Diversity of soil microbial communities: In the perspective of targeting functional genes

Abstract: Abstract

Intensive land use in agriculture can lead to higher loss of biodiversity in soils and subsequently carbon due to tillage and application of pesticides and fertilizers. The microbial communities are pivotal to ecosystem processes in soil such as nutrient cycling, soil formation and plant productivity and thus are affected by land use. The main aim of this thesis is to understand the effects of land-use management on the diversity of both functions and taxonomy of soil microbial communities.
Diversity of microbial enzymes involved is key to understand processes such as carbon cycling in soil. Due to current inefficient methods in obtaining the vast diversity in functional enzymes from environmental samples, we developed a molecular method based on sequence capture to address this issue. As this method is based on oligonucleotide probes, a bioinformatics pipeline to generate probes for targeting mainly diverse functional genes in environmental communities was designed. A web-based implementation of this pipeline was established to make it possible for other researchers to design custom oligos for their own study of interest in understanding ecosystems. The laboratory method ‘captured metagenomics’ was developed and optimized using two soils samples from probes designed to target genes coding for enzymes involved in organic matter degradation. Captured metagenomics was validated and it was superior to current genetic methods such as whole metagenome sequencing.
The land-use management of soils affected the functional composition of microbes in degrading organic matter observed using captured metagenomics. The amount of nitrogen played an important role in defining the functional composition of SOM degrading enzymes while the amount of carbon played a role in defining the taxonomic composition of microbes in the soils. There was no correlation between the functional and taxonomic diversity of microbial communities in the soils that were part of this study. Land-use management also affected the taxonomic composition of AMF and agricultural practices decrease their diversity tremendously. Among the different farming systems, organic farming maintained a higher phylogenetic diversity of AMF with similar cereal production as other strategies. However, the land-use management of soils in this study did not affect bacterial taxonomic composition. These approaches have to be extended to understand microbial responses using enzyme expression to infer their behaviour and adaptation to environmental changes. Similar approaches on functional composition and diversity of microbes in more diverse soils would help us to understand different ecosystems and their functions more clearly.

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