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Djemiel C, Dequiedt S, Bailly A, Tripied J, Lelièvre M, Horrigue W, Jolivet C, Bispo A, Saby N, Valé M, Maron PA, Ranjard L, Terrat S. Biogeographical patterns of the soil fungal:bacterial ratio across France. mSphere 2023; 8:e0036523. [PMID: 37754664 PMCID: PMC10597451 DOI: 10.1128/msphere.00365-23] [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: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 09/28/2023] Open
Abstract
Soils are one of the major reservoirs of biological diversity on our planet because they host a huge richness of microorganisms. The fungal:bacterial (F:B) ratio targets two major functional groups of organisms in soils and can improve our understanding of their importance and efficiency for soil functioning. To better decipher the variability of this ratio and rank the environmental parameters involved, we used the French Soil Quality Monitoring Network (RMQS)-one of the most extensive and a priori-free soil sampling surveys, based on a systematic 16 km × 16 km grid and including more than 2,100 samples. F:B ratios, measured by quantitative PCR targeting the 18S and 16S rDNA genes, turned out to be heterogenously distributed and spatially structured in geographical patterns across France. These distribution patterns differed from bacterial or fungal densities taken separately, supporting the hypothesis that the F:B ratio is not the mere addition of each density but rather results from the complex interactions of the two functional groups. The F:B ratios were mainly influenced by soil characteristics and land management. Among soil characteristics, the pH and, to a lesser extent, the organic carbon content and the carbon:nitrogen (C:N) ratio were the main drivers. These results improved our understanding of soil microbial communities, and from an operational point of view, they suggested that the F:B ratio should be a useful new bioindicator of soil status. The resulting dataset can be considered as a first step toward building up a robust repository essential to any bioindicator and aimed at guiding and helping decision making. IMPORTANCE In the face of human disturbances, microbial activity can be impacted and, e.g., can result in the release of large amounts of soil carbon into the atmosphere, with global impacts on temperature. Therefore, the development and the regular use of soil bioindicators are essential to (i) improve our knowledge of soil microbial communities and (ii) guide and help decision makers define suitable soil management strategies. Bacterial and fungal communities are key players in soil organic matter turnover, but with distinct physiological and ecological characteristics. The fungal:bacterial ratio targets these two major functional groups by investigating their presence and their equilibrium. The aim of our study is to characterize this ratio at a territorial scale and rank the environmental parameters involved so as to further develop a robust repository essential to the interpretation of any bioindicator of soil quality.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Samuel Dequiedt
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Arthur Bailly
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Julie Tripied
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Mélanie Lelièvre
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Walid Horrigue
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | | | | | | | | | - Pierre-Alain Maron
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Lionel Ranjard
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
| | - Sébastien Terrat
- Agroécologie, INRAE, Institut Agro, Université Bourgogne, Franche-Comté, Dijon, France
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Linking Land Use and Plant Functional Diversity Patterns in Sabah, Borneo, through Large-Scale Spatially Continuous Sentinel-2 Inference. LAND 2022. [DOI: 10.3390/land11040572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Global biodiversity losses erode the functioning of our vital ecosystems. Functional diversity is increasingly recognized as a critical link between biodiversity and ecosystem functioning. Satellite earth observation was proposed to address the current absence of information on large-scale continuous patterns of plant functional diversity. This study demonstrates the inference and spatial mapping of functional diversity metrics through satellite remote sensing over a large key biodiversity region (Sabah, Malaysian Borneo, ~53,000 km2) and compares the derived estimates across a land-use gradient as an initial qualitative assessment to test the potential merits of the approach. Functional traits (leaf water content, chlorophyll-a and -b, and leaf area index) were estimated from Sentinel-2 spectral reflectance using a pre-trained neural network on radiative transfer modeling simulations. Multivariate functional diversity metrics were calculated, including functional richness, divergence, and evenness. Spatial patterns of functional diversity were related to land-use data distinguishing intact forest, logged forest, and oil palm plantations. Spatial patterns of satellite remotely sensed functional diversity are significantly related to differences in land use. Intact forests, as well as logged forests, featured consistently higher functional diversity compared to oil palm plantations. Differences were profound for functional divergence, whereas functional richness exhibited relatively large variances within land-use classes. By linking large-scale patterns of functional diversity as derived from satellite remote sensing to land-use information, this study indicated initial responsiveness to broad human disturbance gradients over large geographical and spatially contiguous extents. Despite uncertainties about the accuracy of the spatial patterns, this study provides a coherent early application of satellite-derived functional diversity toward further validation of its responsiveness across ecological gradients.
