Ontology highlight
ABSTRACT:
PROVIDER: PRJNA349159 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4432590.fastq.gz | Fastqsanger.gz | |||
| SRR4432600.fastq.gz | Fastqsanger.gz | |||
| SRR4432610.fastq.gz | Fastqsanger.gz | |||
| SRR4432620.fastq.gz | Fastqsanger.gz | |||
| SRR4432630.fastq.gz | Fastqsanger.gz |
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Project description:Understanding biological diversity and distribution patterns at multiple spatial scales is a central issue in ecology. Here, we investigated the biogeographical patterns of functional genes in soil microbes from 24 arctic heath sites using GeoChip-based metagenomics and principal coordinates of neighbour matrices (PCNM)-based analysis. Functional gene richness varied considerably among sites, while the proportions of each major functional gene category were evenly distributed. Functional gene composition varied significantly at most medium and broad spatial scales, and the PCNM analyses indicated that 14-20% of the variation in total and major functional gene categories could be attributed primarily to relatively broad-scale spatial effects that were consistent with broad-scale variation in soil pH and total nitrogen. The combination of variance partitioning and multi-scales analysis indicated that spatial distance effects contributed 12% to variation in functional gene composition，whereas environmental factors contributed only 3%. This relatively strong influence of spatial as compared to environmental variation in determining functional gene distributions contrasts sharply with typical microbial phylotype/species-based biogeographical patterns in the Arctic and elsewhere. Our results suggest that the distributions of soil functional genes cannot be predicted from phylogenetic distributions because spatial factors associated with historical contingencies are relatively important determinants of their biogeography.
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Project description:Soil qualities and rootstocks are among the main factors that have been acknowledged to influence grape development as well as fruit and wine composition. Despite the role of the soil and rootstock in establishing a successful vineyard in terms of grape quality, almost no molecular evidence linking soil and rootstock properties to the gene expression have been reported. The transcriptome variation in response to different soils and rootstocks was investigated through microarray technology. The cv. Pinot Noir was grown on different soils: sand, turf and vineyard soil. The plants were grafted on the contrasting 101-14 and 1103 Paulsen rootstocks. The modulation of genes expression in response to different soils and rootstocks was evaluated considering their potential impact on primary (carbohydrate) and secondary (phenylpropanoid) metabolisms. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is VV41 at PLEXdb.]
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Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions. We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. We compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during exponential growth and at stationary phase, all in carefully controlled and replicated experimental conditions.
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Project description:The efficacy of inoculation of single pure bacterial cultures into complex microbiomes, for example, in order to achieve increased pollutant degradation rates in contaminated material (i.e., bioaugmentation), has been frustrated by insufficient knowledge on the behaviour of the inoculated bacteria under the specific abiotic and biotic boundary conditions. Here we present a comprehensive analysis of global gene expression of the bacterium Sphingomonas wittichii RW1 in contaminated sand, compared to regular suspended batch growth in liquid culture. RW1 is a well-known bacterium capable of mineralizing polycyclic aromatic hydrocarbons such as dioxins, dibenzofurans and other chlorinated congeners. We tested the reactions of the cells both during the immediate transition phase from liquid culture to sand with or without dibenzofuran, as well during growth and stationary phase in sand. Cells during transition resemble going through stationary phase, showing evidence of stress responses and nutrient scavenging, and even of major adjustments in their primary metabolism if they were not pre-cultured on the same contaminant as found in the soil. Cells growing and surviving in soil show very different signatures as in liquid or in liquid culture exposed to chemicals inducing drought stress, and we obtain evidence for numerous soil-specific expressed genes. We conclude that studies focusing on inoculation efficacy should test behavior under conditions as closely as possible mimicking the intended microbiome conditions We were interested to study the global reactions of bacteria with biodegradative properties under near-environmental as compared to laboratory culture conditions. we compared here the genome-wide responses of RW1 between regular laboratory batch growth on the aromatic substrates DBF and salicylate with growth in sandy soil with or without the same aromatic compounds. We analysed the cellular reactions immediately after introduction into the sand, during lag phase, all in carefully controlled and replicated experimental conditions.
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