Ontology highlight
ABSTRACT:
PROVIDER: PRJNA349092 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR4446845.fastq.gz | Fastqsanger.gz | |||
| SRR4446846.fastq.gz | Fastqsanger.gz |
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Project description:To study whether and how soil nitrogen conditions affect the ecological effects of long-term elevated CO2 on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. Under the aN condition, a majority of microbial function genes, as measured by GeoChip 4.0, were increased in relative abundance or remained unchanged by eCO2. Under the eN condition, most of functional genes associated with carbon, nitrogen and sulfur cycling, energy processes, organic remediation and stress responses were decreased or remained unchanged by eCO2, while genes associated with antibiotics and metal resistance were increased. The eCO2 effects on fungi and archaea were largely similar under both nitrogen conditions, but differed substantially for bacteria. Coupling of microbial carbon or nitrogen cycling genes, represented by positive percentage and density of gene interaction in association networks, was higher under the aN condition. In accordance, changes of soil CO2 flux, net N mineralization, ammonification and nitrification was higher under the aN condition. Collectively, these results demonstrated that eCO2 effects are contingent on nitrogen conditions, underscoring the difficulty toward predictive modeling of soil ecosystem and ecoprocesses under future climate scenarios and necessitating more detailed studies.
2015-04-03 | GSE67531 | GEO
Project description:To study whether and how soil nitrogen conditions affect the ecological effects of long-term elevated CO2 on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. Under the aN condition, a majority of microbial function genes, as measured by GeoChip 4.0, were increased in relative abundance or remained unchanged by eCO2. Under the eN condition, most of functional genes associated with carbon, nitrogen and sulfur cycling, energy processes, organic remediation and stress responses were decreased or remained unchanged by eCO2, while genes associated with antibiotics and metal resistance were increased. The eCO2 effects on fungi and archaea were largely similar under both nitrogen conditions, but differed substantially for bacteria. Coupling of microbial carbon or nitrogen cycling genes, represented by positive percentage and density of gene interaction in association networks, was higher under the aN condition. In accordance, changes of soil CO2 flux, net N mineralization, ammonification and nitrification was higher under the aN condition. Collectively, these results demonstrated that eCO2 effects are contingent on nitrogen conditions, underscoring the difficulty toward predictive modeling of soil ecosystem and ecoprocesses under future climate scenarios and necessitating more detailed studies. Fourty eight samples were collected for four different carbon and nitrogen treatment levels (aCaN,eCaN,aCeN and eCeN) ; Twelve replicates in every elevation
2015-04-03 | E-GEOD-67531 | biostudies-arrayexpress
Project description:During the legume-rhizobium symbiosis, free-living soil bacteria known as rhizobia trigger the formation of root nodules. The rhizobia infect these organs and adopt an intracellular lifestyle within the symbiotic nodule cells where they become nitrogen-fixing bacteroids. Several legume lineages enforce their symbionts into an extreme cellular differentiation, comprising cell enlargement and genome endoreduplication. The antimicrobial peptide transporter BclA is a major determinant of this differentiation process in Bradyrhizobium sp. ORS285, a symbiont of Aeschynomene spp.. In the absence of BclA, Bradyrhizobium sp. ORS285 proceeds until the intracellular infection of nodule cells but the bacteria cannot differentiate into enlarged polyploid bacteroids and fix nitrogen. The nodule bacteria of the bclA mutant constitute thus an intermediate stage between the free-living soil bacteria and the intracellular nitrogen-fixing bacteroids. Metabolomics on whole nodules of Aeschynomene afraspera and Aeschynomene indica infected with the ORS285 wild type or the bclA mutant revealed 47 metabolites that differentially accumulated concomitantly with bacteroid differentiation. Bacterial transcriptome analysis of these nodules discriminated nodule-induced genes that are specific to differentiated and nitrogen-fixing bacteroids and others that are activated in the host microenvironment irrespective of bacterial differentiation and nitrogen fixation. These analyses demonstrated that the intracellular settling of the rhizobia in the symbiotic nodule cells is accompanied with a first transcriptome switch involving several hundreds of upregulated and downregulated genes and a second switch accompanying the bacteroid differentiation, involving less genes but that are expressed to extremely elevated levels. The transcriptomes further highlighted the dynamics of oxygen and redox regulation of gene expression during nodule formation and we discovered that bclA represses the expression of non-ribosomal peptide synthetase gene clusters suggesting a non-symbiotic function of BclA. Together, our data uncover the metabolic and gene expression changes that accompany the transition from intracellular bacteria into differentiated nitrogen-fixing bacteroids.
2019-06-01 | GSE126971 | GEO
Project description:Here we have compared adult wildtype (N2) C. elegans gene expression when grown on different bacterial environments/fod sources in an effort to model naturally occuring nematode-bacteria interactions at the Konza Prairie. We hypothesize that human-induced changes to natural environments, such as the addition of nitrogen fertalizer, have effects on the bacterial community in soils and this drives downstream changes in the structure on soil bacterial-feeding nematode community structure. Here we have used transcriptional profiling to identify candidate genes involved in the interaction of nematodes and bacteria in nature.
