Ammonia-oxidizing Archaea in Kamchatka Hot Springs

REFERENCES

• Clarke , KR . 1993 . Nonparametric multivariate analyses of changes in community structure . Austral J Ecol , 18 : 117 – 143 .
   Web of Science ®Google Scholar
• de la , Torre Jr , Walker , CB , Ingalls , AE , Könneke , M. and Stahl , DA . 2008 . Cultivation of a thermophilic ammonia oxidizing archaeon synthesizing crenarchaeol . Environ Microbiol , 10 : 810 – 818 .
   PubMed Web of Science ®Google Scholar
• DeLong , EF , King , LL , Massana , R. , Cittone , H. , Murray , A. , Schleper , C. and Wakeham , SG . 1998 . Dibiphytanyl ether lipids in nonthermophilic crenarchaeotes . Appl Environ Microbiol , 64 : 1133 – 1138 .
   PubMed Web of Science ®Google Scholar
• Derosa , M. and Gambacorta , A. 1988 . The lipids of Archaebacteria . Prog Lipid Res , 27 : 153 – 175 .
   PubMed Web of Science ®Google Scholar
• Francis , CA , Beman , JM and Kuypers , MMM . 2007 . New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation . ISME , J 1 : 19 – 27 .
   PubMed Web of Science ®Google Scholar
• Francis , CA , Roberts , KJ , Beman , JM , Santoro , AE and Oakley , BB . 2005 . Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean . Proc Natl Acad Sci USA , 102 : 14683 – 14688 .
   PubMed Web of Science ®Google Scholar
• Golovacheva , RS . 1976 . Thermophilic nitrifying bacteria from hot springs . Microbiology English translation of Mikrobiologiya. , 45 : 329 – 331 .
   Web of Science ®Google Scholar
• Hallam , SJ , Mincer , TJ , Schleper , C. , Preston , CM , Roberts , K. , Richardson , PM and DeLong , EF . 2006 . Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine crenarchaeota . PLoS Biol , 4 : 0520 – 0536 .
   Web of Science ®Google Scholar
• Hatzenpichler , R. , Lebedeva , EV , Spieck , E. , Stoecker , K. , Richter , A. , Daims , H. and Wagner , M. 2008 . A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring . Proc Natl Acad Sci USA , 105 : 2134 – 2139 .
   PubMed Web of Science ®Google Scholar
• He , J. , Shen , J. , Zhang , L. , Zhu , Y. , Zheng , Y. , Xu , M. and Di , HJ . 2007 . Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices . Environ Microbiol , 9 : 2364 – 2374 .
   PubMed Web of Science ®Google Scholar
• Hopmans , EC , Schouten , S. , Pancost , RD , van der Meer , MTJ and Damste , JSS . 2000 . Analysis of intact tetraether lipids in archaeal cell material and sediments by high performance liquid chromatography/atmospheric pressure chemical ionization mass spectrometry . Rapid Commun Mass Spectrom , 14 : 585 – 589 .
   PubMed Web of Science ®Google Scholar
• Kemnitz , D. , Kolb , S. and Conrad , R. 2005 . Phenotypic characterization of Rice Cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture . Environ Microbiol , 7 : 553 – 565 .
   PubMed Web of Science ®Google Scholar
• Kemp , PF and Aller , JY . 2004 . Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us . FEMS Microbiol Ecol , 47 : 161 – 177 .
   PubMed Web of Science ®Google Scholar
• Koga , Y. and Morii , H. 2005 . Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects . Biosci Biotech and Biochem , 69 : 2019 – 2034 .
   PubMed Web of Science ®Google Scholar
• Koga , Y. , Akagawamatsushita , M. , Ohga , M. and Nishihara , M. 1993 . Taxonomic significance of the distribution of component parts of polar ether lipids in methanogens . Syst Appl Microbiol , 16 : 342 – 351 .
   Web of Science ®Google Scholar
• Könneke , M. , Bernhard , AE , de la , Torre Jr , Walker , CB , Waterbury , JB and Stahl , DA . 2005 . Isolation of an autotrophic ammonia-oxidizing marine archaeon . Nature , 437 : 543 – 546 .
   PubMed Web of Science ®Google Scholar
• Kowalchuk , GA and Stephen , JR . 2001 . Ammonia-oxidizing bacteria: A model for molecular microbial ecology . Annu Rev Microbiol , 55 : 485 – 529 .
   PubMed Web of Science ®Google Scholar
• Kumar , S. , Tamura , K. and Nei , M. 2004 . MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment . Brief Bioinformat , 5 : 150 – 163 .
