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PROVIDER: PRJNA1209591 | ENA |
REPOSITORIES: ENA
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Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+–N and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics.
2013-07-13 | GSE48820 | GEO
Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, along four sites/elevations of a Tibetan mountainous grassland, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. Cold shock genes were more abundant at higher elevations. Also, gdh converting ammonium into urea was more abundant at higher elevations while ureC converting urea into ammonium was less abundant, which was consistent with soil ammonium contents. Significant correlations were observed between N-cycling genes (ureC, gdh and amoA) and nitrous oxide flux, suggesting that they contributed to community metabolism. Lastly, we found by CCA, Mantel tests and the similarity tests that soil pH, temperature, NH4+M-bM-^@M-^SN and vegetation diversity accounted for the majority (81.4%) of microbial community variations, suggesting that these four attributes were major factors affecting soil microbial communities. Based on these observations, we predict that climate changes in the Tibetan grasslands are very likely to change soil microbial community functional structure, with particular impacts on microbial N cycling genes and consequently microbe-mediated soil N dynamics. Twelve samples were collected from four elevations (3200, 3400, 3600 and 3800 m) along a Tibetan grassland; Three replicates in every elevation
2013-07-13 | E-GEOD-48820 | biostudies-arrayexpress
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.
2017-11-21 | GSE107168 | GEO
Project description:Comparative analysis of tobacco leaves transcriptomes unveils carotenoid pathway potentially determined the characteristics of aroma compounds in different environmental regions. Tobacco (Nicotiana tabacum) is a sensitive crop to environmental changes, and a tobacco with unique volatile aroma fractions always formed in specific ecological conditions. In order to investigate the differential expressed genes caused by environmental changes and reveal the formation mechanism of characteristics of tobacco in three different aroma tobacco regions of Guizhou Province, Agilent tobacco microarray was adapted for transcriptome comparison of tobacco leaves in medium aroma tobacco region Kaiyang and light aroma tobacco regions Weining and Tianzhu. Results showed that there was big difference among the gene expression profiles of tobacco leaves in different environmental conditions. A total of 517 differential expressed genes (DEGs) between Weining and Tianzhu were identified, while 733 and 1,005 genes differentially expressed between Longgang and another two tobacco regions Weining and Tianzhu, respectively. Compared with Longgang, up-regulated genes in Weining and Tianzhu were likely involved in secondary metabolism pathways, especially carotenoid pathway, including PHYTOENE SYNTHASE, PHYTOENE DEHYDROGENASE, LYCOPENE ε-CYCLASE, CAROTENOID β-HYDROXYLASE and CAROTENOID CLEAVAGE DIOXYGENASE 1 genes, while most down-regulated genes played important roles in response to temperature and light radiation, such as heat shock proteins. Gene Ontology and MapMan analyses demonstrated that the DEGs among different environmental regions were significantly enriched in light reaction of photosystem II, response of stimulus and secondary metabolism, suggesting they played crucial roles in environmental adaptation and accumulation of aroma compounds in tobacco plants. Through comprehensive transcriptome comparison, we not only identified several stress response genes in tobacco leaves from different environmental regions but also highlighted the importance of carotenoid pathway genes for characteristics of aroma compounds in specific growing regions. Our study primarily laid the foundation for further understanding the molecular mechanism of environmental adaptation of tobacco plants and molecular regulation of aroma substances in tobacco leaves. In order to investigate the differential expressed genes caused by environmental changes and reveal the formation mechanism of characteristics of tobacco in three different aroma tobacco regions of Guizhou Province, Agilent tobacco microarray was adapted for transcriptome comparison of tobacco leaves in medium aroma tobacco region Kaiyang and light aroma tobacco regions Weining and Tianzhu.
2012-02-23 | E-GEOD-36008 | biostudies-arrayexpress
Project description:To know whether the microarray technique could be used to detect bacterial gene expression in soil, large quantity of RNA was extracted from soil cultures of Pseudomonas putida KT2440 containing a chloroaromatic degrading plasmid at the presence or absence of the growth substrate, 3-chlorobenzoate (3CB). The quality and quantity of the extracted RNA were proper for a typical microarray analysis. Gene expression patterns of soil cultures were analyzed by DNA microarray using the extracted RNA. Among 5346 genes on the array, 5% and 4.5% of genes showed up- or down-regulation. Analysis done at the DAVID Bioinformatics Resources server suggested that the benzoate degradation via hydroxylation pathway had the most significant changes after treatment with 3CB. Expression of the 3CB degradation genes located in the genome was confirmed by real-time RT-PCR. In addition, real time RT-PCR analysis revealed that the fluorescent signals from plasmid genes on the microarray were saturated so that the induction ratio of the genes located in the plasmid was underestimated in microarray analysis. To our best knowledge, this report represents the first trial to use microarray technique to detect genome-wide bacterial gene expression in soil.
2010-04-01 | GSE19516 | GEO