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Rimet F, Canino A, Chonova T, Guéguen J, Bouchez A. Environmental filtering and mass effect are two important processes driving lake benthic diatoms: Results of a DNA metabarcoding study in a large lake. Mol Ecol 2023; 32:124-137. [PMID: 36239474 DOI: 10.1111/mec.16737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
Environmental filtering is often found to dominate assembly rules in diatoms. These microalgae are diverse, especially at subspecies level, and tend to exhibit a niche phylogenetic conservatism. Therefore, other rules, such as competition or mass effects, should be detectable when environmental gradients and dispersal barriers are limited. We used metabarcoding to analyse benthic littoral diatom communities in 153 sites in a large lake (Geneva) exhibiting weak geographical barriers and weak environmental gradients outside river estuaries. We assessed assembly rules using variance partitioning, phylogenetic and source tracking analyses. No phylogenetic over-dispersion of communities, indicative of exclusive competition, was detected. Instead, we found these communities to be phylogenetically over-clustered, indicating environmental filtering, which was even stronger near river estuaries where environmental gradients are stronger. Finally, using a Bayesian method (SourceTracker), we found that rivers flowing into the lake bring communities that settle, especially in sites close to estuaries. Rivers with the highest discharges are primarily responsible for immigration, explaining 27% of lake composition. Therefore, despite favourable conditions to observe other rules, our results support that diatom communities are prominently assembled by environmental filtering and immigration processes, in particular from rivers. However, this does not exclude that other assembly rules may be at play at a finer spatial, temporal and/or phylogenetic scale.
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Affiliation(s)
- Frédéric Rimet
- UMR Carrtel, INRAE, Université Savoie-Mont Blanc, Thonon les Bains, France
| | - Alexis Canino
- UMR Carrtel, INRAE, Université Savoie-Mont Blanc, Thonon les Bains, France.,OFB, Auffargis, France
| | - Teofana Chonova
- UMR Carrtel, INRAE, Université Savoie-Mont Blanc, Thonon les Bains, France
| | - Julie Guéguen
- UMR Carrtel, INRAE, Université Savoie-Mont Blanc, Thonon les Bains, France.,OFB, Auffargis, France
| | - Agnès Bouchez
- UMR Carrtel, INRAE, Université Savoie-Mont Blanc, Thonon les Bains, France
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Influence of Selected Environmental Factors on Diatom β Diversity (Bacillariophyta) and the Value of Diatom Indices and Sampling Issues. WATER 2022. [DOI: 10.3390/w14152315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Human impacts and environmental climate changes have led to a progressive decline in the diversity of diatoms in lakes in the recent past. The components of β diversity (e.g., species turnover and nestedness) and underlying factors are still poorly understood. Here, we report an investigation of two alternative approaches—beta diversity (β diversity) partitioning and local contribution to β diversity (LCBD)—including their responses to selected environmental factors and representativeness of samples in estimating the ecological fitness of a lake. The β diversity of diatoms and their local contributions could be explained by the effects of environmental variables (p < 0.01). The random forest method showed the most contribution to the variance for NO3−, Cl−, and SO42−. PERMANOVA as well as a network analysis in JASP (Jeffrey’s Amazing Statistics Program) showed significant differences between the seasons in diatom assemblages and in the diatom index for Polish lakes (IOJ). Our findings provide insights into the mechanisms responsible for community organizations along environmental gradients from the perspective of β diversity components, and mechanisms of the indication value of diatoms for lakes; the results could be used especially by countries implementing ecological assessments.
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Pérez-Burillo J, Trobajo R, Leira M, Keck F, Rimet F, Sigró J, Mann DG. DNA metabarcoding reveals differences in distribution patterns and ecological preferences among genetic variants within some key freshwater diatom species. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149029. [PMID: 34375267 DOI: 10.1016/j.scitotenv.2021.149029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/16/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Our study evaluates differences in the distribution and ecology of genetic variants within several ecologically important diatom species that are also key for Water Framework Directive monitoring of European rivers: Fistulifera saprophila (FSAP), Achnanthidium minutissimum (ADMI), Nitzschia inconspicua (NINC) and Nitzschia soratensis (NSTS). We used DADA2 to infer amplicon sequence variants (ASVs) of a short rbcL barcode in 531 environmental samples from biomonitoring campaigns in Catalonia and France. ASVs within each species showed different distribution patterns. Threshold Indicator Taxa ANalysis revealed three ecological groupings of ASVs in both ADMI and FSAP. Two of these in each species were separated by opposite responses to calcium and conductivity. Boosted regression trees additionally showed that both variables greatly influenced the occurrence of these groupings. A third grouping in FSAP was characterized by a negative response to total organic carbon and hence was better represented in waters with higher ecological status than the other FSAP ASVs, contrasting with what is generally assumed for the species. In the two Nitzschia species, our analyses confirmed earlier studies: NINC preferred higher levels of calcium and conductivity. Our findings suggest that the broad ecological tolerance of some diatom species results from overlapping preferences among genetic variants, which individually show much more restricted preferences and distributions. This work shows the importance of studying the ecological preferences of genetic variants within species complexes, now possible with DNA metabarcoding. The results will help reveal and understand biogeographical distributions and facilitate the development of more accurate biological indexes for biomonitoring programmes.
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Affiliation(s)
- Javier Pérez-Burillo
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain; Center for Climate Change (C3), Departament de Geografia, Universitat Rovira i Virgili, C/Joanot Martorell 15, E43500 Vila-seca, Tarragona, Spain
| | - Rosa Trobajo
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain.
| | - Manel Leira
- BioCost Research Group, Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA), Universidade de A Coruña, 15071 A Coruña, Spain; Biodiversity and Applied Botany Research Group, Departmento de Botánica, Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - François Keck
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland; Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Frédéric Rimet
- INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - Javier Sigró
- Center for Climate Change (C3), Departament de Geografia, Universitat Rovira i Virgili, C/Joanot Martorell 15, E43500 Vila-seca, Tarragona, Spain
| | - David G Mann
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain; Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK
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