SAN FRANCISCO ESTUARY INVASIVE SPARTINA PROJECT.

Transcription

1 2012 SAN FRANCISCO ESTUARY INVASIVE SPARTINA PROJECT

2 San Francisco Estuary Invasive Spartina Project 2012 ISP Monitoring and Report Prepared by: Tobias Rohmer Olofson Environmental, Inc. Drew Kerr & Ingrid Hogle 1830 Embarcadero Cove, Suite 100 Oakland, California For the State Coastal Conservancy San Francisco Estuary Invasive Spartina Project 1330 Broadway, 13 th Floor Oakland, CA February 2014

3 This report was prepared for the California Coastal Conservancy s San Francisco Estuary Invasive Spartina Project with support and funding from the following contributors: California Coastal Conservancy California Wildlife Conservation Board (MOU # and subsequent)

4 TABLE OF CONTENTS 1 Introduction Species Descriptions and Status Native Pacific Cordgrass (Spartina foliosa) Atlantic Smooth Cordgrass (Spartina alterniflora) and its Hybrids Chilean Cordgrass (Spartina densiflora) and its hybrid with Pacific cordgrass (S. foliosa) English Cordgrass (Spartina anglica) Salt Meadow Cordgrass (Spartina patens) Invasive Spartina Project Program Areas Inventory Monitoring Monitoring California Clapper Rail Monitoring Water Quality Monitoring Restoration Program Progress Through ISP and Monitoring Region 1: Marin Region 2: San Francisco Peninsula Region 3: San Mateo Region 4: Dumbarton South Region 5: Union City Region 6: Hayward Region 7: San Leandro Bay Region 8: Bay Bridge North Region 9: Suisun Region 10: Vallejo Region 11: Petaluma Region 12: Outer Coast Special Topics South Bay Salt Pond Restoration Project Restricted Sites New Infestations and Sub areas Added in Looking Forward to 2013 and Beyond Literature Cited Invasive Spartina Project i 2012 Progress Report

5 TABLE OF FIGURES Figure 1. ISP Reporting Regions with 2012 Spartina alterniflora x foliosa hybrid presence throughout San Francisco Bay Estuary by reporting region and sub area Figure 2. ISP Reporting Regions with 2012 Spartina densiflora presence throughout San Francisco Bay Estuary by reporting region and sub area Figure 3. ISP Reporting Regions with 2012 Spartina densiflora x foliosa hybrid, S. anglica, and S. patens presence throughout San Francisco Bay Estuary by ISP reporting region and sub area Figure 4.. Baywide trend of invasive Spartina from Figure 5. Baywide trends in invasive Spartina infestation from by Reporting Region Figure 6. Distribution of invasive Spartina in 2012 across the 32 sub areas of Reporting Region 1: Marin Figure 7. Distribution of invasive Spartina in 2012 within the Corte Madera Creek Watershed of ISP's Region Figure 8. Distribution of non native Spartina in 2012 across the 35 sub areas of Reporting Region 2: San Francisco Peninsula Figure 9. Distribution of non native Spartina in 2012 across the 26 sub areas of Reporting Region 3: San Mateo Figure 10. Distribution of invasive Spartina in 2012 across the 24 sub areas of Reporting Region 4: Dumbarton South Figure 11. Distribution of invasive Spartina in 2012 across the 21 sub areas of Reporting Region 5: Union City Figure 12. Distribution of invasive Spartina in 2012 across the 28 sub areas of Reporting Region 6: Hayward Figure 13. Distribution of invasive Spartina in 2012 across the 19 sub areas of Reporting Region 7: San Leandro Bay Figure 14. Distribution of invasive Spartina in 2012 across the 12 sub areas of Reporting Region 8: Bay Bridge North Figure 15. Distribution of invasive Spartina in 2012 in the single sub area and adjacent shoreline of Reporting Region 9: Suisun Figure 16.Distribution of invasive Spartina in 2012 across the four sub areas of Reporting Region 10: Vallejo Figure 17. Distribution of invasive Spartina in 2012 across the four sub areas of Reporting Region 11: Petaluma Figure 18. Distribution of invasive Spartina in 2012 across the five sub areas of Reporting Region 12: Outer Coast Figure 19. Map of the South Bay Salt Ponds and neighboring recent restoration projects in South San Francisco Bay. Sites are differentiated based on whether they have been restored to tidal action and if so, whether they have been infested with hybrid Spartina or not as of Figure 20. Distribution map of the 26 ISP sub areas in which treatment of hybrid Spartina was restricted in 2011 and the 11 sub areas in which treatment was restricted for both 2011 and Figure 21. Photo series from 2006 to 2012 showing hybrid Spartina response to continuous treatment, and its subsequent expansion when left untreated. Cargill Mitigation Marsh (13f, Region 5) on the left had no treatment interruptions, while MLK New Marsh (17h, Region 7) on the right was not treated in 2011 and 2012 because of permit restrictions Invasive Spartina Project ii 2012 Progress Report

6 TABLE OF TABLES Table Baywide summary of invasive Spartina area by species Table Baywide summary of invasive Spartina area by Reporting Region Table 3. Summary of 2012 invasive Spartina area by sub area within Reporting Region 1: Marin Table 4. Summary of 2012 invasive Spartina area by sub area within Reporting Region 2: San Francisco Peninsula Table 5. Summary of 2012 invasive Spartina area by sub area within Reporting Region 3: San Mateo Table 6. Summary of 2012 invasive Spartina area by sub area within Reporting Region 4: Dumbarton South Table 7. Summary of 2012 invasive Spartina area by sub area within Reporting Region 5: Union City Table 8. Summary of 2012 invasive Spartina area by sub area within Reporting Region 6: Hayward Table 9. Summary of 2012 invasive Spartina area by sub area within Reporting Region 7: San Leandro Bay Table 10. Summary of 2012 invasive Spartina area by sub area within Reporting Region 8: Bay Bridge North Table 11. Summary of 2012 invasive Spartina area by sub area within Reporting Region 9: Suisun Table 12. Summary of 2012 invasive Spartina area by sub area within Reporting Region 10: Vallejo Table 13. Summary of 2012 invasive Spartina area by sub area within Reporting Region 11: Petaluma Table 14. Summary of 2012 invasive Spartina area by sub area within Reporting Region 12: Outer Coast Table 1. Hybrid Spartina quantities and trends from at the 26 ISP sub areas where treatment was suspended in Invasive Spartina Project iii 2012 Progress Report

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8 1 INTRODUCTION The San Francisco Estuary Invasive Spartina Project (ISP) was established in 2000 by the California State Coastal Conservancy (Conservancy), in partnership with the U.S. Fish and Wildlife Service, in response to the invasion of non native Spartina, or cordgrass, into the marshes and mudflats of the San Francisco Estuary (referred to as Estuary or Bay throughout this report). In the last several decades, four non native cordgrasses, including Spartina alterniflora (Atlantic smooth cordgrass), S. densiflora (Chilean cordgrass), S. anglica (English cordgrass), and S. patens (salt meadow cordgrass), were introduced to the Estuary. Each of these species is known to be invasive outside of its native range, and each has demonstrated varying degrees of invasiveness since establishing in the Estuary. Spartina species are closely related, and both S. alterniflora and S. densiflora subsequently hybridized with native S. foliosa (Daehler and Strong 1996; Ayres, Strong et al. 2003; Ayres, Grotkopp et al. 2008). Offspring of S. alterniflora x foliosa hybrids backcrossed with the parent species and with one another, producing an extremely robust and fertile hybrid swarm, which has invaded habitat throughout the Estuary, threatening the ecological integrity of the existing tidal wetlands and mudflats as well as the potential for future restoration efforts (Daehler and Strong 1996; Goals Project 1999; Ayres, Strong et al. 2003; State Coastal Conservancy 2003; Ayres, Zaremba et al. 2004; Ayres, Grotkopp et al. 2008). Non native Spartina has been determined to pose many serious threats to the Estuary, as was described in the ISP s Programmatic Environmental Impact Statement/Environmental Impact Report (PEIS/EIR) adopted by the Conservancy in 2003 (State Coastal Conservancy 2003). Impacts of non native Spartina include the destruction or degradation of endangered species habitat, loss of flood control capacity, creation of mosquito breeding areas, corruption of salt marsh restoration efforts, and the possible eventual extinction of native Spartina foliosa. The purpose of the ISP is to implement a regional program to eradicate non native Spartina species from the Estuary. This goal is accomplished through a highly coordinated non native Spartina inventory mapping and treatment effort that is planned and supervised by ISP biologists. Mapping and treatment is conducted throughout the growing season each year (normally May through November) over the 50,000 acres of potential Spartina habitat. 1.1 SPECIES DESCRIPTIONS AND STATUS There are one native and four non native species of cordgrass in the San Francisco Estuary. Pacific cordgrass (S. foliosa), the native species, is avoided during treatment and is conserved by controlling the invasive species that have been demonstrated to displace it. Key aspects of the cordgrass species found in the Estuary are contrasted below. All species and hybrids are perennial, salt tolerant grasses that spread both sexually and asexually. The roles these species play in their native habitats give ecologists an indication of their potential to alter the salt marsh ecosystem of San Francisco Bay Native Pacific Cordgrass (Spartina foliosa) California s only native cordgrass, Pacific cordgrass, grows in a narrow range of the tidal spectrum due to its relatively short stature and intolerance for drought. Spartina foliosa is a vital component of the salt marsh plant community, occurring at the lowest intertidal elevation of any native macrophyte. This lower tidal marsh zone occurs at the upper elevation of the mudflat and along channel banks and benches. Na Invasive Spartina Project Progress Report

9 tive cordgrass is also found scattered throughout the next zone in the elevational gradient, the middle tidal marsh zone, or pickleweed marsh plain. Spartina foliosa s slender leafy shoots seldom exceed five feet in height including seed heads, with most shoots ranging from about one to three feet tall. Cordgrass height correlates with its tolerance of submersion, and as such S. foliosa can occupy only a limited range in the lower and middle tidal marsh zones (Cain and Harvey 1983). Its leaves and stems wither in fall and are shed in winter, as the clones die back to the mud substrate. Spartina foliosa is particularly valued as habitat for the endangered California clapper rail (Rallus longirostris obsoletus), which spends most of its time foraging for food within, or close to, the protective canopy of cordgrass. California clapper rails can move within S. foliosa stands, and they spend most of their time under cover of the cordgrass foliar canopy, usually selecting prey items such as benthic and aquatic invertebrates inhabiting the cordgrass stands and their edges. The benthic invertebrate community found in the substrate at the base of S. foliosa is also an important food source to a variety of other consumers including both resident and migratory shorebirds. When stands of S. foliosa are displaced by hybrid S. alterniflora, not only does the biomass of the benthic invertebrates decline by more than 70%, the benthic community also shifts from surface feeders to belowground feeders that are inaccessible to foraging birds (Levin et. al. 2006). While it was widely recognized that hybrid S. alterniflora (discussed in the next section) could potentially threaten the existence of native S. foliosa, control of the hybrids began sufficiently early that the Pacific cordgrass still anchors thousands of acres of tidal marsh throughout the Estuary. Most of the North Bay was relatively unimpacted by hybrid S. alterniflora, and more than 99% of the cordgrass in the remnant marshes throughout the Estuary is still intact S. foliosa. However, S. foliosa was assimilated into the hybrid swarm, and even locally extirpated, in some of the largest infestations around South San Francisco Bay, including the Alameda Flood Control Channel (Site 1) and Eden Landing (Site 13). These sites are the focus of an extensive reintroduction effort by the Conservancy that began in 2010, to establish stands of S. foliosa that will begin to disperse seeds throughout these sites, leveraging the investment in direct planting Atlantic Smooth Cordgrass (Spartina alterniflora) and its Hybrids Atlantic smooth cordgrass is unique among the world s cordgrass species in terms of its growth potential and ecological breadth. Spartina alterniflora is genetically very similar to S. foliosa, but the two species have significant differences. In size, growth rate, pollen and seed production, culm (stem) density and ecological tolerances, S. alterniflora is more robust than S. foliosa (Smart and Barko 1978; Boyer, Callaway et al. 2000). The San Francisco Estuary population of S. alterniflora was introduced from seed collected in Maryland in the early 1970s to aid in a dredge spoils stabilization and marsh restoration experiment (Faber 2000). Genetic similarity to S. foliosa allowed multiple hybridization and eventual backcrossing events that produced the hybrid swarm that has posed the most widespread and intrusive threat to the Estuary (Daehler and Strong 1997). Pollen production, higher fertility, greater tolerance for both inundation and drought, and increased timeframe for flowering make these hybrids a prominent threat to native cordgrass through outcompetition, pollen swamping and hybrid assimilation (Rhymer and Simberloff 1996; Ayres, Garcia Rossi et al. 1999; Anttila, King et al. 2000; Levin, Neira et al. 2006). Invasive Spartina Project Progress Report

10 Hybrid S. alterniflora was well established and widely distributed in the Central and South Bay at the start of the ISP control program, but it was detected early and controlled by ISP in the North Bay. Although a small population established on the shoreline of Southampton Marsh (Site 11) in Benicia State Recreation Area, hybrid S. alterniflora has not yet been detected further into Suisun Bay, despite intensive surveys. Over the years, outlier populations have been detected on the Petaluma River (Site 24), Sonoma Creek (26c), and Mare Island (26b), and single clones were found at both China Camp State Park (23o) and Sonoma Baylands (26d). Pioneering hybrid S. alterniflora populations have also been detected and managed at Drakes Estero, Limantour Estero and Bolinas Lagoon on the Point Reyes peninsula (Site 25). The abundance of hybrid S. alterniflora remains greatest in San Leandro Bay (Oakland), Robert s Landing in San Leandro, and outer Bair Island Ecological Reserve (Redwood City), but has been reduced by 95% baywide by ISP partners, down to 38 net acres since its peak of 805 net acres in Defining Area Chilean Cordgrass (Spartina densiflora) and its hybrid with Pacific cordgrass (S. foliosa) Chilean cordgrass (also called dense flowered cordgrass) is a distinctive cordgrass species native to South America that grows as a bunchgrass in the middle marsh plain, eventually forming tussocks and meadows (Spicher and Josselyn 1985; Kittelson and Boyd 1997).Spartina densiflora was introduced to California in Humboldt Bay by dry ship ballast containing propagules from South American ports that traded lumber(spicher and Josselyn 1985). Thought for most of the 20 th century to be a form of Pacific cordgrass, S. densiflora was deliberately transplanted to a salt marsh restoration at Creekside Park (4g) along Corte Madera Creek in Marin County in the 1970s. Within the salt marshes fringing Corte Madera Creek, it became a locally dominant component of the middle and high salt marsh vegetation, displacing even robust pickleweed. The ISP uses the terms net area and treatment area define the extent of non native Spartina. Net area refers to the size of the infestation if the space between stems were subtracted from the overall footprint of the plant or clump of plants. Net area is the metric typically used in botanical surveys. area describes the area that will be directly affected by treatment. area is a separate measurement used for planning, and it is general 2 to 3 times greater than the net area of given instance of invasive Spartina. While the bulk of the S. densiflora invasion has been contained within Marin around the Corte Madera Creek watershed, other populations have been detected and largely eliminated in Redwood City (19s), Point Pinole Regional Shoreline (Site 10), Burlingame (19k & 19l), Tom s Point (25a) in Tomales Bay, and the shoreline of San Pablo Bay National Wildlife Refuge (26b). Most of the novel population establishments appear to have been the result of active planting by anonymous parties. When established in close proximity to S. foliosa, S. densiflora has produced infertile hybrids with the native cordgrass that spread solely via vegetative growth (Ayres, Zaremba et al. 2008). By 2012, the population of S. densiflora had been reduced to just 105 m 2 Estuary wide, and only 9.8 m 2 of the hybrid between S. foliosa and S. densiflora remains, both reductions of more than 99% since the peak years for each. These successful reductions have been achieved through dedicated implementation of an adaptive Integrated Vegetation Management (IVM) strategy that includes multiple treatment methods. Because of the unique biology of this form of Spartina, any single tool approach would have been ineffective. The efficacy of herbicide treatment (using imazapyr) varies widely between large plants and small Invasive Spartina Project Progress Report

11 plants, as well as between pioneering individuals and established stands. The seed bank viability of S. densiflora is estimated at 3 5 years (as compared to years for S. alterniflora), which increases the time required for full eradication, even after an infestation is effectively reduced to just a few individuals. With these additional challenges, it is fortunate that S. densiflora appears to be somewhat limited in its ability to disperse around the San Francisco Bay ecosystem, and that the infestation has never approached the scale of hybrid S. alterniflora, which both consistently responds well to imazapyr treatment and has shorter seed viability English Cordgrass (Spartina anglica) English cordgrass is an aggressive invader of mudflats and salt marshes in Britain, New Zealand, Australia, and the Pacific Northwest, and thrives in cool temperate climates. It originated in Britain as a fertile hybrid derived from introduced Atlantic smooth cordgrass and common cordgrass (S. maritima). It was introduced to the San Francisco Estuary at Creekside Park (4g) along Corte Madera Creek in Marin County, along with Chilean cordgrass (S. densiflora), in Unlike Atlantic smooth cordgrass and Chilean cordgrass, this species failed to disperse from its point of introduction to expand the infestation beyond Creekside Park. It may be at or near its southern climatic limit on the Pacific Coast in the San Francisco Estuary. Spartina anglica is nearly eradicated from San Francisco Bay, and it is not known to occur in any other location in California. The ISP mapped just 2 m 2 of S. anglica in There are several factors that contributed to this infestation lingering longer than might be expected given its relatively small size and presence at only a single ISP site. Spartina anglica flowers and sets seed in early summer, slightly later than S. densiflora but far ahead of hybrid S. alterniflora. This phenology did not allow for treatment ahead of seed dispersal prior to 2008, when ISP was first permitted to enter the sites before California clapper rail breeding season ends on September 1. In addition, there were several other years where either delayed permits (2011 and 2012 Biological Opinions) or political concerns (delays with Marin County finalizing its revised IPM Policy in 2009) caused the implementing ISP partner, Friends of Corte Madera Creek Watershed, to miss the optimal treatment window for that year. Finally, the remaining S. anglica at Creekside Park is often found growing as a short understory to the native S. foliosa that lines the main channel, which limited the full detection of the target plants, and the desire to preserve as much of the native cordgrass as possible further complicated the matter Salt Meadow Cordgrass (Spartina patens) In its native range on the Atlantic coast, salt meadow cordgrass is naturally restricted to the well drained high salt marsh and relatively moist sandy depressions at or above tidal influence. However, in the San Francisco Estuary, it has thrived along channel banks and on the pickleweed plain. Spartina patens arrived in the Estuary by the early 1960s in Southampton Marsh (Site 11; Benicia State Recreation Area), as evidenced by a sample present in the California Academy of Science s collection from circa At the initiation of treatment by ISP and the California Department of Parks and Recreation (State Parks), 0.65 net acre of salt meadow cordgrass was present in large, discrete patches at Southampton Marsh. In 2012, the net cover was down to only 0.01 acre (up slightly from 2011); however, the work has been stalled because of complications related to the presence of three special status species. Invasive Spartina Project Progress Report

