Sat, 19 Jul 2008 05:18:25 BST CiteULike: vrich's archaea http://www.citeulike.org/user/vrich/tag/archaea CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/vrich/article/1672724 <i>Environmental Microbiology, Vol. 6, No. 1. (2004), pp. 19-34.</i><br /><br />Summary Marine planktonic crenarchaeota have escaped all cultivation attempts to date, all crenarchaeota growing in pure culture so far being hyperthermophiles. Here, we present a comparative genomic analysis of a 16S- plus 23S-rDNA-containing fragment of a crenarchaeote retrieved from an environmental genomic library constructed from picoplankton collected at 500 m depth in the Antarctic Polar Front. The clone DeepAnt-EC39 contained an insert of 33.3 kbp, which was completely sequenced. DeepAnt-EC39 appears to represent a lineage specific to deep-sea waters but widespread geographically, as revealed by the analysis of the 16S-23S-rDNA intergenic spacer region. A comparison with previously sequenced marine crenarchaeotal genomic clones also containing an rrn operon (74A4, 4B7 and Cenarchaeum symbiosum strains A and B) revealed a highly variable structure involving gene rearrangements and insertions/deletions. The surroundings of the rrn operon and the contiguous glutamate-1-semialdehyde aminotransferase gene appear hot spots for recombination. Phylogenetic analyses of all individual predicted proteins revealed the existence of several likely cases of horizontal gene transfer both, between the two archaeal kingdoms and between the two prokaryotic domains. The most frequent horizontal transfers appear to involve genes from mesophilic methanogenic euryarchaeota related to Methanosarcinales. We hypothesise that the acquisition of genes from mesophilic bacteria and euryarchaeota has played a major role in the adaptation of Group I crenarchaeota to life at lower temperatures. Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers Purificacion Lopez-Garcia Celine Brochier David Moreira Francisco Rodriguez-Valera doi:10.1046/j.1462-2920.2003.00533.x Environmental Microbiology, Vol. 6, No. 1. (2004), pp. 19-34. 2007-09-19T01:24:21-00:00 2004 Environmental Microbiology 6 1 19 34 antarctic archaea crens deep_ant hgt http://www.citeulike.org/user/vrich/article/937612 <i>Appl Environ Microbiol, Vol. 63, No. 1. (January 1997), pp. 50-56.</i><br /><br />Newly described phylogenetic lineages within the domain Archaea have recently been found to be significant components of marine picoplankton assemblages. To better understand the ecology of these microorganisms, we investigated the relative abundance, distribution, and phylogenetic composition of Archaea in the Santa Barbara Channel. Significant amounts of archaeal rRNA and rDNA (genes coding for rRNA) were detected in all samples analyzed. The relative abundance of archaeal rRNA as measured by quantitative oligonucleotide hybridization experiments was low in surface waters but reached higher values (20 to 30% of prokaryotic rRNA) at depths below 100 m. Probes were developed for the two major groups of marine Archaea detected. rRNA originating from the euryarchaeal group (group II) was most abundant in surface waters, whereas rRNA from the crenarchaeal group (group I) dominated at depth. Clone libraries of PCR-amplified archaeal rRNA genes were constructed with samples from 0 and 200 m deep. Screening of libraries by hybridization with specific oligonucleotide probes, as well as subsequent sequencing of the cloned genes, indicated that virtually all archaeal rDNA clones recovered belonged to one of the two groups. The recovery of cloned rDNA sequence types in depth profiles exhibited the same trends as were observed in quantitative rRNA hybridization experiments. One representative of each of 18 distinct restriction fragment length polymorphism types was partially sequenced. Recovered sequences spanned most of the previously reported phylogenetic diversity detected in planktonic crenarchaeal and euryarchaeal groups. Several rDNA sequences appeared to be harbored in archaeal types which are widely distributed in marine coastal waters. In total, data suggest that marine planktonic crenarchaea and euryarchaea of temperate coastal habitats thrive in different zones of the water column. The relative rRNA abundance of the crenarchaeal group suggests that its members constitute a significant fraction of the prokaryotic biomass in subsurface coastal waters. Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara Channel. R Massana AE Murray CM Preston EF DeLong Appl Environ Microbiol, Vol. 63, No. 1. (January 1997), pp. 50-56. 2006-11-09T12:08:58-00:00 1997 Appl Environ Microbiol 0099-2240 63 1 50 56 archaea crens eurys santa_barbara_chanel http://www.citeulike.org/user/vrich/article/1562292 <i>Proc Natl Acad Sci U S A, Vol. 103, No. 17. (25 April 2006), pp. 6442-6447.