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Su J, Mazei YA, Tsyganov AN, Chernyshov VA, Mazei NG, Saldaev DA, Yakimov BN. Multi-scale beta-diversity patterns in testate amoeba communities: species turnover and nestedness along a latitudinal gradient. Oecologia 2024; 205:691-707. [PMID: 39115695 DOI: 10.1007/s00442-024-05602-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 07/26/2024] [Indexed: 08/30/2024]
Abstract
The relationship between species diversity and spatial scale is a central topic in spatial community ecology. Latitudinal gradient is among the core mechanisms driving biodiversity distribution on most scales. Patterns of β-diversity along latitudinal gradient have been well studied for aboveground terrestrial and marine communities, whereas soil organisms remain poorly investigated in this regard. The West Siberian Plain is a good model to address diversity scale-dependence since the latitudinal gradient does not overlap with other possible factors such as elevational or maritime. Here, we collected 111 samples following hierarchical sampling (sub-zones, ecosystem types, microhabitat and replicate samples) and performed multi-scale partitioning of β-diversity of testate amoeba assemblages as a model of study. We found that among-ecosystem β-diversity is a leading scale in testate amoeba assemblages variation. Rare species determine β-diversity at all scale levels especially in the northern regions, where rare taxa almost exclusively accounted for the diversity at the ecosystem level. β-Diversity is generally dominated by the turnover component at all scales in lower latitudes, whereas nestedness prevailed at among-ecosystem scale in higher latitudes. These findings indicate that microbial assemblages in northern latitudes are spatially homogeneous and constrained by historical drivers at larger scales, whereas in southern regions, it is dominated by the turnover component both at the microhabitat and ecosystem scales and therefore determined by recent vegetation and environmental heterogeneity. Overall, we have provided the evidence for the existence of negative latitudinal gradient for among-ecosystem β-diversity but not for among-microhabitat and among-sample β-diversity for terrestrial testate amoeba communities.
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Affiliation(s)
- Jiahui Su
- Shenzhen MSU-BIT University, Shenzhen, 518172, China
- Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119991, Russia
| | - Yuri A Mazei
- Shenzhen MSU-BIT University, Shenzhen, 518172, China
- Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119991, Russia
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave. 33, Moscow, 117071, Russia
| | - Andrey N Tsyganov
- Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119991, Russia
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave. 33, Moscow, 117071, Russia
| | | | - Natalia G Mazei
- Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119991, Russia
| | - Damir A Saldaev
- Shenzhen MSU-BIT University, Shenzhen, 518172, China
- Lomonosov Moscow State University, Leninskie Gory 1, Moscow, 119991, Russia
| | - Basil N Yakimov
- Shenzhen MSU-BIT University, Shenzhen, 518172, China.
- Lobachevsky State University of Nizhny Novgorod, Pr. Gagarina 23, Nizhny Novgorod, 603950, Russia.
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2
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Korn R, Berg C, Bersier LF, Gray SM, Thallinger GG. Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands. Environ Microbiol 2024; 26:e16631. [PMID: 38757479 DOI: 10.1111/1462-2920.16631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Peatlands, one of the oldest ecosystems, globally store significant amounts of carbon and freshwater. However, they are under severe threat from human activities, leading to changes in water, nutrient and temperature regimes in these delicate systems. Such shifts can trigger a substantial carbon flux into the atmosphere and diminish the water-holding capacity of peatlands. Microbes associated with moss in peatlands play a crucial role in providing these ecosystem services, which are at risk due to global change. Therefore, understanding the factors influencing microbial composition and function is vital. Our study focused on five peatlands along an altitudinal gradient in Switzerland, where we sampled moss on hummocks containing Sarracenia purpurea. Structural equation modelling revealed that habitat condition was the primary predictor of community structure and directly influenced other environmental variables. Interestingly, the microbial composition was not linked to the local moss species identity. Instead, microbial communities varied significantly between sites due to differences in acidity levels and nitrogen availability. This finding was also mirrored in a co-occurrence network analysis, which displayed a distinct distribution of indicator species for acidity and nitrogen availability. Therefore, peatland conservation should take into account the critical habitat characteristics of moss-associated microbial communities.
