Sediment metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA912230 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR22741937_1.fastq.gz | Fastqsanger.gz | |||
| SRR22741937_2.fastq.gz | Fastqsanger.gz | |||
| SRR22745737_1.fastq.gz | Fastqsanger.gz | |||
| SRR22745737_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 25 |
Similar Datasets
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: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:Dig out the fundamental mechanism of ammonia inhibiting anaerobic digestion by the metaproteomic analysIs via identifying the biotransformation steps in AD, revealing the change characteristics of the active microbiota structure, elucidating the effects of ammonia on microbial enzyme synthesis (transcription and translation), and finding out the key enzymes being inhibited.
2021-02-02 | PXD023948 |
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.
2016-08-02 | GSE85064 | GEO
Project description:HiSpOD is a new efficient functional microarrays probe design algorithm especially dedicated for the microbial ecology and environmental studies. It was used to design 3392 probes targeting 21 genes involved in chlorinated solvent biodegradation pathways and synthesized on a nimblegen microarray. In order to test the probe specificity, the microarray was firstly hybridized to 6 µg of labelled aRNA from sheep rumen content (background aRNA). Secondly, hybridization of 1011 copies of labelled aRNA derived from in vitro transcription of three synthetic genes (mmoC, vcrA and tceA) and mixed with 6 µg of the same complex background material were performed to test their sensibility. Finally, the expression analysis of a contaminated groundwater sample was performed.
2011-04-13 | GSE21492 | GEO
Project description:Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. Three groups of samples, A, B and C. Every group has 3 replicates.
2016-08-02 | E-GEOD-85064 | biostudies-arrayexpress
Project description:Purpose: To study the differential expression of gut bacterial mRNAs during chronic organophosphate treatment. Methods: Balb/c mice were treated with organophosphate (monocrotophos 28 ug/kg body weight/day) directly in drinking water for 180 days. Glucose tolerance tests indicated the induction of glucose intolerance. The total RNA was isolated by using TRIZOL from the cecal tissue that is cleared off fecal contents and subsequently the eukaryotic and bacterial rRNAs were removed by using MicrobExpress and MicrobEnrich kits (Ambion). Subsequently, RNA library was contructed using illumina kit as per manufacturer's instructions. Results: The reads were annotated to the reference human gut microbiome database and we found differential expression of large number of genes especially those involved in organophosphate degradation. Our subsequent studies proved that gut microbial degradation of organophosphates induces glucose intolerance via gluconeogenesis. Conclusions: Chronic organophosphate-induced hyperglycemia is mediated by the organosphosphate-degrading potential of gut microbiota.
2016-12-07 | GSE90843 | GEO
Project description:To study the responses of microbial communities to short-term nitrogen addition and warming,here we examine microbial communities in mangrove sediments subjected to a 4-months experimental simulation of eutrophication with 185 g m-2 year-1 nitrogen addition (N), 3oC warming (W) and nitrogen addition*warming interaction (NW).
2022-03-01 | GSE190739 | GEO