Microorganisms and soil fertility. Jaap Bloem and Peter de Ruiter

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1 Microorganisms and soil fertility Jaap Bloem and Peter de Ruiter

2 Vegetation patches Under harsh conditions plants can survive by living close together: in patches surrounded by bare soil. In fact, the plants then help (facilitate) each other in terms of growth and persistence. In the CASCADE drylands, conditions belowground will be harsh, i.e. in terms of a low soil fertility. In these systems, facilitation is thought to act via the soil by means of positive feedbacks between plants and soil fertility

3 Plant-soil feedbacks: Plant-soil feedbacks can be negative and positive. Negative e.g. when monocultures stimulate growth of soil borne pathogens and diseases. Positive e.g. when plants improve soil fertility in terms of organic matter content, water holding capacity and nutrient availability. Cascade will focus on the analysis of the interplay between plants and the complex of soil fertility parameters. WU will especially look at processes of organic matter dynamics (build-up and decomposition), microbial activity, and nutrient cycling, in order to identify and quantify plant-soil feedbacks. Therefore, WU will make empirical comparisons of this set of soil fertility and microbial parameters within and outside patches. Furthermore, these comparisons can be extended by looking at these parameters along experimental treatments.

4 The soil is full of life But it is mainly invisible Per hectare 3000 kg biomass below ground: 5 cows 60 sheep Per gram soil: a billion bacteria tens of meters of fungal hyphae thousands of species

5 Plant roots and micro-organisms: more litter (SOM), decomposers and mycorrhizal fungi in a sustainable system (Johansson et al., 2004, FEMS Microbiology Ecology 48, 1 13)

6 A closer look: soil particles, plant roots and fungal hyphae (mycorrhiza) Mycorrhizal fungal hyphae greatly extend rhizosphere (access to water and nutrients) Soil aggregates entangled by fungal hyphae Fungi and bacteria produce slime (polysaccharides), gluing soil particles into aggregates Improved retention of water, nutrients and carbon

7 Soil under a microscope (x 400)

8 Under epifluorescence (x400): fungal hyphae and bacteria, closely associated with soil particles Fungal hyphae stained blue (polysaccharides in cell walls) are inactive Fungal hyphae stained red(rna and DNA) are active Bacteria

9 Confocal laser scanning microscope (x 1000): Soil bacteria measured at high resolution Bacteria

10 Soil organisms support ecosystem services Rutgers et al European Journal of Soil Science, 60, Production function nutrient retention (and release) soil structure suppression of plant diseases Resistance and resilience (continuity of land use) Environmental functions degradation organic matter, humus accumulation water balance in soil: storage/retention and drainage climate functions (greenhouse gases N 2 O, CO 2, C sequestration)

11 Production function: microbial indicators of sustainability Nutrient retention (immobilization and release): ratio (net) N mineralization/mineralizable N C mineralization, N mineralization, and ratio fungal to bacterial biomass ratio bacterial growth rate Soil structure: formation of aggregates fungal hyphae labile carbon (extracellular polysaccharides/glue): hot water extractable carbon bacterial growth rate (weathering of rock material)

12 Resistance and resilience: microbial indicators of sustainability Resistance (continuity of land use): to stress and disturbance Total organic matter Labile organic matter: hot water extractable carbon, mineralizable N Amount of fungi, both mycorrhiza and decomposers

13 Environmental functions: microbial indicators of sustainability Degradation organic matter, humus accumulation Ratio C mineralization/net N mineralization Labile C and N Fungal/bacterial biomass ratio water balance in soil: storage/retention and drainage Fungal biomass (hyphae), labile carbon/polysaccharides: aggregates, water holding capacity climate functions Total and labile organic carbon (C-sequestration) Emission of greenhouse gases (CO 2, N 2 O) Denitrifying enzyme activity (N loss and risk of N 2 O production)

14 Microbial indicators: labile organic matter (C and N) Potentially mineralizable nitrogen (anaerobic slurry, 1wk incubation at 40 C) Hot water extractable carbon (16 h extraction at 80 C) Reflects quality of organic matter. Closely related to microbiology, but less dynamic. Changes faster with greater differences than total organic matter (more significant results). Robust practical indicators

15 Biomass of bacteria and fungi measured by direct microscopy Automatic scanning of soil smears Bacteria measured by automatic image analysis Fungal hyphae, active (red) and inactive (blue)

16 Microbial activity Bacterial growth rate: incorporation rate of 3 H-thymidine and 14 C-leucine into bacterial DNA and proteins during a short incubation (1h). Very sensitive. Potential N mineralization: increase in mineral N under standardized conditions in the laboratory (6 wk at 20 C). Reflects net mineralization of plant-available N. Potential C mineralization : O 2 consumption and CO 2 production under standardized conditions in the laboratory(6 wk at 20 C). Basal respiration. Denitrifying Enzyme Activity: N 2 O production in soil slurry during 5h after addition of nitrate and glucose (C-source). Reflects potential N loss and greenhouse gas production.

17 Microbial community structure Phospholipid fatty acid (PLFA) analysis: PLFAs are essential membrane components and reflect the community structure (dominant groups). Saprotrophic fungi, mycorrhizal fungi and groups of bacteria can be distinguished. PLFA fingerprints reflect community composition and show changes in and differences (distances) between microbial communities Provides a quantitative estimate of mycorrhiza Proxy for diversity

18 The end

20 Aerobic and anaerobic N mineralization Aerobic soil incubation 6 wk at 20 C Org. matter net N mineralization Anaerobic slurry 1 wk at 40 C part of microbial biomass killed Difference is proxy for N immobilization Org. matter higher N mineralization (potentially mineralizable N)

III. THE MICROBIAL BIOMASS

III. THE MICROBIAL BIOMASS Required Readings: Ley, R.E., D.A. Lipson and S.K. Schmidt. 2001. Microbial biomass levels in barren and vegetated high altitude talus soils. Soil Sci. Soc. Am. J. 65:111 117.