   PubMed Web of Science ®Google Scholar
• Lam , P. , Jensen , MM , Lavik , G. , McGinnis , DF , Muller , B. Schubert , CJ . 2007 . Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea . Proc Natl Acad Sci USA , 104 : 7104 – 7109 .
   PubMed Web of Science ®Google Scholar
• Lebedeva , EV , Alawi , M. , Fiencke , C. , Namsaraev , B. , Bock , E. and Spieck , E. 2005 . Moderately thermophilic nitrifying bacteria from a hot spring of the Baikal rift zone . FEMS Microbiol Ecol , 54 : 297 – 306 .
   PubMed Web of Science ®Google Scholar
• Leininger , S. , Urich , T. , Schloter , M. , Schwark , L. , Qi , J. Nicol , GW . 2006 . Archaea predominate among ammonia-oxidizing prokaryotes in soils . Nature , 442 : 806 – 809 .
   PubMed Web of Science ®Google Scholar
• Macalady , JL , Vestling , MM , Baumler , D. , Boekelheide , N. , Kaspar , CW and Banfield , JF . 2004 . Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid . Extremophiles , 8 : 411 – 419 .
   PubMed Web of Science ®Google Scholar
• Nicol , GW and Schleper , C . 2006 . Ammonia-oxidising Crenarchaeota: important players in the nitrogen cycle? . Trends Microbiol , 14 : 207 – 212 .
   PubMed Web of Science ®Google Scholar
• Pearson , A. , Huang , Z. , Ingalls , AE , Romanek , CS , Wiegel , J. Freeman , KH . 2004 . Nonmarine crenarchaeol in Nevada hot springs . Appl Environ Microbiol , 70 : 5229 – 5237 .
   PubMed Web of Science ®Google Scholar
• Pearson , A. , Pi , Y. , Zhao , W. , Li , W. , Li , Y. Inskeep , W. 2008 . Factors controlling the distribution of archaeal tetraethers in terrestrial hot springs . Appl Environ Microbiol , 74 : 3523 – 3532 .
   PubMed Web of Science ®Google Scholar
• Prosser , JI and Embley , TM . 2002 . Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers . Anton Van Leeuwen , 81 : 165 – 179 .
   PubMed Web of Science ®Google Scholar
• Prosser , JI and Nicol , GW . 2008 . Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment . Environ Microbiol , 10 : 2931 – 2941 .
   PubMed Web of Science ®Google Scholar
• Purkhold , U. , Pommerening-Roser , A. , Juretschko , S. , Schmid , MC , Koops , HP and Wagner , M. 2000 . Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: Implications for molecular diversity surveys . Appl Environ Microbiol , 66 : 5368 – 5382 .
   PubMed Web of Science ®Google Scholar
• Reigstad , LJ , Richter , A. , Daims , H. , Urich , T. , Schwark , L. and Schleper , C. 2008 . Nitrification in terrestrial hot springs of Iceland and Kamchatka . FEMS Microbiol Ecol , 64 : 167 – 174 .
   PubMed Web of Science ®Google Scholar
• Rotthauwe , JH , Witzel , KP and Liesack , W . 1997 . The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations . Appl Environ Microbiol , 63 : 4704 – 4712 .
   PubMed Web of Science ®Google Scholar
• Schleper , C. , Holben , W. and Klenk , HP . 1997 . Recovery of Crenarchaeotal ribosomal DNA sequences from freshwater-lake sediments . Appl Environ Microbiol , 63 : 321 – 323 .
   PubMed Web of Science ®Google Scholar
• Schleper , C. , Jurgens , G. and Jonuscheit , M. 2005 . Genomic studies of uncultivated archaea . Nat Rev Microbiol , 3 : 479 – 488 .
   PubMed Web of Science ®Google Scholar
• Schloss , PD and Handelsman , J. 2005 . Introducing DOTUR a computer program for defining operational taxonomic units and estimating species richness . Appl Environ Microbiol , 71 : 1501 – 1506 .
   PubMed Web of Science ®Google Scholar
• Schloss , PD , Larget , BR and Handelsman , J. 2004 . Integration of microbial ecology and statistics: a test to compare gene libraries . Appl Environ Microbiol , 70 : 5485 – 5492 .
   PubMed Web of Science ®Google Scholar
• Schouten , S. , Hopmans , EC , Pancost , RD and Damste , JSS . 2000 . Widespread occurrence of structurally diverse tetraether membrane lipids: Evidence for the ubiquitous presence of low-temperature relatives of hyperthermophiles . Proc Natl Acad Sci USA , 97 : 14421 – 14426 .
