| quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. | an ammonia-oxidizing, carbon-fixing archaeon, candidatus "nitrosopumilus maritimus," recently was isolated from a salt-water aquarium, definitively confirming that chemoautotrophy exists among the marine archaea. however, in other incubation studies, pelagic archaea also were capable of using organic carbon. it has remained unknown what fraction of the total marine archaeal community is autotrophic in situ. if archaea live primarily as autotrophs in the natural environment, a large ammonia-oxidi ... | 2006 | 16614070 |
| phylogenetic diversity of planktonic archaea in the estuarine region of east china sea. | to examine the diversity and structure of archaeal communities in the yangtze river estuarine region of east china sea (ecs), the 16s rrna gene clone libraries of two typical sites were constructed with the archaea-specific primers. in total, 71 clones randomly selected were screened by pcr-restriction fragment length polymorphism (pcr-rflp) analysis and 21 clones with unique rflp pattern were sequenced. all the sequences are clustered into the two groups of marine group i (mgi) and marine group ... | 2007 | 16914298 |
| quantitative distribution of presumptive archaeal and bacterial nitrifiers in monterey bay and the north pacific subtropical gyre. | the recent isolation of the ammonia-oxidizing crenarchaeon nitrosopumilus maritimus has expanded the known phylogenetic distribution of nitrifying phenotypes beyond the domain bacteria. to further characterize nitrification in the marine environment and explore the potential crenarchaeal contribution to this process, we quantified putative nitrifying genes and phylotypes in picoplankton genomic libraries and environmental dna samples from coastal and open ocean habitats. betaproteobacteria ammon ... | 2007 | 17472632 |
| potential interactions of particle-associated anammox bacteria with bacterial and archaeal partners in the namibian upwelling system. | recent studies have shown that the anaerobic oxidation of ammonium by anammox bacteria plays an important role in catalyzing the loss of nitrogen from marine oxygen minimum zones (omz). however, in situ oxygen concentrations of up to 25 microm and ammonium concentrations close to or below the detection limit in the layer of anammox activity are hard to reconcile with the current knowledge of the physiology of anammox bacteria. we therefore investigated samples from the namibian omz by comparativ ... | 2007 | 17526789 |
| nitrosomonas nm143-like ammonia oxidizers and nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm. | zero-discharge marine aquaculture systems are an environmentally friendly alternative to conventional aquaculture. in these systems, water is purified and recycled via microbial biofilters. here, quantitative data on nitrifier community structure of a trickling filter biofilm associated with a recirculating marine aquaculture system are presented. repeated rounds of the full-cycle rrna approach were necessary to optimize dna extraction and the probe set for fish to obtain a reliable and comprehe ... | 2008 | 18093145 |
| intact membrane lipids of "candidatus nitrosopumilus maritimus," a cultivated representative of the cosmopolitan mesophilic group i crenarchaeota. | in this study we analyzed the membrane lipid composition of "candidatus nitrosopumilus maritimus," the only cultivated representative of the cosmopolitan group i crenarchaeota and the only mesophilic isolate of the phylum crenarchaeota. the core lipids of "ca. nitrosopumilus maritimus" consisted of glycerol dialkyl glycerol tetraethers (gdgts) with zero to four cyclopentyl moieties. crenarchaeol, a unique gdgt containing a cyclohexyl moiety in addition to four cyclopentyl moieties, was the most ... | 2008 | 18296531 |
| global distribution and diversity of coral-associated archaea and their possible role in the coral holobiont nitrogen cycle. | diversity, distribution and genetic comparison of archaea associated with the surface mucus of corals from three genera, namely acanthastrea sp., favia sp. and fungia sp., from the gulf of eilat, israel and from heron island, australia were studied. sequencing of the 16s rrna gene of the coral-associated archaea revealed dominance of crenarchaeota (79%, on average). in this phylum, 87% of the sequences were similar (>or= 97%) to the thermoprotei, with 76% of these being similar (>or= 97%) to the ... | 2008 | 18707612 |
| ammonia-oxidizing crenarchaeota and nitrification inside the tissue of a colonial ascidian. | marine crenarchaeota represent an abundant component of the oceanic microbiota that play an important role in the global nitrogen cycle. here we report the association of the colonial ascidian cystodytes dellechiajei with putative ammonia-oxidizing crenarchaeota that could actively be involved in nitrification inside the animal tissue. as shown by 16s rrna gene analysis, the ascidian-associated crenarchaeota were phylogenetically related to nitrosopumilus maritimus, the first marine archaeon iso ... | 2008 | 18793310 |