12 Spartina patens has spread into an area of Southampton Marsh that supports a population of an endangered annual hemi parasitic plant, soft bird's beak (Chloropyron molle ssp. molle, formerly Cordylanthus mollis ssp. mollis). The treatment approach initially approved and used in this area of the marsh was to treat the S. patens stands with herbicide in the late fall, after the soft bird s beak had produced seed and senesced, so that the treatment would not negatively affect the soft bird s beak population. However, S. patens itself flowers in May at that location, and by the time herbicide was applied in October, the S. patens plants had also already produced seed and begun senescing. When a plant senesces it is no longer able to uptake and translocate the herbicide, processes that are necessary to kill the plant. It soon was clear that no additional headway was being made toward eradication of S. patens. In 2011, the ISP worked with rare plant researcher Brenda Grewell (USDA ARS) and State Parks to develop a new eradication plan to address the shortcomings of the earlier plan. The new plan would permit limited, temporary impacts to the soft bird s beak so that the S. patens could be treated effectively, and may include collecting and banking seed from the hemi parasite to sow once S. patens has been eradicated and native host plants reestablished. However, implementation of the new plan has now been postponed because of the reappearance of California clapper rail in Southampton Marsh in 2011, after years of absence at the site. In an effort to nurture the potential new clapper rail population, State Parks set up extensive marsh exclusion zones, including areas of S. patens populations, and again restricted entry for treatment until after October 1. The 2012 breeding season surveys did not detect any California clapper rail at the site, but the exclusion zones were still in effect, making it impossible to begin implementing the new strategy. 1.2 INVASIVE SPARTINA PROJECT PROGRAM AREAS The ISP is comprised of three broad programs treatment, monitoring, and restoration, which coordinate closely to achieve the ISP goals. Monitoring is comprised of several programs including Spartina inventory monitoring, treatment monitoring, California clapper rail monitoring, and water quality monitoring. Important tools within the monitoring programs are genetic sampling and analysis of Spartina, and photo point monitoring. The many programs work together to assure and document an effective regional treatment effort, while protecting water quality, wildlife, and the ecosystem structure. The status of each of the program areas is provided below The Program coordinates a multitude of contractors, agencies, landowners and staff to plan and conduct annual treatment of the various non native Spartina species found throughout the Estuary. Pilot efforts to test herbicide methods and coordination mechanisms began in 2004, when the total known footprint of non native Spartina was at that time 758 acres. In 2005, the ISP partners began coordinated, Estuary wide treatment. initially focused on large infestations and areas where partners were most ready to begin work, and expanded to include the total of sites in 2006 and Aerial broadcast treatment by helicopter at several of the large hybrid Spartina monocultures of the central and south bay soon effectively reversed the spread of hybrid Spartina and established control over the infestations. Once continuous meadows of hybrid Spartina at sites like Alameda Flood Control Channel (Site 1), Eden Landing Ecological Reserve (Site 13) in Union City, and Seal Slough (19p) in San Mateo, were reduced to a patchy distribution of plants across each site, the herbicide methods were shifted away from broad Invasive Spartina Project Progress Report

13 cast spray to use of amphibious tracked vehicles on the mudflats and marsh plain, and hauling hose from trucks staged on surrounding levees to accessible marshes. Smaller infestations were treated by applicators with backpack sprayers walking through the marsh, as well as by manual removal of isolated seedlings. Spartina densiflora, a species that grows in a bunchgrass form and doesn t spread significantly by rhizome, was effectively controlled by a strategic combination of herbicide application and digging (see Chilean Cordgrass description in previous section). After several years of regionally coordinated control work, the character of the infestations had changed. Very large meadows of non native Spartina were rare, replaced by sparse infestations spread over larger areas that were more difficult to locate and access. New outlier populations were being discovered in more remote areas of the estuary. By 2008, ISP began to experiment with utilizing airboats on the open mud to allow treatment during low tide, thus maximizing herbicide dry time. The airboats were also used to deploy personnel with backpacks onto the marsh plain of islands and other sites that were inaccessible by land. By 2009, this approach was employed for treatment throughout Don Edwards San Francisco Bay National Wildlife Refuge (DENWR), and by 2012 there were as many as four airboats on a given day working on hybrid Spartina treatment around the Estuary. While the use of airboat in this way is essential at this stage for accessing difficult areas, the vast majority of herbicide treatment is conducted by trained personnel walking through the marsh with backpack herbicide sprayers. There have similarly been shifts in methodology for S. densiflora treatment. By 2012, all sites were using manual removal as the primary technique, with only two sites still requiring an early season application of herbicide to stop seed production until digging can be implemented after California clapper rail breeding season. Mowing was also an important technique used early on in combination with other treatment methods at sites with meadows of S. densiflora, but the reductions achieved through the successful implementation of the adaptive IPM strategies allowed Friends of Corte Madera Creek to discontinue mowing in Control methods used in 2012 are listed by subarea in each of the Reporting Region tables in this report Inventory Monitoring The ISP began Estuary wide inventory monitoring of invasive Spartina in 2000, with annual monitoring of all known infestation sites beginning in The original geographic scope of inventory monitoring was limited to the bayward side of most major highways (Hogle 2008). Since 2006, all potential invasive Spartina habitat identified within the San Francisco Estuary and tidal tributaries, Bolinas Lagoon, Point Reyes National Seashore and Tomales Bay has been surveyed by ISP biologists or its partners. This includes annual surveys over 50,000 acres of tidal marsh and mudflat throughout the Estuary and Outer Coast areas (the inventory area is shown in Figure 1 with summary data for 2012 hybrid Spartina alterniflora). While the area inventoried covers some large remnant marshes as well as many fringe marshes, it also includes miles of flood control channels and many small fragmented marshes, channels and drainage ditches in a matrix of highly urbanized land use. Inventory monitoring is conducted for two purposes: to track change in the extent and net cover of the infestation over time for analyzing and reporting, and to locate and map patches of invasive Spartina to inform management and coordination of Program operations. The ISP typically completes inventory of sites prior to treatment (generally from May through October) to allow for the most efficient use of time and personnel during limited treatment windows. Minimizing time in the marsh during treat Invasive Spartina Project Progress Report

14 ment also serves to minimize potential disturbance to marsh plants and animals. Data is collected using global positioning system (GPS) and managed using a Geographic Information System (GIS). Since 2008, all monitoring has been conducted on the ground or by helicopter for select large and remote sites where large patches of infestation persist. Ground mapping is done mostly on foot, but also by kayak and motorized boats when surveying islands, extensive shorelines and lengthy waterways should be the last year that ISP conducts helicopter monitoring due to its inherent loss of precision as compared to ground mapping. In positive response to treatment, sites monitored in 2012 by helicopter are now reduced to a lower status of infestation level that warrants more detailed ground mapping in the future. A history of the evolution of the ISP Monitoring Program between 2000 and 2012 (Zaremba and Hogle, in progress) will soon be available on the ISP website ( Genetic Sampling and Analysis Genetic analysis is an extremely tool for the ISP and Monitoring programs. Spartina leaf samples are collected and genetically analyzed to distinguish plants with native vs. non native ancestry. Staff collect leaf samples from S. foliosa and hybrid S. alterniflora to verify identification of select plants, guide treatment practices, and keep an eye on new or changing plant morphologies. A genetic sampling plan is developed internally each season to address questions posed by the and Restoration programs and assure efficient use of limited laboratory resources. Samples are shipped to a commercial laboratory for extraction, and then sent to the UCLA Human Genomics Laboratory, where they are analyzed using Simple Sequence Repeats (SSRs; aka microsatellites ) and scored. The laboratory used thirteen SSR loci throughout 2012, with three additional markers added at the end of the season. The ISP analyzes the data from UCLA using the software package Structure (Pritchard Lab, Stanford University) to determine, for every sampled plant, the likelihood of it being descended from S. alterniflora ancestry. The ISP incorporates these results into the program s GIS layers for further analysis and for reference in the field during future treatment and inventory events. Over 2,500 plants have been collected and analyzed in this manner since 2010, allowing the identification and treatment of many otherwise morphologically indistinct hybrid S. alterniflora plants throughout the Estuary. More information regarding the genetic sampling program is available in the Monitoring Program Quality Assurance Document ( and the ISP Spartina Monitoring Program Approach report referenced above Photo Point Monitoring Another tool used by the and Monitoring Programs is photo point monitoring. The ISP established and has maintained 136 permanent locations within 57 sub areas from which staff take consistent photos twice annually to qualitatively monitor marsh changes between seasons and years. Photo points are used to inform the extent of the next treatment effort and to visually document the changes in vegetation occurring at the sites. Visible changes often include rapid disappearance of large areas of nonnative Spartina within 1 3 seasons of treatment, passive (and frequently rapid) establishment of native vegetation, and expansion or rebounding of hybrid Spartina populations when treatment is missed or restricted for one or more seasons. The intra and inter annual visual comparisons of marsh composition are useful to the ISP for monitoring treatment efficacy and for presenting local trends to outside parties. These photos are especially useful to Invasive Spartina Project Progress Report

15 illustrate different marsh trajectories when comparing sites with continuous full treatment with those where treatment was absent or incomplete, as happened in 2011 and 2012as a result of permit restrictions. An example of a photo point sequence is provided later in this report (Figure 21, on page 80). Photo Point photos are available on the web, through Google Maps and Picasa Web Albums, at daadf691d97&t=h&z= Monitoring The ISP began monitoring all treatment events in monitoring involves pairing ISP personnel with the agency or private contractor treatment crews to accomplish the following important objectives: (1) assure protection of California clapper rails and other sensitive species during treatment activities; (2) enhance conservation of native S. foliosa that may be present by delimiting it in no treatment areas for the crew; (3) substantially improve the ability for crews to locate and target plants for treatment by leading them to less obvious plants requiring treatment; and (4) document completed treatment in real time at the patch level. t As previously mapped Spartina locations are revisited, ISP staff update the map features using GPS data loggers to reflect the day s treatment action (e.g. treated, not treated, sub optimally treated etc.). This data is uploaded daily to the ISP s ArcGIS geodatabase for use in the field the next day. Accompanying treatment crews also allows ISP staff to identify, mapping, and concurrently record treatment of patches of invasive Spartina that had not been detected during initial inventory monitoring. monitoring is perhaps the most important of the ISP s new programmatic initiatives, allowing ISP partners to gain ground on the remaining substantial infestations in the West Bay, and greatly accelerating the rate at which eradication may be achieved at all sites. Since the timing of inventory and treatment overlap from mid July through November, the ISP hires additional staff (interns) to conduct treatment monitoring at suitable sites that is, at sites where native Spartina is not present, where hybrid Spartina has been recently mapped by more experienced staff, or where native and hybrid morphologies are sufficiently distinct to allow the interns to make consistently correct determinations. More experienced biologists are thus reserved to inventory and monitor treatment at more complex sites. The ISP employed three interns for the 2012 monitoring season to conduct treatment surveys and assist with inventory California Clapper Rail Monitoring Implementation of Spartina control measures requires annual breeding season surveys of endangered California clapper rail (Rallus longirostris obsoletus) in the marshes affected by the invasion and management of non native Spartina. Annual breeding season surveys provide a standardized measure of clapper rail presence and distribution in marshes throughout the Estuary. This information guides the ISP in the planning, permitting, and implementation of treatment strategies and helps to minimize the impacts of Spartina control on rail populations. Results from California clapper rail surveys help determine the time of year in which ISP monitoring staff and treatment contractors will enter a site so as to not disturb birds present during their breeding season, and are used by USFWS and others for making decisions regarding the ISP program. In 2012, the ISP conducted California clapper rail surveys at 146 Spartina invaded sites between January 15 and April 15. A range of 325 to 422 (average 374) California clapper rails were detected at 48 of the 146 Invasive Spartina Project Progress Report

16 sites surveyed. Detailed survey results from 2012 can be found in the 2012 ISP Clapper Rail Monitoring Report (McBroom 2012) Water Quality Monitoring The application of herbicide for Spartina control is covered under the Statewide General National Pollutant Discharge Elimination System (NPDES) Permit for Application of Aquatic Pesticides for Aquatic Weed Control in Waters of the United States (General Permit No. CAG990005; programs/npdes/docs/aquatic/permit.pdf). To obtain coverage under this permit, each grantee or other ISP partner that will be applying herbicide must submit a Notice of Intent (NOI) to comply with the terms of the General Permit and an annual fee to the Regional Water Quality Control Board (RWQCB). The permit requires preparation of an Aquatic Pesticide Application Plan (APAP) that includes a Water Quality Monitoring Plan (WQMP), which must be updated annually as needed. The ISP arranged with the State Water Resources Control Board and the San Francisco Bay RWQCB to allow the ISP to prepare and implement a programmatic APAP and WQMP on behalf of the ISP partners who submitted NOIs. The ISP prepared a programmatic APAP in 2006 and updates it annually. The APAP is available on the ISP website at The General Permit requires that at least 10% of treated sites be monitored for impacts to water quality. In 2012, 143 ISP sites were treated with herbicide; hence 15 sites were monitored. The permit requires that three sampling events be conducted for each site: one pre treatment background sampling, one treatment event sampling, and one post treatment sampling. Details regarding sampling and analysis methods are provided in the 2012 Aquatic Pesticide Application Plan (Kerr 2012), and the monitoring results are provided in the 2012 Water Quality Monitoring Report (Kerr 2013). As with many substances, there are no State or Federal numeric water quality objectives or limits established for imazapyr herbicide, so concentrations are compared to tested toxicity and effects levels found in the literature. In 2012, concentrations of imazapyr herbicide measured immediately following treatment events were two to four orders of magnitude below those reported in the literature as a concern to humans or the animals that inhabit the tidal marsh ecosystem. Imazapyr is not persistent in the aquatic environment because it is rapidly degraded by sunlight; thus, as expected, the one week post treatment samples with any residual herbicide detected showed a mean reduction of 93.1% over the treatment event levels. The ISP commissioned a focused review of imazapyr herbicide in 2005, prior to adopting it into the treatment program. The review, The use of Imazapyr Herbicide to Control Invasive Cordgrass (Spartina spp.) in the San Francisco Estuary: Water Quality, Biological Resources, and Human Health and Safety (Leson & Associates 2005), is on the ISP website at The Conservancy s findings under CEQA may be found at Restoration Program The Restoration Program was initiated in 2011 to rapidly establish habitat features to benefit California clapper rails in areas where recent removal of non native Spartina has caused decreases in clapper rail habitat. The plan for the program is contained in the California Clapper Rail Habitat Enhancement, Restoration and Monitoring Plan (Olofson Environmental, Inc. 2012). As part of the plan, the Conservancy and other regional ISP partners are employing several habitat enhancement methods including construction of Invasive Spartina Project Progress Report

17 high tide refuge islands, deployment of artificial floating nesting islands, and extensive revegetation, focusing on native tidal marsh plant species that provide foraging, breeding, and high tide refuge cover. In its first two years (autumn 2011 through early 2013) the Restoration Program deployed 125 artificial floating nesting islands in conjunction with USGS (Casazza, Takekawa et al. 2012), constructed six earthen high tide refuge islands (Busnardo and Archbald 2013), and installed 165,000 plants across 30 sites to develop and provide habitat for California clapper rails. The Restoration Program relies on data from the monitoring, treatment, and clapper rail programs to identify suitable areas for revegetation; specifically, these are areas in proximity to California clapper rail populations with suitable elevation and other features, and sufficiently free from hybrid S. alterniflora infestation to safely allow establishment of native plants. This last condition is particularly critical for planting of native S. foliosa, as plantings too near hybrid S. alterniflora would be at risk of being pollinated by the hybrid, resulting in production and spread of more hybrid seeds. Details of the Restoration Program and activities can be found on the ISP website at PROGRESS THROUGH 2011 The ISP has made tremendous progress controlling non native Spartina throughout the San Francisco Estuary and in the neighboring coastal areas of Point Reyes National Seashore and Bolinas Lagoon. In 2011, the ISP mapped a total of 49 net acres of non native Spartina, nearly a 94% estuary wide reduction since the peak of the invasion at 805 acres in In 2011, however, not all non native Spartina was treated, due to permitting restrictions as well as other issues with equipment, timing, weather, and logistics [see the 2011 Report ( Kerr and Grijalva 2012)]. Most significantly, the 2011 Biological Opinion prohibited treatment at 26 sub areas to reduce loss of refuge habitat for endangered California clapper rail potentially caused by removing hybrid S. alterniflora. The untreated sub areas were located within seven of the twelve reporting regions, though predominantly focused around Central and South San Francisco Bay (see Section 3.2 and Figure 20). The interruption in treatment in 2011 resulted in an increase in nonnative Spartina measured at several site in This will be discussed further in the relevant sections that follow, and in Section 3.2. Invasive Spartina Project Progress Report

18 ISP TREATMENT AND MONITORING The ISP s activities and progress are described in this section first from a baywide perspective, and then in more detail for each of the following 12 reporting regions : ISP Reporting Regions Region 1. Marin Region 2. San Francisco Peninsula Region 3. San Mateo Region 4. Dumbarton South Region 5. Union City Region 6. Hayward Region 7. San Leandro Bay Region 8. Bay Bridge North Region 9. Vallejo Region 10. Suisun Region 11. Petaluma Region 12. Outer Coast Figures 1 3 show the location of the reporting regions and provide graphic summaries of the distribution of each non native Spartina species within each reporting region and each sub area. The ISP developed the reporting regions based on regions initially defined by USFWS for assessment of California clapper rail populations. The reporting region boundaries also take into consideration natural and political landscape features, similarity in land management issues, geographic proximity and ecological connectedness of the treatment sub areas, and general impact of non native Spartina invasion on the region. Using these reporting regions allows the ISP to cohesively present treatment and monitoring data in a manner more suitable for correlation with California clapper rail data. The ISP surveyed approximately 50,000 acres of intertidal marsh and mudflat in 2012, and mapped a total of 38 net acres (166 treatment acres) of non native Spartina (Tables 1 and 2, Figure 4). This represents a net 21.7% decrease from 2011, with seven of twelve reporting regions (Marin, San Francisco Peninsula, San Mateo, Union City, San Leandro Bay, Bay Bridge North, and Vallejo) driving the downward trend (Error! Reference source not found., Table 3). Five regions showed a net increase since 2011, three of which (Petaluma, Outer Coast and Suisun) are small and remote infestations of less than 100 m 2. The remaining two regions, Dumbarton South and Hayward, showed an increase in hybrid S. alterniflora, an anticipated result of clonal expansion where treatment was suspended due to permit restrictions in For the regions showing an increase in hybrid S. alterniflora where full treatment occurred (Petaluma, Outer Coast and Suisun), the change totals less than 0.04 acre. Looking over a broader time period, the 38 net acres of non native Spartina cover mapped in 2012 is just 4.75% of the estuary wide cordgrass footprint at its peak in 2006 (805 ac), representing a 95% reduction. Of the remaining non native cordgrass, 94% is distributed among the four most invaded regions (in order of decreasing amount): San Leandro Bay, San Mateo, Hayward and Dumbarton South. There were 11 previously invaded sub areas at which no (zero) non native Spartina was detected in 2012, including China Camp (23o, Region 1); Fisherman's Park (19m, Region 2); two sub areas in Region 5, Old Alameda Creek Upstream of 20 Tide Gates (13g) and Eden Landing Pond 10 (13i); two sub areas in Region 6, Hayward Shoreline Outliers (20p) and Triangle Marsh (20w); two sub areas in Region 10, White Slough / Napa River (26a) and Sonoma Baylands (26d), Grey's Field (24b, Region 11); and two sub areas in region 10, Invasive Spartina Project Progress Report

19 Figure 1. ISP Reporting Regions with 2012 Spartina alterniflora x foliosa hybrid presence throughout San Francisco Bay Estuary by reporting region and sub area. Invasive Spartina Project Progress Report

20 Figure 2. ISP Reporting Regions with 2012 Spartina densiflora presence throughout San Francisco Bay Estuary by reporting region and sub area. Invasive Spartina Project Progress Report

21 Figure 3. ISP Reporting Regions with 2012 Spartina densiflora x foliosa hybrid, S. anglica, and S. patens presence throughout San Francisco Bay Estuary by ISP reporting region and sub area. Invasive Spartina Project Progress Report

