Ontology highlight
ABSTRACT:
PROVIDER: PRJNA718480 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14102348_1.fastq.gz | Fastqsanger.gz | |||
| SRR14102348_2.fastq.gz | Fastqsanger.gz | |||
| SRR14102349_1.fastq.gz | Fastqsanger.gz | |||
| SRR14102349_2.fastq.gz | Fastqsanger.gz | |||
| SRR14102350_1.fastq.gz | Fastqsanger.gz |
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Project description:Waste decomposition in landfills is a complex and microbe-mediated process. Understanding the microbial community composition and structure is critical for accelerating decomposition and reducing adverse impact on the environment. Here, we examined the microbial communities along with landfill depth and age (LDA) in a sanitary landfill in Beijing, China using 16s rRNA Illumina sequencing and GeoChip 4.6. We found that Clostridiales and Methanofollis were the predominant bacteria and archaea in the present landfill, respectively. Interestingly, in contrast with the decreasing trend of microbial diversity in soil, both phylogenetic and functional diversities were higher in deeper and older refuse in the landfill. Phylogenetic compositions were obviously different in the refuse with the same LDA and such difference is mainly attributed to the heterogeneity of refuse instead of random process. Nevertheless, functional structures were similar within the same LDA, indicating that microbial community assembly in the landfill may be better reflected by functional genes rather than phylogenetic identity. Mantel test and canonical correspondence analysis suggested that environmental variables had significant impacts on both phylogenetic composition and functional structure. Higher stress genes, genes for degrading toxic substances and endemic genes in deeper and older refuse indicated that they were needed for the microorganisms to survive in the more severe environments. This study suggests that landfills are a repository of stress-resistant and contaminant-degrading microorganisms, which can be used for accelerating landfill stabilization and enhancing in situ degradation.
2016-06-15 | GSE68712 | GEO
Project description:Waste decomposition in landfills is a complex and microbe-mediated process. Understanding the microbial community composition and structure is critical for accelerating decomposition and reducing adverse impact on the environment. Here, we examined the microbial communities along with landfill depth and age (LDA) in a sanitary landfill in Beijing, China using 16s rRNA Illumina sequencing and GeoChip 4.6. We found that Clostridiales and Methanofollis were the predominant bacteria and archaea in the present landfill, respectively. Interestingly, in contrast with the decreasing trend of microbial diversity in soil, both phylogenetic and functional diversities were higher in deeper and older refuse in the landfill. Phylogenetic compositions were obviously different in the refuse with the same LDA and such difference is mainly attributed to the heterogeneity of refuse instead of random process. Nevertheless, functional structures were similar within the same LDA, indicating that microbial community assembly in the landfill may be better reflected by functional genes rather than phylogenetic identity. Mantel test and canonical correspondence analysis suggested that environmental variables had significant impacts on both phylogenetic composition and functional structure. Higher stress genes, genes for degrading toxic substances and endemic genes in deeper and older refuse indicated that they were needed for the microorganisms to survive in the more severe environments. This study suggests that landfills are a repository of stress-resistant and contaminant-degrading microorganisms, which can be used for accelerating landfill stabilization and enhancing in situ degradation. Fifteen refuse samples with five landfill depths and ages (6m/2a, 12m/4a, 18m/6a, 24m/8a and 30m/10a) were collected from a sanitary landfill in Beijing, China. Three replicates in every landfill depth and age
2016-06-15 | E-GEOD-68712 | biostudies-arrayexpress
Project description:Although the nose, as a gateway for organism-environment interactions, may have a key role in asthmatic exacerbation, the rhinobiome of exacerbated children with asthma was widely neglected to date. Deep nasopharyngeal swab specimens, nasal epithelial spheroid cultures (NAEsp), and blood samples of acute exacerbated wheezers (WH), asthmatics (AB), and healthy controls (HC) were used for culture (n=146), 16 S-rRNA gene amplicon sequencing (n=64), proteomic and cytokine analyses. Interestingly, Proteobacteria were over-represented in WH (WH to AB: p=0.005; WH to HC: p=0.021), whereas Firmicutes and Bacterioidetes were associated with AB. In contrast, Actinobacteria commonly colonized HCs (PermANOVA p=0.005). Moreover, Staphylococcaceae (p<0.05), Enterobacteriaceae (p<0.05), Burkholderiaceae (p<0.05), Xanthobacteraceae (p<0.05), and Sphingomonadaceae (p<0.05) were significantly more abundant in AB compared to WH and HC. The α‐diversity analyses demonstrated an increase of bacterial abundance levels in atopic AB and a decrease in WH samples. Microbiome profiles of atopic WH differed significantly from atopic AB. The NAEsp bacterial exposure with M. catarrhalis, S. aureus and H. influenzae experiments provided a disrupted epithelial cell integrity, a cytokine release and cohort specific proteomic differences especially for M. catarrhalis cultures. Our comprehensive dataset contributes to a deeper insight into the poorly understood plasticity of the nasal microbiota, and, in particular, may enforce our understanding in the pathogenesis of asthma exacerbation in childhood.
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Project description:To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities. In this study, we analyzed the geographic distribution of AMD microbial communities from twenty sites using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes, and the results showed that AMD microbial communities were geographically distributed and had high variations among different sites. Then an AMD-specific microarray was used to further analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them. This study investigated the geographic distribution of Acid Mine Drainages microbial communities using a 16S rRNA gene-based RFLP method and the diversity, composition and structure of AMD microbial communities phylogenetically and functionally using an AMD-specific microarray which contained 1,072 probes ( 571 related to 16S rRNA and 501 related to functional genes). The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11).
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Project description:Samples of oil and production water were collected from five wells of the Qinghai Oilfield, China, and subjected to GeoChip hybridization experiments for microbial functional diversity profiling. Unexpectedly, a remarkable microbial diversity in oil samples, which was higher than that in the corresponding water samples, was observed, thus challenging previously believed assumptions about the microbial diversity in this ecosystem. Hierarchical clustering separated oil and water samples, thereby indicating distinct functional structures in the samples. Genes involved in the degradation of hydrocarbons, organic remediation, stress response, and carbon cycling were significantly abundant in crude oil, which is consistent with their important roles in residing in oil. Association analysis with environmental variables suggested that oil components comprising aromatic hydrocarbons, aliphatic hydrocarbons, and a polar fraction with nitrogen-, sulfur-, and oxygen-containing compounds were mainly influential on the structure of the microbial community. Furthermore, a comparison of microbial communities in oil samples indicated that the structures were depth/temperature-dependent. To our knowledge, this is the first thorough study to profile microbial functional diversity in crude oil samples. From the Qinghai Oilfield located in the Tibetan Plateau, northwest China, oil production mixtures were taken from four oil production wells (No. 813, 516, 48 and 27) and one injection well (No. 517) in the Yue-II block. The floating oil and water phases of the production mixtures were separated overnight by gravitational separation. Subsequently, the microbial community and the characteristics of the water solution (W813, W516, W48, and W27) and floating crude oil (O813, O516, O48, and O27) samples were analyzed. A similar analysis was performed with the injection water solution (W517).
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