Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw

Abstract

BackgroundNew lignocellulolytic enzymes are needed that maintain optimal activity under the harsh conditions present during industrial enzymatic deconstruction of biomass, including high temperatures, the absence of free water, and the presence of inhibitors from the biomass. Enriching lignocellulolytic microbial communities under these conditions provides a source of microorganisms that may yield robust lignocellulolytic enzymes tolerant to the extreme conditions needed to improve the throughput and efficiency of biomass enzymatic deconstruction. Identification of promising enzymes from these systems is challenging due to complex substrate-enzyme interactions and requirements to assay for activity. In this study, metatranscriptomes from compost-derived microbial communities enriched on rice straw under thermophilic and mesophilic conditions were sequenced and analyzed to identify lignocellulolytic enzymes overexpressed under thermophilic conditions. To determine differential gene expression across mesophilic and thermophilic treatments, a method was developed which pooled gene expression by functional category, as indicated by Pfam annotations, since microbial communities performing similar tasks are likely to have overlapping functions even if they share no specific genes.ResultsDifferential expression analysis identified enzymes from glycoside hydrolase family 48, carbohydrate binding module family 2, and carbohydrate binding module family 33 domains as significantly overexpressed in the thermophilic community. Overexpression of these protein families in the thermophilic community resulted from expression of a small number of genes not currently represented in any protein database. Genes in overexpressed protein families were predominantly expressed by a single Actinobacteria genus, Micromonospora.ConclusionsCoupling measurements of deconstructive activity with comparative analyses to identify overexpressed enzymes in lignocellulolytic communities provides a targeted approach for discovery of candidate enzymes for more efficient biomass deconstruction. Glycoside hydrolase family 48 cellulases and carbohydrate binding module family 33 polysaccharide monooxygenases with carbohydrate binding module family 2 domains may improve saccharification of lignocellulosic biomass under high-temperature and low moisture conditions relevant to industrial biofuel production.

The distribution of active β-glucosidase-producing microbial communities in composting

“…Simultaneously, although the gene abundance of GH3E was higher than the gene abundance of GH1B from the overall composting process, in the thermophilic phase of composting, the abundance of fungi gene decreased significantly such as GH3E-6-9 and GH3E-6-14 (Fig 6c), while the abundance of bacterial gene showed D r a f t increasing trends such as GH1-3-8, GH1-2-5, GH1-3-20, GH1-4-24, GH3B-3-16 and GH3B-2-12 (Fig 6a, b). A similar phenomenon was found by Simmons et al (2014) where it was shown that several GH family 1 proteins (i.e., bacterial genes) were significantly overexpressed in the thermophilic community, whereas GH family 3 (predominantly fungal) genes were significantly overexpressed in the mesophilic community. Therefore, we found in our experiment that the GH1 and GH3 family bacteria community play a more important role than the GH3 family fungi community in producting β-glucosidase and degradation cellulose at the later thermophilic stage of composting.…”

Microbial community structure and dynamics in thermophilic composting viewed through metagenomics and metatranscriptomics

“…Except for D99, members from the orders Bacillales, Clostridiales, Actinomycetales, and Thermoanaerobacterales abound throughout the composting process, and most CDSs related to plant biomass degradation were classified as belonging to members of these orders. Actinomycetales are commonly found in compost, particularly in the thermophilic and mature stages11162554, and also in thermophilic microbial consortia enriched from compost3055. Indeed, in our data the relative abundance of CDSs assigned to this order involved with lignocellulosic biomass degradation is largest at D30 and D78 (34.4% and 49%, respectively).…”

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia

“…Previous studies on employing microbial consortia for lignocellulose breakdown utilized both complex373839 and defined media404142.…”