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Affiliation(s)
- Rachel Korn
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | - Sarah M Gray
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gerhard G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
- OMICS Center Graz, BioTechMed, Graz, Austria
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3
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Carvalho da Silva V, Fernandes N. Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest. PeerJ 2023; 11:e15762. [PMID: 37547721 PMCID: PMC10402703 DOI: 10.7717/peerj.15762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
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4
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Jassey VEJ, Hamard S, Lepère C, Céréghino R, Corbara B, Küttim M, Leflaive J, Leroy C, Carrias JF. Photosynthetic microorganisms effectively contribute to bryophyte CO 2 fixation in boreal and tropical regions. ISME COMMUNICATIONS 2022; 2:64. [PMID: 37938283 PMCID: PMC9723567 DOI: 10.1038/s43705-022-00149-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 04/26/2023]
Abstract
Photosynthetic microbes are omnipresent in land and water. While they critically influence primary productivity in aquatic systems, their importance in terrestrial ecosystems remains largely overlooked. In terrestrial systems, photoautotrophs occur in a variety of habitats, such as sub-surface soils, exposed rocks, and bryophytes. Here, we study photosynthetic microbial communities associated with bryophytes from a boreal peatland and a tropical rainforest. We interrogate their contribution to bryophyte C uptake and identify the main drivers of that contribution. We found that photosynthetic microbes take up twice more C in the boreal peatland (~4.4 mg CO2.h-1.m-2) than in the tropical rainforest (~2.4 mg CO2.h-1.m-2), which corresponded to an average contribution of 4% and 2% of the bryophyte C uptake, respectively. Our findings revealed that such patterns were driven by the proportion of photosynthetic protists in the moss microbiomes. Low moss water content and light conditions were not favourable to the development of photosynthetic protists in the tropical rainforest, which indirectly reduced the overall photosynthetic microbial C uptake. Our investigations clearly show that photosynthetic microbes associated with bryophyte effectively contribute to moss C uptake despite species turnover. Terrestrial photosynthetic microbes clearly have the capacity to take up atmospheric C in bryophytes living under various environmental conditions, and therefore potentially support rates of ecosystem-level net C exchanges with the atmosphere.
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Affiliation(s)
- Vincent E J Jassey
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université Toulouse 3-Paul Sabatier (UT3), CNRS, 31062, Toulouse, France.
| | - Samuel Hamard
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université Toulouse 3-Paul Sabatier (UT3), CNRS, 31062, Toulouse, France
| | - Cécile Lepère
- Laboratoire Microorganismes, Génome Et Environnement (LMGE), Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Régis Céréghino
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université Toulouse 3-Paul Sabatier (UT3), CNRS, 31062, Toulouse, France
| | - Bruno Corbara
- Laboratoire Microorganismes, Génome Et Environnement (LMGE), Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Martin Küttim
- Institute of Ecology, School of Natural Sciences and Health, Tallinn University, Uus-Sadama 5, 10120, Tallinn, Estonia
| | - Joséphine Leflaive
- Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Université Toulouse 3-Paul Sabatier (UT3), CNRS, 31062, Toulouse, France
| | - Céline Leroy
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
- ECOFOG, AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles, Campus Agronomique, Kourou, France
| | - Jean-François Carrias
- Laboratoire Microorganismes, Génome Et Environnement (LMGE), Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
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5
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Mazel F, Malard L, Niculita-Hirzel H, Yashiro E, Mod HK, Mitchell EAD, Singer D, Buri A, Pinto E, Guex N, Lara E, Guisan A. Soil protist function varies with elevation in the Swiss Alps. Environ Microbiol 2021; 24:1689-1702. [PMID: 34347350 PMCID: PMC9290697 DOI: 10.1111/1462-2920.15686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/06/2021] [Accepted: 07/25/2021] [Indexed: 11/29/2022]
Abstract
Protists are abundant and play key trophic functions in soil. Documenting how their trophic contributions vary across large environmental gradients is essential to understand and predict how biogeochemical cycles will be impacted by global changes. Here, using amplicon sequencing of environmental DNA in open habitat soil from 161 locations spanning 2600 m of elevation in the Swiss Alps (from 400 to 3000 m), we found that, over the whole study area, soils are dominated by consumers, followed by parasites and phototrophs. In contrast, the proportion of these groups in local communities shows large variations in relation to elevation. While there is, on average, three times more consumers than parasites at low elevation (400–1000 m), this ratio increases to 12 at high elevation (2000–3000 m). This suggests that the decrease in protist host biomass and diversity toward mountains tops impact protist functional composition. Furthermore, the taxonomic composition of protists that infect animals was related to elevation while that of protists that infect plants or of protist consumers was related to soil pH. This study provides a first step to document and understand how soil protist functions vary along the elevational gradient.
