Soils are linked to almost half of the United Nations’ Sustainable Development Goals, mostly through the ecosystem services afforded by soil organic carbon they contain (SOC). Food security, climatic stability, and maintenance of
biodiversity depends upon SOC, which is largely comprised of lignocellulosic plant biomass. In combination with lignocellulose inputs to soil, the microbial
degradation of lignocellulosic polymers into simple sugars is the key regulator of these lifesupporting services. Despite this, the relative importance of different microbial taxa in lignocellulose degradation, or the effects of anthropogenic changes, on microbial lignocellulose decomposition are barely understood. Overarching these two challenges is the dearth of knowledge about soil microbial diversity and function. The largest commercial collection of microorganism isolates contains 20,300 species of an estimated one trillion, with significant bias in the represented groups. Our current knowledge of microbial interactions in soils is therefore severely limited. To address these knowledge gaps, this body of work has focused on (1) increasing knowledge about the relative contributions of microbial species and broad taxonomic groups to the degradative potential of lignocellulose in soils, (2) increasing knowledge about how global changes affect the genetic potential of microbial communities, and (3) increasing the diversity of
cultivated microbial species to improve characterisation and prediction of microbial community dynamics.
Chapter 1 reviews the literature on microbial lignocellulose decomposition in soil. Chapter 2 combines metagenomics, metabolomics, and fibre analysis data on soil from a decade-long field experiment, to understand the impact of plant inputs on grassland microbial community composition and associated genes. The majority of lignocellulolytic genes originated from Actinobacteria, Proteobacteria, Bacillota, Bacteroidota, and Planctomycetes. Decade-long plant
exclusion resulted in communities with high proportions of Bacillales, Thermoproteota, and Proteobacteria, and the composition of lignocellulolytic genes was biased towards the cellulolytic glycoside hydrolase family 5. A single year of plant-exclusion biased the composition of lignocellulolytic genes towards xylanases. Chapter 3 uses data from the UK Soil Security Programme’s UGRASS experiment to understand how agricultural intensification impacts different
phylogenetic and functional microbial groups, and their genes for lignocellulolytic enzymes. Agricultural intensification decreased microbial abundance, drastically increased microbial taxonomic diversity (likely as an artefact of relic DNA), and increased relative abundance of cellulase genes. Chapter 4 used high-throughput in situ cultivation to isolate and cultivate lignocellulose degrading microorganisms from soil. Despite analysis of only 83 isolates, we discovered seven new species from commonly isolated soil microorganisms (predominantly Pseudomonas), highlighting the efficacy of high-throughput in situ cultivation for the isolation of new species. Genome annotation and pan-genome-wide association of accessory genes, from Pseudomonas isolates, identified likely causative genes of degradative phenotypes in in vitro tests, as well as genes which likely contributed to the rate of utilisation of different lignocellulosic
polymers. Chapter 5 highlights emerging challenges for the study of lignocellulose degradation in soils, places the findings from each chapter in the wider context of global challenges, and points the way for future research to aid with societal challenges. This body of work presents advances to
our knowledge of the interactions of genes and microorganisms with the major element of SOC. It addresses knowledge gaps about the identity and relative abundances of microorganisms with lignocellulolytic potential in soils, furthers our understanding of the implications of land use change on microorganisms and genes, and gives broad perspectives on the life-history strategies of Pseudomonas isolates which utilise different lignocellulosic polymers. Deepening our understanding of these processes will allow us to devise more effective management strategies to improve sustainable use of soil carbon for food production, climate change offsetting and biodiversity conservation. Together, these can help to reduce global inequality and allow the better formulation of environmental policy.