Dataset Information

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders.

ABSTRACT: BACKGROUND:Efficient industrial processes for converting plant lignocellulosic materials into biofuels are a key to global efforts to come up with alternative energy sources to fossil fuels. Novel cellulolytic enzymes have been discovered in microbial genomes and metagenomes of microbial communities. However, the identification of relevant genes without known homologs, and the elucidation of the lignocellulolytic pathways and protein complexes for different microorganisms remain challenging. RESULTS:We describe a new computational method for the targeted discovery of functional modules of plant biomass-degrading protein families, based on their co-occurrence patterns across genomes and metagenome datasets, and the strength of association of these modules with the genomes of known degraders. From approximately 6.4 million family annotations for 2,884 microbial genomes, and 332 taxonomic bins from 18 metagenomes, we identified 5 functional modules that are distinctive for plant biomass degraders, which we term "plant biomass degradation modules" (PDMs). These modules incorporate protein families involved in the degradation of cellulose, hemicelluloses, and pectins, structural components of the cellulosome, and additional families with potential functions in plant biomass degradation. The PDMs were linked to 81 gene clusters in genomes of known lignocellulose degraders, including previously described clusters of lignocellulolytic genes. On average, 70% of the families of each PDM were found to map to gene clusters in known degraders, which served as an additional confirmation of their functional relationships. The presence of a PDM in a genome or taxonomic metagenome bin furthermore allowed us to accurately predict the ability of any particular organism to degrade plant biomass. For 15 draft genomes of a cow rumen metagenome, we used cross-referencing to confirmed cellulolytic enzymes to validate that the PDMs identified plant biomass degraders within a complex microbial community. CONCLUSIONS:Functional modules of protein families that are involved in different aspects of plant cell wall degradation can be inferred from co-occurrence patterns across (meta-)genomes with a probabilistic topic model. PDMs represent a new resource of protein families and candidate genes implicated in microbial plant biomass degradation. They can also be used to predict the plant biomass degradation ability for a genome or taxonomic bin. The method is also suitable for characterizing other microbial phenotypes.

SUBMITTER: Konietzny SG

PROVIDER: S-EPMC4189754 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders.

Konietzny Sebastian Ga SG Pope Phillip B PB Weimann Aaron A McHardy Alice C AC

Biotechnology for biofuels 20140909 1

<h4>Background</h4>Efficient industrial processes for converting plant lignocellulosic materials into biofuels are a key to global efforts to come up with alternative energy sources to fossil fuels. Novel cellulolytic enzymes have been discovered in microbial genomes and metagenomes of microbial communities. However, the identification of relevant genes without known homologs, and the elucidation of the lignocellulolytic pathways and protein complexes for different microorganisms remain challeng ...[more]

PMID: 25342967

Similar Datasets

Project description:The microbial degradation of plant-derived compounds under salinity stress remains largely underexplored. The pretreatment of lignocellulose material, which is often needed to improve the production of lignocellulose monomers, leads to high salt levels, generating a saline environment that raises technical considerations that influence subsequent downstream processes. Here, we constructed halotolerant lignocellulose degrading microbial consortia by enriching a salt marsh soil microbiome on a recalcitrant carbon and energy source, i.e., wheat straw. The consortia were obtained after six cycles of growth on fresh substrate (adaptation phase), which was followed by four cycles on pre-digested (highly-recalcitrant) substrate (stabilization phase). The data indicated that typical salt-tolerant bacteria made up a large part of the selected consortia. These were "trained" to progressively perform better on fresh substrate, but a shift was observed when highly recalcitrant substrate was used. The most dominant bacteria in the consortia were Joostella marina, Flavobacterium beibuense, Algoriphagus ratkowskyi, Pseudomonas putida, and Halomonas meridiana. Interestingly, fungi were sparsely present and negatively affected by the change in the substrate composition. Sarocladium strictum was the single fungal strain recovered at the end of the adaptation phase, whereas it was deselected by the presence of recalcitrant substrate. Consortia selected in the latter substrate presented higher cellulose and lignin degradation than consortia selected on fresh substrate, indicating a specialization in transforming the recalcitrant regions of the substrate. Moreover, our results indicate that bacteria have a prime role in the degradation of recalcitrant lignocellulose under saline conditions, as compared to fungi. The final consortia constitute an interesting source of lignocellulolytic haloenzymes that can be used to increase the efficiency of the degradation process, while decreasing the associated costs.

Project description:BackgroundTermites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humification. Lignocellulose is often a principal component of such plant diet, and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While lower termites and their gut flagellates were given larger scientific attention in the past, the gut lignocellulolytic bacteria of higher termites remain less explored. Therefore, in this study, we investigated the structure and function of gut prokaryotic microbiomes from 11 higher termite genera representative of Syntermitinae, Apicotermitinae, Termitidae and Nasutitermitinae subfamilies, broadly grouped into plant fibre- and soil-feeding termite categories.ResultsDespite the different compositional structures of the studied termite gut microbiomes, reflecting well the diet and host lineage, we observed a surprisingly high functional congruency between gut metatranscriptomes from both feeding groups. The abundance of transcripts encoding for carbohydrate active enzymes as well as expression and diversity profiles of assigned glycoside hydrolase families were also similar between plant fibre- and soil-feeding termites. Yet, dietary imprints highlighted subtle metabolic differences specific to each feeding category. Roughly, 0.18% of de novo re-constructed gene transcripts were shared between the different termite gut microbiomes, making each termite gut a unique reservoir of genes encoding for potentially industrially applicable enzymes, e.g. relevant to biomass degradation. Taken together, we demonstrated the functional equivalence in microbial populations across different termite hosts.ConclusionsOur results provide valuable insight into the bacterial component of the termite gut system and significantly expand the inventory of termite prokaryotic genes participating in the deconstruction of plant biomass. Video Abstract.

Project description:In theory, changes in the amount of rainfall can change plant biomass allocation and subsequently influence coupled plant-soil microbial processes. However, testing patterns of combined responses of plants and soils remains a knowledge gap for terrestrial ecosystems. We carried out a comprehensive review of the available literature and conducted a meta-analysis to explore combined plant and soil microbial responses in grasslands exposed to experimental precipitation changes. We measured the effects of experimental precipitation changes on plant biomass, biomass allocation, and soil microbial biomass and tested for trade-offs between plant and soil responses to altered precipitation. We found that aboveground and belowground plant biomass responded asynchronically to precipitation changes, thereby leading to shifts in plant biomass allocation. Belowground plant biomass did not change under precipitation changes, but aboveground plant biomass decreased in precipitation reduction and increased in precipitation addition. There was a trade-off between responses of aboveground plant biomass and belowground plant biomass to precipitation reduction, but correlation wasn't found for precipitation addition. Microbial biomass carbon (C) did not change under the treatments of precipitation reduction. Increased root allocation may buffer drought stress for soil microbes through root exudations and neutralize microbial responses to precipitation reduction. However, precipitation addition increased microbial biomass C, potentially reflecting the removal of water limitation for soil microbial growth. We found that there were positive correlations between responses of aboveground plant biomass and microbial biomass C to precipitation addition, indicating that increased shoot growth probably promoted microbial responses via litter inputs. In sum, our study suggested that aboveground, belowground plant biomass and soil microbial biomass can respond asynchronically to precipitation changes, and emphasizes that testing the plant-soil system as a whole is necessary for forecasting the effects of precipitation changes on grassland systems.

Dataset Information

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders.

Publications

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets