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Original Articles

Bacterial and Archaeal Community Structure of Two Adjacent Calcite Speleothems in Kartchner Caverns, Arizona, USA

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Pages 99-117 | Received 16 Dec 2009, Accepted 11 Feb 2010, Published online: 24 Feb 2011

REFERENCES

  • Aller , JY and Kemp , PF . 2008 . Are archaea inherently less diverse than bacteria in the same environments? . FEMS Microbiol Ecol , 65 : 74 – 87 .
  • Altschul , SF , Madden , TL , Schaffer , AA , Zhang , J. , Zhang , Z. , Miller , W. and Lipman , DJ . 1997 . Gapped BLAST and PSI-BLAST: A new generation of protein database search programs . Nucl Acids Res , 25 : 3389 – 3402 .
  • Ausubel , FM , Brent , R , Kingston , RE , Moore , DD , Seidman , JG , Smith , JA and Struhl , K . 1995 . “ Preparation of genomic DNA from bacteria ” . In Current protocols in molecular biology , Edited by: Ausubel , FM , Brent , R , Kingston , RE , Moore , DD , Seidman , JG , Smith , JA and Struhl , K . 2.4.1 – 2.4.2 . New York : John Wiley & Sons, Inc. .
  • Baker , GC , Smith , JJ and Cowan , DA . 2003 . Review and re-analysis of domain-specific 16S primers . J Microbiol Meth , 55 : 541 – 555 .
  • Barton , HA and Northup , DE . 2007 . Geomicrobiology in cave environments: Past, current and future perspectives . J Cave Karst Stud , 69 : 163 – 178 .
  • Barton , HA , Taylor , NM , Kreate , MP , Springer , AC , Oehrle , SA and Bertog , JL . 2007 . The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments . Int J Speleol , 36 : 93 – 104 .
  • Brodie , EL , DeSantis , TZ , Joyner , DC , Baek , SM , Larsen , JT , Andersen , GL , Hazen , TC , Richardson , PM , Herman , DJ , Tokunaga , TK , Wan , JMM and Firestone , MK . 2006 . Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation . Appl Environ Microbiol , 72 : 6288 – 6298 .
  • Brodie , EL , DeSantis , TZ , Parker , JP , Zubietta , IX , Piceno , YM and Andersen , GL . 2007 . Urban aerosols harbor diverse and dynamic bacterial populations . Proc Natl Acad Sci USA , 104 : 299 – 304 .
  • Buecher , RH . 1999 . Microclimate study of Kartchner Caverns, Arizona . J Cave Karst Stud , 61 : 106 – 120 .
  • Cacchio , P. , Contento , R. , Ercole , C. , Cappuccio , G. , Martinez , MP and Lepidi , A. 2004 . Involvement of microorganisms in the formation of carbonate speleothems in the Cervo Cave (L’Aquila Italy) . Geomicrobiol , J 21 : 497 – 509 .
  • Casamayor , EO , Massana , R. , Benlloch , S. , Ovreas , L. , Diez , B. , Goddard , VJ , Gasol , JM , Joint , I. , Rodriguez-Valera , F. and Pedros-Alio , C. 2002 . Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern . Environ Microbiol , 4 : 338 – 348 .
  • Casamayor , EO , Schafer , H , Baneras , L , Pedros-Alio , C and Muyzer , G . 2000 . Identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis . Appl Environ Microbiol , 66 : 499 – 508 .
  • Chelius , MK and Moore , JC . 2004 . Molecular phylogenetic analysis of archaea and bacteria in Wind Cave, South Dakota . Geomicrobiol J , 21 : 123 – 134 .
  • Chen , Y. , Wu , L. , Boden , R. , Hillebrand , A. , Kumaresan , D. , Moussard , H. , Baciu , M. , Lu , Y. and Colin , Murrell J . 2009 . Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave . ISME , J 3 : 1093 – 1104 .
  • Cole , JR , Chai , B , Farris , RJ , Wang , Q , Kulam , SA , McGarrell , DM , Garrity , GM and Tiedje , JM . 2005 . The Ribosomal Database Project (RDP II): sequences and tools for high-throughput rRNA analysis . Nucleic Acids Res , 33 : D294 – 296 .
  • Cuezva , S. , Sanchez-Moral , S. , Saiz-Jimenez , C. and Canaveras , JC . 2009 . Microbial communities and associated mineral fabrics in Altamira Cave, Spain . Int J Speleol , 38 : 83 – 92 .
  • Danielli , HMC and Edington , MA . 1983 . Bacterial calcification in limestone caves . Geomicrobiol , J 3 : 1 – 16 .
  • DeSantis , TZ , Brodie , EL , Moberg , JP , Zubieta , IX , Piceno , YM and Andersen , GL . 2007 . High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment . Microb Ecol , 53 : 371 – 383 .
  • Derakshani , M. , Lukow , T. and Liesack , W. 2001 . Novel bacterial lineages at the (sub)division level as detected by signature nucleotide targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms . Appl Environ Microbiol , 67 : 623 – 631 .
  • Ferris , MJ , Muyzer , G. and Ward , DM . 1996 . Denaturing gradient gel electrophoresis profiles of 16S rRNA-defined populations inhabiting a hot spring microbial mat community . Appl Environ Microbiol , 62 : 340 – 346 .
