Abstract
BackgroundCompost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are thus important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Studies have revealed substantial diversity in compost microbiomes, yet how this diversity relates to functions and even to the genes encoding lignocellulolytic enzymes remains obscure. Here, we used a metagenomic analysis of the rice straw-adapted (RSA) microbial consortia enriched from compost ecosystems to decipher the systematic and functional contexts within such a distinctive microbiome.ResultsAnalyses of the 16S pyrotag library and 5 Gbp of metagenomic sequence showed that the phylum Actinobacteria was the predominant group among the Bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes. The CAZymes profile revealed that CAZyme genes in the RSA consortia were also widely distributed within these bacterial phyla. Strikingly, about 46.1 % of CAZyme genes were from actinomycetal communities, which harbored a substantially expanded catalog of the cellobiohydrolase, β-glucosidase, acetyl xylan esterase, arabinofuranosidase, pectin lyase, and ligninase genes. Among these communities, a variety of previously unrecognized species was found, which reveals a greater ecological functional diversity of thermophilic Actinobacteria than previously assumed.ConclusionThese data underline the pivotal role of thermophilic Actinobacteria in lignocellulose biodegradation processes in the compost habitat. Besides revealing a new benchmark for microbial enzymatic deconstruction of lignocelluloses, the results suggest that actinomycetes found in compost ecosystems are potential candidates for mining efficient lignocellulosic enzymes in the biofuel industry.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0440-2) contains supplementary material, which is available to authorized users.
Highlights
Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production
These results demonstrate that the rice straw-adapted microbial consortia enriched from the compost ecosystem were capable of degrading lignocellulosic biomass and support previous observations that compost habitats harbor a large number of cellulolytic microbes [3, 7]
Various analysis approaches were used to accurately estimate the microbial diversity within the rice straw-adapted (RSA) consortia, such as MetaPhlAn, mOTUs, Mothur, and SortMeRNA [22,23,24,25]. While these analyses showed minor differences in the rank abundance order, the phylum Actinobacteria was the predominant group among the bacteria in the RSA consortia, followed by Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes (Fig. 1a)
Summary
Compost habitats sustain a vast ensemble of microbes specializing in the degradation of lignocellulosic plant materials and are important both for their roles in the global carbon cycle and as potential sources of biochemical catalysts for advanced biofuels production. Because of the complexity of lignocellulosic enzyme systems and compost microbiomes, it has generally been considered unfeasible to characterize the microbial degradation of lignocellulose in compost ecosystems by applying the above-mentioned techniques, which are principally based on isolated pure strains or 16S rRNA gene cloning. This inhibits furthering our understanding of the functions, interactions and ecology of microbial communities related to the degradation and transformation of lignocellulosic materials, and seriously impedes exploiting the repertoire of novel enzymes and proteins that could enhance the efficiency of biomass conversion in compost ecosystems
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