A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

Abstract

Background: Sugarcane bagasse is a major source of lignocellulosic biomass, yet its economic potential is not fully realised. To add value to bagasse, processing is needed to gain access to the embodied recalcitrant biomaterials. When bagasse is stored in piles in the open for long periods it is colonised by microbes originating from the sugarcane, the soil nearby or spores in the environment. For these microorganisms to proliferate they must digest the bagasse to access carbon for growth. The microbial community in bagasse piles is thus a potential resource for the discovery of useful and novel microbes and industrial enzymes. We used culturing and metabarcoding to understand the diversity of microorganisms found in a uniquely undisturbed bagasse storage pile and screened the cultured organisms for fibre-degrading enzymes. Results: Samples collected from 60 to 80 cm deep in the bagasse pile showed hemicellulose and partial lignin degradation. One hundred and four microbes were cultured from different layers and included a high proportion of oleaginous yeast and biomass-degrading fungi. Overall, 70, 67, 70 and 57% of the microbes showed carboxy-methyl cellulase, xylanase, laccase and peroxidase activity, respectively. These percentages were higher in microbes selectively cultured from deep layers, with all four activities found for 44% of these organisms. Culturing and amplicon sequencing showed that there was less diversity and therefore more selection in the deeper layers, which were dominated by thermophiles and acid tolerant organisms, compared with the top of pile. Amplicon sequencing indicated that novel fungi were present in the pile. Conclusions: A combination of culture-dependent and independent methods was successful in exploring the diversity in the bagasse pile. The variety of species that was found and that are known for biomass degradation shows that the bagasse pile was a valuable selective environment for the identification of new microbes and enzymes with biotechnological potential. In particular, lignin-modifying activities have not been reported previously for many of the species that were identified, suggesting future studies are warranted.

Chemical and microbial characterization of sugarcane mill mud for soil applications

“…Rattanachomsrim, however, reported that Firmicutes were abundant in 3-month-old bagasse whose temperature was ~50°C. This suggests that the latter was still in the thermophilic phase of composting [ 29 , 30 ], which is consistent with the work of Gebbie et al who recently reported resampling the same undisturbed bagasse pile (~ 8 months apart) at multiple depths [ 26 ]. Not surprisingly, they found differences in both bacterial and fungal communities with depth and time.…”

“…The microbial community of aged food waste composts and bagasse are known to vary over time as well as with depth [ 18 , 26 , 28 , 29 ]. Generally, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla present in aged food compost and bagasse, though specifics on the age and chemistry of compost and bagasse piles are often not provided [ 25 , 27 ].…”

Platforms to accelerate biomanufacturing of enzyme and probiotic animal feed supplements: discovery considerations and manufacturing implications

“…While targeting the gut of healthy or high-performing livestock has advantages from a safety perspective, this approach is somewhat limited in scope and there may be microbes in other environments that could provide a stepchange in performance or functional novelty. For example, to find potential probiotics that would synergise and enhance lower-value high-fibre feeds based on sugarcane bagasse, we analysed and characterised the microbial community within a bagasse pile that had been undisturbed for an extended period of time (Gebbie et al 2020). Our hypothesis was that microbes degrading and growing on the fibre in the pile should produce relevant non-starch polysaccharide-degrading enzymes and might therefore be probiotic candidates.…”

Culturable bacteria from an Alpine coniferous forest site: biodegradation potential of organic polymers and pollutants

“…It is recognized that a combination of culture-dependent and culture-independent methods is successful in exploring the abundance and diversity of microorganisms in environmental samples. However, culture-dependent methods are still required to understand microbial functions, physiology, adaptation mechanisms, and community dynamics in their environment and to be able to detect and use microorganisms and their associated bioproducts for biotechnological applications (Gebbie et al 2020 ). Low-temperature environments present a large resource for the discovery of useful microorganisms with a wide range of potential biotechnological applications (Collins and Margesin 2019 ).…”