  • Ford , D and Williams , P . 2007 . Karst hydrogeology and geomorphology , 5 West Sussex : John Wiley & Sons Ltd. .
  • Gelsomino , A , Keijzer-Wolters , AC , Cacco , G and van Elsas , JD . 1999 . Assessment of bacterial community structure in soil by polymerase chain reaction and denaturing gradient gel electrophoresis . J Microbiol Meth , 38 : 1 – 15 .
  • Gonzalez , JM , Portillo , MC and Saiz-Jimenez , C. 2006 . Metabolically active crenarchaeota in Altamira Cave . Naturwissenschaften , 93 : 42 – 45 .
  • 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 .
  • Hayes , SM , White , SA , Thompson , TL , Maier , RM and Chorover , J. 2009 . Changes in lead and zinc lability during weathering-induced acidification of desert mine tailings: Coupling chemical and micro-scale analyses . Appl Geochem , 24 : 2234 – 2245 .
  • Hill , CA . 1999a . Mineralogy of Kartchner Caverns, Arizona . J Cave Karst Stud , 61 : 73 – 78 .
  • Hill , CA . 1999b . Overview of Kartchner Caverns, Arizona . J Cave Karst Stud , 61 : 3
  • Hill , CA and Forti , P . 1997 . 2nd Edition of Cave Minerals of the World , 463 Huntsville, AL : National Speleological Society .
  • Jagnow , DH . 1999 . Geology of Kartchner Caverns State Park, Arizona . J Cave Karst Stud , 61 : 49 – 58 .
  • Laiz , L. , Groth , I. , Schumann , P. , Zezza , F. , Felske , A. , Hermosin , B. and Saiz-Jimenez , C. 2000 . Microbiology of the stalactites from Grotta dei Cervi, Porto Badisco, Italy . Int Microbiol , 3 : 25 – 30 .
  • Lane , DJ . 1991 . “ 16S/23S rRNA sequencing ” . In Nucleic acid techniques in bacterial systematics , Edited by: Stackebrandt , E and Goodfellow , M . 115 – 173 . John Wiley and Sons Ltd. .
  • Macalady , JL , Jones , DS and Lyon , EH . 2007 . Extremely acidic, pendulous cave wall biofilms from the Frasassi cave system, Italy . Environ Microbiol , 9 : 1402 – 1414 .
  • Maddison , DR and Maddison , WP . 2001 . MacClade4: analysis of phylogeny and character evolution , Sunderland, MA : Sinauer Associates .
  • Masuda , N. and Church , GM . 2002 . Escherichia coli gene expression responsive to levels of the response regulator EvgA . Journal of Bacteriology , 184 : 6225 – 6234 .
  • Melim , LA , Shinglman , KM , Boston , PJ , Northup , DE , Spilde , MN and Queen , JM . 2001 . Evidence for microbial involvement in pool finger precipitation, Hidden Cave, New Mexico . Geomicrobiol , J 18 : 311 – 329 .
  • Muyzer , G. , Dewaal , EC and Uitterlinden , AG . 1993 . Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes coding for 16S ribosomal RNA . Appl Environ Microbiol , 59 : 695 – 700 .
  • Northup , DE , Barns , SM , Yu , LE , Spilde , MN , Schelble , RT , Dano , KE , Crossey , LJ , Connolly , CA , Boston , PJ , Natvig , DO and Dahm , CN . 2003 . Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves . Environ Microbiol , 5 : 1071 – 1086 .
  • Portillo , MC , Porca , E , Cuezva , S , Canaveras , JC , Sanchez-Moral , S and Gonzalez , JM . 2009 . Is the availability of different nutrients a critical factor for the impact of bacteria on subterraneous carbon budgets? . Naturwissenschaften , 96 : 1035 – 1042 .
  • Sanchez-Moral , S , Canaveras , JC , Laiz , L , Saiz-Jimenez , C , Bedoya , J and Luque , L . 2003 . Biomediated precipitation of calcium carbonate metastable phases in hypogean environments: A short review . Geomicrobiol J , 20 : 491 – 500 .
  • Schabereiter-Gurtner , C. , Saiz-Jimenez , C. , Pinar , G. , Lubitz , W. and Rolleke , S. 2004 . Phylogenetic diversity of bacteria associated with paleolithic paintings and surrounding rock walls in two spanish caves (Llonin and La Garma) . FEMS Microbiol Ecol , 47 : 235 – 247 .
  • 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 .
  • Spilde , MN , Northup , DE , Boston , PJ , Schelble , RT , Dano , KE , Crossey , LJ and Dahm , CN . 2005 . Geomicrobiology of cave ferromanganese deposits: A field and laboratory investigation . Geomicrobiol , J 22 : 99 – 116 .
  • Swofford , DL . 2006 . PAUP*: phylogenetic analysis using parsimony , Sunderland, MA : Sinauer Associates .
  • Tufts , R. and Tenen , G. 1999 . Discovery and history of Kartchner Caverns, Arizona . J Cave Karst Stud , 61 : 44 – 48 .
  • Wang , Q. , Garrity , GM , Tiedje , JM and Cole , JR . 2007 . Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy . Appl Environ Microbiol , 73 : 5261 – 5267 .

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