Ontology highlight
ABSTRACT:
PROVIDER: PRJNA596584 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10739559.fastq.gz | Fastqsanger.gz | |||
| SRR10739560.fastq.gz | Fastqsanger.gz | |||
| SRR10739561.fastq.gz | Fastqsanger.gz | |||
| SRR10739562.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community at the functional gene level to long-term fertilization, especially integrated fertilization (chemical combined with organic fertilization) remain unclear. Here we used microarray-based GeoChip techniques to explore the shifts of soil microbial functional community in a nutrient-poor paddy soil with long-term (21 years).The long-term fertilization experiment site (set up in 1990) was located in Taoyuan agro-ecosystem research station (28°55’N, 111°27’E), Chinese Academy of Sciences, Hunan Province, China, with a double-cropped rice system. fertilization at various regimes.
2020-09-19 | GSE104014 | GEO
Project description:Microbial decomposition of soil organic carbon (SOC) in Arctic permafrost is one of the most important, but poorly understood, factors in determining the greenhouse gas feedback of tundra ecosystems to climate. Here, we examine changes in the structure of microbial communities in an anoxic incubation experiment at either –2 or 8 °C for up to 122 days using both an organic and a mineral soil collected from the Barrow Environmental Observatory in northern Alaska, USA. Soils were characterized for SOC and geochemistry, and GeoChips 5.0 were used to determine microbial community structure and functional genes associated with C availability and Fe(III) reduction.
2016-11-09 | GSE89644 | GEO
Project description:Soil microbiome dynamics after fertilization with organic versus mineral fertilization
| PRJNA688413 | ENA
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.
2011-01-01 | E-GEOD-24800 | biostudies-arrayexpress
Project description:Arbuscular mycorrhizal (AM) fungi contribute to plant nutrient uptake in systems managed with reduced fertilizer inputs such as organic agriculture and natural ecosystems by extending the effective size of the rhizosphere and delivering mineral. Connecting the molecular study of the AM symbiosis with agriculturally- and ecologically-relevant field environments remains a challenge and is a largely unexplored research topic. This study utilized a cross-disciplinary approach to examine the transcriptional, metabolic, and physiological responses of tomato (Solanum lycopersicum) AM roots to a localized patch of nitrogen (N). A wild-type mycorrhizal tomato and a closely-related nonmycorrhizal mutant were grown at an organic farm in soil that contained an active AM extraradical hyphal network and soil microbe community. The majority of genes regulated by upon enrichment of nitrogen were similarly expressed in mycorrhizal and nonmycorrhizal roots, suggesting that the primary response to an enriched N patch is mediated by mycorrhiza-independent root processes. However where inorganic N concentrations in the soil were low, differential regulation of key tomato N transport and assimilation genes indicate a transcriptome shift towards mycorrhiza-mediated N uptake over direct root supplied N. Furthermore, two novel mycorrhizal-specific tomato ammonium transporters were also found to be regulated under low N conditions. A conceptual model is presented integrating the transcriptome response to low N and highlighting the mycorrhizal-specific ammonium transporters. These results enhance our understanding of the role of the AM symbiosis in sensing and response to an enriched N patch, and demonstrate that transcriptome analyses of complex plant-microbe-soil interactions provide a global snapshot of biological processes relevant to soil processes in organic agriculture. 30 samples were analyzed. There were 2 genotypes (wildtype and mutant) and 3 treatments (two N treatments and a water control) for a total of 6 groups. Each group had 5 biological replicates.
2011-06-29 | E-GEOD-30270 | biostudies-arrayexpress
Project description:Arbuscular mycorrhizal (AM) fungi contribute to plant nutrient uptake in systems managed with reduced fertilizer inputs such as organic agriculture and natural ecosystems by extending the effective size of the rhizosphere and delivering mineral. Connecting the molecular study of the AM symbiosis with agriculturally- and ecologically-relevant field environments remains a challenge and is a largely unexplored research topic. This study utilized a cross-disciplinary approach to examine the transcriptional, metabolic, and physiological responses of tomato (Solanum lycopersicum) AM roots to a localized patch of nitrogen (N). A wild-type mycorrhizal tomato and a closely-related nonmycorrhizal mutant were grown at an organic farm in soil that contained an active AM extraradical hyphal network and soil microbe community. The majority of genes regulated by upon enrichment of nitrogen were similarly expressed in mycorrhizal and nonmycorrhizal roots, suggesting that the primary response to an enriched N patch is mediated by mycorrhiza-independent root processes. However where inorganic N concentrations in the soil were low, differential regulation of key tomato N transport and assimilation genes indicate a transcriptome shift towards mycorrhiza-mediated N uptake over direct root supplied N. Furthermore, two novel mycorrhizal-specific tomato ammonium transporters were also found to be regulated under low N conditions. A conceptual model is presented integrating the transcriptome response to low N and highlighting the mycorrhizal-specific ammonium transporters. These results enhance our understanding of the role of the AM symbiosis in sensing and response to an enriched N patch, and demonstrate that transcriptome analyses of complex plant-microbe-soil interactions provide a global snapshot of biological processes relevant to soil processes in organic agriculture.
2011-06-29 | GSE30270 | 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: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. The experimental sites comprised of three treatments of control, soil erosion and deposition, with 5 replicates of each treatment.
2015-03-28 | E-GEOD-67347 | biostudies-arrayexpress