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Academic literature on the topic 'Ammonia monooxygenase α-subunit (amoA) gene'
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Journal articles on the topic "Ammonia monooxygenase α-subunit (amoA) gene"
1
Avrahami, Sharon, and Ralf Conrad. "Cold-temperate climate: a factor for selection of ammonia oxidizers in upland soil?" Canadian Journal of Microbiology 51, no. 8 (2005): 709–14. http://dx.doi.org/10.1139/w05-045.
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Ammonia-oxidizing bacteria in various upland soils show a rather large diversity with respect to their amoA genes (coding for a subunit of the ammonium monooxygenase). It is known that the community structure of ammonia-oxidizing bacteria in upland soils is influenced by different selective factors, such as pH, gravimetric water content, fertilizer treatment, and temperature. The question, from an ecological point of view, is whether a particular ecophysiological factor, such as temperature, could select for a particular community structure of ammonia oxidizers in upland soils that would be represented by distinct clusters of the amoA gene (AmoA cluster). Studying the literature, including recent publications and our own unpublished results, we found that AmoA clusters 3a, 3b, and 9–12 apparently exhibited no preference for either subtropical/tropical soils (i.e., warm regions) or temperate cold soils. However, AmoA clusters 1 and 4 (and perhaps cluster 2) seem to occur predominantly in soils from cold-temperate regions. Here we review the evidence for a temperature effect on the global distribution of amoA genes in warm- and cold-temperate soils.Key words: nitrifying bacteria, ammonia-oxidizing bacteria, Nitrosospira, ammonium monooxygenase gene, amoA.
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Beman, J. Michael, Kathryn J. Roberts, Linda Wegley, Forest Rohwer, and Christopher A. Francis. "Distribution and Diversity of Archaeal Ammonia Monooxygenase Genes Associated with Corals." Applied and Environmental Microbiology 73, no. 17 (2007): 5642–47. http://dx.doi.org/10.1128/aem.00461-07.
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ABSTRACT Corals are known to harbor diverse microbial communities of Bacteria and Archaea, yet the ecological role of these microorganisms remains largely unknown. Here we report putative ammonia monooxygenase subunit A (amoA) genes of archaeal origin associated with corals. Multiple DNA samples drawn from nine coral species and four different reef locations were PCR screened for archaeal and bacterial amoA genes, and archaeal amoA gene sequences were obtained from five different species of coral collected in Bocas del Toro, Panama. The 210 coral-associated archaeal amoA sequences recovered in this study were broadly distributed phylogenetically, with most only distantly related to previously reported sequences from coastal/estuarine sediments and oceanic water columns. In contrast, the bacterial amoA gene could not be amplified from any of these samples. These results offer further evidence for the widespread presence of the archaeal amoA gene in marine ecosystems, including coral reefs.
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Araki, N., T. Yamaguchi, S. Yamazaki, and H. Harada. "Quantification of amoA gene abundance and their amoA mRNA levels in activated sludge by real-time PCR." Water Science and Technology 50, no. 8 (2004): 1–8. http://dx.doi.org/10.2166/wst.2004.0474.
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The transcription level of amoA mRNA encoding a subunit of ammonia monooxygenase (AMO) in ammonia-oxidizing bacteria (AOB) was quantified by reverse transcription-polymerase chain reaction (RT-PCR) methods in combination with real-time PCR technology. The effects of ammonia concentration and dissolved oxygen (DO) on the transcription levels of amoA mRNA and 16S rRNA in AOB were evaluated in batch experiments with nitrifying sludge taken from a lab-scale reactor treating artificial wastewater. A batch incubation without ammonia resulted in a rapid decrease, within four hours, in the transcription level of amoA mRNA to as low as 1/10 of that at the beginning of the experiment, while the 16S rRNA level in AOB was almost constant. After subsequent incubation with 3 mM ammonia for eight hours, a small increase in the transcription level of amoA mRNA occurred, but ammonia oxidation proceeded in the interim. Copy numbers of amoA mRNA showed an almost fixed value for over eight hours in the absence of dissolved oxygen.
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Hou, Jie, Xiuyun Cao, Chunlei Song, and Yiyong Zhou. "Predominance of ammonia-oxidizing archaea andnirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu)." Canadian Journal of Microbiology 59, no. 7 (2013): 456–64. http://dx.doi.org/10.1139/cjm-2013-0083.
