Sat, 26 Jul 2008 08:09:34 BST CiteULike: vrich's amoa http://www.citeulike.org/user/vrich/tag/amoa CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/vrich/article/1629441 <i>Environmental Microbiology, Vol. 9, No. 10. (October 2007), pp. 2522-2538.</i> Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray Ward B Bess Eveillard Damien Kirshtein D Julie Nelson D Joshua Voytek A Mary Jackson A George doi:10.1111/j.1462-2920.2007.01371.x Environmental Microbiology, Vol. 9, No. 10. (October 2007), pp. 2522-2538. 2007-09-07T03:51:56-00:00 2007 Environmental Microbiology 1462-2912 9 10 2522 2538 Blackwell Publishing ammonia_oxidation amoa fga microarray n_cycle sargasso http://www.citeulike.org/user/vrich/article/2783640 <i>Archives of Microbiology, Vol. 177, No. 2. (1 February 2002), pp. 139-149.</i><br /><br />Autotrophic ammonia-oxidizing bacteria use the essential enzyme ammonia monooxygenase (AMO) to transform ammonia to hydroxylamine. The amo operon consists of at least three genes, amoC, amoA, and amoB; amoA encodes the subunit containing the putative enzyme active site. The use of the amo genes as functional markers for ammonia-oxidizing bacteria in environmental applications requires knowledge of the diversity of the amo operon on several levels: (1) the copy number of the operon in the genome, (2) the arrangement of the three genes in an individual operon, and (3) the primary sequence of the individual genes. We present a database of amo gene sequences for pure cultures of ammonia-oxidizing bacteria representing both the &#35- and the &#37-subdivision of Proteobacteria in the following genera: Nitrosospira (6 strains), Nitrosomonas (5 strains) and Nitrosococcus (2 strains). The amo operon was found in multiple (2-3) nearly identical copies in the &#35-subdivision representatives but in single copies in the &#37-subdivision ammonia oxidizers. The analysis of the deduced amino acid sequence revealed strong conservation for all three Amo peptides in both primary and secondary structures. For the amoA gene within the &#35-subdivision, nucleotide identity values are approximately 85% within the Nitrosomonas or the Nitrosospira groups, but approximately 75% when comparing between these groups. Conserved regions in amoA and amoC were identified and used as primer sites for PCR amplification of amo genes from pure cultures, enrichments and the soil environment. The intergenic region between amoC and amoA is variable in length and may be used to profile the community of ammonia-oxidizing bacteria in environmental samples. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-001-0369-z. Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria Jeanette Norton Javier Alzerreca Yuichi Suwa Martin Klotz doi:10.1007/s00203-001-0369-z Archives of Microbiology, Vol. 177, No. 2. (1 February 2002), pp. 139-149. 2008-05-11T02:48:43-00:00 2002 Archives of Microbiology 177 2 139 149 amoa autotrophs lh-pcr http://www.citeulike.org/user/vrich/article/2783068 <i>Appl. Environ. Microbiol., Vol. 71, No. 5. (1 May 2005), pp. 2642-2652.</i><br /><br />We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to "RA 14" or "WB5FH-A," which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of nonsynonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors. 10.1128/AEM.71.5.2642-2652.2005 Methane-Oxidizing Bacteria in a California Upland Grassland Soil: Diversity and Response to Simulated Global Change Hans-Peter Horz Virginia Rich Sharon Avrahami Brendan Bohannan doi:10.1128/AEM.71.5.2642-2652.2005 Appl. Environ. Microbiol., Vol. 71, No. 5. (1 May 2005), pp. 2642-2652. 2008-05-10T17:09:54-00:00 2005 Appl. Environ. Microbiol. 71 5 2642 2652 amoa global_change jasper_ridge stats trflp