Depth Distribution of Ammonia Oxidation Rates and Ammonia-Oxidizer Community Composition in the Sargasso Sea
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA179550 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Ammonia oxidizer community structure were examined in a depth profile from 20 to 2000 m at the Bermuda Atlantic Time-series Study using a functional gene microarray to look at amoA diversity
2012-11-15 | GSE42287 | GEO
Project description:Ammonia oxidizer community structure were examined in a depth profile from 20 to 2000 m at the Bermuda Atlantic Time-series Study using a functional gene microarray to look at amoA diversity Two color array (cy3 and cy5): the universal standard 20 bp oligo (fluoresced with cy5) is printed to the slide with a 70-mer. Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer will bind to it. Signal is the cy3/cy5. Two replicate arrays were run on duplicate targets.
2012-11-15 | E-GEOD-42287 | biostudies-arrayexpress
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone.
2013-08-24 | GSE50164 | GEO
Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone. Two color array (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. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.
2013-08-24 | E-GEOD-50164 | biostudies-arrayexpress
Project description:Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation-reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another - yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O(2), [Formula: see text], and [Formula: see text]) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24-0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 10(7) genes g(-) (1)) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria.
| S-EPMC3403348 | biostudies-literature
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
Project description:Hydrodynamic conditions shape ammonia-oxidizer communities in the central Baltic Sea water column
| PRJNA216927 | ENA
Project description:The abundance of bacterial (AOB) and archaeal (AOA) ammonia oxidisers, assessed using quantitative PCR measurements of their respective a-subunit of the ammonia monooxygenase (amoA) genes, and ammonia oxidation rates were measured in four contrasting coastal sediments in the Western English Channel. Sediment was sampled bimonthly from July 2008 to May 2011, and measurements of ammonia oxidiser abundance and activity compared to a range of environmental variables including salinity, temperature, water column nutrients and sediment carbon and nitrogen content. Despite a higher abundance of AOA amoA genes within all sediments, and at all time-points, rates of ammonia oxidation correlated with AOB and not AOA amoA gene abundance. Other than ammonia oxidation rate, sediment particle size was the only variable that correlated with the spatial and temporal patterns of AOB amoA gene abundance, implying a preference of the AOB for larger sediment particles. This is possibly due to deeper oxygen penetration into the sandier sediments, increasing the area available for ammonia oxidation to occur, higher concentrations of inhibitory sulphide with pore waters of muddier sediments or a combination of both oxygen and sulphide concentrations. Similar to many other temporal studies of nitrification within estuarine and coastal sediments, decreases in AOB amoA gene abundance were evident during summer and autumn, with maximum abundance and ammonia oxidation rates occurring in winter and early spring. The lack of correlation between AOA amoA gene abundance and ammonium oxidation rate suggests an alternative role for amoA-carrying AOA within these sediments.
2013-08-24 | GSE50163 | 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: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