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Can we accurately predict the distribution of soil microorganism presence and relative abundance?

Verdon, Valentin; Malard, Lucie; Collart, Flavien et al.

2024 • In Ecography

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https://hdl.handle.net/2268/321746

DOI
10.1111/ecog.07086

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Keywords :

amplicon sequencing; archaea; bacteria; cross-validation; eDNA; fungi; protist; species distribution model; topsoil

Abstract :

[en] Soil microbes play a key role in shaping terrestrial ecosystems. It is therefore essential to understand what drives their distribution. While multivariate analyses have been used to characterise microbial communities and drivers of their spatial patterns, few studies have focused on predicting the distribution of amplicon sequence variants (ASVs). Here, we evaluate the potential of species distribution models (SDMs) to predict the presence–absence and relative abundance distribution of bacteria, archaea, fungi, and protist ASVs in the western Swiss Alps. Advanced automated selection of abiotic covariates was used to circumvent the lack of knowledge on the ecology of each ASV. Presence–absence SDMs could be fitted for most ASVs, yielding better predictions than null models. Relative abundance SDMs performed less well, with low fit and predictive power overall, but displayed a good capacity to differentiate between sites with high and low relative abundance of the modelled ASV. SDMs for bacteria and archaea displayed better predictive power than for fungi and protists, suggesting a closer link of the former with the abiotic covariates used. Microorganism distributions were mostly related to edaphic covariates. In particular, pH was the most selected covariate across models. The study shows the potential of using SDM frameworks to predict the distribution of ASVs obtained from topsoil DNA. It also highlights the need for further development of precise edaphic mapping and scenario modelling to enhances prediction of microorganism distributions in the future.

Disciplines :

Environmental sciences & ecology

Author, co-author :

Verdon, Valentin ; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland

Malard, Lucie ; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland

Collart, Flavien ; Université de Liège - ULiège > Département de Biologie, Ecologie et Evolution > Biologie de l'évolution et de la conservation - Unité aCREA-Ulg (Conseils et Recherches en Ecologie Appliquée) ; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland

Adde, Antoine ; Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland

Yashiro, Erika ; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland

Lara Pandi, Enrique ; Real Jardín Botánico-CSIC, Madrid, Spain

Mod, Heidi ; Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland

Singer, David ; Changins College for Viticulture and Enology, University of Sciences and Art Western Switzerland, Nyon, Switzerland

Niculita-Hirzel, Hélène ; Department of Occupational Health and Environment, Centre for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland

Guex, Nicolas ; Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland

Guisan, Antoine ; Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland ; Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland ; Centre Interdisciplinaire de Recherche sur la Montagne, University of Lausanne, Lausanne, Switzerland

Language :

English

Title :

Can we accurately predict the distribution of soil microorganism presence and relative abundance?

Publication date :

2024

Journal title :

Ecography

ISSN :

0906-7590

eISSN :

1600-0587

Publisher :

John Wiley and Sons Inc

Peer reviewed :

Peer Reviewed verified by ORBi

Funding text :

\u2013 AG received funding from the Swiss National Science Foundation (SNSF, grant no. 184908).

Available on ORBi :

since 05 September 2024

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