22 Table Baywide summary of invasive Spartina area by species. Spartina species Net Cover 2012 Net Cover 2011 Change Since 2011 % Change Since 2011 Peak Year Peak Amount (ac) Change Since Peak % Change Since Peak % Remaining since Peak S. alterniflora x foliosa ac ac ac. 21.6% ac ac 95.2% 4.8% S. densiflora 0.03 ac 0.09 ac 0.06 ac. 66.7% ac 4.14 ac 99.3% 0.7% S. densiflora x foliosa 8.81 m m m % m m % 2.5% S. anglica 1.86 m m m % m m % 0.5% S. patens 0.01 ac ac ac % ac 0.64 ac 98.5% 1.5% Table Baywide summary of invasive Spartina area by Reporting Region. Region # Reporting Region Name # Sub Areas Area suitable for invasive Spartina colonization (ac) Net Cover 2012 (ac) Change Since 2011 (ac) % Change Since 2011 Peak Year Peak Amount (ac) Change Since Peak (ac) % Change Since Peak % Remaining since Peak 1 Marin 32 2, % % 3.1% 2 SF Peninsula % % 0.9% 3 San Mateo 26 4, % % 5.0% 4 Dumbarton South 24 7, % % 12.8% 5 Union City 21 3, % % 0.2% 6 Hayward 28 1, % % 3.4% 7 San Leandro Bay % % 17.8% 8 Bay Bridge North 12 1, % % 10.2% 9 Suisun % % 2.3% 10 Vallejo 4 19, % % 7.3% 11 Petaluma 4 5, % % 8.4% 12 Outer Coast 5 2, % % 39.6% ALL SFB Estuary , % % 4.7% Invasive Spartina Project Progress Report

23 Invasive Spartina Acreage by Year Since Peak Net ac. Ac.* 590 Acres ** Year Figure 4.. Baywide trend of invasive Spartina from * acre measurements began in 2008 **2007 data are artificially low due to constraints of aerial photo interpretation that year. Net Acres Invasive Spartina by Region Year Marin San Francisco Peninsula San Mateo Dumbarton South Union City Hayward San Leandro Bay Bay Bridge North Suisun Vallejo Petaluma Outer Coast Figure 5. Baywide trends in invasive Spartina infestation from by Reporting Region. Invasive Spartina Project Progress Report

24 Limantour Estero (25b) and Bolinas Lagoon, South (25e). For some of these locations, 2012 was the second year of no detection. The Program completed treatment within 184 sub areas in With the exception of some manual removal of Spartina densiflora in late spring, treatment was conducted between August 21 st, when the USFWS issued the Biological Opinion (BO) was received, and early December. crews used backpack sprayers and airboats to accomplish most of the work, with truck used at several sites, a Marshmaster amphibious tracked vehicle used at Calaveras Marsh (5a.2) in DENWR, and helicopter used on the northeastern portion of Bair Island s B2 (2c & 2d). Aside from 0.01 acre of untreated Spartina patens described previously (on page 4), all sites authorized for treatment in the 2012 BO were treated in However, because treatment could not begin at many sites until the BO was issued on August 21, 2012, the program had to work within a shortened treatment window, which resulted in some of the target plants not being treated before they senesced 1. At many sites, senescence only impacted a small percentage of the infestation. However, as the treatment continued into November and December, a greater proportion of the plants were typically senesced, and treatment was likely less effective than it would have been if conducted earlier in the year. in 2012 continued to be restricted at 11 of the 26 sub areas that were restricted in 2011, again to limit the removal of potential California clapper rail refuge provided by hybrid Spartina (see summary of site restrictions on page 76). Seed suppression 2 was authorized at one of the restricted sites, B2 North Quadrant East (2c.1b) 3, and implemented to maintain the treatment progress at that site and to limit reinfestation of neighboring Bair Island marshes. The next sections describe the treatment and inventory completed within each of the 12 reporting regions in Relevant background and site information is included, and a synopsis of California clapper rail survey results and revegetation work is provided within the regional context. 1 The systemic herbicide used for Spartina treatment, imazapyr, must be applied to actively growing plants to allow for uptake and translocation into the plants root structure. Once the plants have senesced, the window of opportunity for control has passed for the year. 2 Seed suppression entails the application, normally by helicopter, of a dilute solution of herbicide to arrest the development of the target plants (i.e., stop seed production and vegetative/asexual expansion), while not causing plant mortality. It is used in special circumstances by the ISP to maintain the above ground biomass of the hybrid Spartina so that it can continue to provide refuge for California clapper rail, while slowing down plant growth and spread. 3 More information regarding restriction of treatment by permits in 2011 and 2012 is provided in Section 3.2. Invasive Spartina Project Progress Report

25 2.1 REGION 1: MARIN The Marin Region is composed of marsh tracts lining the eastern side of Marin County from the Golden Gate Bridge to the mouth of the Petaluma River. The region is influenced by several large freshwater inputs creating a spectrum of fully tidal, brackish and freshwater wetlands. Though filling of marshlands for development and agriculture has decreased and fragmented existing marshes, some of the remnants are large and diverse. The region maintains several large contiguous tracts of marsh, most notably those around the Novato Creek, Corte Madera Creek and Las Gallinas Creek Watersheds, which also includes one of the Estuary s oldest extant tidal marshes, China Camp State Park. While the Marin Region has never had a very sizeable infestation in terms of acreage, there were many small infestations scattered throughout the marshes and creek banks. The region also has the most diverse infestation, with four non native Spartina species present (S. alterniflora x foliosa hybrids, S. densiflora, S. densiflora x foliosa hybrids, and S. anglica), the majority occurring in the Corte Madera Creek Watershed. Creekside Park (4g) along Corte Madera Creek is the original introduction site for S. densiflora and S. anglica to the Estuary and is also the only sub area where S. anglica can be found. The ISP inventoried this region s 32 sub areas on foot when accessible, and by kayak or whaler for the upstream portions of watersheds and the jagged shorelines that are less traversable by foot. Survey by helicopter was employed to revisit historic points and survey the long and remote shoreline north of Las Gallinas Creek. Figures 6 & 7 show the locations of the treatment sites, and Table 3 presents site information, including treatment and monitoring data. A total of 0.19 acres of non native cordgrass of four species was found in 2012, which represents just 3.1% of the 6.1 acres present at the height of the infestation in this region, in While hybrid S. alterniflora comprises the bulk of the infestation, 99% of the Estuary s S. densiflora was found in Marin with 104 m 2 (0.03ac) of net cover. Spartina anglica persists at Creekside Park but in drastically reduced abundance with only 1.9 m 2 of net cover, down from over 36 m 2 in 2011 and 383 m 2 at its highest levels in of S. densiflora was conducted manually by digging at all sites. Spartina densiflora tends to be a discretely rooted bunchgrass in the San Francisco Estuary, not normally spreading by creeping rhizomes. As a result, each individual plant is pulled or dug with a trowel or shovel depending on the size, taking care to capture as much of the roots as possible. Since no large, mature plants remain, the ISP is essentially working to exhaust the seed bank by surveying twice each year in late spring and early winter. This timing allows for the highest possible detection of the target plants; in late spring the S. densiflora often has a flower stalk sticking up above the surrounding vegetation and in early winter the pickleweed is either red or senescent which allows the green S. densiflora to stand out. Seed viability for this species is estimated to be 3 5 years, and this is consistent with the ISP s recent experience. Manual methods are more effective than herbicide on small plants, probably due to the nature of the in rolled leaves of S. densiflora that possess a very thick cuticle. Along with these characteristics, there may simply be too little leaf surface on these small plants to uptake sufficient herbicide. At two locations with S. densiflora and also California clapper rail populations, Creekside Park (4g) and the north bank at the mouth of Corte Madera Creek (4j), herbicide was applied in early summer to halt plant development and prevent dispersal of seed. This was followed by several days of manual removal later in the season (after September 1), when crews could access the sites without potentially disrupting nesting California clapper rails. These are the two largest remaining S. densiflora infestations in the Estuary. Invasive Spartina Project Progress Report

26 The other location, behind Larkspur Ferry Terminal on the north bank of the mouth of Corte Madera Creek (4j) was among those not permitted for treatment in 2011, and the infestation had both rebounded and dispersed seed by A substantial control effort was required at both of these sites in 2012, including the early summer herbicide application, followed by multiple days of manual removal with the Conservation Corps North Bay (CCNB). Hybrid S. alterniflora has always been a minor component of the Corte Madera Creek non native Spartina infestation, but its management poses special challenges in this area. There is a great deal of native cordgrass intact throughout the lower watershed, and as a result it can be difficult to detect nascent hybrid infestations until they reach a detectible critical mass or manifest distinct morphological characteristics. Invasive Spartina Project Progress Report

27 Figure 6. Distribution of invasive Spartina in 2012 across the 32 sub areas of Reporting Region 1: Marin. Invasive Spartina Project Progress Report

28 Figure 7. Distribution of invasive Spartina in 2012 within the Corte Madera Creek Watershed of ISP's Region 1. In addition, there are many residential properties along these tidelands, each with its own unique shoreline configuration where new infestations can gain a foothold (some with both a front and backyard composed of salt marsh habitat). The ISP and the Friends of Corte Madera Creek Watershed have worked to adapt inventory methods to address these areas, including shifting from kayak/boat surveys to contacting each landowner and surveying long stretches of private properties on the ground. Hybrid S. alterniflora. treatment in 2012 consisted of herbicide applications on small clones or individual, scattered plants, which were conducted using a four gallon backpack sprayer or a smaller one gallon pump sprayer. Clapper rail surveys conducted by the ISP and Point Blue Conservation Science at 30 sites indicated a steady or slight increase in clapper rail populations from those observed in 2011 (McBroom 2012). The ISP has not targeted the Marin Region for habitat enhancement because there are an abundance of large native marshes of high quality clapper rail habitat, and the impact of non native Spartina and its treatment is generally quite minimal. The exception is Creekside Park, where the infestation by multiple Spartina species displaced many native marsh plants. Here, Friends of Corte Madera Creek Watershed has installed 1,200 native Grindelia stricta plants since January 2011 to supplement nesting substrate and high tide refuge cover for resident California clapper rails. Additionally, abundant native cordgrass and little threat from hybrid allowed the ISP to collect S. foliosa from two nearby Marin County marshes, Starkweather Park (23l) and Strawberry Cove (23i), for propagation and future outplanting by the Restoration Program in Invasive Spartina Project Progress Report

29 Table 4. Summary of 2012 invasive Spartina area by sub area within Reporting Region 1: Marin. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 1: MARIN 03a: Blackie's Creek (above bridge) Yes 8/23 Dug, Backpack m² 0.5 m² 3 m² 2005 >99% 94% 03b: Blackie's Creek Mouth Yes 8/23 Dug, Backpack 0 22 m² 0.2 m² 22 m² 39 m² % 11% 04a: Corte Madera Ecological Reserve 04b: College of Marin Ecological Study Area Yes 6/27 ; 9/12; 11/23 Dug, Backpack 0.1 m² 54 m² 0.7 m² 55 m² 144 m² % 1080% increase (50 m²) Yes 8/7 Dug 0.1 m² m² 0.2 m² 0.4 m² 2004 >99% 1588% increase (0.2 m²) 04c: Piper Park East Yes 6/26 Dug 0.2 m² 0.8 m² 1 m² 2 m² 8 m² % 73% 04d: Piper Park West Yes 6/26 Dug 0.02 m² m² 0.4 m² 2 m² 2001 >99% 37% increase (0.1 m²) 04e: Larkspur Ferry Landing Area Yes 8/22 Dug, Backpack m² 0.05 m² 0.1 m² 0.3 m² 2005 >99% >99% 04f: Riviera Circle Yes 7/5 7/6; 7/19 Dug, Backpack 0.5 m² 5 m² 9 m² 15 m² 43 m² 2003 >99% 58% 04g: Creekside Park Yes 8/22 Dug, Backpack, 2 m² 0.03 m² 32 m² 35 m² 334 m² 2001 >99% 78% 04h: Upper Corte Madera Creek (Above Bon Air Rd) 04i: Lower Corte Madera Creek (Bon Air Rd to HWY 101) 04j.1: Corte Madera Creek Mouth North Bank 04j.2: Corte Madera Creek Mouth South Bank Yes 8/22; 1/7/13 Yes 5/24; 8/22; 12/18 No 8/22; 12/ m² Dug, Backpack 2 m² 2 m² 2 m² 11 m² 37 m² 2003 >99% 89% Dug, Backpack 2 m² 114 m² 18 m² 133 m² 370 m² % 40% Dug, Backpack m² 226 m² 25 m² 251 m² 938 m² % 137% increase (145 m²) Yes 7/5; 9/17 Dug, Backpack m² 47 m² 2 m² 49 m² 192 m² % 60% 04k: Boardwalk No. 1 (Arkites) Yes 7/6 Dug 0.6 m² 0 9 m² 10 m² 25 m² % 34% 04l: Murphy Creek Yes 8/20 Dug m² 0.02 m² 09: Tiscornia Marsh / Pickleweed Park Yes 6/23; 9/12; 10/ m² 2007 >99% >99% Dug, Backpack 0.01 m² 8 m² 0.1 m² 8 m² 26 m² 2004 >99% 47% Invasive Spartina Project Progress Report

30 Table 3. Summary of 2012 invasive Spartina area by sub area within Reporting Region 1: Marin (continued). Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 1: MARIN (continued) 23a: Brickyard Cove Yes 5/25 Dug 0 1 m² 0.2 m² 1 m² 6 m² % 464% increase (1 m²) 23b: Beach Drive Yes 8/23; 11/23 Backpack 0 24 m² 0 24 m² 191 m² % 80% 23c: Loch Lomond Marina Yes 9/4 Backpack m² m² 6 m² 2004 >99% 98% 23d.1: San Rafael Canal Mouth East Yes 9/4 Dug, Backpack 0 18 m² 0 18 m² 113 m² % 71% 23d.2: San Rafael Canal Mouth West 23e: Muzzi and Martas Marsh Yes 7/9; 9/4; 9/27; 11/23 Yes 9/4; 10/24 Dug, Backpack 0 9 m² 0.3 m² 10 m² 32 m² % 6% increase (0.5 m²) Dug, Backpack 0.1 m² 50 m² 2 m² 52 m² 324 m² % 78% 23f: Paradise Cay Yes 7/27; 8/2 Dug, Backpack m² 0.6 m² 1 m² 7 m² 2004 >99% 74% 23g: Greenwood Cove Yes 9/28 Dug 2 m² m² 2 m² 6 m² % 61% increase (0.9 m²) 23h: Strawberry Point Yes 5/21 Dug m² 1 m² 3 m² 2005 >99% 845% increase (1 m²) 23i: Strawberry Cove Yes 8/23 Backpack 0 38 m² 0 38 m² 110 m² % 4% increase (2 m²) 23j: Bothin Marsh Yes 9/17 Backpack 0 1 m² 0 1 m² 15 m² 2006 >99% 91% 23k: Sausalito Yes 8/29 Backpack m² m² 4 m² 2004 >99% 49% 23l: Starkweather Park Yes 5/25; 9/27 Dug 0.3 m² m² 0.4 m² 1 m² 2006 >99% 291% increase (0.3 m²) 23m: Novato Yes 9/27 Backpack 0 13 m² 0 13 m² 19 m² % 28% 23n: Triangle Marsh and shoreline Yes 9/16 Backpack m² 0.1 m² 0.7 m² 4 m² 2007 >99% 93% 23o: China Camp Yes No invasive Spartina % 100% REGION 1 TOTAL 2 m ac 104 m ac 0.7 ac % 45% 10 m 2 Invasive Spartina Project Progress Report

31 2.2 REGION 2: SAN FRANCISCO PENINSULA The San Francisco Peninsula Region extends from the Golden Gate Bridge to the San Mateo Bridge, including Angel, Yerba Buena and Treasure Islands (Figure 8). Historically, vast areas of tidal marsh extended from the convergence of Colma and San Bruno Creeks in South San Francisco (Site 18) south to modernday Foster City (19q), with smaller marshes to the north at the mouths of Islais and Mission creeks in San Francisco. In the mid 20 th century, widespread filling of marshes for urban development and construction of San Francisco International Airport (SFO) drastically reduced tidal marsh habitat to a few small, disjunct marshes, stretches of bay fringe, rip rap shoreline and open tidal flat. Despite spanning over 25 miles of shoreline, the region currently contains only 1,217 acres of tidal habitat. Heavy colonization by hybrid Spartina alterniflora had tremendous impact on this region as clones coalesced along the nearshore mudflats, eventually forming meadows and continuous tracts of homogeneous invasive cordgrass marshes. The region s 35 sub areas (Figure 8, Table 4) were thoroughly surveyed by foot in 2012, which resulted in the mapping of 1.12 acres of net Spartina cover within 5.56 treatment acres. This represents a 56% decline in the San Francisco Peninsula Region infestation from 2011 and a 99% reduction in Spartina cover from the peak of the infestation in 2004 (125 ac). Other species remain in small amounts at isolated subareas: 16 individual S. densiflora plants and four instances of nearby S. densiflora hybrid, totaling 0.3 m 2 and 0.05 m 2 respectively, were found at two contiguous sub areas, Sanchez Marsh (19k) and Burlingame Lagoon (19l). Spartina densiflora has been present at these marshes since the start of ISP coordinated treatment in 2005, and current treatment efforts are focused on exhausting the seed bank. The locations of S. densiflora and its hybrids in the San Francisco Peninsula region indicate that these plants did not disperse here on their own, but rather were intentionally transplanted to Sanchez Marsh by an anonymous party, and then spread to adjacent the Burlingame Lagoon sub area. All treatment of S. densiflora in Region 2 is conducted manually by digging the plants, and is conducted twice annually. In 30 of the 35 sub areas in this region, infestations have been reduced to just a trace of their former extent (< 1.0%) (see Table 4). Throughout the Colma Creek/San Bruno Complex (Site 18, see Figure 8 inset) there was only 0.04 acre mapped and treated a 99.9% reduction from the peak of 54.4 acres in The 2012 inventory included the mapping of two large clones (totaling 69 net m 2 ) on Confluence Marsh (18f), a site that was not permitted for treatment in 2011 but was permitted in at two other sub areas, SFO Shoreline (19h) and Seal Slough Mouth Central Marsh (19p.1), was also restricted in 2011; however, because of an error in interpreting maps of site boundaries, three mudflat clones on SFO Shoreline (19h) were mistakenly treated in 2011, which resulted in the 2012 inventory measuring a decline of hybrid S. alterniflora at this marsh. One sub area, Fisherman s Park (19m), situated between Anza Lagoon (19r) and Coyote Point County Park, reached its first year of zero detection of hybrid S. alterniflora in The ISP collaborates with the San Mateo County Mosquito and Vector Control District (SMCMVCD) for the vast majority of treatment in the San Francisco Peninsula Region. Most hybrid S. alterniflora sites in this region were treated with herbicide by backpack sprayer, but airboat applications were essential at several sites because target plants were growing too far out onto the extensive mudflats to allow access by foot. SMCMVCD previously used Argos (amphibious tracked vehicles) at many of these soft mud sites but tracked vehicles were no longer permitted in the 2011 and 2012 Biological Opinions. Airboats were used Invasive Spartina Project Progress Report

32 Figure 8. Distribution of non native Spartina in 2012 across the 35 sub areas of Reporting Region 2: San Francisco Peninsula. Invasive Spartina Project Progress Report