2009-05-02 | GSE15923 | GEO
Project description:Bacteria are major drivers of organic matter decomposition and play crucial roles in global nutrient cycling. Although the degradation of dead fungal biomass (necromass) is increasingly recognized as an important contributor to soil carbon (C) and nitrogen (N) cycling, the genes and metabolic pathways involved in necromass degradation are under characterized. In particular, how bacteria degrade necromass containing different quantities of melanin, which largely control rates of necromass decomposition in situ, is largely unknown. To address this gap, we conducted a multi-timepoint transcriptomic analysis using three Gram-negative, bacterial species grown on low or high melanin necromass of Hyaloscypha bicolor. The bacterial species, Cellvibrio japonicus, Chitinophaga pinensis, and Serratia marcescens, belong to genera known to degrade necromass in situ. We found that while bacterial growth was consistently higher on low than high melanin necromass, the CAZyme-encoding gene expression response of the three species was similar between the two necromass types. Interestingly, this trend was not shared for genes encoding nitrogen utilization, which varied in C. pinensis and S. marcescens during growth on high versus low melanin necromass. Additionally, this study tested the metabolic capabilities of these bacterial species to grow on a diversity of C and N sources and found that the three bacteria have substantially different abilities to utilize carbon and nitrogen compounds. Collectively, our data suggests that as necromass changes chemically over the course of degradation, certain bacterial species are favored based on their differential metabolic capacities.
2024-05-29 | GSE268149 | GEO
Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated.
2011-02-15 | GSE21213 | GEO
Project description:Aeolian soil erosion, exacerbated by anthropogenic perturbations, has become one of the most alarming processes of land degradation and desertification. By contrast, dust deposition might confer a potential fertilization effect. To examine how they affect topsoil microbial community, we conducted a study GeoChip techniques in a semiarid grassland of Inner Mongolia, China. We found that microbial communities were significantly (P<0.039) altered and most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or remained unaltered in relative abundance by both erosion and deposition, which might be attributed to acceleration of organic matter mineralization by the breakdown of aggregates during dust transport and deposition. As a result, there were strong correlations between microbial carbon and nitrogen cycling genes. amyA genes encoding alpha-amylases were significantly (P=0.01) increased by soil deposition, reflecting changes of carbon profiles. Consistently, plant abundance, total nitrogen and total organic carbon were correlated with functional gene composition, revealing the importance of environmental nutrients to soil microbial function potentials. Collectively, our results identified microbial indicator species and functional genes of aeolian soil transfer, and demonstrated that functional genes had higher susceptibility to environmental nutrients than taxonomy. Given the ecological importance of aeolian soil transfer, knowledge gained here are crucial for assessing microbe-mediated nutrient cyclings and human health hazard.
2015-03-28 | GSE67347 | GEO
Project description:It has long been recognized that species occupy a specific ecological niche within their ecosystem. The ecological niche is defined as the number of conditions and resources that limit species distribution. Within their ecological niche, species do not exist in a single physiological state but in a number of states we call the Natural Operating Range. In this paper we link ecological niche theory to physiological ecology by measuring gene expression levels of collembolans exposed to various natural conditions. The soil-dwelling collembolan Folsomia candida was exposed to 26 natural soils with different soil characteristics (soil type, land use, practice, etc). The animals were exposed for two days and gene expression levels were measured. The main factor found to regulate gene expression was the soil type (sand or clay), in which 18.5% of the measured genes were differentially expressed. Gene Ontology analysis showed animals exposed to sandy soils experience general stress, affecting cell homeostasis and replication. Multivariate analysis linking soil chemical data to gene expression data revealed that soil fertility influences gene expression. Land-use and practice had less influence on gene expression; only forest soils showed a different expression pattern. A variation in gene expression variation analysis showed overall low variance in gene expression. The large difference in response to soil type was caused by the soil physicochemical properties where F. candida experiences clay soils and sandy soils as very different from each other. This collembolan prefers fertile soils with high organic matter content, as soil fertility was found to correlate with gene expression and animals exposed to sandy soils (which, in general, have lower organic matter content) experience more general stress. Finally, we conclude that there is no such thing as a fixed physiological state for animals in their ecological niche and the boundary between the ecological niche and a stressed state depends on the genes/pathways investigated. Test animals were exposed to 26 natural soils + 2 control soils. 4 biological replicates per soil containing 25 grams of soil and 30 23-day-old animals per replicate, RNA was isolated after two days of exposure. for the micro-array hybridization design we made use of an interwoven loop design. from the four replicates per soil two were labeled with Cy3 and 2 with Cy5. It was made sure that now two replicates of the same soil were ever hybridized against the same soil.
2011-02-15 | E-GEOD-21213 | biostudies-arrayexpress