</i><br /><br />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-oxidizing population would play a significant role in marine nitrification. Here we use the natural distribution of radiocarbon in archaeal membrane lipids to quantify the bulk carbon metabolism of archaea at two depths in the subtropical North Pacific gyre. Our compound-specific radiocarbon data show that the archaea in surface waters incorporate modern carbon into their membrane lipids, and archaea at 670 m incorporate carbon that is slightly more isotopically enriched than inorganic carbon at the same depth. An isotopic mass balance model shows that the dominant metabolism at depth indeed is autotrophy (83%), whereas heterotrophic consumption of modern organic carbon accounts for the remainder of archaeal biomass. These results reflect the in situ production of the total community that produces tetraether lipids and are not subject to biases associated with incubation and/or culture experiments. The data suggest either that the marine archaeal community includes both autotrophs and heterotrophs or is a single population with a uniformly mixotrophic metabolism. The metabolic and phylogenetic diversity of the marine archaea warrants further exploration; these organisms may play a major role in the marine cycles of nitrogen and carbon. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. AE Ingalls SR Shah RL Hansman LI Aluwihare GM Santos ER Druffel A Pearson doi:10.1073/pnas.0510157103 Proc Natl Acad Sci U S A, Vol. 103, No. 17. (25 April 2006), pp. 6442-6447. 2007-08-15T09:42:31-00:00 2006 Proc Natl Acad Sci U S A 0027-8424 103 17 6442 6447 archaea lipids pacific http://www.citeulike.org/user/vrich/article/2776714 <i>Proceedings of the National Academy of Sciences, Vol. 103, No. 10. (7 March 2006), pp. 3846-3851.</i><br /><br />Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane-carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100-2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea. 10.1073/pnas.0600035103 Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru Jennifer Biddle Julius Lipp Mark Lever Karen Lloyd Ketil Sorensen Rika Anderson Helen Fredricks Marcus Elvert Timothy Kelly Daniel Schrag Mitchell Sogin Jean Brenchley Andreas Teske Christopher House Kai-Uwe Hinrichs doi:10.1073/pnas.0600035103 Proceedings of the National Academy of Sciences, Vol. 103, No. 10. (7 March 2006), pp. 3846-3851. 2008-05-09T21:43:30-00:00 2006 Proceedings of the National Academy of Sciences 103 10 3846 3851 16srrna archaea fish lipids http://www.citeulike.org/user/vrich/article/2689375 <i>ISME J, Vol. 2, No. 1. (November 2007), pp. 3-18.</i> Uncultured archaea in deep marine subsurface sediments: have we caught them all? Andreas Teske Ketil Sorensen doi:10.1038/ismej.2007.90 ISME J, Vol. 2, No. 1. (November 2007), pp. 3-18. 2008-04-18T19:56:37-00:00 2007 ISME J 2 1 3 18 International Society for Microbial Ecology archaea pcr_bias http://www.citeulike.org/user/vrich/article/2295498 <i>ISME J (24 January 2008)</i><br /><br />Whale-falls represent localized areas of extreme organic enrichment in an otherwise oligotrophic deep-sea environment. Anaerobic remineralization within these habitats is typically portrayed as sulfidogenic; however, we demonstrate that these systems are also favorable for diverse methane-producing archaeal assemblages, representing up to 40% of total cell counts. Chemical analyses revealed elevated methane and depleted sulfate concentrations in sediments under the whale-fall, as compared to surrounding sediments. Carbon was enriched (up to 3.5%) in whale-fall sediments, as well as the surrounding sea floor to at least 10 m, forming a 'bulls eye' of elevated carbon. The diversity of sedimentary archaea associated with the 2893 m whale-fall in Monterey Canyon (California) varied both spatially and temporally. 16S rRNA diversity, determined by both sequencing and terminal restriction fragment length polymorphism analysis, as well as quantitative PCR of the methyl-coenzyme M reductase gene, revealed that methanogens, including members of the Methanomicrobiales and Methanosarcinales, were the dominant archaea (up to 98%) in sediments immediately beneath the whale-fall. Temporal changes in this archaeal community included the early establishment of methylotrophic methanogens followed by development of methanogens thought to be hydrogenotrophic, as well as members related to the newly described methanotrophic lineage, ANME-3. In comparison, archaeal assemblages in 'reference' sediments collected 10 m from the whale-fall primarily consisted of Crenarchaeota affiliated with marine group I and marine benthic group B. Overall, these results indicate that whale-falls can favor the establishment of metabolically and phylogenetically diverse methanogen assemblages, resulting in an active near-seafloor methane cycle in the deep sea.The ISME Journal advance online publication, 24 January 2008; doi:10.1038/ismej.2007.103. Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California. Shana K Goffredi Regina Wilpiszeski Ray Lee Victoria J Orphan doi:10.1038/ismej.2007.103 ISME J (24 January 2008) 2008-01-27T22:06:30-00:00 2008 ISME J 1751-7362 archaea methanogens trflp http://www.citeulike.org/user/vrich/article/2750707 <i>Nature, Vol. 409, No. 6819. (25 January 2001), pp. 507-510.</i> Archaeal dominance in the mesopelagic zone of the Pacific Ocean Markus Karner Edward Delong David Karl doi:10.1038/35054051 Nature, Vol. 409, No. 6819. (25 January 2001), pp. 507-510. 2008-05-03T21:10:36-00:00 2001 Nature 409 6819 507 510 archaea crens fish gi