Nitrification along a grassland gradient
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ABSTRACT:
PROVIDER: PRJEB85752 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:It is assumed that climate and land-use changes cause increasing stress to pollinators, which play pivotal roles in almost all terrestrial ecosystems, with consequences on population growth, diversity and ecosystem functions. While these responses to global change drivers are well located, the molecular pathways triggering the response are poorly understood. We analysed the transcriptomic response of Bombus lucorum workers in their systematic responses to temperature and livestock grazing, sampled along an elevational gradient from 650 – 1930 m.a.s.l., and from differently managed grassland sites (livestock grazing vs. unmanaged) in and around the National Park Berchtesgaden (German Alps).
2022-09-14 | GSE198931 | 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+–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:bacterial diversity along elevation gradient Metagenome
| PRJNA906103 | ENA
Project description:Metagenomic samples from along a rainfall gradient
| PRJNA930013 | ENA
Project description:Developmental profiling study along the maize leaf gradient
| PRJEB48470 | ENA
Project description:Metagenomic analysis of sediments along a uranium gradient
| PRJEB6942 | ENA
Project description:The ecophysiology of complete ammonia oxidizing Nitrospira (CMX) and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the relevance of their activity from the ecosystem-level process perspective has remained unclear. We investigated oligotrophic carbonate rock aquifers as a model system to assess the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen. CMX accounted for up to 95% of the ammonia oxidizer communities. Nitrification rates were positively correlated to CMX clade A-associated phylotypes and AOB affiliated with Nitrosomonas ureae. Surprisingly, short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed more than 90% to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOA and AOB was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater is primarily governed by AOB. Higher growth yields at lower NH4+ turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations. Activity measurements combined with differential inhibition allowed a refined understanding of ammonia oxidizer coexistence, competition and cooperation beyond the insights from molecular data alone.
2023-10-24 | PXD039573 | Pride
Project description:gene expression profiling in different zones along the gradient of the growing maize leaf balde aover a time course of dirunal cycle and carbon starvation by extension of the night Plants assimilate carbon in their photosynthetic tissues in the light. However, carbon is required during the night, and in non-photosynthetic organs. It is therefore essential that plants manage their carbon resources spatially and temporally and coordinate growth with carbon availability. In growing maize (Zea mays) leaf blades a defined developmental gradient facilitates analyses in the cell division, elongation and mature zones. We investigated the responses of the metabolome and transcriptome and polysome loading, as a qualitative proxy for protein synthesis, at dusk, dawn and 6, 14 and 24 hours into an extended night, and tracked whole leaf elongation over this time course. Starch and sugars are depleted by dawn in the mature zone, but only after an extension of the night in the elongation and division zones. Sucrose recovers partially between 14 and 24 h into the extended night in the growth zones but not the mature zone. The global metabolome and transcriptome track these zone-specific changes in sucrose. Leaf elongation and polysome loading in the growth zones also remain high at dawn, decrease between 6 and 14 h into the extended night and then partially recover indicating that growth processes are determined by local carbon status. The level of sucrose-signaling metabolite trehalose-6-phosphate, and the trehalose-6-phosphate:sucrose ratio are much higher in growth than mature zones at dusk and dawn but fall in the extended night. Candidate genes were identified by searching for transcripts that show characteristic temporal response patterns or contrasting responses to carbon starvation in growth and mature zones. 3 repliucates per time point and leaf region, each pooled form 5 indiviual plants
2016-08-24 | E-GEOD-85963 | biostudies-arrayexpress
Project description:gene expression profiling in different zones along the gradient of the growing maize leaf balde aover a time course of dirunal cycle and carbon starvation by extension of the night Plants assimilate carbon in their photosynthetic tissues in the light. However, carbon is required during the night, and in non-photosynthetic organs. It is therefore essential that plants manage their carbon resources spatially and temporally and coordinate growth with carbon availability. In growing maize (Zea mays) leaf blades a defined developmental gradient facilitates analyses in the cell division, elongation and mature zones. We investigated the responses of the metabolome and transcriptome and polysome loading, as a qualitative proxy for protein synthesis, at dusk, dawn and 6, 14 and 24 hours into an extended night, and tracked whole leaf elongation over this time course. Starch and sugars are depleted by dawn in the mature zone, but only after an extension of the night in the elongation and division zones. Sucrose recovers partially between 14 and 24 h into the extended night in the growth zones but not the mature zone. The global metabolome and transcriptome track these zone-specific changes in sucrose. Leaf elongation and polysome loading in the growth zones also remain high at dawn, decrease between 6 and 14 h into the extended night and then partially recover indicating that growth processes are determined by local carbon status. The level of sucrose-signaling metabolite trehalose-6-phosphate, and the trehalose-6-phosphate:sucrose ratio are much higher in growth than mature zones at dusk and dawn but fall in the extended night. Candidate genes were identified by searching for transcripts that show characteristic temporal response patterns or contrasting responses to carbon starvation in growth and mature zones.
2016-08-24 | GSE85963 | GEO