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Stephenson F, Hewitt JE, Torres LG, Mouton TL, Brough T, Goetz KT, Lundquist CJ, MacDiarmid AB, Ellis J, Constantine R. Cetacean conservation planning in a global diversity hotspot: dealing with uncertainty and data deficiencies. Ecosphere 2021. [DOI: 10.1002/ecs2.3633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Judi E. Hewitt
- National Institute of Water and Atmosphere (NIWA) Hamilton New Zealand
- Department of Statistics University of Auckland Auckland New Zealand
| | - Leigh G. Torres
- Department of Fisheries and Wildlife Marine Mammal Institute Oregon State University Newport Oregon USA
| | - Théophile L. Mouton
- Marine Biodiversity Exploitation, and Conservation (MARBEC) UMR IRD‐CNRS‐UM‐IFREMER 9190 Université de Montpellier Montpellier34095France
| | - Tom Brough
- National Institute of Water and Atmosphere (NIWA) Hamilton New Zealand
| | - Kimberly T. Goetz
- National Oceanic and Atmospheric Administration National Marine Fisheries Service Marine Mammal Laboratory Alaska Fisheries Science Center Seattle Alaska USA
- National Institute of Water and Atmosphere (NIWA) Wellington New Zealand
| | - Carolyn J. Lundquist
- National Institute of Water and Atmosphere (NIWA) Hamilton New Zealand
- Institute of Marine Science University of Auckland Auckland New Zealand
| | | | - Joanne Ellis
- School of Science University of Waikato Tauranga New Zealand
| | - Rochelle Constantine
- Institute of Marine Science University of Auckland Auckland New Zealand
- School of Biological Sciences University of Auckland Auckland New Zealand
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Sturbois A, De Cáceres M, Sánchez-Pinillos M, Schaal G, Gauthier O, Mao PL, Ponsero A, Desroy N. Extending community trajectory analysis: New metrics and representation. Ecol Modell 2021. [DOI: 10.1016/j.ecolmodel.2020.109400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Aglieri G, Baillie C, Mariani S, Cattano C, Calò A, Turco G, Spatafora D, Di Franco A, Di Lorenzo M, Guidetti P, Milazzo M. Environmental DNA effectively captures functional diversity of coastal fish communities. Mol Ecol 2020; 30:3127-3139. [PMID: 33078500 DOI: 10.1111/mec.15661] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 01/04/2023]
Abstract
Robust assessments of taxonomic and functional diversity are essential components of research programmes aimed at understanding current biodiversity patterns and forecasting trajectories of ecological changes. Yet, evaluating marine biodiversity along its dimensions is challenging and dependent on the power and accuracy of the available data collection methods. Here we combine three traditional survey methodologies (underwater visual census strip transects [UVCt], baited underwater videos [BUV] and small-scale fishery catches [SSFc]), and one novel molecular technique (environmental DNA metabarcoding [eDNA]-12S rRNA and cytochrome oxidase subunit 1 [COI]) to investigate their efficiency and complementarity in assessing fish diversity. We analysed 1,716 multimethod replicates at a basin scale to measure the taxonomic and functional diversity of Mediterranean fish assemblages. Taxonomic identities were investigated at species, genus and family levels. Functional identities were assessed using combinations of morphological, behavioural and trophic traits. We show that: (a) SSFc provided the higher taxonomic diversity estimates followed by eDNA, and then UVCt and BUV; (b) eDNA was the only method able to gather the whole spectrum of considered functional traits, showing the most functionally diversified and least redundant fish assemblages; and (c) the effectiveness of eDNA in describing functional structure reflected its lack of selectivity towards any considered functional trait. Our findings suggest that the reach of eDNA analysis stretches beyond taxon detection efficiency and provides new insights into the potential of metabarcoding in ecological studies.
