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ABSTRACT:
PROVIDER: PRJNA430737 | ENA |
REPOSITORIES: ENA
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Project description:Inhibition of the anaerobic digestion process through accumulation of volatile fatty acids (VFA) is a recurring problem which is the result of unbalanced growth between acidogenic bacteria and methanogens. A speedy recovery is essential for an establishment of a feasible economical biogas productions. Yet, little is known regarding the organisms participating in the recovery. In this study the organisms involved in the recovery were studied using protein-stable isotope probing (Protein-SIP) and mapping this data onto a binned metagenome. Under acetate-accumulated simulating conditions a formation of 13C-labeled CO2 and CH4 was detected immediately after the addition of [U-13C]acetate, indicative of a high turnover rate of acetate. Several labeled peptides were detected in protein-SIP analysis. These 13C-labeled peptides were mapped onto a binned metagenome for improved taxanomical classification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia and one Bacteroidetes. The organisms affiliating with Clostridia and Bacteroidetes all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis; indicating that these organisms are possible syntrophic acetate-oxidizing bacteria (SAOB) that can facilitate acetate consumption via syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms involved in specific pathways.
2016-05-11 | PXD002996 | Pride
Project description:Syntrophic acetate oxidation in haloalkaline environments
| PRJNA484800 | ENA
Project description:Biogas plants (BGPs) produce methane and carbon dioxide through the anaerobic digestion of agricultural waste. Identification of strategies for more stable biogas plant operation and increased biogas yields require better knowledge about the individual degradation steps and the interactions within the microbial communities. The metaprotein profiles of ten agricultural BGPs and one laboratory reactor were investigated using a metaproteomics pipeline. Fractionation of samples using SDS-PAGE was combined with a high resolution Orbitrap mass spectrometer, metagenome sequences specific for BGPs, and the MetaProteomeAnalyzer software. This enabled us to achieve a high coverage of the metaproteome of the BGP microbial communities. The investigation revealed approx. 17,000 protein groups (metaproteins), covering the majority of the expected metabolic networks of the biogas process such as hydrolysis, transport, fermentation processes, amino acid metabolism, methanogenesis and bacterial C1-metabolism. Biological functions could be linked with the taxonomic composition. Two different types of BGPs were classified by the abundance of the acetoclastic methanogenesis and by abundance of enzymes implicating syntrophic acetate oxidation. Linking of the identified metaproteins with the process steps of the Anaerobic Digestion Model 1 proved the main model assumptions but indicated also some improvements such as considering syntrophic acetate oxidation. Beside the syntrophic interactions, the microbial communities in BGPs are also shaped by competition for substrates and host-phage interactions causing cell lysis. In particular, larger amounts of Bacteriophages for the bacterial families Bacillaceae, Enterobacteriaceae and Clostridiaceae, exceeding the cell number of the Bacteria by approximately four-fold. In contrast, less Bacteriophages were found for Archaea, but more CRISPR proteins were detected. On the one hand, the virus induced turnover of biomass might cause slow degradation of complex biomass in BGP. On the other hand, the lysis of bacterial cells allows cycling of essential nutrients.
2019-05-03 | PXD009349 | Pride
Project description:Syntrophus aciditrophicus is a model syntrophic bacterium that degrades fatty and aromatic acids into acetate, CO2, formate and H2 that are utilized by methanogens and other hydrogen-consuming microbes. The degradation of benzoate by S. aciditrophicus proceeds by a multi-step pathway that involves many reactive acyl-Coenzyme A species (RACS) as intermediates which can potentially result in Nε-acylation of lysine residues in proteins. Herein, we investigate post-translational modifications in the S. aciditrophicus proteome to identify and characterize a variety of acyl-lysine modifications that correspond to RACS present in the benzoate degradation pathway. Modification levels are sufficient to support post-translational modification analyses without antibody enrichment, enabling the study of a range of acylations located, presumably, on the most extensively acylated proteins. Seven types of acyl modifications were identified throughout the proteome, six of which correspond directly to RACS that are intermediates in the benzoate degradation pathway. Benzoate–degrading proteins are heavily represented among acylated proteins. The presence of functional deacylase enzymes in S. aciditrophicus indicates a potential regulatory system/mechanism by which these bacteria modulate acylation. Uniquely, Nε-acyl-lysine RACS are highly abundant in these syntrophic bacteria, raising the compelling possibility of enzyme modulation during benzoate degradation in this, and potentially, other syntrophic bacteria. Our results outline candidates to further study the impact of acylations within syntrophic systems.
2022-03-16 | PXD025631 | Pride
Project description:Macrotene chromosomes provides insights to a new mechanism of high-order gene amplification in eukaryotes
| PRJEB7917 | ENA
Project description:In the syntrophic interaction between fermentative bacteria (Pelotomaculum thermopropionicum) and methanogenic archaea (methanogens: Methanothemobacter thermautotrophicus), reducing equivalents (e.g., H2) produced by fermentative bacteria should efficiently be consumed by methanogens in order for the fermentation of volatile fatty acids (VFA, e.g., butyrate, propionate, and acetate) to be thermodynamically feasible. It has been known that physical approximation (e.g., coaggregation) between VFA-fermenting syntrophic bacteria (syntrophs) and hydrogenotrophic methanogens is necessary for efficient H2 transfer between them. Our previous study has shown that, at an early exponential growth phase of syntrophic coculture, cells of Pelotomaculum thermopropionicum (syntroph) were connected to cells of Methanothermobacter thermautotrophicus (methanogen) via unidentified extracellular filamentous appendages, after which they started to coaggregate, suggesting that the filamentous appendages may have been important for their syntrophic interaction. The filamentous appendages seemed to specifically connect these syntrophic partners, since such pairwise connection has been observed neither in single-species cultures (monocultures) nor in mixtures with other microbes.<br>We found that P. thermopropionicum has putative gene clusters for flagellum and pilus, while no extracellular filament gene was identified in the M. thermautotrophicus genome. So we examined transcriptome responses of M. thermautotrophicus to the contact with flagellar filament protein (FliC) and flagellar cap protein (FliD) of P. thermopropionicum.
2009-01-06 | E-MEXP-1971 | biostudies-arrayexpress