Ammonia oxidizing bacterial communities in TWW irrigated soil
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR528080.fastq.gz | Fastqsanger.gz | |||
| ERR528081.fastq.gz | Fastqsanger.gz | |||
| ERR528082.fastq.gz | Fastqsanger.gz | |||
| ERR528083.fastq.gz | Fastqsanger.gz | |||
| ERR528084.fastq.gz | Fastqsanger.gz |
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Project description:Ecology of soil bacterial active community under TWW irrigation in an Olive orchard.
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Project description:Ecology of soil bacterial active community under TWW irrigation in an Olive orchard
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Project description:Ecology of ammonia oxidizing and nitrite oxidizing microorganisms in the Namibian coastal upwelling oxygen minimum zone
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Project description:The oxidation of ammonia to nitrite, which constitutes the initial and rate-limiting step in the nitrification process, plays a pivotal role in the transformation of ammonia within soil ecosystems. Due to its susceptibility to a range of pollutants, such as heavy metals, pesticides, and pharmaceuticals, nitrification serves as a valuable indicator in the risk assessment of chemical contaminants in soil environments. Here, we analyzed the effects of cadmium (Cd) treatment on soil potential nitrification rate (PNR), and the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. The results showed that, under 1 day incubation, the soil PNR with Cd 0.5 mg kg-1 was a little higher but not statistically significant than that with zero mg kg-1. Then, the soil PNR increased with the increasing Cd concentration from 0.5 to one mg kg-1, and continuously declined from 1 to 10 mg kg-1. Moreover, we predicted the bacterial functions of samples with hormetic Cd dose (one mg kg-1) by PICURSt (Phylogenetic Investigation of Communities Reconstruction of Unobserved States), and found that the expression of protein disulfide isomerase (PDI) increased with the hormetic Cd dose. PDI is known to enhance the activity of compounds containing -SH or -S-S which can help prevent oxidative damage to membranes. The soil PNR was significantly correlated with AOA abundance rather than AOB, even the abundance of AOB was higher than that of AOA, indicating that AOA functionally predominated over AOB. Our study effectively evaluated the Cd toxicity on soil microbial community and clearly illustrated the ecological niches of AOA and AOB in the agricultural soil system studied, which will be instructive for the sustainable development of agriculture.
| S-EPMC11849506 | biostudies-literature
Project description:Nitrification is a key process in soil nitrogen (N) dynamics, but relatively little is known about it in tropical soils. In this study, we examined soils from Trinidad to determine the edaphic drivers affecting nitrification levels and community structure of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in non-managed soils. The soils were naturally vegetated, ranged in texture from sands to clays and spanned pH 4 to 8. The AOA were detected by qPCR in all soils (ca. 10(5) to 10(6) copies archaeal amoA g(-1) soil), but AOB levels were low and bacterial amoA was infrequently detected. AOA abundance showed a significant negative correlation (p<0.001) with levels of soil organic carbon, clay and ammonium, but was not correlated to pH. Structures of AOA and AOB communities, as determined by amoA terminal restriction fragment (TRF) analysis, differed significantly between soils (p<0.001). Variation in AOA TRF profiles was best explained by ammonium-N and either Kjeldahl N or total N (p<0.001) while variation in AOB TRF profiles was best explained by phosphorus, bulk density and iron (p<0.01). In clone libraries, phylotypes of archaeal amoA (predominantly Nitrososphaera) and bacterial amoA (predominanatly Nitrosospira) differed between soils, but variation was not correlated with pH. Nitrification potential was positively correlated with clay content and pH (p<0.001), but not to AOA or AOB abundance or community structure. Collectively, the study showed that AOA and AOB communities were affected by differing sets of edaphic factors, notably that soil N characteristics were significant for AOA, but not AOB, and that pH was not a major driver for either community. Thus, the effect of pH on nitrification appeared to mainly reflect impacts on AOA or AOB activity, rather than selection for AOA or AOB phylotypes differing in nitrifying capacity.
| S-EPMC3938500 | 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:Response of estuarine ammonia-oxidizing communities to constant and fluctuating salinity regimes
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Project description:The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the beta subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 microg of NH(4)(+)-N ml(-1), to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function.
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Project description:Microcosm Soil Freshwater or TWW Irrigated Raw sequence reads
| PRJNA668737 | ENA