A methodological framework to embrace soil biodiversity

Stefan Geisen; Maria J.I. Briones; Huijie Gan; Valerie M. Behan-Pelletier; Ville-Petri Friman; G. Arjen de Groot; S.Emilia Hannula; Zoë Lindo; Laurent Philippot; Alexei V. Tiunov; Diana H. Wall

doi:10.1016/j.soilbio.2019.107536

A methodological framework to embrace soil biodiversity

Stefan Geisen (Corresponding author), Maria J.I. Briones, Huijie Gan, Valerie M. Behan-Pelletier, Ville-Petri Friman, G. Arjen de Groot, S.Emilia Hannula, Zoë Lindo, Laurent Philippot, Alexei V. Tiunov, Diana H. Wall

NIOO - Terrestrial Ecology (TE)

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

Abstract

Soils host the vast majority of life on Earth including microorganisms and animals, and supporting all terrestrial vegetation. While soil organisms are pivotal for ecosystem functioning, the assemblages of different biota from a taxonomic and functional perspective, as well as how these different organisms interact, remains poorly known. We provide a brief overview of the taxonomic and functional diversity of all major groups of soil biota across different scales and organism sizes, ranging from viruses to prokaryotes and eukaryotes. This reveals knowledge gaps in relation to all soil biodiversity groups, which are especially evident for viruses, protists, micro- and meso-fauna. We review currently-available methods to study the taxonomic and functional diversity of soil organisms by grouping all commonly-used methods into morphological, biochemical and molecular approaches. We list potentials and limitations of the methods to reveal that there is, as yet, no single method to fully characterize the biodiversity even of a single group of soil biota. Yet, we stress that we now have the methods available to enable scientists to disentangle the taxonomic and functional diversity of virtually all soil organisms. We provide a user-friendly guide to help researchers address a wider variety of soil biodiversity in their studies by discussing and critically analysing the various potentials and limitations of diverse methods to study distinct groups of soil life. We highlight that integrative methodological approaches, ideally in collaborative interactions, are key to advancing our understanding of soil biodiversity, such as the combination of morphological and molecular approaches to overcome method-specific limitations. Together, integrative efforts can provide information on the abundance, biomass, diversity and function of several groups of soil biota simultaneously. This newly-obtained integrative information on soil biodiversity will help to define the importance of soil biodiversity in ecosystem processes, functions, and services, and serve to refine food-web and earth system models.

Original language	English
Article number	107536
Journal	Soil Biology & Biochemistry
Volume	136
DOIs	https://doi.org/10.1016/j.soilbio.2019.107536
Publication status	Published - 2019

Keywords

international
Plan_S-Compliant_NO
Molecular methods
Food-webs
Biodiversity
Soil functions and health
Microorganisms

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title = "A methodological framework to embrace soil biodiversity",

abstract = "Soils host the vast majority of life on Earth including microorganisms and animals, and supporting all terrestrial vegetation. While soil organisms are pivotal for ecosystem functioning, the assemblages of different biota from a taxonomic and functional perspective, as well as how these different organisms interact, remains poorly known. We provide a brief overview of the taxonomic and functional diversity of all major groups of soil biota across different scales and organism sizes, ranging from viruses to prokaryotes and eukaryotes. This reveals knowledge gaps in relation to all soil biodiversity groups, which are especially evident for viruses, protists, micro- and meso-fauna. We review currently-available methods to study the taxonomic and functional diversity of soil organisms by grouping all commonly-used methods into morphological, biochemical and molecular approaches. We list potentials and limitations of the methods to reveal that there is, as yet, no single method to fully characterize the biodiversity even of a single group of soil biota. Yet, we stress that we now have the methods available to enable scientists to disentangle the taxonomic and functional diversity of virtually all soil organisms. We provide a user-friendly guide to help researchers address a wider variety of soil biodiversity in their studies by discussing and critically analysing the various potentials and limitations of diverse methods to study distinct groups of soil life. We highlight that integrative methodological approaches, ideally in collaborative interactions, are key to advancing our understanding of soil biodiversity, such as the combination of morphological and molecular approaches to overcome method-specific limitations. Together, integrative efforts can provide information on the abundance, biomass, diversity and function of several groups of soil biota simultaneously. This newly-obtained integrative information on soil biodiversity will help to define the importance of soil biodiversity in ecosystem processes, functions, and services, and serve to refine food-web and earth system models.",

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author = "Stefan Geisen and Briones, {Maria J.I.} and Huijie Gan and Behan-Pelletier, {Valerie M.} and Ville-Petri Friman and {de Groot}, {G. Arjen} and S.Emilia Hannula and Zo{\"e} Lindo and Laurent Philippot and Tiunov, {Alexei V.} and Wall, {Diana H.}",

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AU - Geisen, Stefan

AU - Briones, Maria J.I.