| ammonia-oxidizing archaea involved in nitrogen removal. | ammonia oxidation is critical to global nitrogen cycling and is often thought to be driven only by ammonia-oxidizing bacteria. the recent finding of new ammonia-oxidizing organisms belonging to the archaeal domain challenges this perception. two major microbial groups are now believed to be involved in ammonia oxidation: chemolithotrophic ammonia-oxidizing bacteria (aob) and ammonia-oxidizing archaea (aoa). candidatus "nitrosopumilus maritimus", the first isolated ammonia-oxidizing archaeon from ... | 2009 | 19232671 |
| archaeal diversity and the prevalence of crenarchaeota in salt marsh sediments. | crenarchaeal 16s rrna sequences constituted over 70% of the archaeal clones recovered from three salt marsh sites dominated by different grasses. group i.1a crenarchaeota dominated at two sites, while group i.3b crenarchaeota sequences were most abundant at a third site. abundances of 16s rrna genes related to "candidatus nitrosopumilus maritimus" differed by site and sampling date. | 2009 | 19395565 |
| ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. | the discovery of ammonia oxidation by mesophilic and thermophilic crenarchaeota and the widespread distribution of these organisms in marine and terrestrial environments indicated an important role for them in the global nitrogen cycle. however, very little is known about their physiology or their contribution to nitrification. here we report oligotrophic ammonia oxidation kinetics and cellular characteristics of the mesophilic crenarchaeon 'candidatus nitrosopumilus maritimus' strain scm1. unli ... | 2009 | 19794413 |
| distribution and diversity of archaeal and bacterial ammonia oxidizers in salt marsh sediments. | diversity and abundance of ammonia-oxidizing betaproteobacteria (beta-aob) and archaea (aoa) were investigated in a new england salt marsh at sites dominated by short or tall spartina alterniflora (sas and sat sites, respectively) or spartina patens (sp site). aoa amoa gene richness was higher than beta-aob amoa richness at sat and sp, but aoa and beta-aob richness were similar at sas. beta-aob amoa clone libraries were composed exclusively of nitrosospira-like amoa genes. aoa amoa genes at sat ... | 2009 | 19801456 |
| crenarchaeol dominates the membrane lipids of candidatus nitrososphaera gargensis, a thermophilic group i.1b archaeon. | analyses of archaeal membrane lipids are increasingly being included in ecological studies as a comparatively unbiased complement to gene-based microbiological approaches. for example, crenarchaeol, a glycerol dialkyl glycerol tetraether (gdgt) with a unique cyclohexane moiety, has been postulated as biomarker for ammonia-oxidizing archaea (aoa). crenarchaeol has been detected in nitrosopumilus maritimus and 'candidatus nitrosocaldus yellowstonii' representing two of the three lineages within th ... | 2010 | 20033067 |
| high abundance of ammonia-oxidizing archaea in coastal waters, determined using a modified dna extraction method. | molecular characterizations of environmental microbial populations based on recovery and analysis of dna generally assume efficient or unbiased extraction of dna from different sample matrices and microbial groups. appropriate controls to verify this basic assumption are rarely included. here three different dna extractions, performed with two commercial kits (fastdna and ultraclean) and a standard phenol-chloroform method, and two alternative filtration methods (sterivex and 25-mm-diameter poly ... | 2010 | 20118363 |
| homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context. | ammonia-oxidizing archaea are frequent and ubiquitous inhabitants of terrestrial and marine environments. as they have only recently been detected, most aspects of their metabolism are yet unknown. here we report on the occurrence of genes encoding potential homologues of copper-dependent nitrite reductases (nirk) in ammonia-oxidizing archaea of soils and other environments using metagenomic approaches and pcr amplification. two pairs of highly overlapping 40 kb genome fragments, each containing ... | 2010 | 20132279 |
| nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. | ammonia-oxidizing archaea are ubiquitous in marine and terrestrial environments and now thought to be significant contributors to carbon and nitrogen cycling. the isolation of candidatus "nitrosopumilus maritimus" strain scm1 provided the opportunity for linking its chemolithotrophic physiology with a genomic inventory of the globally distributed archaea. here we report the 1,645,259-bp closed genome of strain scm1, revealing highly copper-dependent systems for ammonia oxidation and electron tra ... | 2010 | 20421470 |
| synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(ii) and 2-oxoglutarate-dependent dioxygenase ectd. | as a response to high osmolality, many microorganisms synthesize various types of compatible solutes. these organic osmolytes aid in offsetting the detrimental effects of low water activity on cell physiology. one of these compatible solutes is ectoine. a sub-group of the ectoine producer's enzymatically convert this tetrahydropyrimidine into a hydroxylated derivative, 5-hydroxyectoine. this compound also functions as an effective osmostress protectant and compatible solute but it possesses prop ... | 2010 | 20498719 |
| relevance of a crenarchaeotal subcluster related to candidatus nitrosopumilus maritimus to ammonia oxidation in the suboxic zone of the central baltic sea. | marine pelagic redoxclines are areas of enhanced biogeochemical cycling inhabited by distinct functional groups of prokaryotes. in this study, the diversity and abundance of archaeal and bacterial nitrifying populations throughout a pelagic redoxcline in the central baltic sea were examined using a suite of molecular methods. 16s rrna/rrna gene as well as bacterial and archaeal amoa mrna/amoa gene fingerprints and clone libraries revealed that the putative nitrifying assemblages consisted solely ... | 2010 | 20535219 |
| distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum thaumarchaeota. | globally distributed archaea comprising ammonia oxidizers of moderate terrestrial and marine environments are considered the most abundant archaeal organisms on earth. based on 16s rrna phylogeny, initial assignment of these archaea was to the crenarchaeota. by contrast, features of the first genome sequence from a member of this group suggested that they belong to a novel phylum, the thaumarchaeota. here, we re-investigate the thaumarchaeota hypothesis by including two newly available genomes, ... | 2010 | 20598889 |
| phylogenetic evidence of noteworthy microflora from the subsurface of the former homestake gold mine, lead, south dakota. | molecular characterization of subsurface microbial communities in the former homestake gold mine, south dakota, was carried out by 16s rdna sequence analysis using a water sample and a weathered soil-like sample. geochemical analyses indicated that both samples were high in sulphur, rich in nitrogen and salt, but with significantly different metal concentrations. microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (otus) belonging to the archaeal phyl ... | 2010 | 20662386 |
| comparative metagenomics of bathypelagic plankton and bottom sediment from the sea of marmara. | to extend comparative metagenomic analyses of the deep-sea, we produced metagenomic data by direct 454 pyrosequencing from bathypelagic plankton (1000 m depth) and bottom sediment of the sea of marmara, the gateway between the eastern mediterranean and the black seas. data from small subunit ribosomal rna (ssu rrna) gene libraries and direct pyrosequencing of the same samples indicated that gamma- and alpha-proteobacteria, followed by bacteroidetes, dominated the bacterial fraction in marmara d ... | 2011 | 20668488 |
| molecular signatures for the crenarchaeota and the thaumarchaeota. | crenarchaeotes found in mesophilic marine environments were recently placed into a new phylum of archaea called the thaumarchaeota. however, very few molecular characteristics of this new phylum are currently known which can be used to distinguish them from the crenarchaeota. in addition, their relationships to deep-branching archaeal lineages are unclear. we report here detailed analyses of protein sequences from crenarchaeota and thaumarchaeota that have identified many conserved signature ind ... | 2011 | 20711675 |
| characterization of archaeal community in contaminated and uncontaminated surface stream sediments. | archaeal communities from mercury and uranium-contaminated freshwater stream sediments were characterized and compared to archaeal communities present in an uncontaminated stream located in the vicinity of oak ridge, tn, usa. the distribution of the archaea was determined by pyrosequencing analysis of the v4 region of 16s rrna amplified from 12 streambed surface sediments. crenarchaeota comprised 76% of the 1,670 archaeal sequences and the remaining 24% were from euryarchaeota. phylogenetic anal ... | 2010 | 20725722 |
| cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. | the role of ammonia-oxidizing archaea (aoa) in nitrogen cycling in marine sediments remains poorly characterized. in this study, we enriched and characterized aoa from marine sediments. group i.1a crenarchaea closely related to those identified in marine sediments and "candidatus nitrosopumilus maritimus" (99.1 and 94.9% 16s rrna and amoa gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (sob). the selective enrichment o ... | 2010 | 20870784 |