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The coupled nitrification–denitrification process plays a pivotal role in cycling and removal of nitrogen in aquatic ecosystems. In the present study, the communities of ammonia oxidizers and denitrifiers in the sediments of 2 basins (Guozhenghu Basin and Tuanhu Basin) of a large urban eutrophic lake (Lake Donghu) were determined using the ammonia monooxygenase subunit A (amoA) gene and the nitrite reductase gene. At all sites of this study, the archaeal amoA gene predominated over the bacterial amoA gene, whereas the functional gene for denitrification nirK gene far outnumbered the nirS gene. Spatially, compared with the Tuanhu Basin, the Guozhenghu Basin showed a significantly greater abundance of the archaeal amoA gene but less abundance of the nirK and nirS genes, while there was no significant difference of bacterial amoA gene copy numbers between the 2 basins. Unlike the archaeal amoA gene, the nirK gene showed a significant difference in community structure between the 2 basins. Archaeal amoA diversity was limited to the water–sediment cluster of Crenarchaeota, in sharp contrast with nirK for which 22 distinct operational taxonomic units were found. Accumulation of organic substances were found to be positively related to nirK and nirS gene copy numbers but negatively related to archaeal amoA gene copy numbers, whereas the abundance of the bacterial amoA gene was related to ammonia concentration.
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Beman, J. Michael, and Christopher A. Francis. "Diversity of Ammonia-Oxidizing Archaea and Bacteria in the Sediments of a Hypernutrified Subtropical Estuary: Bahía del Tóbari, Mexico." Applied and Environmental Microbiology 72, no. 12 (2006): 7767–77. http://dx.doi.org/10.1128/aem.00946-06.
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ABSTRACT Nitrification within estuarine sediments plays an important role in the nitrogen cycle, both at the global scale and in individual estuaries. Although bacteria were once thought to be solely responsible for catalyzing the first and rate-limiting step of this process, several recent studies have suggested that mesophilic Crenarchaeota are capable of performing ammonia oxidation. Here we examine the diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) within sediments of Bahía del Tóbari, a hypernutrified estuary receiving substantial amounts of ammonium in agricultural runoff. Using PCR primers designed to specifically target the archaeal ammonia monooxygenase α-subunit (amoA) gene, we found AOA to be present at five sampling sites within this estuary and at two sampling time points (January and October 2004). In contrast, the bacterial amoA gene was PCR amplifiable from only 40% of samples. Bacterial amoA libraries were dominated by a few widely distributed Nitrosomonas-like sequence types, whereas AOA diversity showed significant variation in both richness and community composition. AOA communities nevertheless exhibited consistent spatial structuring, with two distinct end member assemblages recovered from the interior and the mouths of the estuary and a mixed assemblage from an intermediate site. These findings represent the first detailed examination of archaeal amoA diversity in estuarine sediments and demonstrate that diverse communities of Crenarchaeota capable of ammonia oxidation are present within estuaries, where they may be actively involved in nitrification.
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Stopnišek, Nejc, Cécile Gubry-Rangin, Špela Höfferle, Graeme W. Nicol, Ines Mandič-Mulec, and James I. Prosser. "Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment." Applied and Environmental Microbiology 76, no. 22 (2010): 7626–34. http://dx.doi.org/10.1128/aem.00595-10.
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ABSTRACT Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and “deep peat” lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.
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Oved, Tamar, Avi Shaviv, Tal Goldrath, Raphi T. Mandelbaum, and Dror Minz. "Influence of Effluent Irrigation on Community Composition and Function of Ammonia-Oxidizing Bacteria in Soil." Applied and Environmental Microbiology 67, no. 8 (2001): 3426–33. http://dx.doi.org/10.1128/aem.67.8.3426-3433.2001.
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ABSTRACT The effect of effluent irrigation on community composition and function of ammonia-oxidizing bacteria (AOB) in soil was evaluated, using techniques of molecular biology and analytical soil chemistry. Analyses were conducted on soil sampled from lysimeters and from a grapefruit orchard which had been irrigated with wastewater effluent or fertilizer-amended water (FAW). Specifically, comparisons of AOB community composition were conducted using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of the gene encoding the α-subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and subsequent sequencing of relevant bands. A significant and consistent shift in the population composition of AOB was detected in soil irrigated with effluent. This shift was absent in soils irrigated with FAW, despite the fact that the ammonium concentration in the FAW was similar. At the end of the irrigation period, Nitrosospira-like populations were dominant in soils irrigated with FAW, while Nitrosomonas-like populations were dominant in effluent-irrigated soils. Furthermore, DGGE analysis of the amoA gene proved to be a powerful tool in evaluating the soil AOB community population and population shifts therein.
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Stephen, John R., Yun-Juan Chang, Sarah J. Macnaughton та ін. "Effect of Toxic Metals on Indigenous Soil β-Subgroup Proteobacterium Ammonia Oxidizer Community Structure and Protection against Toxicity by Inoculated Metal-Resistant Bacteria". Applied and Environmental Microbiology 65, № 1 (1999): 95–101. http://dx.doi.org/10.1128/aem.65.1.95-101.1999.
