Mining the biomass deconstructing capabilities of rice yellow stem borer symbionts

Rahul Singh,Simon J Mcqueen-Mason,Mayank Gupta,Medha Sharma,Syed Shams Yazdani,Neil C Bruce,Adam A Dowle,Danish Eqbal,Joseph P Bennett,Anna M Alessi

doi:10.1186/s13068-019-1603-8

Abstract

BackgroundEfficient deconstruction of lignocellulosic biomass into simple sugars in an economically viable manner is a prerequisite for its global acceptance as a feedstock in bioethanol production. This is achieved in nature by suites of enzymes with the capability of efficiently depolymerizing all the components of lignocellulose. Here, we provide detailed insight into the repertoire of enzymes produced by microorganisms enriched from the gut of the crop pathogen rice yellow stem borer (Scirpophaga incertulas).ResultsA microbial community was enriched from the gut of the rice yellow stem borer for enhanced rice straw degradation by sub-culturing every 10 days, for 1 year, in minimal medium with rice straw as the main carbon source. The enriched culture demonstrated high cellulolytic and xylanolytic activity in the culture supernatant. Metatranscriptomic and metaexoproteomic analysis revealed a large array of enzymes potentially involved in rice straw deconstruction. The consortium was found to encode genes ascribed to all five classes of carbohydrate-active enzymes (GHs, GTs, CEs, PLs, and AAs), including carbohydrate-binding modules (CBMs), categorized in the carbohydrate-active enzymes (CAZy) database. The GHs were the most abundant class of CAZymes. Predicted enzymes from these CAZy classes have the potential to digest each cell-wall components of rice straw, i.e., cellulose, hemicellulose, pectin, callose, and lignin. Several identified CAZy proteins appeared novel, having an unknown or hypothetical catalytic counterpart with a known class of CBM. To validate the findings, one of the identified enzymes that belong to the GH10 family was functionally characterized. The enzyme expressed in E. coli efficiently hydrolyzed beechwood xylan, and pretreated and untreated rice straw.ConclusionsThis is the first report describing the enrichment of lignocellulose degrading bacteria from the gut of the rice yellow stem borer to deconstruct rice straw, identifying a plethora of enzymes secreted by the microbial community when growing on rice straw as a carbon source. These enzymes could be important candidates for biorefineries to overcome the current bottlenecks in biomass processing.

Highlights

Efficient deconstruction of lignocellulosic biomass into simple sugars in an economically viable man‐ ner is a prerequisite for its global acceptance as a feedstock in bioethanol production
Microbial diversity of a rice yellow stem borer gut consortium Rice yellow stem borer (YSB) larvae were collected from paddy fields and the larvae gut dissected to facilitate the collection of the gut fluid. 16S ribosomal RNA (rRNA) analysis of the microbial community present in the gut identified various operational taxonomic units (OTUs) that were affiliated to 178 genera belonging to 13 different phyla (Table 1)
A similar trend existed in terms of total number of unique OTUs detected under each category (Fig. 1b)

Summary

Introduction

Efficient deconstruction of lignocellulosic biomass into simple sugars in an economically viable man‐ ner is a prerequisite for its global acceptance as a feedstock in bioethanol production. This is achieved in nature by suites of enzymes with the capability of efficiently depolymerizing all the components of lignocellulose. None of the current formulations of biomass degrading enzymes fully meet the requirements of the biofuels’ industry [15] To overcome these limitations, a diverse range of lignocellulosic degrading organisms are being explored for new enzyme activities, including insects, which have evolved to digest wider range of lignocellulosic substrates [16,17,18]

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Conclusion