| induced cooperation between marine nitrifiers and anaerobic ammonium-oxidizing bacteria by incremental exposure to oxygen. | in oxygen-limited marine ecosystems cooperation between marine nitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria is of importance to nitrogen cycling. strong evidence for cooperation between anammox bacteria and nitrifiers has been provided by environmental studies but little is known about the development of such communities, the effects of environmental parameters and the physiological traits of their constituents. in this study, a marine laboratory model system was developed. coo ... | 2010 | 20956064 |
| metatranscriptomic analysis of ammonia-oxidizing organisms in an estuarine bacterioplankton assemblage. | quantitative pcr (qpcr) analysis revealed elevated relative abundance (1.8% of prokaryotes) of marine group 1 crenarchaeota (mg1c) in two samples of southeastern us coastal bacterioplankton, collected in august 2008, compared with samples collected from the same site at different times (mean 0.026%). we analyzed the mg1c sequences in metatranscriptomes from these samples to gain an insight into the metabolism of mg1c population growing in the environment, and for comparison with ammonia-oxidizin ... | 2010 | 21085199 |
| ribosomal tag pyrosequencing of dna and rna from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds. | ribosomal tag libraries based on dna and rna in coral reef sediment from hawaii show the microbial community to be dominated by the bacterial phyla proteobacteria, firmicutes and actinobacteria, the archaeal order nitrosopumilales and the uncultivated divisions marine group iii (euryarchaeota) and marine benthic group c (crenarchaeota). operational taxonomic units (otus) number in the high thousands, and richness varies with site, presence or absence of porewater sulfide (sediment depth), and nu ... | 2010 | 21176054 |
| environmental shaping of sponge associated archaeal communities. | archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood. | 2010 | 21209889 |
| microbial metatranscriptomics in a permanent marine oxygen minimum zone. | simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (omzs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. here, we present a metatranscriptomic survey of microbial community metabolism in the eastern tropical south pacific omz off northern chile. community rna was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycline ... | 2011 | 21210935 |
| genomic signatures of fifth autotrophic carbon assimilation pathway in bathypelagic crenarchaeota. | marine crenarchaeota, ubiquitous and abundant organisms in the oceans worldwide, remain metabolically uncharacterized, largely due to their low cultivability. identification of candidate genes for bicarbonate fixation pathway in the cenarchaeum symbiosum a was an initial step in understanding the physiology and ecology of marine crenarchaeota. recent cultivation and genome sequencing of obligate chemoautotrophic nitrosopumilus maritimus scm1 were a major breakthrough towards understanding of the ... | 2010 | 21255356 |
| complete-fosmid and fosmid-end sequences reveal frequent horizontal gene transfers in marine uncultured planktonic archaea. | the extent of horizontal gene transfer (hgt) among marine pelagic prokaryotes and the role that hgt may have played in their adaptation to this particular environment remain open questions. this is partly due to the paucity of cultured species and genomic information for many widespread groups of marine bacteria and archaea. molecular studies have revealed a large diversity and relative abundance of marine planktonic archaea, in particular of thaumarchaeota (also known as group i crenarchaeota) ... | 2011 | 21346789 |
| genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. | ammonia-oxidizing archaea (aoa) are thought to be among the most abundant microorganisms on earth and may significantly impact the global nitrogen and carbon cycles. we sequenced the genome of aoa in an enrichment culture from low-salinity sediments in san francisco bay using single-cell and metagenomic genome sequence data. five single cells were isolated inside an integrated microfluidic device using laser tweezers, the cells' genomic dna was amplified by multiple displacement amplification (m ... | 2011 | 21364937 |
| functional analysis of archaeal mbf1 by complementation studies in yeast. | multiprotein-bridging factor 1 (mbf1) is a transcriptional co-activator that bridges a sequence-specific activator (basic-leucine zipper (bzip) like proteins (e.g. gcn4 in yeast) or steroid/nuclear-hormone receptor family (e.g. ftz-f1 in insect)) and the tata-box binding protein (tbp) in eukaryotes. mbf1 is absent in bacteria, but is well- conserved in eukaryotes and archaea and harbors a c-terminal cro-like helix turn helix (hth) domain, which is the only highly conserved, classical hth domain ... | 2011 | 21392374 |