33 Table 5. Summary of 2012 invasive Spartina area by sub area within Reporting Region 2: San Francisco Peninsula. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 2: SAN FRANCISCO PENINSULA 12a: Pier 94 Yes 9/2 Backpack m² m² 0.6 m² 2003 >99% 99% 12b: Pier 98 / Heron's Head Yes 11/7 Backpack 0 36 m² 0 36 m² 370 m² % 29% 12c: India Basin Yes 9/2 Backpack m² m² 0.02 m² 2005 >99% 1100% increase (< 0.1 m²) 12d: Hunters Point Naval Reserve Yes 10/24 Backpack m² m² 6 m² 2008 >99% 6% increase (< 0.1 m²) 12e: Yosemite Channel Yes 9/27 Backpack 0 23 m² 0 23 m² 39 m² 2004 >99% 80% increase (10 m²) 12f: Candlestick Cove Yes 9/27 Backpack m² m² 0.4 m² 2006 >99% >99% 12g: Crissy Field Yes 9/20 Dug 0 2 m² 0 2 m² 5 m² 2002 >99% 269% increase (1 m²) 12h: Yerba Buena Island Yes Not surveyed in n/a n/a 12i: Mission Creek Yes 9/2 Backpack m² m² 1 m² 2009 >99% 83% 18a: Colma Creek Yes 8/23 Backpack 0 1 m² 0 1 m² 9 m² 2005 >99% 95% 18b: Navigable Slough Yes 8/23 Backpack 0 8 m² 0 8 m² 14 m² 2006 >99% 72% 18c: Old Shipyard Yes 8/23 Backpack m² m² 3 m² 2006 >99% >99% 18d: Inner Harbor Yes 8/23; 10/9 Backpack, Airboat 18e: Sam Trans Peninsula Yes 8/23 Backpack, Airboat 18f: Confluence Marsh No 8/23; 10/9 Backpack, Airboat 18g: San Bruno Marsh Yes 8/23; 10/9 Backpack, Airboat m² m² 4 m² 2001 >99% 99% 0 12 m² 0 12 m² 61 m² 2001 >99% 73% 0 69 m² 0 69 m² 201 m² 2004 >99% 48% 0 14 m² 0 14 m² 91 m² 2004 >99% 97% 18h: San Bruno Creek Yes 8/23 Backpack 0 50 m² 0 50 m² 152 m² 2001 >99% 36% 19a: Brisbane Lagoon Yes 8/22 Backpack 0 3 m² 0 3 m² 12 m² 2006 >99% 93% 19b: Sierra Point Yes 8/22 Backpack 0 6 m² 0 6 m² 14 m² 2004 >99% 92% 19c: Oyster Cove Yes 8/22 Backpack 0 2 m² 0 2 m² 5 m² 2006 >99% >99% Invasive Spartina Project Progress Report

34 Table 4. Summary of 2012 invasive Spartina area by sub area within Reporting Region 2: San Francisco Peninsula (continued). Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 2: SAN FRANCISCO PENINSULA (continued) 19d: Oyster Point Marina Yes 8/22 Backpack m² m² 2 m² 2006 >99% 87% 19e: Oyster Point Park Yes 8/22 Backpack 0 1 m² 0 1 m² 6 m² 2005 >99% 98% 19f: Point San Bruno Yes 8/22 Backpack 0 9 m² 0 9 m² 86 m² 2005 >99% 62% 19g: Seaplane Harbor Yes 10/23 Backpack, Airboat 19h: SFO Shoreline No 10/23; 12/7 Backpack, Airboat 19i: Mills Creek Mouth Yes 10/3; 10/9 Backpack, Airboat 19j: Easton Creek Mouth Yes 10/9 Backpack, Airboat 19k: Sanchez Marsh Yes 10/4 Dug, Backpack 0.05 m² 158 m² m² 19l: Burlingame Lagoon Yes 10/4 Dug, Backpack m² 25 m² m² 0 4 m² 0 4 m² 40 m² 2004 >99% 155% increase (3 m²) m² m² 0.4 ac % 73% 0 8 m² 0 8 m² 21 m² 2005 >99% 95% 0 4 m² 0 4 m² 13 m² 2004 >99% 99% 158 m² 0.3 ac % 65% 25 m² 183 m² 2004 >99% 60% 19m: Fisherman's Park Yes No invasive Spartina % 100% 19n: Coyote Point Marina / Marsh Yes 8/24 Backpack m² m² 2 m² 2003 >99% 98% 19o: San Mateo Creek / Ryder Park Yes 8/24 Backpack 0 3 m² 0 3 m² 11 m² 2006 >99% 83% 19p.1: Seal Slough Mouth Central Marsh 19p.2: Seal Slough Mouth Peripheral Marshes No 11/7 Backpack, Airboat Yes 8/24; 11/7 Backpack, Airboat 19r: Anza Lagoon Yes 10/4 Backpack m² m² ac ac 4.2 ac % 34% m² m² 0.3 ac 2004 >99% 72% 0.05 m² 2004 >99% >99% REGION 2 TOTAL 0.05 m ac 0.3 m ac 5.6 ac 2004 >99% 56% Invasive Spartina Project Progress Report

35 at the largest remaining infestation in the region, Seal Slough Mouth Central Marsh (19p.1), primarily to deploy personnel with backpack sprayers throughout the 97 acre marsh and to access and treat along the bay front edges. The ISP surveyed 35 sites in the San Francisco Peninsula Region for California clapper rails in 2012 and saw a slight decline from numbers over the prior two years (McBroom 2012). However, the 4 6 birds detected reflects a significant decline from 2007, when hybrid S. alterniflora dominated multiple shorelines and provided a large amount of non native habitat for clapper rails at the Colma Creek/San Bruno complex in South San Francisco. With the removal of invasive hybrid monocultures that had infested this area, the naturally occurring mudflats are now restored to their original extent. Because of the low elevation of the natural and historic mudflats in this area, this region is severely limited in the amount of area where any native vegetation can establish. With no significant opportunity to enhance habitat that could support sustainable populations of California clapper rail, revegetation efforts have been very limited and experimental in this region. A pilot project to introduce Spartina foliosa along Colma Creek was begun in 2011 and continued in 2012 by W. Thornton (San Francisco State University s Romberg Tiburon Center), and Grindelia stricta plants were installed on the marsh plain. Invasive Spartina Project Progress Report

36 2.3 REGION 3: SAN MATEO The San Mateo Region is comprised of the bay shore between Foster City and Menlo Park, and includes a varied mosaic of urbanized historic marsh, diked salt ponds, tidal marsh and expansive tidal flats. Within this region is the South Bay s largest remnant tract of ancient marsh, Greco Island, which is owned by the US Fish and Wildlife Service and managed as part of Don Edwards San Francisco Bay National Wildlife Refuge (DENWR). Because of development, what once was a three to four kilometer wide band of historic marsh lining the entire shoreline has now been reduced to fragmented marsh islands separated from the mainland by diked ponds managed for salt production. However, these remnants still provide thousands of acres of high quality tidal marsh habitat, albeit greatly reduced in scale from the historical footprint. This region has been heavily impacted by the hybrid S. alterniflora invasion, which quickly colonized the shoreline, marshes, and newly breached areas undergoing restoration from agriculture or salt production back to fully tidal marsh. Several large salt ponds are still slated for future restoration. It is critical to continue monitoring and treating new infestations in newly opened ponds, or restoration success could be severely threatened. The San Mateo Region s 26 sub areas (Figure 9, Table 5) were monitored on foot, by various boats and by helicopter to survey potential cordgrass habitat on the prominent islands and in the many large sloughs, ponds and newly breached marshes of this region. Aerial surveys for hybrid Spartina were completed using helicopters at the few large sites that have formidable persisting hybrid populations: Bird Island (2a.3) and the neighboring B2 North Quadrant (2c) and B2 South Quadrant (2d) portions of Outer Bair Island. The ISP identified a total of 8 acres of hybrid S. alterniflora in Region 3, despite the 57% decline since 2011 and 94% decline since the height of the infestation in 2004, when there were 135 acres. Restrictions in 2011 prohibited treatment at six sites in this region, including (in decreasing order of hybrid cover): B2 North Quadrant (2c), B2 South Quadrant (2d), Ravenswood Slough and Mouth (2i), Belmont Slough Mouth (2a.1), West Point Slough NW (2e) and Bird Island (2a.3). Two small patches of S. densiflora remained in this region at Maple Street Channel (19s) in 2012, both of which were new seedlings (totaling 0.22 m 2 ) from the seed bank left behind from plants discovered and treated during the 2010 monitoring season. Achieving complete and thorough treatment over the entirety of the San Mateo Region in any given year has been an enormous challenge for ISP partners. Over one thousand acres of tidal marsh have been impacted by either moderate or heavy infestations of hybrid Spartina, the majority located on islands, with many other areas that are difficult to access on foot due to very soft mud. Helicopter treatment was essential in reversing the spread and beginning to gain control of hundreds of acres of hybrid S. alterniflora in this region. The ISP has transitioned to ground based treatment whenever possible, but there have been significant obstacles to that strategy here that were not present at some of the other large infestations, such as the Alameda Flood Control Channel (Site 1) and Eden Landing Ecological Reserve (Site 13) on the East Bay shoreline, where access to hybrid populations is simpler. For example, due to permit restrictions in the 2011 and 2012 Biological Opinions, SMCMVCD could not deploy Argos onto Greco Island (2f & 2h) or Bair Island (2b, 2c, 2d, 2k & 2m), or out into some soft mud of Belmont Slough (2a) and Ravenswood Slough (2i), and tackling these infestations with backpack applications alone was not feasible. Using a boat with a propeller motor has serious limitations, because propeller motors require a depth of water, which is normally counter to the ebb tide conditions needed for sufficient herbicide dry time. Invasive Spartina Project Progress Report

37 Figure 9. Distribution of non native Spartina in 2012 across the 26 sub areas of Reporting Region 3: San Mateo. Invasive Spartina Project Progress Report

38 Table 6. Summary of 2012 invasive Spartina area by sub area within Reporting Region 3: San Mateo. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 3: SAN MATEO 02a.1a: Belmont Slough Mouth No 9/5 9/7; 10/2 10/3; 11/19 11/20 Backpack, Airboat ac ac 2.4 ac % 43% 02a.1b: Belmont Slough Mouth South 02a.2: Upper Belmont Slough and Redwood Shores No 9/5 9/7; 10/2 Backpack, Airboat ac ac 1.4 ac % 4% Yes 9/4 9/5 Backpack, Airboat ac ac 1.8 ac % 60% 02a.3: Bird Island No 11/19 11/20 Backpack, Airboat m² m² 0.9 ac % 32% 02a.4: Redwood Shores Mitigation Bank n/a New Subarea No in m² 0 6 m² 32 m² 2012 n/a n/a 02b.1: Corkscrew Slough Yes 12/6 Backpack, Airboat ac ac 1 ac % 60% 02b.2: Steinberger Slough South, Redwood Creek Northwest Yes 9/7; 11/19 11/20; 12/6 Backpack, Airboat ac ac 2.4 ac % 65% 02c.1a: B2 North Quadrant West No 10/18 10/19; 11/20 Backpack, Airboat ac ac 7.6 ac % 5% 02c.1b: B2 North Quadrant East No 8/31 Aerial: Broadcast ac ac 13.2 ac % 53% 02c.2: B2 North Quadrant South Yes 10/17 10/18 Backpack, Airboat 0 1 ac 0 1 ac 5 ac % 58% 02d.1a: B2 South Quadrant West No 11/1 11/2; 11/19 02d.1b: B2 South Quadrant East No 11/1 11/2; 11/19 02d.2: B2 South Quadrant (2) Yes 11/1 11/2; 11/19 02d.3: B2 South Quadrant (3) Yes 10/18; 11/1; 11/19 02e: West Point Slough NW No 10/6; 11/27; 12/6 Backpack, Airboat ac ac 4.9 ac % 41% Backpack, Airboat m² m² 0.6 ac 2004 >99% 54% Backpack, Airboat m² m² 0.7 ac % 80% Backpack 0 53 m² 0 53 m² 661 m² 2001 >99% 55% Airboat m² m² 1 ac % 33% Invasive Spartina Project Progress Report

39 Table 5. Summary of 2012 invasive Spartina area by sub area within Reporting Region 3: San Mateo (continued). Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 3: SAN MATEO (continued) 02f: Greco Island North Yes 9/19; 9/21 9/22; 9/24 Backpack, Airboat ac ac 4.9 ac % 63% 02g: West Point Slough SW and East Yes 10/5; 11/27; 12/6 Backpack m² m² 0.4 ac 2005 >99% 55% 02h: Greco Island South Yes 9/19; 9/21 9/22; 10/6 Backpack, Airboat ac ac 3.5 ac % 78% 02i: Ravenswood Slough and Mouth No 11/6; 11/27 Backpack, Airboat ac ac 5.9 ac % 24% increase (590 m²) 02j.1: Ravenswood Open Space Preserve (N of Hwy 84) 10/5; 11/27 Backpack, Airboat 0 9 m² 0 9 m² 79 m² % 90% 02k: Redwood Creek and Deepwater Slough Yes 9/18; 11/5; 12/6 Backpack, Airboat m² m² 1.5 ac % 91% 02l: Inner Bair Yes 9/18 Backpack 0 13 m² 0 13 m² 200 m² 2006 >99% 87% 02m: Pond B3 Yes 11/19 11/20 Airboat m² m² 0.4 ac 2012 n/a 165% increase (179 m²) 19q: Foster City Yes 8/24 Backpack m² m² 2 m² 2004 >99% 87% 19s: Maple Street Channel Yes 5/31; 11/15 Dug 0 4 m² 0.2 m² 5 m² 11 m² % 90% REGION 3 TOTAL ac 0.2 m² 8.1 ac 59.6 ac % 57% Invasive Spartina Project Progress Report

40 After a successful pilot project testing an airboat as a treatment platform and several years of successful implementation throughout portions of DENWR, the Coastal Conservancy acquired an airboat that is used, maintained, and housed by SMCMVCD for use at these San Mateo Region sites. The 2012 treatment season was the first year of full implementation using the new airboat, and it allowed for the first year of full treatment of all sub areas in the region. In 2012, 20 sub areas in the San Mateo Region were treated by airboat (Table 5), which represents 83% of the ISP sites in this region. Crews utilized backpack applicators deployed onto the marsh plain from the airboat to treat scattered plants or to access infestations beyond reach of the 300 feet of airboat hose. With two airboats available, ISP partners were able to complete the most thorough treatment to date of such challenging areas of Region 3 as B2 North Quadrant (2c), Deepwater Slough (2k), Pond B3 (2m), and Greco Island South (2h). However, with the late start due to permitting delays, two sites, Belmont Slough (2a) and Ravenswood Slough (2i), experienced a high percentage of senescence by the time of treatment. Meanwhile, many hybrid plants within some areas of Bair Island were still green and actively growing well into December. The ISP noted these phenological differences between sites, with the knowledge gained being folded into the planning for subsequent treatment seasons in an attempt to catch all plants before they set seed, and certainly before they senesce. The ISP surveys 19 California clapper rail sites in the San Mateo Region, and all were surveyed in 2012 (18 sites by the ISP and one site by Point Blue Conservation Science) data show a continued positive trend in rail numbers over the last four years (McBroom 2012), despite the continuous and significant annual decrease in hybrid Spartina cover resulting from effective treatment. The presence of abundant S. foliosa and concurrent persisting hybrid in this region left little opportunity in 2012 for native cordgrass planting by the Restoration Program. Instead, four high tide refuge islands were constructed and planted two along Belmont Slough (2a.1 2), one on Bird Island (2a.3), and one at Bair Island (B2 North Quadrant [2c]). In addition, 25 artificial floating nesting islands were placed on Greco Island North (2f). Extensive revegetation has occurred for two years ( and ) at Greco Island North and Bair Island (B2 North) with more than 10,100 plants, primarily Grindelia stricta, installed by the Restoration Program. Invasive Spartina Project Progress Report

41 2.4 REGION 4: DUMBARTON SOUTH The Dumbarton South Region includes all intertidal lands south of the Dumbarton Bridge, and includes a total of 20 sub areas (Figure 10, Table 6). The landscape in this portion of the bay is a mosaic of wetland habitats including salt marsh, salt ponds, mudflats, and vernal pools, predominantly owned and managed by the Don Edwards San Francisco Bay National Wildlife Refuge (DENWR). The marshes in this region are of a wide variety of age classes ranging from historic (Laumeister Marsh [part of 15b], Dumbarton and Audubon Marshes [5b]), to well developed restoration marshes (Faber Marsh [part of 15b], La Riviere Marsh [5d] and Palo Alto Baylands [8]), to recently breached restoration sites (Island Ponds [05i], Knapp Tract [15a.6], and Pond A17). The Dumbarton South Region has seen a net increase in tidal wetlands over the last 50 years due to high sedimentation rates and subsequent marsh accretion, as well as accomplishments by the South Bay Salt Pond Restoration Project (SBSP). This region includes the bulk of the former salt evaporators that are slated to become tidal wetlands as part of the SBSP. These increases in tidal marsh have resulted in a large increase to the habitat that the ISP has to survey annually and potentially treat; over 2,000 acres have been added to the area surveyed by the ISP in this region since The expansive amount of tidal wetland area to survey as well as the large remaining amount of hybrid Spartina present in the Dumbarton South Region led to a higher reliance on helicopter inventory over any other region in The large and remote sub areas of Calaveras Marsh (5a.2), Coyote Creek including Ogilvie Island (15a), Mowry Slough and Mowry Marsh (5a.1) were all mapped via helicopter in The remaining 18 sub areas were inventoried by foot and kayak. The Dumbarton South Region contained 5acres of non native Spartina, exclusively hybrid S. alterniflora, which reflects a 9% increase from the invasion level in 2011 and ranks it currently as the fourth most invaded region in the Estuary. This increase is driven by uninhibited hybrid expansion at the only three sub areas in the region where treatment was not permitted in 2011: Inner Cooley Landing (16.2), Alviso Slough (15a.4) and Calaveras Marsh (5a.2). Hybrid S. alterniflora is currently at 13% of its peak footprint of 40 acres in 2008, with ISP partners achieving 87% control of the invasion as of 2012 in this region. However, the Dumbarton South Region did have the only instance of a new infestation as defined as hybrid discovered more than 1km from any detection in prior years. Three new clones were found extending barely more than a kilometer upstream from 2011 locations in the upper reaches of Mowry Slough (05a.1). These clones were treated by backpack in Between , hybrid S. alterniflora treatment was severely limited in the Dumbarton South Region by a September 1 marsh entry date that marks the end of clapper rail breeding season. The entry restriction allowed hybrid S. alterniflora to continue spreading for several additional years after the start of the Program, and resulted in the peak of the invasion not occurring until 2008, 2 3 years later than most other regions. There were too many infestation sites to inventory and treat before the plants senesced each year, and many members of the hybrid swarm would set seed by late September. This was especially true for the vast marshes of DENWR, most of which contain high quality clapper rail habitat. The region also contains hundreds of acres of native cordgrass, and since the hybrid invasion was just moving into the area, there were still many nascent infestations and cryptic forms that could escape detection until they began to stand out from the surrounding S. foliosa. In addition, since helicopter monitoring was necessary to efficiently inventory the area each year, smaller and more cryptic forms of hybrid may not have been detected. Invasive Spartina Project Progress Report

42 Figure 10. Distribution of invasive Spartina in 2012 across the 24 sub areas of Reporting Region 4: Dumbarton South Invasive Spartina Project Progress Report

43 Table 7. Summary of 2012 invasive Spartina area by sub area within Reporting Region 4: Dumbarton South. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 4: DUMBARTON SOUTH 02j.2: Ravenswood Open Space Preserve (S of Hwy 84) Yes 10/5; 11/27 Backpack, Airboat 0 31 m² 0 31 m² 209 m² 2006 >99% 75% 02n: SF2 n/a New Subarea No in m² 0 1 m² 25 m² 2012 n/a n/a 05a.1: Mowry Marsh and Slough Yes 9/7; 9/18; 11/12; 12/10; 12/14 Backpack, Airboat m² m² 1.5 ac % 90% increase (314 m²) 05a.2: Calaveras Marsh No 10/3 10/5 Backpack, Amphibious vehicle, Airboat ac ac 6.7 ac % 45% increase (920 m²) 05b: Dumbarton/Audubon Yes 8/23 8/24; 9/7 Backpack, Airboat ac ac 1 ac % 65% 05c.1: Newark Slough West Yes 10/8 Backpack, Airboat 0 68 m² 0 68 m² 537 m² % 67% 05c.2: Newark Slough East Yes 9/7; 10/8 Backpack, Airboat m² m² 1008 m² % 90% 05d: LaRiviere Marsh Yes 9/8 Backpack 0 58 m² 0 58 m² 800 m² 2006 >99% 89% 05e: Mayhew's Landing Yes 9/8 Backpack m² m² 589 m² % 68% 05f: Coyote Creek Alameda County Yes Not surveyed in n/a no data in g: Cargill Pond (W Hotel) Yes 9/8 Backpack 0 4 m² 0 4 m² 24 m² 2010 >99% 89% 05h: Plummer Creek Mitigation Marsh Yes 9/14 Backpack 0 3 m² 0 3 m² 26 m² % 98% 05i: Island Ponds n/a 12/14 Backpack 0 5 m² 0 5 m² 39 m² 2012 n/a n/a 08: Palo Alto Baylands Yes 8/27; 9/3 Truck, Backpack ac ac 1 ac % 15% 15a.1: Charleston Slough to Mountainview Slough Yes 9/4 9/5 Truck, Backpack 0 52 m² 0 52 m² 334 m² 2004 >99% 70% 15a.2: Stevens Creek to Guadalupe Slough Yes 9/5; 9/17 Truck, Backpack 0 36 m² 0 36 m² 189 m² % 44% Invasive Spartina Project Progress Report

