"Omnidia": software for taxonomy, calculation of diatom indices and inventories management

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1 Hydrobiologia 269/270 : , H. van Dam (ed.), Twelfth nternational Diatom Symposium Kluwer Academic Publishers. Printed in Belgium. 509 "Omnidia": software for taxonomy, calculation of diatom indices and inventories management C. Lecointe', M. Coste 2 & J. Prygiel 3 1 CL C, Haut-Poulvere, Monbazillac, France ; 2 Cemagref Bordeaux, 50 avenue de Verdun, Gazinet, Cestas, France ; 3 Agence de l'eau Artois-Picardie, 764 boulevard Lahure, Douai, France Key words : Bacillariophyceae, data base, index, monitoring, freshwater Abstract Software for calculation of 6 diatom indices and diversity indices has been created for both Macintosh and BM compatible computers. This software runs with the data base Omnis 5 under Windows 3.0. t includes three taxonomic files : families, genera and species, and an inventories file. Four types of data inputs are possible. t is always possible to operate simulations and to carry out investigations with simple or combined characters. All files and results of investigations can be listed in different ways. This data base is compatible with both word processing and spreadsheet systems. ntroduction Diatom indices are rarely utilized in studies related to water quality. Some criticisms have been formulated, but undoubtedly, the lack of a data base for calculation of indices is the main obstacle to a more frequent application of such indices. The Agence de l'eau Artois-Picardie has adopted diatom indices for monitoring rivers (Agence de l'eau Artois-Picardie, 1992 ; Prygiel, 1991). Utilization of such methods for routine survey in a large basin requires suitable software. The Omnidia program has been developed for this purpose. The data processing company CLC developed, together with the Cemagref of Bordeaux and the Agence de l'eau Artois-Picardie, a specific software program for both Macintosh and BM compatible computers. This program has been carried out with Omnis 5 (Blyth software) and Windows 3 (Microsoft). This program allows the calculation of the following six indices : CEC index (Descy & Coste, 1991), Descy's index (1979), Generic Diatom ndex or GD (Coste & Ayphassorho, 1991), Leclercq & Maquet's index (1987), Sladecek's index (1986), SP or Specific Pollution Sensitivity ndex (Coste in Cemagref, 1982). The CEC index is calculated from a two-entry table which contains 208 taxa. Horizontally, there are 8 groups of taxa ranked according decreasing tolerance to pollution by biodegradable organic matters from left to right and vertically, there are 4 subgroups of more stenoecous species representing the upstream-downstream successions along a theorical running water ecosystem. The other indices are calculated from the formula of Zelinka & Marvan (1961) : D = E Aj iy,/e A1 vj where A3 is the relative abundance of the taxon j, vj is the indicator value of the taxon j and i; is the sensitivity to pollution of the taxon j. More details about these indices are given in Coste et al. (1991). The Omnidia program includes 4 main functions : management of three taxonomic files, inventories management, investigations and listings.

2 510 The Omnidia program Management of taxonomic files Species file This file includes 2035 taxa according to recent taxonomy (Krammer & Lange-Bertalot, : Round et al., 1990). The following data is given for each taxon : a unique 4-letter code, name (including author(s) and year of description), references, synonyms, family, genera and sensitivity and indicator values for each of the 6 indices except the CEC index for which only the membership of a group or a subgroup is given (Fig. 1). Spaces have been reserved for other indices (salinity, eutrophication, etc.) and the possibility is offered to present a scanned photograph of each species and to enter details on the structure of frustule. Genera file The genera file includes 308 genera according to the classification of Round et al. (1990), with a 4-letter code, sensitivity and indicator values for each genus. These values allow the calculation of GD. This indice is directly derived from SP. Coefficient values are average values calculated from those given to the species belonging to the considered genera. FCHER DES DRTOMEES Denomination Gomphonema olivaceum (Hornemann) Brebisson var. olivaceum 4 References 1838 KLB86p374f165(1-18)KLB91p424f Synonymies' (=GOLV) Genre GOMP GOMPHONEMA C.G. Ehrenberg CEE Famille NA NAVCULACEES Groupe 3 PS DESCY SLAD L&M Troph PH Satin. T 02 Sapr Hab Sensibilite 4,0 4 2,0 3, Valeur indicatrice 1, nserer Modifier Trouuer 4 ~ FF~ Fig. 1. Extract of the species file. Screen image of page on Gomphonema olivaceum (Hornemann) Breb. This taxon is coded GOL and is described in Krammer & Lange-Bertalot (1986) page 374 for the text and Fig. 165 (1-18) for the photographs. GOLV (Gomphonema olivacea (Homemann) Dawnson ex Ross & Sims) is the only synonym of GOLL The genus and family of GOL as well as the value for sensitivity to pollution and the indicator value for indices calculated from the formula of Zelinka and Marvan (1961) are given. For the CEC index, the group or subgroup is precised. Some spaces have been reserved for future indices such as the salinity index (satin.) or ph index. This file can be deleted by selecting the dustbin icon or printed by selecting the printer icon. By selecting the microscope icon, it is possible to get a scanned photograph of the taxon and to have details on the structure of the frustule (length, width, number of striae per l0µ, etc). These topics have to be added by the user.