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Affiliation(s)
- Florent Mazel
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Lucie Malard
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland
| | - Hélène Niculita-Hirzel
- Department of Occupational Health and Environment, Center for Primary Care and Public Health (Unisanté), University of Lausanne, Epalinges, CH-1066, Switzerland
| | - Erika Yashiro
- Center for Microbial Communities, Section of Biotechnology, Aalborg University, Aalborg, Denmark
| | - Heidi K Mod
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, Neuchâtel, CH-2000, Switzerland
| | - David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, CH-2000, Switzerland.,UMR CNRS 6112 LPG-BIAF, Université d'Angers, Angers Cedex 1, France
| | - Aline Buri
- Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
| | - Eric Pinto
- Terrabiom Association, Dörflistrasse 32, Oberrieden, Zürich, 8942, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Enrique Lara
- Real Jardín Botánico, CSIC, Plaza de Murillo 2, Madrid, 28014, Spain
| | - Antoine Guisan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.,Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, 1015, Switzerland
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7
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Ritson JP, Alderson DM, Robinson CH, Burkitt AE, Heinemeyer A, Stimson AG, Gallego-Sala A, Harris A, Quillet A, Malik AA, Cole B, Robroek BJM, Heppell CM, Rivett DW, Chandler DM, Elliott DR, Shuttleworth EL, Lilleskov E, Cox F, Clay GD, Diack I, Rowson J, Pratscher J, Lloyd JR, Walker JS, Belyea LR, Dumont MG, Longden M, Bell NGA, Artz RRE, Bardgett RD, Griffiths RI, Andersen R, Chadburn SE, Hutchinson SM, Page SE, Thom T, Burn W, Evans MG. Towards a microbial process-based understanding of the resilience of peatland ecosystem service provisioning - A research agenda. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143467. [PMID: 33199011 DOI: 10.1016/j.scitotenv.2020.143467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/12/2020] [Accepted: 10/24/2020] [Indexed: 06/11/2023]
Abstract
Peatlands are wetland ecosystems with great significance as natural habitats and as major global carbon stores. They have been subject to widespread exploitation and degradation with resulting losses in characteristic biota and ecosystem functions such as climate regulation. More recently, large-scale programmes have been established to restore peatland ecosystems and the various services they provide to society. Despite significant progress in peatland science and restoration practice, we lack a process-based understanding of how soil microbiota influence peatland functioning and mediate the resilience and recovery of ecosystem services, to perturbations associated with land use and climate change. We argue that there is a need to: in the short-term, characterise peatland microbial communities across a range of spatial and temporal scales and develop an improved understanding of the links between peatland habitat, ecological functions and microbial processes; in the medium term, define what a successfully restored 'target' peatland microbiome looks like for key carbon cycle related ecosystem services and develop microbial-based monitoring tools for assessing restoration needs; and in the longer term, to use this knowledge to influence restoration practices and assess progress on the trajectory towards 'intact' peatland status. Rapid advances in genetic characterisation of the structure and functions of microbial communities offer the potential for transformative progress in these areas, but the scale and speed of methodological and conceptual advances in studying ecosystem functions is a challenge for peatland scientists. Advances in this area require multidisciplinary collaborations between peatland scientists, data scientists and microbiologists and ultimately, collaboration with the modelling community. Developing a process-based understanding of the resilience and recovery of peatlands to perturbations, such as climate extremes, fires, and drainage, will be key to meeting climate targets and delivering ecosystem services cost effectively.
