Overview
ABSTRACT
The new meta-omics techniques have upset the field of microbial ecology, particularly due to the contribution of the new high-throughput sequencing technologies. This revolution has benefited from fundamental research point of view but also by giving access to tools dedicated to new measurements and to carry out soil microbial quality diagnosis. What are the bio-indicators used? How are they studied and applied on a large scale? This article will be focused on the different meta-omic techniques illustrated by valid or undergoing validation examples, as well as future developments in order to answer the essential challenge of a better understanding and preservation of the soil.
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Christophe DJEMIEL : Post-doctoral fellow at INRA Dijon, PhD in environmental and population biology and ecology from the University of Lille. - UMR 1347 Agroecology – INRA/Université de Bourgogne/AgroSup, BIOmE pole – BIOCOM team, Dijon, France
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Sébastien TERRAT : Lecturer at the Dijon-Auxerre Institute of Technology, PhD in soil microbial ecology from Blaise Pascal University (Clermont II). - UMR 1347 Agroecology – INRA/Université de Bourgogne/AgroSup, BIOmE pole – BIOCOM team, Dijon, France
INTRODUCTION
Over the past two decades, microbial ecology has not escaped the data explosion known as "Big Data", due in particular to the emergence of very high-throughput sequencing techniques, generating massive quantities of data. . The use of these new technologies, grouped together under the term "meta-omics", combined with the ability to obtain biological material (DNA, RNA, proteins) directly from an ecosystem, have made it possible to understand the ecosystem not at the scale of a single organism ("omics" methods), but by characterizing all the communities of organisms in an ecosystem. . This revolution has increased our knowledge of the complexity of the microbiome of various natural ecosystems, such as soils .
Soils play a central role in many functions, and their microbiomes provide numerous ecosystem services to maintain environmental quality, all of which are impacted by human activities. . For example, soil micro-organisms are involved in numerous biogeochemical cycles, but also in other functions such as plant productivity or pathogen barrier. In addition, it has been possible to identify a series of factors (e.g. anthropization, climate disruption) involved in changing soil quality, and consequently its microbiome.
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KEYWORDS
Microbiology | Next generation sequencing | meta-omics | diagnosis | bioindicator | soil
New meta-omics techniques for diagnosis of soil microbial quality
Using micro-organisms to assess the biological quality of soils
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