44 Table 6. Summary of 2012 invasive Spartina area by sub area within Reporting Region 4: Dumbarton South (continued). Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 4: DUMBARTON SOUTH (continued) 15a.3: Guadalupe Slough Yes 9/19 Truck, Backpack m² m² 0.3 ac % 21% increase (70 m²) 15a.4: Alviso Slough No 9/18; 10/5; 11/3; 11/12 Backpack, Airboat 0 1 ac 0 1 ac 3.7 ac % 198% increase (0.7 ac) 15a.5: Coyote Creek to Artesian Slough Yes 11/3; 11/12 Truck, Backpack, Airboat 0 66 m² 0 66 m² 161 m² % 344% increase (51 m²) 15b: Faber / Laumeister Marsh Yes 9/7 Backpack m² m² 0.3 ac % 37% 15c: Shoreline Regional Park Yes 9/13 Backpack m² m² 0.3 ac % 32% 16.1: Cooley Landing Central No 9/17 9/18, 11/9 Backpack, Airboat ac ac 7.6 ac % 352% increase (1.2 ac) 16.2: Cooley Landing West Yes 9/17 9/18 Truck, Backpack, Airboat ac ac 4.5 ac % 46% REGION 4 TOTAL ac ac 27.8 ac % 9% increase Invasive Spartina Project Progress Report

45 Airboats were used for treatment at 10 sub areas in the Dumbarton South Region in 2012 (Table 6), representing 50% of the region total, while the remaining sites were primarily treated via backpack applications, with a small number by hose application from a trucks on an adjacent levee. An amphibious tracked vehicle (Marshmaster ) was permitted for use on a single site, Calaveras Marsh (5a.2), due to the difficulty of remote access of that 700+ acre marsh. This marsh is up to 900 m wide from the bay front to the high marsh transition at an impassable levee, a distance too great for backpack applicators to repeatedly traverse for treatment and refilling of backpacks. Aside from Palo Alto Baylands (8) which still contains a moderate infestation of hybrid Spartina on southeast Hooks Island, and the airboat sites discussed above, the rest of the work in the region is comprised of treating lightly infested marshes (e.g. Faber/Laumeister [15b], Stevens Creek Tidal Marsh[15c]) or widely scattered clones along the many miles of shoreline on the banks of the sloughs and creeks at the edge of the far south bay (including Alviso, Guadalupe, Stevens, Permanente, and Charleston within 15a). The rapid colonization by Spartina in the Island Ponds (A19 21) of Coyote Creek was previously thought to be composed solely of native recruits. In 2012, researchers with the SBSP discovered a well established clone of obvious hybrid S. alterniflora, and it was treated. This discovery highlights the inherent risk of restoring salt ponds to tidal marsh in areas near invasive hybrid Spartina stands. The ISP and the SBSP coordinate to monitor and treat new infestations in order to protect the investments in both projects. Through the efforts of the ISP, DENWR, and Point Blue Conservation Science, 30 sites were surveyed for California clapper rails in the Dumbarton South Region in This region includes some of the highest quality clapper rail habitat in the Estuary, and survey results revealed detection increases since 2011 (McBroom 2012; Wood 2013). Sites in this region generally have abundant S. foliosa and are not a high priority for ISP revegetation efforts. However, the ISP and partners constructed one high tide refuge island at Cooley Landing (16.2) in No other habitat enhancements were installed in 2012 within Region 4, though the Restoration Program harvested S. foliosa from three marshes Permanente Creek [15a.1], Alviso Slough [15a.4], Coyote Creek [15a.5] for propagation and planting in other regions around the Estuary. Invasive Spartina Project Progress Report

46 2.5 REGION 5: UNION CITY The Union City Region extends from San Mateo Bridge to the Dumbarton Bridge marshes on the eastern side of the Bay, and was once the delta of the largest watershed in the south bay (the Alameda Creek watershed). Since the early 1900s, hydrology in this region has been altered by high density development upstream, with the resulting water flow channelized into two creeks: Old Alameda Creek and the Alameda Flood Control Channel. Land use in the downstream portion of this region was primarily agricultural (salt ponds and cattle grazing), which resulted in only minimal amounts of urban development along the shoreline stretching inland for about three miles. This area is instead a wide expanse of former salt evaporators and grazing pastures in various stages of management (muted, tidal, or ponded). The first marsh reestablishment in the region began in the 1930s with a natural flooding event that created Whale s Tail and Ideal Marshes. By 2009, over 800 acres of marsh were being reestablished as former salt evaporators were restored to tidal action. The largest of these projects occurred within the Eden Land Ecological Reserve as part of the SBSP. In future years, over 2,000 additional acres are slated for restoration to tidal action. The Union City Region is one of the regions most affected by hybrid S. alterniflora. Pond 3 (1f), adjacent to the Alameda Flood Control Channel (Site 1) was the original introduction location of Spartina alterniflora in the 1970s during an experiment in dredge spoils stabilization and habitat restoration conducted by the Army Corps of Engineers. By the mid 1990s, S. alterniflora had spread throughout the Estuary and researchers discovered that it had hybridized with native S. foliosa. As the infestation expanded in the absence of coordinated treatment, native Spartina was almost completely extirpated from most of the marshes in the Union City Region as a result of displacement and assimilation by hybrid S. alterniflora. All restoration projects in this region that were breached and restored to full tidal action quickly became infested with hybrid Spartina. By 2004, there were over 135 net acres of hybrid Spartina at the Alameda Flood Control Channel (Site 1) and another 64 net acres throughout Eden Landing Ecological Reserve (Site 13). To a greater degree than anywhere else in the Estuary, entire marshes were dominated by tall meadows of cordgrass that excluded native marsh plants, and mudflats and channels were extensively colonized. Fortunately, residential and commercial development was mainly sequestered to the east of these marsh complexes, and the areas were either closed to the public or contained only a few levee access points, which could be effectively closed by the land manager. This allowed the ISP to use aerial broadcast applications of herbicide from to gain control of the infestation and stop seed and propagule dispersal. None of the sites in the Union City Region are islands, and all of the infestations are easily accessible from levees. Once the aerial broadcast work had substantially reduced the infestation, the Alameda County Flood Control District (ACFCD) was able to implement ground based treatment on a large scale with their Argo (amphibious tracked vehicle). The 21 sub areas within the Union City Region (Figure 11, Table 7) were monitored extensively on foot, supplemented by kayak surveys of Old Alameda Creek (13a 13c) and the recently breached Pond E8a [13m] in the Eden Landing Complex. With once the largest invasion in the Estuary (233 acres of hybrid in 2004), only 0.42 acres of non native cordgrass was mapped here in This drastic decline is the result of aerial broadcast of herbicide during the initial treatment of hybrid monocultures in and the persistent follow up treatment by Argo and truck in , bringing the invasion footprint down to 0.18% of Invasive Spartina Project Progress Report

47 Figure 11. Distribution of invasive Spartina in 2012 across the 21 sub areas of Reporting Region 5: Union City. Invasive Spartina Project Progress Report

48 Table 8. Summary of 2012 invasive Spartina area by sub area within Reporting Region 5: Union City. Net Spartina Coverage By Species All Invasive Spartina Cover Split Sub area REPORTING REGION 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 5: UNION CITY 01a: AFCC Channel Mouth Yes 8/22 Truck, Backpack 0 14 m² 0 14 m² 42 m² 2004 >99% 53% 01b: AFCC Lower Channel Yes 8/22 8/23 Truck, Backpack 0 46 m² 0 46 m² 261 m² 2004 >99% 90% 01c: AFCC Upper Channel Yes 8/22 8/23 Truck, Backpack 0 17 m² 0 17 m² 111 m² 2004 >99% 74% 01d: AFCC Upper Channel Union City Blvd to I e: Strip Marsh No. of Channel Mouth Yes 8/23 Truck, Backpack m² m² 444 m² 2005 >99% 30% Yes 8/22 Truck, Backpack 0 1 m² 0 1 m² 4 m² 2004 >99% 372% increase (1 m²) 01f: Pond 3 AFCC Yes 8/22 Backpack 0 6 m² 0 6 m² 16 m² 2001 >99% 97% 13a: Old Alameda Creek North Bank Yes 8/22 Truck, Backpack m² m² 15 m² 2005 >99% 95% 13b: Old Alameda Creek Island Yes 8/23 Backpack 0 31 m² 0 31 m² 232 m² 2001 >99% 60% 13c: Old Alameda Creek South Bank Yes 8/23, 10/19 Truck, Backpack 0 2 m² 0 2 m² 8 m² 2001 >99% 69% 13d: Whale's Tail North Fluke Yes 8/23 Backpack m² m² 841 m² 2005 >99% 104% increase (189 m²) 13e: Whale's Tail South Fluke Yes 9/3 Backpack 0 4 m² 0 4 m² 45 m² 2001 >99% 96% 13f: Cargill Mitigation Marsh Yes 8/23 Backpack 0 40 m² 0 40 m² 130 m² 2004 >99% 85% 13g: Upstream of 20 Tide Gates Yes No invasive Spartina 2011 or % n/a 13h: Eden Landing North Creek Yes 9/7 Truck, Backpack 0 11 m² 0 11 m² 58 m² 2007 >99% 1319% increase (11 m²) 13i: Eden Landing Pond 10 Yes No invasive Spartina 2011 or % n/a 13j: Eden Landing Mt Eden Creek Yes 8/22 Backpack 0 6 m² 0 6 m² 19 m² % 73% 13k: Eden Landing Reserve South North Creek Marsh 13l: Eden Landing Reserve North Mt Eden Creek Marsh Yes 8/22 Backpack 0 31 m² 0 31 m² 85 m² % 27% Yes 9/7, 10/19 Backpack 0 3 m² 0 3 m² 5 m² % 93% Invasive Spartina Project Progress Report

49 Table 7. Summary of 2012 invasive Spartina area by sub area within Reporting Region 5: Union City (continued). Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 5: UNION CITY (continued) 13m: Eden Landing Ponds E8A, E9, and E8X New Subarea No Invasive Spartina in n/a n/a n/a 21a: Ideal Marsh North Yes 8/24 Backpack 0 44 m² 0 44 m² 346 m² 2001 >99% 95% 21b: Ideal Marsh South Yes 8/24; 10/8 Backpack, Airboat m² m² 1 ac 2006 >99% 52% REGION 5 TOTAL ac ac 1.7 ac 2004 >99% 62% Invasive Spartina Project Progress Report

50 its 2004 amount. In this region, there are two sub areas with a history of hybrid infestation (Upstream of 20 Tide Gates on Old Alameda Creek [13g] and Eden Landing Pond 10 [13i]) where no invasive Spartina has been detected since To date, no invasive cordgrass species other than hybrid S. alterniflora has been discovered in this region. of the minimal remnant amount of hybrid S. alterniflora in the Union City Region is conducted exclusively by backpack, with applicators led to previously mapped patches by ISP biologists. As these sites which are near eradication, the remaining hybrids are often very sparse and widely scattered, resulting in the majority of the time spent on mobilization and moving applicators across marsh plains and through muddy sloughs with very little time spent actually applying herbicide. This distribution of remaining hybrids highlights the necessity of the treatment surveys that the ISP began in 2009 (see description above in Invasive Spartina Project Program Areas ) for achieving complete coverage of the infestation at each site. In 2012, the ISP conducted a pilot of round two inventory to determine if it would be valuable to revisit sites that are approaching eradication towards the end of the season to catch plants that were missed in the first round. Some plants can be hard to detect or identify due to being hidden by tall pickleweed or other vegetation or grazing by birds, while others may not have been sprayed sufficiently or were simply overlooked. Based on the results of this pilot, some of these sites will be prioritized in 2013 for a second round of inventory and followed up with spot treatment to maintain an eradication trajectory. The Union City Region includes 20 California clapper rail sites, eleven of which were surveyed by the ISP in 2012 and the remaining nine sites by staff at DENWR. Survey results were consistent with past years results, indicating a stable trend for rail populations in the region (McBroom 2012). Since most formerly native cordgrass was assimilated by the hybrid invasion and subsequently treated and removed from many marshes in this region, the ISP took advantage of the ample opportunities for S. foliosa reintroduction. Extensive revegetation has occurred throughout the region, with over 71,360 Grindelia and S. foliosa plants installed during the first two seasons ( and ) along the Alameda Flood Control Channel (1a & 1b) and at multiple sites within Eden Landing Ecological Reserve (13b, 13c, 13d, 13e, 13f, 13j, and 13k). Native cordgrass reintroduction has proven highly successful at two sites in particular: Alameda Flood Control Channel (1a & 1b) and North Creek Marsh (13k). In 2012, 25 artificial floating nesting islands were placed at Whale s Tail South (13e) in collaboration with USGS. Invasive Spartina Project Progress Report

51 2.6 REGION 6: HAYWARD Extending from Oakland Airport south to the San Mateo Bridge, the Hayward Region is one of the most heavily urbanized shorelines in the Estuary. It has not historically supported abundant tidal marsh habitat, the most prominent tract of which was filled and developed for Oakland International Airport during World War II. Today the region is primarily comprised of a broad band of tidal mudflat and three recently restored marsh complexes with minimal interconnectivity: Cogswell Marsh (restored 1980), Robert s Landing (restored 1995), and Oro Loma (restored 1997). These mostly low and mid elevation marshes are predominantly vegetated by pickleweed and lack the higher elevation zones needed to support a more diverse suite of native plants. Channel development at these sites is also simple, lacking the complex branching and sinuosity derived from more mature geomorphology. As of 2012, the establishing vegetation in these relatively young restored marshes has not been sufficient to provide quality native habitat for California clapper rails and other marsh species. The coincidental timing of the baywide spread of hybrid Spartina and the restoration of tidal connection to these previously diked sites provided an unfortunate optimal scenario for quick and complete invasion of the marsh complexes and associated shorelines. By 2005 the region was infested with 226 acres of hybrid S. alterniflora, and the native marsh plant community that had begun to develop at each site since restoration was being replaced by hybrid cordgrass meadows. In addition, many miles of unvegetated mudflats along the remnant strip marshes and rip rap shoreline of the Hayward Region became dominated by hybrid Spartina, and flood control channels became clogged with the tall, dense cordgrass. From , ISP partners relied on aerial broadcast applications of herbicide by helicopter to gain control over the heavy infestations at the large sites in the Hayward Region. Since these sites are fragmented from other tidal marshes by urban development, and several lack the vegetative structure and geomorphology of more mature systems, treatment was phased in at several locations to reduce impacts to the resident California clapper rails, which had been drawn to and were becoming reliant on the extensive stands of hybrid S. alterniflora. In Region 6, this phase in took the form of gradually adding portions of Cogswell Marsh (20m o) to the annual treatment program until the entire site was included. The substantial reductions in hybrid Spartina cover achieved through 2011 have allowed for shifts in treatment methodologies in response to changing conditions. Work at large sites such as Cogswell Marsh (20m o) and Oro Loma Marsh (7a & 7b) transitioned from broadcast aerial herbicide applications to a combination of airboat and backpack applications, while the use of Argos was discontinued along the flood control channels and rip rap shoreline that can now be adequately managed by spot treatment from backpack alone. The ISP monitored its 28 Hayward Region sub areas (Figure 12, Table 8) exclusively on foot in 2012, mapping 7.57 acres of hybrid S. alterniflora net cover. No other invasive Spartina species is present in this region. This represents an increase of 2.73 acres (56.4%) of net hybrid coverage, the largest increase in the Estuary. The most significant increases were observed in the three sub areas where treatment was prohibited in 2011, including (in order of decreasing hybrid extent): Cogswell Marsh B (20n), Citation Marsh (20d) and North Marsh (20f). Two sub areas in this region experienced the first year where the ISP did not detect any hybrid: Hayward Shoreline Outliers [20p] and Triangle Marsh [20w], both adjacent to Cogswell Marsh, Quadrant A [20m]. Invasive Spartina Project Progress Report

52 Figure 12. Distribution of invasive Spartina in 2012 across the 28 sub areas of Reporting Region 6: Hayward. Invasive Spartina Project Progress Report

53 Table 9. Summary of 2012 invasive Spartina area by sub area within Reporting Region 6: Hayward. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 6: HAYWARD 07a: Oro Loma Marsh East Yes 9/4,9/11 Backpack, Airboat m² m² 0.3 ac 2008 >99% 70% 07b: Oro Loma Marsh West Yes 9/4 5, 9/11 Backpack, Airboat m² m² 0.7 ac 2005 >99% 73% 20a: Oyster Bay Regional Shoreline Yes 8/24, 9/4 5 Truck, Backpack m² m² 534 m² 2004 >99% 43% 20b: Oakland Metropolitan Golf Links Yes 10/4, 10/19 Truck, Backpack m² m² 0.4 ac % 125% increase (224 m²) 20c: Dog Bone Marsh Yes 9/20 Truck, Backpack 0 35 m² 0 35 m² 92 m² 2006 >99% 766% increase (31 m²) 20d.1: Citation Marsh South No 9/21 Backpack 0 85 m² 0 85 m² 576 m² % 215% increase (58 m²) 20d.2: Citation Marsh North No No Allowed in ac ac 4.1 ac % 67% increase (1813 m²) 20e: East Marsh Yes 9/20 Truck, Backpack m² m² 2 m² 2004 >99% 97% 20f.1: North Marsh North No No Allowed in ac ac 1 ac % 401% increase (980 m²) 20f.2: North Marsh South No No Allowed in ac ac 3 ac % 53% increase (566 m²) 20g: Bunker Marsh No No Allowed in ac ac 1.1 ac % 23% increase (217 m²) 20h.1: San Lorenzo Creek and Mouth North 20h.2: San Lorenzo Creek and Mouth South No No Allowed in m² 0 75 m² 672 m² 2004 >99% 57% Yes 9/20 Backpack m² m² 462 m² 2004 >99% 60% 20i: Bockmann Channel Yes 8/22 Truck m² m² 2 m² 2004 >99% 86% 20j: Sulphur Creek Yes 8/22 Truck 0 3 m² 0 3 m² 4 m² 2001 >99% 3918% increase (3 m²) 20k: Hayward Landing Yes 8/22 Truck, Backpack m² m² 1 m² 2001 >99% 14% Invasive Spartina Project Progress Report

54 Table 8. Summary of 2012 invasive Spartina area by sub area within Reporting Region 6: Hayward (continued). Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 6: HAYWARD (continued) 20l: Johnson's Landing Yes 8/22 Backpack m² m² 0.5 m² 2005 >99% 91% 20m: Cogswell Marsh, Quadrant A Yes 8/22 Backpack 0 46 m² 0 46 m² 166 m² 2005 >99% 96% 20n: Cogswell Marsh, Quadrant B No No Allowed in ac ac 10.1 ac % 162% increase (2.6 ac) 20o: Cogswell Marsh, Quadrant C No No Allowed in ac ac 1.5 ac % 9% 20p: Hayward Shoreline Outliers Yes No Invasive Spartina % 100% 20q: San Leandro Shoreline Outliers 20r: Oakland Airport Shoreline and Channels Yes 9/20 Truck m² m² 0.4 ac % 415% increase (688 m²) Yes 10/4 Truck, Backpack m² m² 1002 m² % 84% increase (167 m²) 20s: H.A.R.D. Marsh Yes 8/22 Backpack, Airboat 0 3 m² 0 3 m² 8 m² % 77% 20t: San Leandro Marina Yes 9/20 Truck m² m² 3 m² % 79% 20u: Estudillo Creek Channel 20v: Hayward Landing Canal Yes 9/20 Truck 0 20 m² 0 20 m² 71 m² % 31% increase (5 m²) Yes 9/21 Backpack m² m² 242 m² 2005 >99% 178% increase (74 m²) 20w: Triangle Marsh Yes No Invasive Spartina % 100% REGION 6 TOTAL ac ac 23.7 ac % 56% increase Invasive Spartina Project Progress Report

