Abstract
BackgroundLignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform “community-level” metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes.ResultsHere, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis, Leadbetterella and Truepera. The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of hydrolytic cellulases, hemicellulases and carbohydrate-binding modules involved in lignocellulose degradation. The expression of these activities correlated to the changes in the biomass composition observed by FTIR and ssNMR measurements.ConclusionsA combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks. In addition to the expected carbohydrate-active enzymes, our studies reveal a large number of unknown proteins, some of which may play a crucial role in community-based lignocellulose degradation.
Highlights
Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere
Dynamics of wheat straw degradation Wheat straw was selected as the sole carbon source for shake flask cultures which were inoculated with wheat straw compost
Dried and milled wheat straw samples were subsequently analysed by Fourier transform infrared (FTIR)
Summary
Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. Single-species approaches are, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes. Soil and composting microbiomes are diverse and complex microbial communities that degrade plant cell wall biomass. These microbiomes make a significant contribution to the release of nutrients and recycling of carbon from this highly abundant yet recalcitrant material [1]; due to the complexity and the diversity of species, questions about the roles of community members remain unanswered. The community structure depends on many environmental factors such as oxygen content, plant origin, soil residues, temperature, pH, phase of the lignocellulose degradation and chemical nature of the exposed biomass [3]. A comprehensive assessment of the microbial community to degrade lignocellulose, can only be achieved through the combination of ‘omics techniques [4,5,6]
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