3 511 Management of inventories nventories are grouped in a single file. The record number must be unique. There are no restrictions on number of taxa in a sample. Taxa are arranged in alphabetical order, even after adding new taxa (Fig. 2). Two types of entering data are possible. One way is to use grids. Each key of the keyboard is assigned to a taxon (Fig. 3). Every time you press a key, you increase the quantity of this species by one. According to the medium (calcareous, acid or brackish) the attribution of the keys is different. The user has only to select the medium he wants to study before entering the data. Another way is to enter the 4-letter codes of the taxa and their abundance. When a same taxon appears many times in a same record,the program adds them up. Moreover, this program allows to carry out simulations. These simulations make it possible to calculate new indices after having modified the number and/or the nature of the taxa. This operation can be made without changing the original record. For instance, it allows to see the part played by the dominant species in the calculations of indices. When data entering is finished, the details of the inventory, the scores of the different types of indices and its characteristics are displayed on the screen. t is then possible to modify some items like slide number, river, date etc. and also the counts (adding and deleting a species, modifying quantities). Then, lists of species, taxa numbers and all indices can be obtained again. nvestigations and printings Details of a record can be printed. Species are listed in decreasing order of importance with code, name (including author(s) and year of de- a SEP 88 ( SOMME NEVRE FLEXCOURT PONT DU CD 123 (Y41220 ( (6D01 Curage recent Aval barrage Cours d'eau tres ombrage NUENTRRES PS SLADECEK DESCY NB especes Effectif Diversite 1 3,98 Equitabilite [ 0,68 10,3 12,3 11,6 Calc ul d es in dic es L& M GENRE CEE 12,7 11,0 11,1 ALAN AN AMJA APED CAFF CCS CDEL C HEN CHC CHN CPED CPLA CPLE CSN DTE DVUE FCVA Trouuer Sommer 2 preparations Lire un fichier de comptage Simulation Creer ) Modifier Fig. 2. Extract of the inventory file. Example related to slide number Different details can be entered such as the date, the river, the hydrographic basin, the exact locality and some topics related to the geographic localization of the site (PK = distance from the source). Species and their abundance values are listed in alphabetical order of the codes. The six diatom indices and some other parameters (number of taxa, number of counted individuals, Shannon diversity and equitability) are presented simultaneously. As for the taxonomic files, each inventory can be deleted, modified and listed.

