Anaerobic digester metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA433870 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6725470_1.fastq.gz | Fastqsanger.gz | |||
| SRR6725470_2.fastq.gz | Fastqsanger.gz | |||
| SRR6725480_1.fastq.gz | Fastqsanger.gz | |||
| SRR6725480_2.fastq.gz | Fastqsanger.gz | |||
| SRR6725490_1.fastq.gz | Fastqsanger.gz |
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Project description:We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Array (âMaize GeneChipâ). Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and amplified fragment length polymorphism (AFLP) methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Due to large amounts of repetitive, mobile DNA, the maize genome requires a target preparation method that offers both a high level of gene enrichment and accurate scoring of SFPs. The objectives of this research are (i) to determine which target preparation method (CF, MF, mRNA, or AFLP) optimally enriches for gene sequences complementary to probe sequences on the Affymetrix GeneChip Maize Genome Array and (ii) to estimate SFP detection power for each target method. The AFLP technology is covered by patents, and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. GeneChip. This work was supported in part by U.S. National Science Foundation grant DBI-0321467 and USDA-ARS. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Michael Gore. The equivalent experiment is ZM10 at PLEXdb.] Experiment Overall Design: protocol: mRNA - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: mRNA - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: mRNA - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred(3-replications)
2008-10-25 | E-GEOD-12770 | biostudies-arrayexpress
Project description:Sludge recirculation mixing in anaerobic digesters is essential for the stable operation of the digestion process. While often neglected, the configuration of the sludge inlet has a substantial influence on the efficiency of the mixing process. The fluid is either injected directly into the enclosed fluid domain or splashes onto the free surface of the slurry flow. In this paper, the aim was to investigate the effect of the inlet configuration by means of computational fluid dynamics-using ANSYS Fluent. Single-phase and multi-phase models are applied for a submerged and splashing inlet, respectively. To reduce the high computational demand, we also develop surrogate single-phase models for the splashing inlet. The digester mixing is analyzed by comparing velocity contours, velocity profiles, mixing time and dead volume. The non-Newtonian characteristics of the sludge is considered, and a [Formula: see text] model is employed for obtaining turbulence closure. Our method is validated by means of a previous study on the same geometry. Applying a submerged inlet configuration, the resulting dead volume in the tank is estimated around 80 times lower than for the case of a splashing inlet. Additionally, by emulating the multi-phase model for splashing inlet configurations with a single-phase one, the simulation clock time reduced to 15%.
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Project description:The rise of agro-industrial activities over recent decades has exponentially increased lignocellulose biomasses (LCB) production. LCB serves as a cost-effective source for fermentable sugars and other renewable chemicals. This study explores the use of microbial consortia, particularly thermophilic consortia, for LCB deconstruction. Thermophiles produce stable enzymes that retain activity under industrial conditions, presenting a promising approach for LCB conversion. This research focused on two microbial consortia (i.e., microbiomes) that were analyzed for enzyme production using a cheap medium, i.e., a mixture of spent mushroom substrate (SMS) and digestate. The secreted xylanolytic enzymes were characterized in terms of temperature and pH optima, thermal stability, and hydrolysis products from LCB-derived polysaccharides. These enzymes showed optimal activity aligning with common biorefinery conditions and outperformed a formulated enzyme mixture in thermostability tests in the digestate. Phylogenetic and genomic analyses highlighted the genetic diversity and metabolic potential of these microbiomes. Bacillus licheniformis was identified as a key species, with two distinct strains contributing to enzyme production. The presence of specific glycoside hydrolases involved in the cellulose and hemicellulose degradation underscores these consortia's capacity for efficient LCB conversion. These findings highlight the potential of thermophilic microbiomes, isolated from an industrial environment, as a robust source of robust enzymes, paving the way for more sustainable and cost-effective bioconversion processes in biofuel and biochemical production and other biotechnological applications.