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Affiliation(s)
- Giorgio Aglieri
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Salford, UK
| | - Stefano Mariani
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Carlo Cattano
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.,Department of Integrative Marine Ecology, Sicily, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo (complesso Roosevelt), Palermo, Italy
| | - Antonio Calò
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,UMR 7035 ECOSEAS, CNRS, Université Côte d'Azur, Nice, France
| | - Gabriele Turco
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Davide Spatafora
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
| | - Antonio Di Franco
- Department of Integrative Marine Ecology, Sicily, Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo (complesso Roosevelt), Palermo, Italy.,UMR 7035 ECOSEAS, CNRS, Université Côte d'Azur, Nice, France
| | - Manfredi Di Lorenzo
- Institute for Biological Resources and Marine Biotechnologies, National Research Council (IRBIM-CNR), Mazara del Vallo, Italy
| | - Paolo Guidetti
- Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy.,UMR 7035 ECOSEAS, CNRS, Université Côte d'Azur, Nice, France.,Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marco Milazzo
- Department of Earth and Marine Sciences (DiSTeM), University of Palermo, Palermo, Italy.,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa), Rome, Italy
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Sarker SK, Reeve R, Paul NK, Matthiopoulos J. Modelling spatial biodiversity in the world’s largest mangrove ecosystem—The Bangladesh Sundarbans: A baseline for conservation. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12887] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Swapan Kumar Sarker
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences University of Glasgow Glasgow UK
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences University of Glasgow Glasgow UK
| | - Nirmal K. Paul
- Management Plan Division Bangladesh Forest Department Khulna Bangladesh
| | - Jason Matthiopoulos
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical Veterinary and Life Sciences University of Glasgow Glasgow UK
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Scherrer D, D'Amen M, Fernandes RF, Mateo RG, Guisan A. How to best threshold and validate stacked species assemblages? Community optimisation might hold the answer. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.13041] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Scherrer
- Department of Ecology and EvolutionUniversity of Lausanne, Biophore Lausanne Switzerland
| | - Manuela D'Amen
- Department of Ecology and EvolutionUniversity of Lausanne, Biophore Lausanne Switzerland
| | - Rui F. Fernandes
- Department of Ecology and EvolutionUniversity of Lausanne, Biophore Lausanne Switzerland
| | - Rubén G. Mateo
- Department of Ecology and EvolutionUniversity of Lausanne, Biophore Lausanne Switzerland
- ETSI de MontesForestal y del Medio NaturalUniversidad Politécnica de Madrid Madrid Spain
| | - Antoine Guisan
- Department of Ecology and EvolutionUniversity of Lausanne, Biophore Lausanne Switzerland
- Institute of Earth Surface DynamicsUniversity of Lausanne, Géopolis Lausanne Switzerland
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Talluto MV, Mokany K, Pollock LJ, Thuiller W. Multifaceted biodiversity modelling at macroecological scales using Gaussian processes. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Matthew V. Talluto
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB); Berlin Germany
- Laboratoire d'Écologie Alpine (LECA); CNRS; Université Grenoble Alpes; Grenoble France
| | | | - Laura J. Pollock
- Laboratoire d'Écologie Alpine (LECA); CNRS; Université Grenoble Alpes; Grenoble France
| | - Wilfried Thuiller
- Laboratoire d'Écologie Alpine (LECA); CNRS; Université Grenoble Alpes; Grenoble France
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