Anaerobic microorganisms
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA982777 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24895997_1.fastq.gz | Fastqsanger.gz | |||
| SRR24895997_2.fastq.gz | Fastqsanger.gz | |||
| SRR24895998_1.fastq.gz | Fastqsanger.gz | |||
| SRR24895998_2.fastq.gz | Fastqsanger.gz | |||
| SRR24895999_1.fastq.gz | Fastqsanger.gz |
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Project description:Anaerobic digestion is a popular and effective microbial process for waste treatment. The performance of anaerobic digestion processes is contingent on the balance of the microbial food web in utilizing various substrates. Recently, co-digestion, i.e., supplementing the primary substrate with an organic-rich co-substrate has been exploited to improve waste treatment efficiency. Yet the potential effects of elevated organic loading on microbial functional gene community remains elusive. In this study, functional gene array (GeoChip 5.0) was used to assess the response of microbial community to the addition of poultry waste in anaerobic digesters treating dairy manure. Consistent with 16S rRNA gene sequences data, GeoChip data showed that microbial community compositions were significantly shifted in favor of copiotrophic populations by co-digestion, as taxa with higher rRNA gene copy number such as Bacilli were enriched. The acetoclastic methanogen Methanosarcina was also enriched, while Methanosaeta was unaltered but more abundant than Methanosarcina throughout the study period. The microbial functional diversity involved in anaerobic digestion were also increased under co-digestion.
2017-01-12 | GSE93419 | GEO
Project description:Anaerobic degradation (AD) of heterogeneous agricultural substrates is a complex process involving a diverse microbial community. While microbial community composition of a variety of biogas plants (BPs) is well described, little is known about metabolic processes and microbial interaction patterns. Here, we analyzed 16 large-scale BPs using metaproteomics. All metabolic steps of AD were observed in the metaproteome, and multivariate analyses indicated that they were shaped by temperature, pH, volatile fatty acid content and substrate types. Biogas plants can be subdivided into hydrogenotrophic, acetoclastic or a mixture of both methanogenic pathways based on their process parameters, taxonomic and functional metaproteome. Network analyses showed large differences in metabolic and microbial interaction patterns. Both, number of interactions and interaction partners were highly dependent on the prevalent methanogenic pathway for most species. Nevertheless, we observed a highly conserved metabolism of different abundant Pseudomonas spp. for all BPs indicating a key role during AD in carbohydrate hydrolysis irrespectively of variabilities in substrate input and process parameters. Thus, Pseudomonas spp. are of high importance for robust and versatile AD food webs, which highlight a large variety of downstream metabolic processes for their respective methanogenic pathways.
2019-11-11 | PXD014605 | Pride
Project description:Two parallel anaerobic digestion lines were designed to match a "bovid-like" digestive structure. Each of the lines consisted of two Continuous Stirred Tank Reactors placed in series and separated by an acidic treatment step. The first line was inoculated with industrial inocula whereas the second was seeded with cow digestive tract contents. After three month of continuous sewage sludge feeding, samples were recovered for shotgun metaproteomic and DNA-based analysis. Strikingly, protein inferred and 16S rDNA tags based taxonomic community profiles were not fully consistent. Principal Component analysis however revealed a similar clustering pattern of the samples, suggesting that reproducible methodological and/or biological factors underlie this observation. The performances of the two digestion lines did not differ significantly and the cow derived inocula did not establish in the reactors. A low throughput metagenomic dataset (3.4x106 reads, 1.1 Gb) was also generated for one of the samples. It allowed a substantial increase of the analysis depth (increase of the spectral identification rate). For the first time, a high level of proteins expressed by members of the "Candidatus Competibacter" group is reported in an anaerobic digester, a key microbial player in environmental bioprocess communities.
2015-08-12 | PXD002420 | Pride
Project description:Effect of certain microorganisms on mouse gut microbial communities in aged group.
2021-09-24 | GSE180087 | GEO
Project description:Meta-proteomics analysis approach in the application of biogas production from anaerobic digestion has many advantages that has not been fully uncovered yet. This study aims to investigate biogas production from a stable 2-stage chicken manure fermentation system in chemical and biological perspective. The diversity and functional protein changes from the 1st stage to 2nd stage is a good indication to expose the differential metabolic processes in anaerobic digestion. The highlight of identified functional proteins explain the causation of accumulated ammonia and carbon sources for methane production. Due to the ammonia stress and nutrient limitation, the hydrogenotrophic methanogenic pathway is adopted as indicative of meta-proteomics data involving the key methanogenic substrates (formate and acetate). Unlike traditional meta-genomic analysis, this study could provide both species names of microorganism and enzymes to directly point the generation pathway of methane and carbon dioxide in investigating biogas production of chicken manure.
2021-02-08 | PXD022498 | Pride
Project description:In anaerobic digestion plants (ADP) homogenization of the feed, the fermenter content and the microbial communities represents a precondition for effective and robust biogas production,but also a major energy consumer. For a 850 m3 agricultural AD-P equipped with eight sampling ports we investigated whether different feeding and stirring regimes enable a sufficient homogenization of the microbial communities using metaproteome and TRFLP analysis. Systematic comparison of the samples by scatter plots and students t-test revealed only a limited number of slightly changed metaproteins, taxonomies and biological processes, indicating no systematic differences between the microbial communities in center and rim as well as between top and bottom. However, comparison of the amount of shared identified metaproteins between the sample ports showed minor variation, which might be correlated with the applied stirring strategy. In sum, the applied stirring and feeding conditionswere sufficient to homogenize the microbial communities in AD-Ps largely.
2021-04-27 | PXD016213 | Pride
Project description:The anaerobic digestion microbiomes has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and phenotypics, in their ability to reflect the full-scale anaerobic digestion microbiome. The phenotypic fingerprinting reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and phenotypic traits, yielded certain similar features yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, phenotypic fingerprinting is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.
2021-05-26 | PXD024788 | Pride
Project description:Microorganisms in anaerobic digestion of chicken manure Raw sequence reads
| PRJNA938737 | ENA