55 In 2012 the ISP surveyed 25 California clapper rail sites in the Hayward Region. Interestingly, there were decreases in rail detections at several sites where treatment was not permitted in 2011, most notably at Citation Marsh (20d) in the Robert s Landing complex. Despite these local decreases, regional rail numbers appeared to be stable from (McBroom 2012). The young status of the restoration marshes in this region and their immediate infestation by hybrid Spartina and subsequent treatment has resulted in an absence of both native cordgrass and marsh gumplant (Grindelia stricta), both of which the Restoration Program is working to enhance through extensive revegetation projects. High density plantings have occurred throughout the region with 25,750 plants installed during the first two seasons ( and ) at the Cogswell, Oro Loma and Robert s Landing marsh complexes. Additionally, 50 artificial floating nesting islands were placed at the Cogswell Marsh and Robert s Landing in Invasive Spartina Project Progress Report

56 2.7 REGION 7: SAN LEANDRO BAY The San Leandro Bay Region is a highly urbanized portion of the Bay that extends north from the Oakland Airport to the Bay Bridge. The once extensive marshes in this region have largely fallen victim to bay fill and development. Only one historic marsh, Arrowhead Marsh, exists in this region, and even its creation was caused by human intervention (the collapse of the upstream Lake Chabot dam in 1874, which was potentially exacerbated by logging practices). San Leandro Bay has been impacted by urbanization and industrial land use, with the Port of Oakland, Oakland International Airport, Oakland Coliseum complex and the Nimitz Freeway (I 880) all surrounding the water body and built on former marshland. Bay Farm Island and portions of Alameda Island were created by bay fill and now have only fringing marshes associated with them. Currently this region contains a series of small marshes with relatively simple elevation and vegetative structure, riprap shoreline, and narrow fringing shoreline marshes. This region was among the most impacted by hybrid Spartina, which created and expanded marsh habitat where primarily mudflat previously occurred. As in the Hayward Region (Region 6, discussed above), the ISP initially relied on aerial broadcast treatment from helicopter where appropriate to reduce the monocultures of hybrid Spartina that dominated the remnant tidal marshes and colonized the unvegetated mudflats and channels. The hybrid S. alterniflora meadows at Elsie Roemer (included in 17a) were treated from by broadcast application of herbicide from a large amphibious tracked vehicle (Marsh Mog ), while the flood control channels throughout the Oakland Coliseum complex (17i) were treated from the smaller Argos. Both amphibious vehicles have a very low ground pressure to allow access to soft muddy areas where a backpack applicator could not walk, and they accommodate the transport of the larger quantity of herbicide that was necessary to efficiently treat these monocultures of hybrid S. alterniflora. The highly fragmented nature of the marshes in this urbanized region required that treatment be phased in to reduce the impacts to resident California clapper rails, the population of which had increased in this region in the 2000s presumably due to hybrid S. alterniflora expansion. In addition to increasing the proportion treated over several seasons, the ISP utilized seed suppression (described in footnote 2 on page 17) at Arrowhead Marsh East (17c.2) and MLK New Marsh (17h) to slowly increase the treatment footprint. The 19 sub areas of the San Leandro Bay Region (Figure 13, Table 9) were monitored on foot in 2012, with the exception of Oakland Inner Harbor (17f) and Crab Cove (a small portion of 17a), which were surveyed on foot and also by boat. Hybrid S. alterniflora was the only non native cordgrass species found in Region 7, with a net cover of 15 acres, almost identical to the amount found in San Leandro Bay remains the most invaded region, harboring 39% of the remaining non native cordgrass in the entire Estuary (15 of 38 acres). The four sites exhibiting the largest increases in 2012 occurred either in marshes where treatment was prohibited in 2011 or along the shoreline between them where treatment was authorized (in order of decreasing hybrid extent): Arrowhead Marsh West (17c.1), Damon Marsh (17d.4), Fan Marsh (17j) and Fan Marsh Shoreline (17d.1). The two sub areas that contain the largest amount of hybrid S. alterniflora, Arrowhead Marsh East (17c.2) and MLK New Marsh (17h), showed slight decreases in the reported area of the invasive, which are attributable to differences in assessment of cover in the field while surveying the larger expanses of hybrid that grew in the absence of treatment, and are not likely actual declines in hybrid cover. Hybrid extent in San Leandro Bay stands at 18% of its peak infestation in 2006 (15 of 83 acres), and has not changed significantly since Invasive Spartina Project Progress Report

57 Figure 13. Distribution of invasive Spartina in 2012 across the 19 sub areas of Reporting Region 7: San Leandro Bay. Invasive Spartina Project Progress Report

58 Table 10. Summary of 2012 invasive Spartina area by sub area within Reporting Region 7: San Leandro Bay. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 7: SAN LEANDRO BAY 17a: Alameda Island South (Elsie Roemer Bird Sanctuary, Crown Memorial State Beach, Crab Cove) Yes 8/22 Backpack m² m² 0.4 ac % 38% increase (172 m²) 17b: Bay Farm Island Yes 8/22 Backpack m² m² 609 m² 2005 >99% 549% increase (96 m²) 17c.1: Arrowhead Marsh West No 9/6, 9/24, 9/25, 10/9 Backpack, Airboat ac ac 7.1 ac % 19% increase (0.4 ac) 17c.2: Arrowhead Marsh East No No Allowed in ac ac 15.9 ac % 3% 17d.1: MLK Regional Shoreline Fan Marsh Shoreline 17d.2: Airport Channel MLK Shoreline No 9/6, 9/7, 10/9 Yes 9/7,9/8, 10/26 Truck, Airboat m² m² 0.5 ac % 249% increase (513 m²) Backpack m² m² 0.6 ac % 372% increase (563 m²) 17d.3: East Creek MLK Shoreline Yes 8/22 Backpack 0 28 m² 0 28 m² 90 m² 2004 >99% 91% 17d.4: MLK Regional Shoreline Damon Marsh 17d.5: Damon Slough / Elmhurst Creek MLK Shoreline No No Allowed in ac ac 1.5 ac % 75% increase (583 m²) Yes 8/23 Backpack 0 70 m² 0 70 m² 144 m² 2005 >99% 73% 17e.1: San Leandro Creek North No 8/24 Backpack 0 2 m² 0 2 m² 10 m² 2003 >99% 69% 17e.2: San Leandro Creek South Yes 8/24, 9/21, 10/24 17f: Oakland Inner Harbor Yes 10/5, 10/8, 10/24 Backpack 0 26 m² 0 26 m² 93 m² 2003 >99% 75% Truck, Backpack, Airboat 17g: Coast Guard Island Yes 10/19 Backpack, Airboat m² m² 869 m² % 68% 0 1 m² 0 1 m² 8 m² 2003 >99% 79% 17h: MLK New Marsh No No Allowed in ac ac ac % 11% 17i: Coliseum Channels Yes 9/21, 10/19 Truck, Backpack m² m² 554 m² % 21% Invasive Spartina Project Progress Report

59 Table 9. Summary of 2012 invasive Spartina area by sub area within Reporting Region 7: San Leandro Bay (continued). Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 7: SAN LEANDRO BAY (continued) 17j: Fan Marsh No No Allowed in m² m² 2.52 ac % 67% increase (313 m²) 17k: Airport Channel Yes 9/7 Truck, Airboat 0 16 m² 0 16 m² 68 m² 2005 >99% 71% 17l: Doolittle Pond Yes 9/18 Truck, Airboat 0 7 m² 0 7 m² 73 m² 2004 >99% 86% 17m: Alameda Island (Aeolian Yacht Club and East Shore) Yes 8/22 Backpack, Airboat REGION 7 TOTAL ac m² m² 0.7 ac % 22% ac 43.8 ac % 1% Invasive Spartina Project Progress Report

60 Aside from the sites with treatment restrictions currently in place, the infestations throughout the San Leandro Bay Region have been largely eliminated by effective annual treatment with herbicide from In 2012, backpack applications were used to maintain the eradication trajectory throughout the region. Limited airboat spot applications were conducted at several sites due to access challenges and soft mudflats. Portions of Oakland Inner Harbor (17f) are best approached from the water due to the extensive industrial development along the banks, and these were treated by backpack from shallow bottom boat. In 2012, the ISP surveyed 14 California clapper rail sites in the San Leandro Bay Region and data show a decline of about 44% from 2009 (McBroom 2012). Much of this decline is driven by the trend at Arrowhead Marsh (17c), a small but highly invaded site which supports a dense population of California clapper rail. Due to the lack of treatment at this site over the years, hybrid Spartina is still the dominant vegetative cover for clapper rails at Arrowhead Marsh. restrictions at numerous sites in this region currently leave few opportunities for California clapper rail habitat enhancement, due to risk of hybrid S. alterniflora encroaching on and overwhelming new plantings in the absence of control efforts. Plantings of S. foliosa in proximity to hybrid S. alterniflora also have a high likelihood of being pollinated by the hybrids, which would cause the native plants to produce hybrid seeds and spread the infestation. Although the opportunities are limited, ISP revegetation projects have installed more than 670 Grindelia stricta plants at MLK New Marsh (17h) and Damon Marsh (17d.4). Save The Bay, in collaboration with the ISP, has installed more than 2,400 plants over the past two seasons ( and ) in Arrowhead Marsh West (17c.1) where treatment was permitted and where hybrids are largely controlled. In 2012, 25 artificial floating nesting islands were placed on Arrowhead Marsh and one high tide refuge island was constructed and planted at MLK New Marsh. In addition, research conducted in collaboration with San Francisco State University s Romberg Tiburon Center (W. Thornton) and the University of California, Davis has reintroduced approximately 1,000 Spartina foliosa seedlings to the Elsie Roemer Bird Sanctuary in Alameda where the net hybrid cordgrass footprint was reduced below 500 m 2 by Invasive Spartina Project Progress Report

61 2.8 REGION 8: BAY BRIDGE NORTH The Bay Bridge North Region includes all East Bay shoreline marshes north of the Bay Bridge and southwest of the Carquinez Strait. In the southern portion of this region, which extends from the Bay Bridge to the Richmond/San Rafael Bridge, marshes are mostly small and fragmented, such as Emeryville Crescent (6a & 6b) and Stege Marsh (22d), or isolated pocket marshes like Golden Gate Fields and Central Avenue Marsh. Marshes here are often connected only by riprap shoreline and most currently have no potential for expansion due to the hardscape of adjacent freeway and urban development at the upland edge. North of the Richmond Bridge, there is a greater diversity of marsh types and maturation, but they too are disjunct and tenuously connected by riprap or narrow marsh fringe. The Bay Bridge North Region includes the historic marshes of Point Pinole Regional Shoreline (including Whittell Marsh [10a] and Giant Marsh [10c]), notable for the presence of vernal pools and a relatively high proportion of rare plant species, and the vast expanse of mixed salt and brackish marshes that make up Wildcat Marsh (22a) and San Pablo Marsh (22b.1 and 22b.2) sub areas. Only a handful of marshes in this region were significantly impacted by non native Spartina, and native cordgrass remains the dominant macrophyte of the low marsh zone throughout the North Bay. Water flow from the Delta pushing out towards the Golden Gate discouraged northbound dispersal of propagules and the establishment of hybrid S. alterniflora since the core infestations were in the marshes of Central and South San Francisco Bay. However, over time repeated tidal action allowed for some dispersal against the predominant directional flow. This resulted in net cover of 4.92 acres at the height of the infestation in 2009 on the vast mudflats and natural channel complex of San Pablo Marsh (22b.1 and 22b.2), the largest hybrid S. alterniflora infestation in the North Bay. Throughout the rest of the region, the ISP was able to catch the infestations early and begin implementation of treatment plans, never allowing coverage to increase above a small proportion of the remnant marshes and shorelines in this area. This successful rapid response to the invasive in these areas results in fewer loci of dispersal that would increase the cost of future mapping and treatment and prolong the time to eradication. While the extent of the hybrid infestation in the Bay Bridge North Region never warranted broadcast treatment from helicopter, a significant mudflat infestation occurred at San Pablo Marsh that could not be managed with the available technologies, until the ISP piloted the use of airboats here to maximize access and available tidal windows for Spartina treatment. While several populations were large enough to require spot treatment from truck or Hydrotraxx (amphibious tracked vehicle) up through 2010, the vast majority never advanced beyond the level of backpack sprayer, and the tidal areas north of Point Pinole only harbored a few widely scattered clones or individual plants. has continued to be very effective and the challenge has been detecting nascent infestations in the abundant S. foliosa throughout, which can require genetic analysis to discern native from non native plants when morphological or phenological traits (e.g. timing of flowering or senescence) are insufficient. The Bay Bridge North Region also contained three relatively minor infestations of S. densiflora that likely spread from the Corte Madera Creek introduction site in Marin. Herbicide was applied in the initial years, but rapid reductions allowed transition to only manual removal by digging by Of these three sites, only Whittell Marsh (10a) had any S. densiflora detected in 2012 (0.33 m 2 ). This was dug and removed during inventory to continue progress towards eliminating the seed bank. Invasive Spartina Project Progress Report

62 Figure 14. Distribution of invasive Spartina in 2012 across the 12 sub areas of Reporting Region 8: Bay Bridge North. Invasive Spartina Project Progress Report

63 Table 11. Summary of 2012 invasive Spartina area by sub area within Reporting Region 8: Bay Bridge North. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 8: BAY BRIDGE NORTH 06a: Emeryville Crescent East Yes 9/6 Backpack 0 30 m² 0 30 m² 265 m² 2004 >99% 93% 06b: Emeryville Crescent West Yes 9/18 Backpack 0 2 m² 0 2 m² 19 m² 2004 >99% 97% 10a: Whittell Marsh Yes 6/28 Dug m² 0.3 m² 1 m² 2005 >99% 623% increase (0.3 m²) 10b: Southern Marsh Yes 5/30; 9/17 Dug, Backpack 0 1 m² 0 1 m² 24 m² 2010 >99% 97% 10c: Giant Marsh Yes 5/30; 9/17 Backpack 0 14 m² 0 14 m² 52 m² % 54% 22a: Wildcat Marsh Yes 9/6 Backpack, Airboat m² m² 975 m² % 163% increase (174 m²) 22b.1: San Pablo Marsh East No 9/4 9/6 Backpack, Airboat ac ac 1.1 ac % 13% 22b.2: San Pablo Marsh West Yes 9/5 9/6; 10/24 Backpack, Airboat m² m² 0.8 ac % 57% 22c: Breuner Marsh (Rheem Creek) Yes 9/17 Backpack, Airboat m² m² 0.3 ac % 76% 22d: Stege Marsh Yes 9/10 Backpack 0 32 m² 0 32 m² 85 m² % 22e: Hoffman Marsh Yes 8/29 Backpack m² m² 2 m² 2004 >99% 10% increase (3 m²) no data in f: Richmond / Albany / Pinole Shoreline Yes 9/6; 11/23 Backpack 0 26 m² 0 28 m² 186 m² % 84% REGION 8 TOTAL ac 0.3 m² 0.7 ac 2.5 ac % 48% Invasive Spartina Project Progress Report

64 ISP surveyed the 12 sub areas (Figure 14, Table 10) in Region 8 mostly on foot in Helicopter was also used to help monitor Wildcat Marsh (22a), and various boats were used to survey the long and remote shorelines between marshes. A total of 0.66 acre of non native cordgrass was found, predominantly hybrid S. alterniflora, though 13 instances of S. densiflora covering 0.33 m 2 were also mapped within a single sub area, Whittell Marsh (10a). The extent of 2012 invasive cordgrass net coverage in this region reflects a 90% total reduction since the peak infestation in 2009 and a 48% decline since The highest amount of S. densiflora (17.5 m 2 ) was found in 2004, and 2012 levels are less than 2% of that total. Twelve California clapper rail sites in this region were surveyed in 2012, ten by ISP and two by Point Blue Conservation Science. From , the ISP has consistently decreased hybrid S. alterniflora cover in this region, while California clapper rail survey results over the same time period indicate a positive fouryear trend. Ample well developed rail habitat at Wildcat Marsh (22a) and San Pablo Marsh(22b) drive this trend. The ISP did not implement any revegetation projects in this region in However, S. foliosa was collected from Golden Gate Fields in 2011 for propagation and planting at other sites around the Estuary. Invasive Spartina Project Progress Report

65 2.9 REGION 9: SUISUN The Suisun Bay includes an enormous amount of wetland acreage formed by flow from the Sacramento and San Joaquin Rivers as they merge with the Bay. The Suisun Region is bounded to the west by the Carquinez Strait and extends east approximately to Antioch where the salinity transitions to freshwater wetlands within the Delta. This region was historically a vast complex of tidal and brackish marshes, the majority of which were diked in the early 20 th Century for agricultural development. The diked baylands in the region, now largely managed for waterfowl habitat and some agriculture, are currently threatened by subsidence, sea level rise, and diminishing sustainability of the earthen levee network. Because of the limited connectivity to the rest of the Estuary via the Carquinez Strait, predominant direction of water flow, and the distance from the site of Spartina alterniflora introduction some 35 miles to the south, the Suisun Region has only had minimal invasion by hybrid S. alterniflora. The extent of ISP s monitoring efforts is focused predominantly on Southampton Marsh (11) in Benicia State Recreation Area where the largest non native Spartina presence is from Spartina patens. This is the only location where S. patens is found in the Estuary (as well as throughout California), and samples of S. patens from this location can be found at the California Academy of Sciences dating back to Hybrid S. alterniflora is also present at a very low level (Figure 15, Table 11), having been first detected by the ISP in autumn of both hybrid S. alterniflora and S. patens has been difficult to plan and execute over the years due timing and habitat considerations as a result of the presence of endangered annual hemiparasite soft bird s beak (Chloropyron molle molle, formerly Cordylanthus mollis mollis), and as well as the return ofcalifornia clapper rail to the site after many years of absence (see salt meadow cordgrass discussion, Section 1.1.5). Fortunately for the continuity of treatment efforts, the hybrid S. alterniflora population has established only near the bayfront and mouth of the main tidal channel of Southampton, so while there have been some treatment restrictions at the site, they have not significantly impacted hybrid control. But the presence of the endangered annual plant has been a major challenge to S. patens treatment since the onset of ISP, and the recent addition of California clapper and black rail exclusion zones have further exacerbated the timing and seasonal habitat issues, making it impossible to achieve any level of effective treatment of S. patens. From , State Parks applied herbicide to S. patens after the C. m. molle had set seed and senesced so as not to impact the endangered soft bird s beak. This technique eliminated the big clones of S. patens by 2007, but year after year there was little progress towards eradication because S. patens was senesced by the time of herbicide application (October November) and was less prone to effective uptake and translocation of herbicide. In 2011 ISP biologists, USDA ARS researcher Brenda Grewell, and California State Parks and Recreation Department staff developed a plan that would include minor impacts to C. m. molle in order to treat the S. patens properly. Also in 2011, California clapper rail were detected in breeding season call counts at Southampton Marsh, and exclusion zones were established throughout the marsh (mostly along the channel network) that prohibited entry during the time period that was essential to implement the S. patens treatment plan. These exclusions zones were still in place during the 2012 season and treatment was not authorized for S. patens, but treatment was permitted for hybrid S. alterniflora. Invasive Spartina Project Progress Report

