Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

Abstract

Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity—the backbone of the regulation of ecosystem services and “soil health” maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.

Biogeographical patterns of the soil fungal:bacterial ratio across France

“…The organic carbon content and the C:N ratio were indeed the main drivers of the soil fungal and bacterial densities taken separately (highlighting the amount and quality of C substrates available for microbial development), but the relative contributions of bacteria and fungi differed, as evidenced by variance partitioning ( Table S1 ). As a consequence, the F:B ratio reflected the complex interactions of these two different functional groups—another key aspect of the understanding of soil microbial communities ( 9 ). Taken together, these results evidence that the F:B ratio provides good complementarity information regarding bacterial and fungal communities, both implied in soil functioning.…”

“…Despite differences, they have altogether showed good repeatability. However, there is a clear need to standardize methods like the DNA extraction procedure for qPCR ( 8 ) or specific biochemical steps for PLFA analyses ( 7 ) to obtain comparable results across studies or laboratories and evaluate the biological status of soils ( 9 ). A first recent meta-analysis going into this direction focused on 1,323 measurements of the soil F:B ratio using PLFA analyses among 11 major biomes to produce the first global maps of F:B biomass ratios ( 10 ).…”

“…The soil ecological quality—defined as the capacity of a soil to host a great quantity and diversity of interacting living organisms implied in its functioning—has been intensively studied as a consequence of the current need for an agroecological transition of soils and of the development of modern research tools ( 11 , 12 ). There is now a clear need to have access to robust molecular tools to efficiently reflect the complex interactions of the bacterial and fungal soil microbial communities ( 9 ), particularly in agricultural soils such as croplands or managed grasslands.…”

Current Challenges and Pitfalls in Soil Metagenomics

“…These challenges are also applicable to metatranscriptomics, metabolomics, and metaproteomics [ 75 ]. However, these disciplines are largely underexplored for soil microbial communities due to operational challenges [ 76 ]. The challenges motivating these guidelines need to be solved to ensure that the field of soil metagenomics continues to expand.…”

Living Fungi in an Opencast Limestone Mine: Who Are They and What Can They Do?

“…Furthermore, it should be noted that functional assignment in this study may not cover all possible functions contributed by the community. Previous studies have demonstrated that fungal functions, predicted by PICRUSt2 and FungalTrait, may be limited by the number of genes available in the database and poor taxonomic classification [ 30 , 31 , 66 ].…”