| core and intact polar glycerol dibiphytanyl glycerol tetraether lipids of ammonia-oxidizing archaea enriched from marine and estuarine sediments. | glycerol dibiphytanyl glycerol tetraether (gdgt)-based intact membrane lipids are increasingly being used as complements to conventional molecular methods in ecological studies of ammonia-oxidizing archaea (aoa) in the marine environment. however, the few studies that have been done on the detailed lipid structures synthesized by aoa in (enrichment) culture are based on species enriched from nonmarine environments, i.e., a hot spring, an aquarium filter, and a sponge. here we have analyzed core ... | 2011 | 21441324 |
| enrichment of a novel marine ammonia-oxidizing archaeon obtained from sand of an eelgrass zone. | ammonia-oxidizing archaea (aoa) are generally cultivated at ammonium concentrations of less than 2 mm. the physiology and abundance in the environment of aoa suggest an important role in the nitrogen cycle. we report here a novel marine ammonia-oxidizing crenarchaeote, strain nm25 belonged to 'candidatus nitrosopumilus', that was enriched from coastal sand of an eelgrass zone and grew in a medium containing 15 mm ammonium at 30°c. a phylogenetic analysis based on the 16s rrna gene revealed this ... | 2011 | 21487199 |
| nitrogen metabolism and kinetics of ammonia-oxidizing archaea. | the discovery of ammonia-oxidizing mesophilic and thermophilic group i archaea changed the century-old paradigm that aerobic ammonia oxidation is solely mediated by two small clades of beta- and gammaproteobacteria. group i archaea are extremely diverse and ubiquitous in marine and terrestrial environments, accounting for 20-30% of the microbial plankton in the global oceans. recent studies indicated that many of these organisms carry putative ammonia monooxygenase genes and are more abundant th ... | 2011 | 21514476 |
| nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. | genes of archaea encoding homologues of ammonia monooxygenases have been found on a widespread basis and in large amounts in almost all terrestrial and marine environments, indicating that ammonia oxidizing archaea (aoa) might play a major role in nitrification on earth. however, only one pure isolate of this group from a marine environment has so far been obtained, demonstrating archaeal ammonia oxidation coupled with autotrophic growth similar to the bacterial counterparts. here we describe th ... | 2011 | 21525411 |
| archaea in yellowstone lake. | the yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the archaea. this study continues on this theme, examining yellowstone lake and its lake floor hydrothermal vents. significant archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. phylogenetic diversity was assessed using 454-flx sequencing (∼51 000 ... | 2011 | 21544103 |
| characteristics of the microbial community associated with ammonia oxidation in a full-scale rockwool biofilter treating malodors from livestock manure composting. | the relationship between the activity and community structure of microbes associated with the oxidation of ammonia in a full-scale rockwool biofilter was examined by kinetic, denaturing gradient gel electrophoresis (dgge), and sequence analyses. the packing materials were sampled from two different depths at 3 sites. estimated k(m) values were similar among depths at same sampling sites, while v(max) differed in the mid-point sample. the lower depth of this site had the highest v(max). a corresp ... | 2010 | 21576861 |
| ammonia-oxidizing bacteria dominates over ammonia-oxidizing archaea in a saline nitrification reactor under low do and high nitrogen loading. | a continuous nitrification reactor treating saline wastewater was operated for almost one year under low dissolved oxygen (do) levels (0.15 to 0.5 mg/l) and high nitrogen loadings (0.26-0.52 kg-n/(m(3) d)) in four phases. the diversity and abundance of ammonia-oxidizing archaea (aoa) and ammonia-oxidizing bacteria (aob) were analyzed by cloning, terminal restriction fragment length polymorphism (t-rflp) and quantitative polymerase chain reaction (qpcr). the results showed that there were only on ... | 2011 | 21618465 |
| molecular characterization of the microbial community in hydrogenetic ferromanganese crusts of the takuyo-daigo seamount, northwest pacific. | the abundance and phylogenetic diversity of the microbial community in the hydrogenetic ferromanganese crust, sandy sediment and overlying seawater were investigated by culture-independent molecular analysis based on the 16s rrna gene. these samples were carefully collected from the takuyo-daigo seamount, located in the northwest pacific ocean, by a remotely operated vehicle. based on quantitative pcr analysis, archaea occupy a significant portion of the prokaryotic communities in the ferromanga ... | 2011 | 21631576 |
| abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical south pacific. | we assessed the abundance and molecular phylogeny of archaeoplankton in the oxygen minimum zone (omz) of the eastern tropical south pacific, using specific-probe hybridization and phylogenetic analysis of the ssu-rrna gene. euryarchaea from marine group-ii (mg-ii) were most abundant in the surface oxic layer, representing 4.0±2.0% of the total picoplankton, while crenarchaea from group i.1a (g-i.1a) peaked at the oxyclines, with a relative abundance of 8.1±4.3% (upper oxycline). in most of the s ... | 2011 | 21696407 |
| differential photoinhibition of bacterial and archaeal ammonia oxidation. | inhibition by light potentially influences the distribution of ammonia oxidizers in aquatic environments and is one explanation for nitrite maxima near the base of the euphotic zone of oceanic waters. previous studies of photoinhibition have been restricted to bacterial ammonia oxidizers, rather than archaeal ammonia oxidizers, which dominate in marine environments. to compare the photoinhibition of bacterial and archaeal ammonia oxidizers, specific growth rates of two ammonia-oxidizing archaea ... | 2011 | 22093004 |
| Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine. | Thaumarchaea, which represent as much as 20% of prokaryotic biomass in the open ocean, have been linked to environmentally relevant biogeochemical processes, such as ammonia oxidation (nitrification) and inorganic carbon fixation. We have used culture-independent methods to study this group because current cultivation limitations have proved a hindrance in studying these organisms. From a metagenomic data set obtained from surface waters from the Gulf of Maine, we have identified 36 111 sequence ... | 2011 | 22050608 |
| Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus. | Cell division is mediated by different mechanisms in different evolutionary lineages. While bacteria and euryarchaea utilize an FtsZ-based mechanism, most crenarchaea divide using the Cdv system, related to the eukaryotic ESCRT-III machinery. Intriguingly, thaumarchaeal genomes encode both FtsZ and Cdv protein homologues, raising the question of their division mode. Here, we provide evidence indicating that Cdv is the primary division system in the thaumarchaeon Nitrosopumilus maritimus. We also ... | 2011 | 21923770 |
| enrichment and characterization of an autotrophic ammonia-oxidizing archaeon of mesophilic crenarchaeal group i.1a from an agricultural soil. | soil nitrification is an important process for agricultural productivity and environmental pollution. though one cultivated representative of ammonia-oxidizing archaea from soil has been described, additional representatives warrant characterization. we describe an ammonia-oxidizing archaeon (strain my1) in a highly enriched culture derived from agricultural soil. fluorescence in situ hybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cel ... | 2011 | 22003023 |
| variability of prokaryotic community structure in a drinking water reservoir (marathonas, greece). | the structure of the bacteria and archaea community in a large drinking water reservoir (marathonas, greece; mr) was investigated in october 2007 and september 2008, using 16s rrna gene clone libraries. the bacterial communities were more diverse than archaeal communities (shannon diversity index h´ 0.81-3.28 and 1.36-1.77, respectively). the overall bacterial community composition was comparable to bacterioplankton community described in other freshwater habitats. within the bacteria, betaprote ... | 2011 | 21971081 |
| Split decision: a thaumarchaeon encoding both FtsZ and Cdv cell division proteins chooses Cdv for cytokinesis. | Cytoskeletal proteins play a pivotal role in cytokinesis in prokaryotes and eukaryotes. Most bacteria and a major branch of the archaea called the Euryarchaeota harbour a tubulin homologue, FtsZ, which assembles into a dynamic polymeric ring structure required for cytokinesis. However, Crenarchaeota, another branch of the archaea, lack FtsZ and instead use Cdv proteins, which are homologues of the ESCRT-III-like system involved in vesicular sorting and cytokinesis in eukaryotes, for cell divisio ... | 2011 | 21895799 |
| amoa-based consensus phylogeny of ammonia-oxidizing archaea and deep sequencing of amoa genes from soils of four different geographic regions. | ammonia-oxidizing archaea (aoa) play an important role in nitrification and many studies exploit their amoa genes as marker for their diversity and abundance. we present an archaeal amoa consensus phylogeny based on all publicly available sequences (status june 2010) and provide evidence for the diversification of aoa into four previously recognized clusters and one newly identified major cluster. these clusters, for which we suggest a new nomenclature, harboured 83 aoa species-level otu (using ... | 2011 | 22141924 |
| Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1. | Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite. | 2011 | 21914867 |