66 Figure 15. Distribution of invasive Spartina in 2012 in the single sub area and adjacent shoreline of Reporting Region 9: Suisun. Invasive Spartina Project Progress Report

67 Table 12. Summary of 2012 invasive Spartina area by sub area within Reporting Region 9: Suisun. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 9: SUISUN 11: Southampton Marsh Yes 9/5 Backpack 51 m² 8 m² 0 59 m² 321 m² % 121% increase (32 m²) REGION 9 TOTAL 51 m² 8 m² 0 59 m² 321 m² % 121% increase Invasive Spartina Project Progress Report

68 The ISP surveyed Southampton Marsh extensively on foot in 2012 and found a total of 0.01 acre of nonnative Spartina, including 51 m 2 of S. patens and 8.3 m 2 of hybrid S. alterniflora. The S. patens footprint reflects a 98% reduction since its peak in 2005, while the hybrid cover is at less than 2% of its peak in The Suisun Region, with its extensive brackish and freshwater marshes, has a very low density of California clapper rails, which generally prefer more saline conditions. Avocet Research and Associates surveyed Southampton Marsh in 2012 and did not detect any California clapper rails at the site (J. Evens, pers. comm.). Though tracts of native cordgrass extend along its shorelines, the hydrology of this region and the resulting marshes do not support a significant California clapper rail population. No habitat enhancement efforts have been undertaken here by the ISP to date. Invasive Spartina Project Progress Report

69 2.10 REGION 10: VALLEJO The Vallejo Region covers the northern portion of San Pablo Bay bounded by the mouth of the Petaluma River on the west, the City of Vallejo to the east, and extending eight miles inland to the north. The extensive historic tidal marsh footprint in this region was formed in the delta where the Sonoma Creek and Napa River watersheds converged with San Pablo Bay. Currently the region is a composite of diked agricultural lands and salt ponds, tidal marshes, tidal flats and open ponds managed primarily for waterfowl. Extant tidal marsh is limited to wide bayshore bands in areas, and fringing S. foliosa along the sloughs of the two rivers, which are bounded by levees protecting agricultural lands and decommissioned salt production ponds. The non native Spartina presence in the Vallejo Region has been primarily hybrid S. alterniflora on Mare Island, though there has been local colonization by S. densiflora along that same shoreline, and one other isolated incidence in Napa Sonoma Marsh. The most prominent hybrid S. alterniflora clones established along the western shore of Mare Island (26b) and also just upstream of the mouth of Sonoma Creek (26c), where they expressed a novel phenology, flowering and senescing distinctly earlier than elsewhere around the Bay, requiring earlier inventory mapping and treatment to be effective. From , Mare Island contained the only known infestation in in this region, and since it contained S. densiflora the area was surveyed early in the season to stop seed dispersal by late June/early July. Surveying so early in the hybrid growing season was problematic for the thorough detection of a nascent hybrid presence, as well as for accurate and thorough mapping amongst substantial tracts of native cordgrass. Since 2009, helicopter and airboat treatment has reduced the invasive Spartina footprint sufficiently to allow effective treatment solely by backpack in both 2011 and A story of successful early detection and rapid response is found at Sonoma Baylands (26d) where a single large and well established hybrid S. alterniflora clone was discovered in 2010 amidst expansive tracts of recruiting native Spartina. After a single herbicidal treatment in the same year, no hybrid has been detected and the regrowth in its former footprint has been genetically tested and verified as S. foliosa marks the second year of zero detection of invasive cordgrass in this sub area located in a remote and otherwise uninfested portion of the Estuary. Since the four Region 10 locations (Figure 16, Table 12) contain very little non native Spartina within a vast acreage of tidal marsh habitat, the sites were monitored in 2012 by helicopter, airboat and whaler with additional groundwork by staff biologists in areas of historic non native detections. In two of the four locations (San Pablo Bay NWR and Mare Island [26b] and Sonoma Creek [26c]), non native Spartina was detected covering 80 m 2, all of which was hybrid S. alterniflora, except for five S. densiflora plants covering 0.11 m 2 along the northern Mare Island shoreline. The majority of hybrid S. alterniflora (74 m 2 ) was found along Sonoma Creek, while the historically more massive clones along the Mare Island Shoreline had been dramatically decreased from a peak of 0.31 acres in 2009 to 20 m 2 in The strong freshwater influence and the very young status of many of the restoration sites in the Vallejo Region currently results in few resident California clapper rail, though there is considerable future potential clapper rail habitat. In 2012, ISP, Point Blue Conservation Science, and staff of San Pablo Bay NWR surveyed ten sites and detected low numbers of California clapper rails consistent with prior years (Wood 2013). With hybrid Spartina only colonizing two remote areas within this vast region, native cordgrass has Invasive Spartina Project Progress Report

70 Figure 16.Distribution of invasive Spartina in 2012 across the four sub areas of Reporting Region 10: Vallejo. Invasive Spartina Project Progress Report

71 Table 13. Summary of 2012 invasive Spartina area by sub area within Reporting Region 10: Vallejo. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 10: VALLEJO 26a: White Slough / Napa River Yes No invasive Spartina 2011 or % n/a 26b: San Pablo Bay NWR and Mare Island Yes 7/23 Dug, Backpack 0 20 m² 0.1 m² 20 m² 37 m² % 77% 26c: Sonoma Creek Yes 8/22 Backpack 0 74 m² 0 74 m² 422 m² % 72% 26d: Sonoma Baylands Yes No invasive Spartina 2011 or % n/a REGION 10 TOTAL 0 94 m m² 94 m m % 73% Invasive Spartina Project Progress Report

72 very successfully established itself at recent restoration sites like Tolay Creek and Sonoma Baylands. No ISP revegetation efforts have been directed to this region due to observed natural recruitment of native plants. The ISP Restoration Program collected Spartina foliosa from the banks of the Napa River and propagated for planting at sites in other regions. Invasive Spartina Project Progress Report

73 2.11 REGION 11: PETALUMA The Petaluma Region consists of the wetlands lining the tidal portions of the Petaluma River and its tributaries in Marin and Sonoma Counties, from downtown Petaluma to the river s mouth in northwestern San Pablo Bay. Heavily influenced by the interaction between the volume of freshwater from the Petaluma River with the tidal contribution from the Bay, Region 11 includes a considerable amount of brackish tidal marsh. This once vast expanse of contiguous wetlands has been partially converted to diked agricultural lands with the exception of Petaluma Marsh, which is one of the largest ancient tracts of tidal marsh in the Estuary. The hybrid S. alterniflora population along the upper Petaluma River (24a) is geographically removed from the bulk of the bay wide invasion and stands as the northernmost extent of hybrid in the Estuary. It is unlikely the infestation was dispersed to this upstream location naturally because there has never been any hybrid found in the southernmost several miles of the Petaluma River, through which propagules would have passed if spread from another North Bay infestation on the tides. Colonization in these upper reaches may have been caused by accidental introduction of hybrid seed and/or propagules by a dredge or other watercraft returning from an infested marsh in another part of the Bay. In 2012, the infestation was treated with herbicide by backpack sprayer from a shallow bottom boat on a receding tide. This work did not occur until late in the treatment season due to permitting delays, which may impact efficacy and allowed hybrid seeds to develop and potentially disperse. Similar to the Vallejo Region, the ISP monitored the four expansive sub areas (Figure 17, Table 13) in the Petaluma Region primarily by boat and helicopter, with biologists surveying by foot only in limited areas of the historic invasion. A total of 0.01 acre (52 m 2 ) of hybrid S. alterniflora was found here in 2012, down from the peak of 0.15 acre in 2007, but showing an increase from the 23 m 2 mapped in This increase is likely due to the Petaluma sites having been treated late in the 2011 season which can result in reduced efficacy. The Petaluma Region s high quality rail habitat is largely surveyed by Point Blue Conservation Science, though in 2012 the ISP surveyed a small portion of Upper Petaluma River (24a). Results from 2012 surveys indicate continuing declines in rail numbers from 2010 in this region (Wood 2013). As control of hybrid Spartina has been very limited in this region and because there is abundant S. foliosa, no ISP revegetation projects were implemented in One location in this region, Sonoma Marina, was used as a donor source for S. foliosa collection and propagation for planting elsewhere around the Bay. Invasive Spartina Project Progress Report

74 Figure 17. Distribution of invasive Spartina in 2012 across the four sub areas of Reporting Region 11: Petaluma. Invasive Spartina Project Progress Report

75 Table 14. Summary of 2012 invasive Spartina area by sub area within Reporting Region 11: Petaluma. Net Spartina Coverage By Species All Invasive Spartina Cover REPORTING REGION Split Sub area 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 11: PETALUMA 24a: Upper Petaluma River Upstream of Grey's Field Yes 10/29 Backpack, Airboat 0 45 m² 0 45 m² 77 m² % 102% increase (23 m²) 24b: Grey's Field Yes No invasive Spartina 2011 or % n/a 24c: Petaluma Marsh Yes 10/29 Backpack, Airboat 0 7 m² 0 7 m² 10 m² % 2729% increase (6 m²) REGION 11 TOTAL 0 52 m² 0 52 m² 87 m % 130% increase Invasive Spartina Project Progress Report

76 2.12 REGION 12: OUTER COAST The Outer Coast Region is the only area of hybrid S. alterniflora infestation outside of the San Francisco Estuary and includes the following geographically isolated watersheds on the western border of Marin County: Tomales Bay (25a), Bolinas Lagoon (25d & 25e), Estero de Limantour (25b) and Drakes Estero (25c). This region is impacted only minimally by development, and most of the lands are under the protection of the U.S. National Parks Service as part of the Point Reyes National Seashore. A majority of the remaining land is protected and/or managed by other public agencies, most notably California Department of Fish & Wildlife, National Oceanic & Atmospheric Administration and Marin County Parks and Open Space District. Threat from non native Spartina in this Region has been very limited due to reduced connectivity with San Francisco Estuary and its invasive populations. However, isolated clones of hybrid S. alterniflora have established in Drakes Estero (25c), Estero de Limantour (25b), and Bolinas Lagoon (25d & e), while S. densiflora established in two locations within Tomales Bay (25a). The ISP has effectively used tarping for the various infestations of hybrid S. alterniflora on the marsh plain in the Outer Coast Region due to restrictions on herbicide use, and digging of S. densiflora has greatly reduced those isolated colonies to near eradication. Native cordgrass has lined the shore of Bolinas Lagoon since the mid 20 th century, but it began colonizing and proliferating on the mudflat in the mid 2000s with increased sediment deposition from upstream anthropogenic activities. The new establishment and rapid expansion closely resembled that of the hybrid from the San Francisco Estuary, and ISP attention was quickly directed to this area of high ecological concern. Extensive monitoring and genetic sampling of plants around the Lagoon have identified a minor hybrid S. alterniflora presence and a much more extensive and proliferating population of native Spartina foliosa. The Outer Coast Region is broken into five large locations (Figure 18, Table 14) that were all monitored in 2012 from various types of boats, supplemented by foot survey in accessible areas. The hybrid S. alterniflora presence expanded as a whole from 5.6 m 2 in 2011 to 77.2 m 2 (0.02ac), driven entirely by the rapid expansion of two clones on the eastern shore of Bolinas Lagoon that were not treated (except for inflorescence clipping) in 2011 while the use of herbicide was evaluated for permitting. Marin County Parks is working with Gulf of the Farallones National Marine Sanctuary to develop a plan for treating this expanding infestation located out on the soft mudflats where tarping or excavation are not viable treatment options, and they will be conducting a CEQA review in The hybrid clones treated by tarping along the Bolinas Coast (25d & 25e) and in Estero de Limantour (25b) in prior years were absent in 2012, and the tarped clone in Home Bay of Drakes Estero (25c) was reduced by 56% from 0.18 m 2 in 2011 to 0.08 m 2 in Spartina densiflora is this region s other invasive cordgrass, but it was found in greatly reduced amounts after extensive foot survey of the two areas in Tomales Bay where it has been found in the past (25a, the marshes of Tom s Point and Hog Island Oyster Company). With the help of Audubon Canyon Ranch, the S. densiflora presence in Tomales Bay has been reduced to 0.01 m 2 of net cover in 2012, which is 0.22% of the 5 m 2 present at its peak in In fact, all 18 instances of mapped and dug S. densiflora plants in 2012 were young recruits found during the earlier of two rounds of survey at Tom s Point. The 3 5 year seed viability of S. densiflora, however, allows new recruits to emerge years after all adult plants have been eliminated and it requires diligent monitoring and removal to ensure that no additions are made to the seed bank. Invasive Spartina Project Progress Report

77 Figure 18. Distribution of invasive Spartina in 2012 across the five sub areas of Reporting Region 12: Outer Coast. Invasive Spartina Project Progress Report

78 Table 15. Summary of 2012 invasive Spartina area by sub area within Reporting Region 12: Outer Coast. Net Spartina Coverage By Species All Invasive Spartina Cover Split Sub area REPORTING REGION 2011 Auth Dates 2012 Method anglica patens densiflora x foliosa alterniflora x foliosa densiflora Net Area Area Peak Year Net Area Decline Since Peak Since 2011 REGION 12: OUTER COAST 25a: Tom's Point, Tomales Yes 5/30 Dug m² 0.01 m² 0.1 m² 2010 >99% 97% 25b: Limantour Estero Yes No invasive Spartina % 100% 25c: Drakes Estero Yes 6/11 Tarped m² m² 3 m² 2002 >99% 56% 25d: Bolinas Lagoon, North Yes 10/29 Tarped, Mowed 0 77 m² 0 77 m² 100 m² 2012 n/a 1719% increase (73 m²) 25e: Bolinas Lagoon, South Yes No invasive Spartina % 100% REGION 12 TOTAL 0 77 m m² 77 m m % 1208% increase Invasive Spartina Project Progress Report

79 The present range of the California clapper rail is limited to the tidal marshes of the San Francisco Estuary, with the exception of occasional observations along the Outer Coast. In October of 2012, the ISP detected a California clapper rail in Tomales Bay during a Spartina survey. The ISP did not conduct clapper rail surveys at the marshes in the Outer Coast Region, and no ISP revegetation projects were implemented in this region in Invasive Spartina Project Progress Report

80 3 SPECIAL TOPICS 3.1 SOUTH BAY SALT POND RESTORATION PROJECT The South Bay Salt Pond Restoration Project (SBSP), managed by the State Coastal Conservancy, is the largest tidal restoration effort on the West Coast, with a goal of restoring native wetland ecosystem functioning to the 15,100 acres acquired from Cargill in This ambitious project has a timeline of approximately 50 years to restore the decommissioned salt ponds to salt marsh and a variety of other tidal habitats. In addition, within the SBSP area of San Francisco Bay south of the San Mateo Bridge, there are several thousand additional acres adjacent (sometimes contiguous) with the SBSP sites that are in the process of tidal restoration from other land uses such as agriculture. As these systems mature, they promise to provide much needed support to a variety of species that have been seriously impacted by the loss of 85 90% of the historic wetlands around the Estuary since the turn of the 20 th Century. However, when these sites are first breached, and for several years hence until the plant community begins to mature, they are the most vulnerable to invasion and rapid domination by hybrid S. alterniflora of any habitat in the Estuary. While the initial elevation of the restoration sites varies greatly due to subsidence or the import of fill, they all lack vegetation initially. With the absence of competition and biotic resistance, hybrid Spartina can freely colonize and quickly expand vegetatively through the soft mud. Once hybrid Spartina is well established, it can significantly alter the hydrology and development of the plant community, pushing the site off a native marsh development trajectory. To protect these sites, the ISP places a high priority on monitoring them at least once annually, and rapidly following up with treatment if necessary. However, the burden of adding large tracts to the 50,000 acres already inventoried each year is significant, and typically these new marshes are remote and very challenging to access at the proper tide for a thorough assessment of hybrid Spartina presence or for treatment. Figure 19 shows the sites within SBSP, as well as other neighboring restoration marshes, and the status of infestation by hybrid S. alterniflora. Within the Alviso and Ravenswood focal areas of SBSP, the ISP has detected and treated nascent hybrid Spartina infestations within the westernmost Island Pond (Pond A21 in [05i]) along Coyote Creek, and Pond SF2 (02n), just south of western landfall of the Dumbarton Bridge. Multiple other infestations have been discovered and treated in the northern portion of SBSP s Eden Landing (Baumberg) focal area, including North Creek (13h), Pond E10 (13i), Mt. Eden Creek (13j), North Creek Marsh (13k), and Mt. Eden Creek Marsh (13l). In 2012, the net area of hybrid S. alterniflora throughout these SBSP sites was 58 m 2, 89% of which was located in Eden Landing. Some of the areas within this complex were breached before comprehensive Spartina treatment began, and the abundance of propagules from neighboring hybrid stands flooded the new areas and established without resistance. Several other recent restoration sites near SBSP sites became infested and are being actively managed by the ISP to eliminate the threat to the health of the tidal ecosystem. Bair Island s Pond B3 (2m) was breached in 2008 when there was still a substantial infestation surrounding the site, and the ISP has been working with San Mateo Mosquito & Vector Control District to control the invasion and reduce the competition pressure on native Spartina so it can colonize and flourish. Pond B3 (02m) is the most infested of the recently breached restoration sites of the south bay, with 287 m 2 of hybrid mapped and treated in Invasive Spartina Project Progress Report

81 2012 within the 411 acre site. Ravenswood Open Space Preserve (2j) contains a 52 acre breached pond immediately north of the western landfall of the Dumbarton Bridge, and this site contains a pioneering infestation of hybrid Spartina (40 m 2 ). The Redwood Shores Mitigation Bank (02a.4) at the mouth of Belmont Slough was breached in 2010, and hybrid propagules quickly colonized the new restoration site. However, the elevation was only appropriate for hybrid establishment on the habitat islands within the site, so only a trace amount was mapped by ISP biologists in Invasive Spartina Project Progress Report

82 Figure 19. Map of the South Bay Salt Ponds and neighboring recent restoration projects in South San Francisco Bay. Sites are differentiated based on whether they have been restored to tidal action and if so, whether they have been infested with hybrid Spartina or not as of Invasive Spartina Project Progress Report

83 3.2 RESTRICTED TREATMENT SITES As mentioned periodically throughout the report, treatment of invasive Spartina was not permitted at 26 sub areas in 2011 and at 11 sub areas in The restrictions were required by USFWS in the Section 7 Biological Opinion for each year, and were intended to limit adverse impacts on California clapper rails potentially caused by removal of refuge habitat provided by the non native Spartina plants. Figure 20 shows the locations of the precluded sub areas in each year. In 2011, the 26 restricted sub areas were distributed throughout much of the Estuary, in seven of the 12 reporting regions (reporting regions 1 4 and 6 8; Table 15). In the Marin Region (Region 1), treatment was restricted at Corte Madera Creek Mouth North (04j.1). In the San Francisco Peninsula Region (Region 2), there were three restricted sub areas including Confluence Marsh (18f), SFO Shoreline (19h), and Seal Slough Mouth (19p.1). In the San Mateo Region (Region 3), there were six restricted sub areas including Belmont Slough (02a.1), Bird Island (02a.3), the northern portions of B2 North Quadrant (02c.1a and 02c.1b), most of B2 South Quadrant (02d.1a, and 02d.1b), West Point Slough NW (02e), and Ravenswood Slough and Mouth (02i). In the Dumbarton South Region (Region 4), treatment was restricted at three large marshes, including Calaveras Marsh (05a.2), Alviso Slough (15a.4), and the eastern part of Cooley Landing Marsh (16.1). In the Hayward Region (Region 6), treatment was restricted at six sub areas, including Citation Marsh (20d.1 and 20d.2), North Marsh (20f.1 and 20f.2), Bunker Marsh (20g), San Lorenzo Creek and Mouth North (20h.1), and quadrants B and C of Cogswell Marsh (20n and 20o). In the San Leandro Bay Region (Region 7), treatment was restricted at six sub areas, including Fan Marsh and shoreline (17j and 17d.1), Damon Marsh (17d.4), San Leandro Creek North (17e.1), MLK New Marsh (17h) and Arrowhead Marsh (17c.1 and 17c.2). Finally, in the Bay Bridge North Region (Region 8), treatment was restricted on the eastern portion of San Pablo Marsh (22b.1). In 2012, the 11 restricted sub areas were consolidated mainly to the East Bay to reduce risk of additional damage to marsh habitat potentially caused by retaining active invasive Spartina propagule sources in so many areas of the Estuary. Ten of the 11 restricted sub areas were located in the Hayward and San Leandro Bay regions (reporting regions 6 and 7, respectively). In the Hayward Region (Region 6), restricted sub areas again included quadrants B and C of Cogswell Marsh (20n & 20o) along the Hayward Regional Shoreline, and four sub areas within the Robert s Landing Complex to the north, including Bunker Marsh (20g), Citation Marsh North (20d.2), North Marsh (20f) and San Lorenzo Creek Mouth North (20h.1). In the San Leandro Bay (Region 7), restricted sub areas again included Fan Marsh (17j), Damon Marsh (17d.4), MLK New Marsh (17h) and Arrowhead Marsh East (17c.2). The final sub area, B2 North Quadrant East (02c.1b), is in the San Mateo Region (Region 3). Seed suppression (described in footnote 2 on page 17) was authorized here, allowing the ISP to limit reinfestation of the neighboring Bair Island and other USFWS Refuge marshes. ISP inventoried the 2011 restricted sites in the summer of 2012 and mapped acres of hybrid S. alterniflora, which comprises 79% of the remaining baywide total acreage of non native Spartina. The results showed that the net area of hybrid S. alterniflora at the 26 untreated sub areas increased significantly at eight of the sub areas over one season. At 15 of the sub areas, no significant change in net cover was Invasive Spartina Project Progress Report