   PubMed Web of Science ®Google Scholar
• Schouten , S , Hopmans , EC , Schefuss , E and Damste , JSS . 2002 . Distributional variations in marine crenarchaeotal membrane lipids: A new tool for reconstructing ancient sea water temperatures? . Earth Planet Sci Lett , 204 : 265 – 274 .
   Web of Science ®Google Scholar
• Schouten , S , van der Meer , MTJ , Hopmans , EC , Rijpstra , WIC , Reysenbach , A-L , Ward , DM and Sinninghe Damste , JS . 2007 . Archaeal and bacterial glycerol dialkyl glycerol tetraether lipids in hot springs of Yellowstone National Park . Appl Environ Microbiol , 73 : 6181 – 6191 .
   PubMed Web of Science ®Google Scholar
• Shen , J. , Zhang , L. , Zhu , Y. , Zhang , J. and He , J. 2008 . Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam . Environ Microbiol , 10 : 1601 – 1611 .
   PubMed Web of Science ®Google Scholar
• Spear , JR , Barton , HA , Robertson , CE , Francis , CA and Pace , NR . 2007 . Microbial community biofabrics in a geothermal mine adit . Appl Environ Microbiol , 73 : 6172 – 6180 .
   PubMed Web of Science ®Google Scholar
• Uda , I. , Sugai , A. , Itoh , Y. H. and Itoh , T. 2001 . Variation in molecular species of polar lipids from Thermoplasma acidophilum depends on growth temperature . Lipids , 36 : 103 – 105 .
   PubMed Web of Science ®Google Scholar
• Urakawa , H. , Tajima , Y. , Numata , Y. and Tsuneda , S. 2008 . Low temperature decreases the phylogenetic diversity of ammonia-oxidizing archaea and bacteria in aquarium biofiltration systems . Appl Environ Microbiol , 74 : 894 – 900 .
   PubMed Web of Science ®Google Scholar
• Venter , JC , Remington , K. , Heidelberg , JF , Halpern , AL , Rusch , D. Eisen , JA . 2004 . Environmental genome shotgun sequencing of the Sargasso Sea . Science , 304 : 66 – 74 .
   PubMed Web of Science ®Google Scholar
• Wang , S. , Xiao , X. , Jiang , L. , Peng , X. , Zhou , H. , Meng , J. and Wang , F. 2009 . Diversity and abundance of ammonia-oxidizing Archaea in hydrothermal vent chimneys of the Juan de Fuca Ridge . Appl Environ Microbiol , 75 : 4216 – 4220 .
   PubMed Web of Science ®Google Scholar
• Weidler , GW , Dornmayr-Pfaffenhuemer , M. , Gerbl , FW , Heinen , W. and Stan-Lotter , H. 2007 . Communities of archaea and bacteria in a subsurface radioactive thermal spring in the Austrian Central Alps and evidence of ammonia-oxidizing Crenarchaeota . Appl Environ Microbiol , 73 : 259 – 270 .
   PubMed Web of Science ®Google Scholar
• Weijers , JWH , Schouten , S. , Spaargaren , OC and Damste , JSS . 2006 . Occurrence and distribution of tetraether membrane lipids in soils: Implications for the use of the TEX86 proxy and the BIT index . Org Geochem , 37 : 1680 – 1693 .
   Web of Science ®Google Scholar
• White , DC , Davis , WM , Nickels , JS , King , JD and Bobbie , RJ . 1979 . Determination of the sedimentary microbial biomass by extractible lipid phosphate . Oecologia , 40 : 51 – 62 .
   PubMed Web of Science ®Google Scholar
• Wuchter , C. , Abbas , B. , Coolen , MJL , Herfort , L. , van Bleijswijk , J. and Timmers , P. et al . 2006 . Archaeal nitrification in the ocean . Proc Natl Acad Sci USA , 103 : 12317 – 12322 .
   PubMed Web of Science ®Google Scholar
• Zhang , C. , Pearson , A. , Li , YL , Mills , G. and Wiegel , J. 2006 . Thermophilic temperature optimum for crenarchaeol synthesis and its implication for archaeal evolution . Appl Environ Microbiol , 72 : 4419 – 4422 .
   PubMed Web of Science ®Google Scholar
• Zhang , C. , Ye , Q. , Huang , Z. , Li , W. , Chen , J. and Song , Z. et al . 2008 . Global occurrence and biogeographic patterning of putative archaeal amoA genes in terrestrial hot springs . Appl Environ Microbiol , 74 : 6417 – 6426 .
   PubMed Web of Science ®Google Scholar