AU - Gan, Huijie

AU - Behan-Pelletier, Valerie M.

AU - Friman, Ville-Petri

AU - de Groot, G. Arjen

AU - Hannula, S.Emilia

AU - Lindo, Zoë

AU - Philippot, Laurent

AU - Tiunov, Alexei V.

AU - Wall, Diana H.

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N2 - Soils host the vast majority of life on Earth including microorganisms and animals, and supporting all terrestrial vegetation. While soil organisms are pivotal for ecosystem functioning, the assemblages of different biota from a taxonomic and functional perspective, as well as how these different organisms interact, remains poorly known. We provide a brief overview of the taxonomic and functional diversity of all major groups of soil biota across different scales and organism sizes, ranging from viruses to prokaryotes and eukaryotes. This reveals knowledge gaps in relation to all soil biodiversity groups, which are especially evident for viruses, protists, micro- and meso-fauna. We review currently-available methods to study the taxonomic and functional diversity of soil organisms by grouping all commonly-used methods into morphological, biochemical and molecular approaches. We list potentials and limitations of the methods to reveal that there is, as yet, no single method to fully characterize the biodiversity even of a single group of soil biota. Yet, we stress that we now have the methods available to enable scientists to disentangle the taxonomic and functional diversity of virtually all soil organisms. We provide a user-friendly guide to help researchers address a wider variety of soil biodiversity in their studies by discussing and critically analysing the various potentials and limitations of diverse methods to study distinct groups of soil life. We highlight that integrative methodological approaches, ideally in collaborative interactions, are key to advancing our understanding of soil biodiversity, such as the combination of morphological and molecular approaches to overcome method-specific limitations. Together, integrative efforts can provide information on the abundance, biomass, diversity and function of several groups of soil biota simultaneously. This newly-obtained integrative information on soil biodiversity will help to define the importance of soil biodiversity in ecosystem processes, functions, and services, and serve to refine food-web and earth system models.

AB - Soils host the vast majority of life on Earth including microorganisms and animals, and supporting all terrestrial vegetation. While soil organisms are pivotal for ecosystem functioning, the assemblages of different biota from a taxonomic and functional perspective, as well as how these different organisms interact, remains poorly known. We provide a brief overview of the taxonomic and functional diversity of all major groups of soil biota across different scales and organism sizes, ranging from viruses to prokaryotes and eukaryotes. This reveals knowledge gaps in relation to all soil biodiversity groups, which are especially evident for viruses, protists, micro- and meso-fauna. We review currently-available methods to study the taxonomic and functional diversity of soil organisms by grouping all commonly-used methods into morphological, biochemical and molecular approaches. We list potentials and limitations of the methods to reveal that there is, as yet, no single method to fully characterize the biodiversity even of a single group of soil biota. Yet, we stress that we now have the methods available to enable scientists to disentangle the taxonomic and functional diversity of virtually all soil organisms. We provide a user-friendly guide to help researchers address a wider variety of soil biodiversity in their studies by discussing and critically analysing the various potentials and limitations of diverse methods to study distinct groups of soil life. We highlight that integrative methodological approaches, ideally in collaborative interactions, are key to advancing our understanding of soil biodiversity, such as the combination of morphological and molecular approaches to overcome method-specific limitations. Together, integrative efforts can provide information on the abundance, biomass, diversity and function of several groups of soil biota simultaneously. This newly-obtained integrative information on soil biodiversity will help to define the importance of soil biodiversity in ecosystem processes, functions, and services, and serve to refine food-web and earth system models.

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KW - Plan_S-Compliant_NO

KW - Molecular methods

KW - Food-webs

KW - Biodiversity

KW - Soil functions and health

KW - Microorganisms

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DO - 10.1016/j.soilbio.2019.107536

M3 - Article

SN - 0038-0717

VL - 136

JO - Soil Biology & Biochemistry

JF - Soil Biology & Biochemistry

M1 - 107536

ER -

A methodological framework to embrace soil biodiversity

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Keywords

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