4 512 COMPTAGE MLEU CALCARE is AFOR = DEHR / DTE 6 FPN + MCR 1 SACU & CMEN [ CPST AAMB R STN z NHEU Z SHAN Y GVRT u NPU U NHU $ NROM q NSOC Q LAVER G CCRE h GTER H CS N M GORR!5 OPAR w NCTE b NLAN B MEN N CPRO 9 NVEN < NCRY > NVRO * SDE 7 DTCR 2 SRAM 3 STTU MDL ' RUGA e NAC E NAR i NGR HNT $ SKPO S NSO j CMN J CPED W NATO x NCPR n NPUP NGOE a RBBB a SOP 8 DVUL 9 FCAP - FCON SULN, CRTO CCAS < AUGR MVAR ) CBAC r NOS R NAMP t NFT NLSU 0 NLN p CPST AMN D ALAN f APED k CPLA K CPLE RLAU X NFRU c NEXT C NOOE 2 NPER ; NMN : NURO SOYA 4 FGRE 5 CCDM u CKUT - SOUB a STTU T NCPL y NFR P NPAL NREC F RLB g CAFF L OTRU m GMN v NTPT U NGRE } SERE \ NTRU Preparation n 5361 Commencer ie comptage A ST N 1 Arreter le comptage Nombre d'especes 7 Effect if 1 10 Fig. 3. Detail of the calcareous grid used to enter diatom data. Each key of the keyboard is assigned to a taxon. Every time the key is pressed, you increase the quantity of this species by one. Three similar grids exist for acid, brackish and generic taxa. The taxa which are not included in the grid can be entered directly by typing the 4-letter codes followed by the counts. Of course, all the results of inventories can be entered this way. scription) and relative abundance. Several records can be printed at once too. Two levels of selection are possible. n a first run, selections can be carried out on slides, dates, rivers, drainage basins, etc. n a second run, the first selection can be improved by determining levels of abundance for 4 species at maximum. Selection of more than 4 species may be obtained by programming Omnis. Four types of listings are possible : list of inventories with only codes and relative abundances, one by one inventories with codes, complete denominations, abundances and scores of indices, tables with 14 inventories maximum and tables with indices. To print tables with more than 14 inventories, selections must be exported on spreadsheets and then on wordprocessing systems. Conclusion Only the main functions of Omnidia program have been mentioned. Other possibilities exist such as modifying taxon names in inventories to follow the updating of taxonomy. The main ad- vantage of Omnidia is its versatility. Everyone may update taxonomy and program Omnis to provide for his own needs. Spaces reserved to other indices, for example eutrophication, go in this way. This program and the database can be ordered at CLC for about 4,000 French francs. A free demonstration (BM-PC or Macintosh) version can be obtained from the senior author. Acknowledgements We thank Dr E. F. Stoermer for his help with the English rendering of the text. References Agence de 1'Eau Artois-Picardie, Carte de qualite hydrobiologique des cours d'eau du bassin Artois-Picardie. Document Agence de 1'Eau Artois- Picardie, 15 pp + carte. Cemagref, Etude des methodes biologiques quantitatives d'appreciation de la qualite des eaux. Rapport Division Qualite des Eaux Lyon - Agence financiere de Bassin Rhone - Mediterranee - Corse, Pierre-Benite, 28 pp. Coste M. & H. Ayphassorho, Etude de la qualite des eaux du Bassin Artois-Picardie a 1'aide des communautes de diatomees benthiques (Application des indices dia-

5 513 tomiques). Rapport Cemagref, Bordeaux - Agence de 1'Eau Artois-Picardie, Douai 227 pp. Coste M., C. Bosca & A. Dauta, Use of algae for monitoring rivers in France. n B. A. Whitton, E. Rott & G. Friedrich (eds), Use of algae for monitoring rivers, Dnsseldorf, E. Rott, nnsbruck : Descy J. P., A new approach to water quality estimation using diatoms. Nova Hedwigia 64: Descy J. P. &M. Coste, A test of methods for assessing water quality based on diatoms. Verh. nternat. Verein. Limnol. 24 : Krammer K. & H. Lange-Bertalot, Bacillariophyceae. Sosswasserflora von Mitteleuropa. 2 (1-4). G. Fischer, Stuttgart. Leclercq L. & Maquet B., Deux nouveaux indices chimique et diatomique de qualite d'eau courante. Appli- cation au Samson et a ses affluents (bassin de la Meuse beige). Comparaison avec d'autres indices chimiques, biocenotiques et diatomiques. nstitut Royal des Sciences Naturelles de Belgique, document de travail 28, 113 pp. Prygiel J., Use of benthic diatoms in surveillance of the Artois-Picardie basin hydrobiological quality. n B. A. Whitton, E. Rott & G. Friedrich (eds), Use of algae for monitoring rivers, Dusseldorf, E. Rott, nnsbruck : Round F. E., R. Crawford & D. G. Mann, The diatoms. Cambridge University Press, Cambridge, 747 pp. Sladecek V., Diatoms as indicators of organic pollution. Acta Hydrochim. Hydrobiol. 14 : Zelinka M. & P. Marvan, Zur Prazisierung der biologischen Klassifikation des Rheinheit fliessender Gewasser. Arch. Hydrobiol. 57 :

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