Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies

Abstract\ud \ud Background\ud Lignocellulose is one of the most abundant forms of fixed carbon in the biosphere. Current industrial approaches to the degradation of lignocellulose employ enzyme mixtures, usually from a single fungal species, which are only effective in hydrolyzing polysaccharides following biomass pre-treatments. While the enzymatic mechanisms of lignocellulose degradation have been characterized in detail in individual microbial species, the microbial communities that efficiently breakdown plant materials in nature are species rich and secrete a myriad of enzymes to perform “community-level” metabolism of lignocellulose. Single-species approaches are, therefore, likely to miss important aspects of lignocellulose degradation that will be central to optimizing commercial processes.\ud \ud \ud Results\ud Here, we investigated the microbial degradation of wheat straw in liquid cultures that had been inoculated with wheat straw compost. Samples taken at selected time points were subjected to multi-omics analysis with the aim of identifying new microbial mechanisms for lignocellulose degradation that could be applied in industrial pre-treatment of feedstocks. Phylogenetic composition of the community, based on sequenced bacterial and eukaryotic ribosomal genes, showed a gradual decrease in complexity and diversity over time due to microbial enrichment. Taxonomic affiliation of bacterial species showed dominance of Bacteroidetes and Proteobacteria and high relative abundance of genera Asticcacaulis, Leadbetterella and Truepera. The eukaryotic members of the community were enriched in peritrich ciliates from genus Telotrochidium that thrived in the liquid cultures compared to fungal species that were present in low abundance. A targeted metasecretome approach combined with metatranscriptomics analysis, identified 1127 proteins and showed the presence of numerous carbohydrate-active enzymes extracted from the biomass-bound fractions and from the culture supernatant. This revealed a wide array of hydrolytic cellulases, hemicellulases and carbohydrate-binding modules involved in lignocellulose degradation. The expression of these activities correlated to the changes in the biomass composition observed by FTIR and ssNMR measurements.\ud \ud \ud Conclusions\ud A combination of mass spectrometry-based proteomics coupled with metatranscriptomics has enabled the identification of a large number of lignocellulose degrading enzymes that can now be further explored for the development of improved enzyme cocktails for the treatment of plant-based feedstocks. In addition to the expected carbohydrate-active enzymes, our studies reveal a large number of unknown proteins, some of which may play a crucial role in community-based lignocellulose degradation.This work was funded by Biotechnology and Biological Sciences Research\ud Council (BBSRC) Grants BB/1018492/1, BB/K020358/1 and BB/P027717/1, the\ud BBSRC Network in Biotechnology and Bioenergy BIOCATNET and São Paulo\ud Research Foundation (FAPESP) Grant 10/52362-5. ERdA thanks EMBRAPA\ud Instrumentation São Carlos and Dr. Luiz Alberto Colnago for providing the\ud NMR facility and CNPq Grant 312852/2014-2. The authors would like to thank\ud Deborah Rathbone and Susan Heywood from the Biorenewables Develop‑\ud ment Centre for technical assistance in rRNA amplicon sequencing

Observation of an exotic narrow doubly charmed tetraquark

Conventional, hadronic matter consists of baryons and mesons made of three quarks and a quark-antiquark pair, respectively(1,2). Here, we report the observation of a hadronic state containing four quarks in the Large Hadron Collider beauty experiment. This so-called tetraquark contains two charm quarks, a (u) over bar and a (d) over tilde quark. This exotic state has a mass of approximately 3,875 MeV and manifests as a narrow peak in the mass spectrum of (DD0)-D-0 pi(+) mesons just below the D*D-+(0) mass threshold. The near-threshold mass together with the narrow width reveals the resonance nature of the state

Constraints on the CKM angle gamma from B-+/- -> Dh(+/-) decays using D -> h(+/-)h'(-/+)pi(0) final states

A data sample collected with the LHCb detector corresponding to an integrated luminosity of 9 fb(-1) is used to measure eleven CP violation observables in B-+/- -> Dh(+/-) decays, where h is either a kaon or a pion. The neutral D meson decay is reconstructed in the three-body final states: K-+/-pi(-/+)pi(0); pi(+)pi(-)pi(0); K+ K- pi(0) and the suppressed pi K-+(-/+)pi(0) combination. The mode where a large CP asymmetry is expected, B-+/- -> [K-+/-pi(-/+)pi(0)] K-D(+/-), is observed with a significance greater than seven standard deviations. The ratio of the partial width of this mode relative to that of the favoured mode, B-+/- -> [K-+/-pi(-/+)pi(0)] K-D(+/-), is R-ADS(K) = (1.27 +/- 0.16 +/- 0.02) x 10(-2). Evidence for a large CP asymmetry is also seen: A(ADS(K)) = - 0.38 +/- 0.12 +/- 0.02. Constraints on the CKM angle gamma are calculated from the eleven reported observables