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Affiliation(s)
- Jonathan P Ritson
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.
| | - Danielle M Alderson
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Clare H Robinson
- Department of Earth & Environmental Sciences, The University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | | | - Andreas Heinemeyer
- Stockholm Environment Institute, Department of Environment & Geography, York YO10 5NG, UK
| | - Andrew G Stimson
- North Pennines AONB Partnership, Weardale Business Centre, The Old Co-op building, 1 Martin Street, Stanhope, County Durham DL13 2UY, UK
| | - Angela Gallego-Sala
- Department of Geography, University of Exeter, Laver, North Park Road, Exeter EX4 4QE, UK
| | - Angela Harris
- Department of Geography, The University of Manchester, Manchester M13 9PL, UK
| | - Anne Quillet
- Department of Geography and Environmental Science, University of Reading, Whiteknights RG6 6AB, UK
| | - Ashish A Malik
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK
| | - Beth Cole
- School of Geography, Geology and the Environment, University of Leicester, LE1 7RH, UK
| | - Bjorn J M Robroek
- Dept. of Aquatic Ecology & Environmental Biology, Institute for Water and Wetlands Research, Radboud University, Nijmegen, the Netherlands
| | - Catherine M Heppell
- School of Geography, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Damian W Rivett
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Dave M Chandler
- Moors for the Future Partnership, The Moorland Centre, Fieldhead, Edale, Derbyshire S33 7ZA, UK
| | - David R Elliott
- Environmental Sustainability Research Centre, University of Derby, Derby DE22 1GB, UK
| | - Emma L Shuttleworth
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Erik Lilleskov
- USDA Forest Service, Northern Research Station, Houghton, MI 49931, USA
| | - Filipa Cox
- Department of Earth and Environmental Sciences, University of Manchester, M13 9PL, UK
| | - Gareth D Clay
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Iain Diack
- Natural England, Parkside Court, Hall Park Way, Telford, Shropshire TF3 4LR, UK
| | - James Rowson
- Department of Geography and Geology, Edge Hill University, St Helens Road, Ormskirk Lancs L39 4QP, UK
| | - Jennifer Pratscher
- School of Energy, Geoscience, Infrastructure and Society, The Lyell Centre, Heriot-Watt University, Edinburgh EH14 4AP, UK
| | - Jonathan R Lloyd
- Department of Earth & Environmental Sciences, The University of Manchester, Williamson Building, Oxford Road, Manchester M13 9PL, UK
| | | | - Lisa R Belyea
- School of Geography, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Marc G Dumont
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Mike Longden
- Lancashire Wildlife Trust, 499-511 Bury new road, Bolton Bl2 6DH, UK
| | - Nicholle G A Bell
- School of Chemistry, University of Edinburgh, King's Buildings, David Brewster Road, Edinburgh EH93FJ, UK
| | - Rebekka R E Artz
- Ecological Sciences, The James Hutton Institute, Craigiebuckler, Aberdeen AB15 8QH, UK
| | - Richard D Bardgett
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester M13 9PT, UK
| | | | - Roxane Andersen
- Environmental Research Institute, University of the Highlands and Islands, Castle St., Thurso KW14 7JD, UK
| | - Sarah E Chadburn
- College of Engineering, Mathematics and Physical Sciences, University of Exeter, Stocker Road, Exeter EX4 4PY, UK
| | - Simon M Hutchinson
- School of Science, Engineering and Environment, University of Salford, Salford M5 4WT, UK
| | - Susan E Page
- School of Geography, Geology and the Environment, University of Leicester, LE1 7RH, UK
| | - Tim Thom
- Yorkshire Peat Partnership, Yorkshire Wildlife Trust, Unit 23, Skipton Auction Mart, Gargrave Road, Skipton, North Yorkshire BD23 1UD, UK
| | - William Burn
- Stockholm Environment Institute, Department of Environment & Geography, York YO10 5NG, UK
| | - Martin G Evans
- School of Environment Education and Development, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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8
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Francioli D, Lentendu G, Lewin S, Kolb S. DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. Microorganisms 2021; 9:361. [PMID: 33673098 PMCID: PMC7918050 DOI: 10.3390/microorganisms9020361] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
| | - Guillaume Lentendu
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland;
| | - Simon Lewin
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
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9
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Protistan and fungal diversity in soils and freshwater lakes are substantially different. Sci Rep 2020; 10:20025. [PMID: 33208814 PMCID: PMC7675990 DOI: 10.1038/s41598-020-77045-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/04/2020] [Indexed: 11/14/2022] Open
Abstract
Freshwater and soil habitats hold rich microbial communities. Here we address commonalities and differences between both habitat types. While freshwater and soil habitats differ considerably in habitat characteristics organismic exchange may be high and microbial communities may even be inoculated by organisms from the respective other habitat. We analyze diversity pattern and the overlap of taxa of eukaryotic microbial communities in freshwater and soil based on Illumina HiSeq high-throughput sequencing of the amplicon V9 diversity. We analyzed corresponding freshwater and soil samples from 30 locations, i.e. samples from different lakes across Germany and soil samples from the respective catchment areas. Aside from principle differences in the community composition of soils and freshwater, in particular with respect to the relative contribution of fungi and algae, soil habitats have a higher richness. Nevertheless, community similarity between different soil sites is considerably lower as compared to the similarity between different freshwater sites. We show that the overlap of organisms co-occurring in freshwater and soil habitats is surprisingly low. Even though closely related taxa occur in both habitats distinct OTUs were mostly habitat–specific and most OTUs occur exclusively in either soil or freshwater. The distribution pattern of the few co-occurring lineages indicates that even most of these are presumably rather habitat-specific. Their presence in both habitat types seems to be based on a stochastic drift of particularly abundant but habitat-specific taxa rather than on established populations in both types of habitats.
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10
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Reczuga MK, Seppey CVW, Mulot M, Jassey VE, Buttler A, Słowińska S, Słowiński M, Lara E, Lamentowicz M, Mitchell EA. Assessing the responses of Sphagnum micro-eukaryotes to climate changes using high throughput sequencing. PeerJ 2020; 8:e9821. [PMID: 32999758 PMCID: PMC7505061 DOI: 10.7717/peerj.9821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 08/05/2020] [Indexed: 11/20/2022] Open
Abstract
Current projections suggest that climate warming will be accompanied by more frequent and severe drought events. Peatlands store ca. one third of the world's soil organic carbon. Warming and drought may cause peatlands to become carbon sources through stimulation of microbial activity increasing ecosystem respiration, with positive feedback effect on global warming. Micro-eukaryotes play a key role in the carbon cycle through food web interactions and therefore, alterations in their community structure and diversity may affect ecosystem functioning and could reflect these changes. We assessed the diversity and community composition of Sphagnum-associated eukaryotic microorganisms inhabiting peatlands and their response to experimental drought and warming using high throughput sequencing of environmental DNA. Under drier conditions, micro-eukaryotic diversity decreased, the relative abundance of autotrophs increased and that of osmotrophs (including Fungi and Peronosporomycetes) decreased. Furthermore, we identified climate change indicators that could be used as early indicators of change in peatland microbial communities and ecosystem functioning. The changes we observed indicate a shift towards a more "terrestrial" community in response to drought, in line with observed changes in the functioning of the ecosystem.
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Affiliation(s)
- Monika K. Reczuga
- Climate Change Ecology Research Unit, Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, Poznań, Poland
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
- Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Christophe Victor William Seppey
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
- Department of Arctic and Marine Biology, Faculty of Biosciences Fisheries and Economics, University of Tromsø, Tromsø, Norway
| | - Matthieu Mulot
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
| | - Vincent E.J. Jassey
- Laboratoire Ecologie Fonctionelle et Environnement, Université de Toulouse, CNRS, Toulouse Cedex, France
- Ecological Systems Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Site Lausanne, Switzerland
| | - Alexandre Buttler
- Ecological Systems Laboratory, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research, Site Lausanne, Switzerland
| | - Sandra Słowińska
- Department of Geoecology and Climatology, Institute of Geography and Spatial Organization, Polish Academy of Sciences, Warsaw, Poland
| | - Michał Słowiński
- Past Landscape Dynamics Laboratory, Institute of Geography and Spatial Organization, Polish Academy of Sciences, Warsaw, Poland
| | - Enrique Lara
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
- Real Jardín Botánico, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mariusz Lamentowicz
- Climate Change Ecology Research Unit, Faculty of Geographical and Geological Sciences, Adam Mickiewicz University, Poznań, Poland
| | - Edward A.D. Mitchell
- Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
- Jardin Botanique de Neuchâtel, Neuchâtel, Switzerland
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