Characterising microbial lignocellulose degradation in soils using high-throughput in situ cultivation and metagenomics

Soils are a major reservoir of global carbon, containing 3.3 and 4.5 times the atmospheric and biotic carbon pool, respectively. Lignocellulose is the most abundant organic polymer in the biosphere and the primary source of recalcitrant carbon in global soils. Consequently, the microbial-mediated decomposition of lignocellulose is a key feature of the global carbon cycle. However, the synergistic interactions of hydrolytic soil microbial communities have made them largely intractable to isolation and cultivation via traditional culture-based approaches, and consequently, our knowledge of the true diversity and hydrolytic enzyme pool of biodegradative microbial communities in soils is significantly limited. Recently, high-throughput microbial cultivation devices, such as the 'iChip', which are deployed in situ to replicate environmental conditions, have enabled the cultivation of up to 50% of bacterial cells from soils, a significant improvement on the <1% that is typically achieved using conventional methods. In combination with metagenomic sequencing, these technologies now allow more comprehensive inventories of microbial diversity and function in soils, where lignocellulose decomposition has previously been assessed only by taxonomic overviews based on phylogenetic marker genes (e.g. rRNA/ITS1). Consequently, the functional diversity of lignocellulolytic microorganisms in soils represents a blind spot in our understanding of ecosystem function. To address this, we will combine high-throughput in situ cultivation, metagenomics, and quantitative hydrolase enzyme assays with analysis of key soil quality indicators to address the identity and activity of key cellulolytic microorganisms in oxic and anoxic soils. Finally, these data will be integrated to develop models to assess cellulose decomposition rates in situ. The study would represent the most comprehensive analysis of lignocellulose-degrading microorganisms in soils to date, providing a step-change in our understanding of soil microorganisms involved in the largest flow of carbon in the biosphere.