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ABSTRACT Contamination of soils with toxic metals is a major problem on military, industrial, and mining sites worldwide. Of particular interest to the field of bioremediation is the selection of biological markers for the end point of remediation. In this microcosm study, we focus on the effect of addition of a mixture of toxic metals (cadmium, cobalt, cesium, and strontium as chlorides) to soil on the population structure and size of the ammonia oxidizers that are members of the beta subgroup of the Proteobacteria (β-subgroup ammonia oxidizers). In a parallel experiment, the soils were also treated by the addition of five strains of metal-resistant heterotrophic bacteria. Effects on nitrogen cycling were measured by monitoring the NH3 and NH4 + levels in soil samples. The gene encoding the α-subunit of ammonia monooxygenase (amoA) was selected as a functional molecular marker for the β-subgroup ammonia oxidizing bacteria. Community structure comparisons were performed with clone libraries of PCR-amplified fragments of amoA recovered from contaminated and control microcosms for 8 weeks. Analysis was performed by restriction digestion and sequence comparison. The abundance of ammonia oxidizers in these microcosms was also monitored by competitive PCR. All amoA gene fragments recovered grouped with sequences derived from culturedNitrosospira. These comprised four novel sequence clusters and a single unique clone. Specific changes in the community structure of β-subgroup ammonia oxidizers were associated with the addition of metals. These changes were not seen in the presence of the inoculated metal-resistant bacteria. Neither treatment significantly altered the total number of β-subgroup ammonia-oxidizing cells per gram of soil compared to untreated controls. Following an initial decrease in concentration, ammonia began to accumulate in metal-treated soils toward the end of the experiment.
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Hoshino, Tatsuhiko, Naohiro Noda, Satoshi Tsuneda, Akira Hirata, and Yuhei Inamori. "Direct Detection by In Situ PCR of theamoA Gene in Biofilm Resulting from a Nitrogen Removal Process." Applied and Environmental Microbiology 67, no. 11 (2001): 5261–66. http://dx.doi.org/10.1128/aem.67.11.5261-5266.2001.
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ABSTRACT Ammonia oxidation is a rate-limiting step in the biological removal of nitrogen from wastewater. Analysis of microbial communities possessing the amoA gene, which is a small subunit of the gene encoding ammonia monooxygenase, is important for controlling nitrogen removal. In this study, the amoA gene present in Nitrosomonas europaea cells in a pure culture and biofilms in a nitrifying reactor was amplified by in situ PCR. In this procedure, fixed cells were permeabilized with lysozyme and subjected to seminested PCR with a digoxigenin-labeled primer. Then, the amplicon was detected with an alkaline phosphatase-labeled antidigoxigenin antibody and HNPP (2-hydroxy-3-naphthoic acid-2′-phenylanilide phosphate), which was combined with Fast Red TR, and with an Alexa Fluor 488-labeled antidigoxigenin antibody. The amoAgene in the biofilms was detected with an unavoidable nonspecific signal when the former method was used for detection. On the other hand, the amoA gene in the biofilms was detected without a nonspecific signal, and the cells possessing the amoAgene were clearly observed near the surface of the biofilm when Alexa Fluor 488-labeled antidigoxigenin antibody was used for detection. Although functional gene expression was not detected in this study, detection of cells in a biofilm based on their function was demonstrated.
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Tietz, A., R. Hornek, G. Langergraber, N. Kreuzinger, and R. Haberl. "Diversity of ammonia oxidising bacteria in a vertical flow constructed wetland." Water Science and Technology 56, no. 3 (2007): 241–47. http://dx.doi.org/10.2166/wst.2007.505.
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Vertical flow constructed wetlands (VFCWs) with intermittent loading are very suitable for nitrification. Ammonia oxidising bacteria (AOB) are the limiting step of nitration. Therefore the AOB community of a full-scale VFCW, receiving municipal wastewater, was investigated within this study. The diversity of the functional gene encoding the α–subunit of the ammonia monooxygenase (amoA), present only in AOB, was assessed by denaturing gradient gel electrophoresis (DGGE). Only very few amoA sequence types dominated the wetland filter substrate; nevertheless a stable nitrification performance could be observed. During the cold season the nitrification was slightly reduced, but it has been shown that the same AOB could be identified. No spatial AOB pattern could be observed within the filter body of the VFCW. The most prominent bands were excised from DGGE gels and sequenced. Sequence analyses revealed two dominant AOB lineages: Nitrosomonas europaea/“Nitrosococcus mobilis” and Nitrosospira. Species of the Nitrosomonas lineage are commonly found in conventional wastewater treatment plants (WWTPs). In contrast, members of the Nitrosospira lineage are rarely present in WWTPs. Our observations indicate that the AOB community in this VFCW is similar to that found in horizontal flow constructed wetlands, but differs from common WWTPs regarding the presence of Nitrosospira.