84 Figure 20. Distribution map of the 26 ISP sub areas in which treatment of hybrid Spartina was restricted in 2011 and the 11 sub areas in which treatment was restricted for both 2011 and Invasive Spartina Project Progress Report

85 Table 16. Hybrid Spartina quantities and trends from at the 26 ISP sub areas where treatment was suspended in Spartina amounts presented in this table are the mean value within the range of estimated net cover area. The seemingly steady trends (symbolized as ) denote that an annual net change could not be accurately determined due to overlaps in the minima and maxima of these cover ranges. Sub areas shown in red were also not authorized for treatment in 2012**. Reporting Region Subarea # Sub area Name 04j.1 Net 2009 (ac) Net 2010 (ac) Net 2011 (ac) Net 2012 (ac) Trend Trend Corte Madera Creek Mouth North Bank f Confluence Marsh Trend 19h SFO Shoreline * Seal Slough Mouth Central 19p.1 Marsh a.1 Belmont Slough Mouth a.3 Bird Island c.1 B2 North Quadrant** d.1 B2 South Quadrant e West Point Slough NW Ravenswood Slough and 02i Mouth Cooley Landing Central a.2 Calaveras Marsh a.4 Alviso Slough d Citation Marsh f North Marsh g Bunker Marsh San Lorenzo Creek and Mouth 20h.1 North n Cogswell Marsh, Quadrant B o Cogswell Marsh, Quadrant C c Arrowhead Marsh d.1 17d.4 MLK Regional Shoreline Fan Marsh Shoreline MLK Regional Shoreline Damon Marsh e.1 San Leandro Creek North m m 2 * 17h MLK New Marsh j Fan Marsh b.1 San Pablo Marsh East Total * The decrease in net area of hybrid S. alterniflora at SFO Shoreline (19h) and San Leandro Creek North (17e.1) likely resulted from mistaken treatment of several shoreline clones caused by misinterpretation of revised site boundaries (see discussion in Section 2.3). ** A portion of B2 North Quadrant (02c.1) was authorized for seed suppression in Invasive Spartina Project Progress Report

86 Measured, and at four sub areas a net decrease in area was mapped (Table 15). The changes in net area of hybrid S. alterniflora at each of the 26 untreated sub areas ranged from an increase of 350% (Cooley Landing Central [16.1]) to a decrease of 50% (San Lorenzo Creek and Mouth [20h.i]) 4, while total net area for the two years was about the same (27.87 net acres in 2011, and net acres in 2012), with a total net increase over one growing season of about 10%. While the number of net acres increase is not dramatic, the very rapid expansion of hybrid S. alterniflora at many of the untreated sites in just a single season provides a sobering reminder of the remarkable vigor of this ecosystem engineer. Figure 21 illustrates what these changes look like in the field. The marsh on the left, Cargill Mitigation Marsh (13f, Region 5), was treated annually from 2006 through This 49 acre restoration site was opened in 1998, and by 2005 it was dominated by hybrid S. alterniflora (22 net acres). The ISP began annual treatment in The photo progression in Figure 21 shows a view of the site in 2006, 2010, 2011, and By 2010, nearly all hybrid S. alterniflora was removed, and by 2012, this view shows a single remaining clone (there was a total of 0.04 acre at the site). Missing from this picture and the site after treatment is native Spartina foliosa and tall gumplant to provide structure and refuge habitat. With the hybrid S. alterniflora completely under control, the ISP Revegetation Program was able to begin planting at Cargill Mitigation Marsh in the winter of The marsh on the right in Figure 21, MLK New Marsh (17h, Region 7), was partially treated from 2007 through 2010, and then not treated in 2011 or This 70.6 acre restoration site was opened in 1998, and was immediately populated with hybrid S. alterniflora seed from the adjacent Arrowhead Marsh (17c). The view in the photo progression shows a marked expansion of the footprint area in 2011, and an even greater increase by The patches in 2011 and 2012 appear sparse, which accounts for the surprisingly low net area (~4 net acres) cover. Without treatment, however, it can be expected that these sparse areas will continue to fill in and the population will expand over time to a greater area of the site. Figure 21 illustrates how a seemingly small net area of untreated hybrid S. alterniflora can expand rapidly, and over the course of only two years, can reverse years of progress towards eradication. Research from UC Davis documented that hybrid S. alterniflora is capable of spreading at a greater than exponential rate in the conditions of the San Francisco Estuary (Ayres and Strong, 2003). The criteria provided by USFWS for removal or reduction of the treatment restrictions at the 11 sites is that there be a measured increase of 80 California clapper rails (over a 2010 baseline), sustained for three years. Annual surveys by the ISP and others indicate that baywide California clapper rail numbers have been stable since 2009, with no major increases or decreases in annual population estimates. The Conservancy initiated a habitat restoration program in 2011 to rapidly establish habitat features to benefit California clapper rails at strategic locations near where recent removal of non native Spartina has caused decreases in local California clapper rail populations. The program has installed 165,000 plants across 30 sites and constructed six earthen high tide refuge islands (Busnardo and Archbald 2013) to develop and provide habitat for California clapper rails, although it is unlikely that these substantial efforts will increase clapper rail numbers in the near term. See Section for more information on this program. 4 Analysis omits data from SFO Shoreline (19h) Invasive Spartina Project Progress Report

87 Cargill Mitigation Marsh (13f) Annual MLK New Marsh (17h) Annual No Extensive hybrid S. alterniflora cover at both sites 2010 Hybrid S. alterniflora cover greatly reduced at both sites after four years of treatment Reduction in the marsh at right is less because treatments were not as thorough Hybrid cover continues to diminish at treated site Hybrid cover visually increases at site with no treatment in Hybrid virtually gone from treated site Hybrid footprint expanded to nearly pre treatment area after two years without treatment. (Sparse patches expected to fill in in following years.) Figure 21. Photo series from 2006 to 2012 showing hybrid Spartina response to continuous treatment, and its subsequent expansion when left untreated. Cargill Mitigation Marsh (13f, Region 5) on the left had no treatment interruptions, while MLK New Marsh (17h, Region 7) on the right was not treated in 2011 and 2012 because of permit restrictions. Invasive Spartina Project Progress Report

88 3.3. NEW INFESTATIONS AND SUB AREAS ADDED IN 2012 The Dumbarton South Region (Region 4) had the only instance of a new infestation as defined by the ISP ( non native Spartina discovered more than 1km from any detection in prior years ). Three new clones of hybrid S. alterniflora were found approximately one kilometer upstream from previous locations in the upper reaches of Mowry Slough (05a.1, Region 4). These clones were treated by backpack in The Redwood Shores Mitigation Bank (02a.4, Region 3) was breached in 2010 and hybrid propagules likely from the adjacent Belmont Slough quickly colonized the new restoration site. However, the elevation of the marsh was only suitable for hybrids to establish on the habitat islands constructed within the site. A small amount was hybrid S. alterniflora (6 m 2 net area) was mapped there in Clones of hybrid S. alterniflora were discovered for the first time and treated in Pond A21, the westernmost marsh of the Coyote Creek Island Ponds (05i, Region 4), as well as small patches in the newlybreached Pond SF2 (02n, Region 3), just south of western landfall of the Dumbarton Bridge (see discussion of South Bay Salt Ponds Restoration in Section 3.1). Both of these areas were also in close proximity to hybrid S. alterniflora populations not permitted for treatment in Invasive Spartina Project Progress Report

89

90 4 LOOKING FORWARD TO 2013 AND BEYOND The goal of the Invasive Spartina Project is to eradicate non native Spartina from the San Francisco Estuary in order to restore and preserve native tidal marsh. Over the past eight years ( ), the ISP and its partners have made great progress towards this goal, having reduced the cover of the invasion by 95% since its peak at 805 net acres in 2005, and with many sites approaching eradication. In 2012 there were less than 40 net acres of non native Spartina Estuary wide, and 11 previously invaded sub areas had recorded the first or second year with no invasive Spartina having been detected (see Section 2). The final phase of eradication is the most challenging for any large scale noxious weed control program, because finding and removing the last few plants dispersed throughout a large area is inherently difficult. The task for the ISP is further complicated by (1) challenges identifying some forms of hybrid S. alterniflora in their early growth stages, when they can appear similar to S. foliosa, and (2) the presence of the endangered California clapper rail, which has resulted in suspension of treatment at 10 sites for an indeterminate length of time. Both of these conditions have the potential to significantly affect the course and timeline for achieving the goal of eradication, and each is discussed below. Hybrid Identification The ISP has worked over the years initially with University of California, Davis, researchers and in recent years with the University of California, Los Angeles, Human Genomics Laboratory to refine methods for laboratory testing and data analysis to better identify plants with S. alterniflora ancestry (i.e., hybrid S. alterniflora plants; see Section ). In 2012, the ISP employed an evolutionary ecologist and geneticist to work with the laboratory and guide this process, and to advise the ISP regarding sampling plan design and data interpretation. As the genetic testing methods have improved, the ISP has been able to also refine field identification methods to allow more efficient data collection during inventory monitoring. While it is still challenging to make field identifications in some situations, the methods have evolved in step with the need, and continue to be generally adequate for the project s purposes. However, because of the time required to prepare, test, and analyze plant samples (frequently four or more weeks), treatment crews are not always able to make decisions based on current year data, which may result in failure to treat plants that subsequently are identified as hybrid S. alterniflora. This inefficiency results in a small percentage of plants being unnecessarily left untreated in a given year, and crews must return to the spot to treat a year later potentially after the plant has expanded or even set seed. Achieving eradication will require identifying and treating all hybrid S. alterniflora plants each season. The ISP will continue to pursue improved methods and modified sampling strategies to reduce analysis time and keep pace with the program s needs. Effect of Restrictions on Eradication Timeline Many forms of hybrid S. alterniflora are tall and dense, and the endangered California clapper rail may be attracted there for cover from prey and refuge during high tides. Concern for the California clapper rail led USFWS to prohibit treatment of hybrid S. alterniflora at 26 sub areas in 2011, and in 2012, to prohibit treatment at 10 sites and limit it at one site in 2012 (See Section 3.2). The sub areas where treatment was restricted in 2012 comprise 21 net acres (55%) of the 38 net acres of non native Spartina mapped in It is unknown how long treatment at these sub areas may be suspended, as removal or reduction of the restriction is dependent upon a substantial increase in the California clapper rail population sustained over a period of three years. Invasive Spartina Project Progress Report

91 Untreated, the hybrid S. alterniflora at the restricted sites will increase in net area and in footprint (the area over which the Spartina is distributed). Based on data collected in the San Francisco Estuary before treatment began in 2005, researchers from UC Davis documented that hybrid S. alterniflora is capable of spreading at a greater than exponential rate (Ayres and Strong, 2003). Depending on the amount of time before treatment is reinitiated at these sites, the populations may be several times larger than they are now. The ISP has demonstrated that even very large areas of non native Spartina can be controlled and drastically reduced within 2 4 years of initiating treatment; however, following achievement of initial control, there will be a period of several years of annual monitoring and treatment before eradication can be achieved (similar to the process that many sites are undergoing now). Thus, eradication at the restricted sub areas may be many years behind the remainder of the sites. Moving Forward The ISP will continue treatment at the unrestricted sites to achieve eradication of the remaining 17 net acres of non native Spartina as quickly and efficiently as possible. It is presently unknown whether seed and propagules from the untreated sites will cause significant invasion pressure on the treated sites; an effort will be made to assess this and to adapt the management approach if feasible. The ISP also will continue implementation of the Restoration Program, with intensive planting of native marsh plants at strategic locations to rapidly establish and enhance habitat for California clapper rails. Work to date in this area looks promising, but it is not certain whether this effort will promote increase of clapper rail populations in the near term. The ISP, Conservancy, and DENWR will continue to work with staff and management at USFWS to further clarify conservation and regulatory objectives and timelines, and develop a viable strategy for achieving California clapper rail conservation objectives and eradication of invasive Spartina from the San Francisco Estuary. Invasive Spartina Project Progress Report

92 5 LITERATURE CITED Anttila, C. K., R. A. King, et al. (2000). "Reciprocal hybrid formation of Spartina in San Francisco Bay." Molecular Ecology 9(6): Ayres, D. R., D. Garcia Rossi, et al. (1999). "Extent and degree of hybridization between exotic (Spartina alterniflora) and native (S foliosa) cordgrass (Poaceae) in California, USA determined by random amplified polymorphic DNA (RAPDs)." Molecular Ecology 8(7): Ayres, D. R., E. Grotkopp, et al. (2008). "Hybridization between invasive Spartina densiflora (Poaceae) and native S foliosa in San Francisco Bay, California, USA." American Journal of Botany 95(6): Ayres, D. R., D. R. Strong, et al. (2003). "Spartina foliosa a common species on the road to rarity?" Madrono 50: Ayres, D. R., K. Zaremba, et al. (2008). "Sexual reproduction of cordgrass hybrids (Spartina foliosa x alterniflora) invading tidal marshes in San Francisco Bay." Diversity and Distributions 14(2): Ayres, D. R., K. Zaremba, et al. (2004). "Extinction of a common native species by hybridization with an invasive congener." Weed Technology 18: Boyer, K. E., J. C. Callaway, et al. (2000). "Evaluating the progress of restored cordgrass (Spartina foliosa) marshes: belowground biomass and tissue nitrogen." Estuaries 23: Busnardo, M. and G. Archbald (2013). Lessons Learned from Construction of California Clapper Rail Earthen High Tide refuge Islands, Prepared for the California State Coastal Conservancy San Francisco Invasive Spartina Project, 1330 Broadway, 13th Floor, Oakland, CA : 15. Cain, D. and H. Harvey (1983). "Evidence of salinity induced ecophenic variation in cordgrass(spartina foliosa Trin.)." Madrono 30(1): Casazza, M., J. Takekawa, et al. (2012). California clapper rail alterificial island study quartely progress report, FY12, Quarter 2, Prepared for the California State Coastal Conservancy San Francisco Invasive Spartina Project, 1330 Broadway, 13th Floor, Oakland, CA Daehler, C. C. and D. R. Strong (1996). "Status, prediction and prevention of introduced cordgrass Spartina spp invasions in Pacific estuaries, USA." Biological Conservation 78(1 2): Daehler, C. C. and D. R. Strong (1997). "Hybridization between introduced smooth cordgrass (Spartina alterniflora; Poaceae) and native California cordgrass (S foliosa) in San Francisco Bay, California, USA." American Journal of Botany 84(5): Faber, P. (2000). "Grass Wars Good Intentions Gone Awry. Why would anyone Bring an Alien Cordgrass into S. F. Bay?" California Coast & Ocean 16(2): Goals Project (1999). Baylands Ecosystem Habitat Goals. A report of habitat recommendations prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project., U.S. Environmental Protection Agency, San Francisco, CA / San Francisco Bay Regional Water Quality Board, Oakland, CA. Hogle, I. (2008) Monitoring Report. Berkeley, CA, Prepared for the California State Coastal Conservancy San Francisco Invasive Spartina Project, 1330 Broadway, 13th Floor, Oakland, CA : 42. Invasive Spartina Project Progress Report

93 Hogle, I. and K. Zaremba. (in preparation). San Francisco Estuary Invasive Spartina Project Spartina Monitoring Program Approach Prepared by Olofson Environmental, Inc. for the California State Coastal Conservancy, 1330 Broadway, 13th Floor, Oakland, CA Olofson Environmental, Inc. (2012). San Francisco Estuary Invasive Spartina Project California Clapper Rail Habitat Enhancement Restoration and Monitoring Plan, Prepared for the California State Coastal Conservancy San Francisco Invasive Spartina Project, 1330 Broadway, 13th Floor, Oakland, CA : 94. Kerr, D. and E. Grijalva (2012). San Francisco Estuary Invasive Spartina Project 2011 Report, Prepared for the California State Coastal Conservancy San Francisco Invasive Spartina Project, 1330 Broadway, 13th Floor, Oakland, CA Kerr, D. (2012). San Francisco Estuary Invasive Spartina Project 2012 Aquatic Pesticide Application Plan., Prepared for the California State Coastal Conservancy San Francisco Invasive Spartina Project, 1330 Broadway, 13th Floor, Oakland, CA Kerr, D. (2013). San Francisco Estuary Invasive Spartina Project 2012 Water Quality Monitoring Report., Prepared for the California State Coastal Conservancy San Francisco Invasive Spartina Project, 1330 Broadway, 13th Floor, Oakland, CA : 52. Kittelson, P. M. and M. J. Boyd (1997). "Mechanisms of expansion for an introduced species of cordgrass, Spartina densiflora, in Humboldt Bay, California." Estuaries 20(4): Leson & Associates. (2005). Use of Imazapyr Herbicide to Control Invasive Cordgrass (Spartina spp.) in the San Francisco Estuary: Water Quality, Biological Resources, and Human Health and Safety, prepared for the San Francisco Estuary Invasive Spartina Project. Levin, L. A., C. Neira, et al. (2006). "Invasive cordgrass modifies wetland trophic function." Ecology 87(2): McBroom, J. T. (2012). Clapper Rail Surveys for the San Francisco Estuary Invasive Spartina Project. Berkeley, CA, Olofson Environmental, Inc.: 120. Neira, C., E. D. Grosholz, et al. (2006). "Mechanisms generating modification of benthos following tidal flat invasion by a Spartina hybrid." Ecological Applications 16(4): Rhymer, J. M. and D. Simberloff (1996). "Extinction by hybridization and introgression." Annual Review of Ecological Systems 27: Smart, R. M. and J. W. Barko (1978). "Influence of sediment salinity and nutrients on the physiological ecology of selected salt marsh plants.." Estuarine and Coastal Marine Science 7: Spicher, D. and M. Josselyn (1985). "Spartina(Gramineae) in northern California: Distribution and taxonomic notes." Madrono 32(3): State Coastal Conservancy (2003). Final Programmatic Environmental Impact Statement/Environmental Impact Report, San Francisco Estuary Invasive Spartina Project: Spartina Control Program. Oakland, CA. Volume 1: Final Programmatic Environmental Impact Statement/Environmental Impact Report. Wood, J. a. E., M. (2013) Annual Report to U.S. Fish and Wildlife Service: California Clapper Rail (Rallus longirostris obsoletus) TE P. C. Science. Petaluma, CA, PRBO Conservation Science. Invasive Spartina Project Progress Report