Biobio exp
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21633 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2023660_1.fastq.gz | Fastqsanger.gz | |||
| ERR2023660_2.fastq.gz | Fastqsanger.gz | |||
| ERR2023661_1.fastq.gz | Fastqsanger.gz | |||
| ERR2023661_2.fastq.gz | Fastqsanger.gz | |||
| ERR2023662_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
2019-03-15 | PXD013103 | Pride
Project description:Pure cultures of ammonia oxidizing bacterium, Nitrosomonas europaea, are exposed to cyanide in pseudo-steady state batch reactor in presence of ammonia. Nitrosomonas europaea are generally regarded as the most sensitive organism to various inhibitors commonly encountered in the wastewater treatment plants (WWTP). To find stress genes of Nitrosomonas europaea to cyanide known as inhibitor of respiratory process, whole-genome transcript response to cyanide was determined in this research using microarray and qRT-PCR. When 1 uM NaCN inhibits nitrification about 50 %, transcript levels of 35 genes were increased while transcript levels of 29 genes were decreased, showing more than 2-fold in total 2460 genes. moeZ (NE2353), homologue with rhodanases related to detoxification of CN-, showed 7-fold up regulation and gene cluster including moeZ also showed significant up regulation. Keywords: cyanide, stress response, moeZ The 1 uM NaCN caused more than 50 % inhibition in physiological response for 1 hour incubation. Transcriptional levels of the cells inhibited by cyanide were compared with the cells under control condition.
2010-05-26 | E-GEOD-10664 | biostudies-arrayexpress
Project description:Pure cultures of ammonia oxidizing bacterium, Nitrosomonas europaea, are exposed to cyanide in pseudo-steady state batch reactor in presence of ammonia. Nitrosomonas europaea are generally regarded as the most sensitive organism to various inhibitors commonly encountered in the wastewater treatment plants (WWTP). To find stress genes of Nitrosomonas europaea to cyanide known as inhibitor of respiratory process, whole-genome transcript response to cyanide was determined in this research using microarray and qRT-PCR. When 1 uM NaCN inhibits nitrification about 50 %, transcript levels of 35 genes were increased while transcript levels of 29 genes were decreased, showing more than 2-fold in total 2460 genes. moeZ (NE2353), homologue with rhodanases related to detoxification of CN-, showed 7-fold up regulation and gene cluster including moeZ also showed significant up regulation. Keywords: cyanide, stress response, moeZ
2008-06-21 | GSE10664 | GEO
Project description:Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions. Recent reports indicate a decrease in oceanic nitrification rates under experimentally lowered pH. How composition and abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) assemblages respond to decreasing oceanic pH, however, is unknown. We sampled microbes from two different acidification experiments and used a combination of qPCR and functional gene microarrays for the ammonia monooxygenase gene (amoA) to assess how acidification alters the structure of ammonia oxidizer assemblages. We show that despite widely different experimental conditions, acidification consistently altered the community composition of AOB by increasing the relative abundance of taxa related to the Nitrosomonas ureae clade. In one experiment this increase was sufficient to cause an increase in the overall abundance of AOB. There were no systematic shifts in the community structure or abundance of AOA in either experiment. These different responses to acidification underscore the important role of microbial community structure in the resiliency of marine ecosystems. amoA gene diversity from two ocean acidification experiments, Monterey Bay experiment (two time points, ambient and acidified) and Vineyard Sound experiment (ambient and acifidied, with and without nutrients) examined with 2 two-color arrays (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5.
2013-08-27 | E-GEOD-49956 | biostudies-arrayexpress
Project description:Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions. Recent reports indicate a decrease in oceanic nitrification rates under experimentally lowered pH. How composition and abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) assemblages respond to decreasing oceanic pH, however, is unknown. We sampled microbes from two different acidification experiments and used a combination of qPCR and functional gene microarrays for the ammonia monooxygenase gene (amoA) to assess how acidification alters the structure of ammonia oxidizer assemblages. We show that despite widely different experimental conditions, acidification consistently altered the community composition of AOB by increasing the relative abundance of taxa related to the Nitrosomonas ureae clade. In one experiment this increase was sufficient to cause an increase in the overall abundance of AOB. There were no systematic shifts in the community structure or abundance of AOA in either experiment. These different responses to acidification underscore the important role of microbial community structure in the resiliency of marine ecosystems. SUBMITTER_CITATION: Title: Acidification alters the composition of ammonia oxidizing microbial assemblages in marine mesocosms Journal: Marine Ecology Progress Series Issue: 492 Pages: 1-8 DOI: 10.3354/meps 10526 Authors: Jennifer L Bowen Patrick J Kearns Michael Holcomb Bess B Ward
2013-08-27 | GSE49956 | GEO