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Project description:In a previous study, we analyzed the molecular diversity of Planctomycetales by PCR amplification and sequencing of 16S rRNA clone libraries generated from a municipal wastewater plant, using planctomycete-specific and universal primer sets (R. Chouari, D. Le Paslier, P. Daegelen, P. Ginestet, J. Weissenbach, and A. Sghir, Appl. Environ. Microbiol. 69:7354-7363, 2003). Only a small fraction (4%) of the 16S rRNA gene sequences of the digester clone library corresponded to the Planctomycetales division. Importantly, 85.9% of the digester clone sequences are grouped into two different clusters named WWE1 (81.4% of the sequences) and WWE2 (4.5%) and are distantly affiliated with unidentified bacterial sequences retrieved from a methanogenic reactor community and from a termite gut, respectively. In phylogenetic analysis using 16S rRNA gene sequence representatives of the main phylogenetic bacterial divisions, the two clusters are monophyletic, branch apart from each other, and are distantly related to Planctomycetales and other bacterial divisions. A novel candidate division is proposed for WWE1, while the WWE2 cluster strongly affiliates with the recently proposed Lentisphearae phylum. We designed and validated a 16S rRNA probe targeting WWE1 16S rRNA sequences by both fluorescent in situ hybridization (FISH) and dot blot hybridization (DBH). Results of FISH analysis show that WWE1 representative microorganisms are rods or filamentous shaped, while DBH shows that WWE1 accounts for 12% of the total bacterial rRNA within the anaerobic digester. The remaining 16S rRNA gene sequences are affiliated with Verrucomicrobia or recently described candidate divisions with no known pure culture representatives, such as OD1, BRC1, or NBL-UPA2, making up less than 3.5% of the clone library, respectively. This inventory expands the known diversity of the latter bacterial division-level lineages.
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Project description:The microbial diversity and metabolic potential of a methanogenic consortium residing in a 3785-liter anaerobic digester, fed with wastewater algae, was analyzed using 454 pyrosequencing technology. DNA was extracted from anaerobic sludge material and used in metagenomic analysis through PCR amplification of the methyl-coenzyme M reductase ? subunit (mcrA) gene using primer sets ML, MCR, and ME. The majority of annotated mcrA sequences were assigned taxonomically to the genera Methanosaeta in the order Methanosarcinales. Methanogens from the genus Methanosaeta are obligate acetotrophs, suggesting this genus plays a dominant role in methane production from the analyzed fermentation sample. Numerous analyzed sequences within the algae fed anaerobic digester were unclassified and could not be assigned taxonomically. Relative amplicon frequencies were determined for each primer set to determine the utility of each in pyrosequencing. Primer sets ML and MCR performed better quantitatively (representing the large majority of analyzed sequences) than primer set ME. However, each of these primer sets was shown to provide a quantitatively unique community structure, and thus they are of equal importance in mcrA metagenomic analysis.
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Project description:Influenced by feedstock type and microbial inoculum, different microbial groups must precisely interact for high-quality biogas yields. As a first approach for optimization, this study aimed to identify through time the biogas-producing microbial community in a 10-ton dry anaerobic digester treating cattle manure by denaturing gradient gel electrophoresis (DGGE) and metagenomics. Moreover, the associated bovine residues or feedstocks (leachate, manure, oxidation lagoon water, rumen) were also characterized to determine their contribution. A diverse and dynamic community characterized by Bacteria (82%-88%) and a considerable amount of Archaea (8%-15%) presented profiles particular to each stage of biogas production. Eukaryotes (2.6%-3.6%), mainly fungi, were a minor but stable component. Proteobacteria represented 47% of the community at the start of the run but only 18% at the end, opposite to the Bacteroidetes/Chlorobi group (8% and 20%, respectively), while Firmicutes (12%-18%) and Actinobacteria (12%-32%) remained relatively constant. Methanogens of the order Methanomicrobiales represented by several species of Methanoculleus were abundant at the end of the run (77%) contrary to Methanosarcinales (11%) and Methanobacteriales (0.7%). Therefore, methanogenesis mainly occurred by the hydrogenotrophic pathway. Manure and oxidation lagoon water seemed to contribute key microorganisms, while rumen dominated by Methanobrevibacter (72%) did not proliferate in the digester. Manure particularly possessed Methanoculleus (24%) and uncultured methanogens identified by DGGE, whereas oxidation lagoon was exclusively abundant in Methanolinea (18%) and Methanosaeta (19%). Leachate, as the microbial inoculum from a previous run, adequately preserved the biogas-producing community. These results could lead to higher biogas yields through bioaugmentation strategies by incorporating higher proportions or an enriched inoculum from the relevant feedstocks.
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