Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1093157 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28492000_1.fastq.gz | Fastqsanger.gz | |||
| SRR28492000_2.fastq.gz | Fastqsanger.gz | |||
| SRR28492001_1.fastq.gz | Fastqsanger.gz | |||
| SRR28492001_2.fastq.gz | Fastqsanger.gz | |||
| SRR28492002_1.fastq.gz | Fastqsanger.gz |
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Project description:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon.
2011-01-01 | GSE24800 | GEO
Project description:The melting of permafrost and its potential impact on greenhouse gas emissions is a major concern in the context of global warming. The fate of the carbon trapped in permafrost will largely depend on soil physico-chemical characteristics, among which are the quality and quantity of organic matter, pH and water content, and on microbial community composition. In this study, we used microarrays and real-time PCR (qPCR) targeting 16S rRNA genes to characterize the bacterial communities in three different soil types representative of various Arctic settings. The microbiological data were linked to soil physico-chemical characteristics and CO2 production rates. Microarray results indicated that soil characteristics, and especially the soil pH, were important parameters in structuring the bacterial communities at the genera/species levels. Shifts in community structure were also visible at the phyla/class levels, with the soil CO2 production rate being positively correlated to the relative abundance of the Alphaproteobacteria, Bacteroidetes, and Betaproteobacteria. These results indicate that CO2 production in Arctic soils does not only depend on the environmental conditions, but also on the presence of specific groups of bacteria that have the capacity to actively degrade soil carbon. Three different soil types from the Canadian high Arctic were sampled at two depths within the active layer of soil and at two sampling dates (winter and summer conditions), for a total of 20 samples.
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Project description:Relentless mining operations have destroyed our environment significantly. Soil inhabiting microbes play a significant role in ecological restoration of these areas. Microbial weathering processes like chemical dissolution of rocks significantly promotes the soil properties and enhances the rock to soil ratio respectively. Earlier studies have reported that bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, rock-dissolving mechanisms of the bacterium remain to be unclear till date. Thus, we have performed rock-dissolution experiments followed by genome and transcriptome sequencing of novel Pseudomonas sp.NLX-4 strain to explore the efficiency of microbe-mediated habitat restoration and its molecular mechanisms underlying this biological process. Results obtained from initial rock dissolution experiments revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids with elevated concentrations of potassium, silicon and aluminium elements. The rock dissolution experiments of NLX-4 strain exhibited an initial increase in particle diameter variation values between 0-15 days and decline after 15 days-time respectively. The 6,771,445-base pair NLX-4 genome exhibited 63.21 GC percentage respectively with a total of 6041 protein coding genes. Genome wide annotations of NLX-4 strain exhibits 5045-COG, 3996-GO, 5342-InterPro, 4386-KEGG proteins respectively Transcriptome analysis of NLX-4 cultured with/without silicate rocks resulted in 539 (288-up and 251-down) differentially expressed genes (DEGs). Fifteen DEGs encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated by cultured with silicate rocks. This study has not only provided a new strategy for the ecological restoration of rock mining areas, but also enriched the applicable bacterial and genetic resources.
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Project description:Anthropogenic activities have dramatically increased the inputs of reactive nitrogen (N) into terrestrial ecosystems, with potentially important effects on the soil microbial community and consequently soil C and N dynamics. Our analysis of microbial communities in soils subjected to 14 years of 7 g N m-2 year-1 Ca(NO3)2 amendment in a Californian grassland showed that the taxonomic composition of bacterial communities, examined by 16S rRNA gene amplicon sequencing, was significantly altered by nitrate amendment, supporting the hypothesis that N amendment- induced increased nutrient availability, yielded more fast-growing bacterial taxa while reduced slow-growing bacterial taxa. Nitrate amendment significantly increased genes associated with labile C degradation (e.g. amyA and xylA) but had no effect or decreased the relative abundances of genes associated with degradation of more recalcitrant C (e.g. mannanase and chitinase), as shown by data from GeoChip targeting a wide variety of functional genes. The abundances of most N cycling genes remained unchanged or decreased except for increases in both the nifH gene (associated with N fixation), and the amoA gene (associated with nitrification) concurrent with increases of ammonia-oxidizing bacteria. Based on those observations, we propose a conceptual model to illustrate how changes of functional microbial communities may correspond to soil C and N accumulation.
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Project description:<p>Carbonate-type saline-alkaline stress severely constrains maize production; however, the synergistic response mechanisms between rhizosphere microorganisms and metabolites remain unclear. This study focused on maize fields in the carbonate chernozem region of the Songnen Plain in Northeast China. Through field experiments and the integration of soil chemical factor analysis, microbial high-throughput sequencing (16S rRNA and ITS), and non-targeted metabolomics (LC-MS), we systematically investigated the response mechanisms of the rhizosphere micro-ecosystem under saline-alkaline stress. The results indicated that saline-alkaline stress significantly increased soil pH and electrical conductivity (EC), and led to decreases in soil organic matter (SOM), total nitrogen (TN), and total phosphorus (TP) contents. However, the rhizosphere zone exhibited a certain buffering capacity, maintaining a higher cation exchange capacity (CEC). Microbial community analysis revealed that bacterial alpha diversity increased under stress. In contrast, fungal diversity significantly decreased, and the community structure shifted towards a pathogen-dominated community, primarily within Ascomycota, especially the genus Fusarium. Co-occurrence network analysis further revealed that saline-alkaline conditions enhanced the complexity and connectivity of bacterial networks but led to the contraction and structural simplification of fungal networks. Metabolite analysis showed that saline-alkaline stress induced significant reprogramming of the rhizosphere metabolic profile. Organophosphorus compounds, nucleotides, and their analogs were significantly enriched, while defensive secondary metabolites such as Cajanol specifically accumulated in the saline-alkaline rhizosphere. Pathway analysis indicated the activation of stress resistance and oxidative stress mitigation-related pathways, including Betalain biosynthesis, flavonoid biosynthesis, tryptophan metabolism, and arginine metabolism. Multi-omics integration analysis identified soil EC and total potassium (TK) as key environmental factors driving the differentiation of microbial and metabolite communities. Key differential metabolites showed significant positive correlations with saline-alkaline-enriched microbial taxa (e.g., Sphingomonas), revealing a metabolite-mediated microbial recruitment mechanism. This study, through multi-omics analysis, discovered that the maize rhizosphere, under saline-alkaline stress, undergoes metabolic reprogramming (e.g., enriching defensive metabolites like Cajanol) to directionally recruit beneficial bacteria such as Sphingomonas and maintains higher bacterial network complexity, while also leading to the pathologization of the fungal community. Our study reveals that maize recruits beneficial microbes via rhizosphere metabolic reprogramming, providing a mechanistic basis for microbiome-assisted saline-alkaline soil remediation.</p>
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