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Original Articles

Meter-Scale Diversity of Microbial Communities on a Weathered Pegmatite Granite Outcrop in the Wicklow Mountains, Ireland; Evidence for Mineral Induced Selection?

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Pages 1-14 | Received 16 Jan 2009, Accepted 07 Jul 2009, Published online: 15 Jan 2010

REFERENCES

  • Adams , J J , Pal , G , Jia , Z and Smith , S P . 2006 . Mechanism of bacterial cell-surface attachment revealed by the structure of cellulosomal type II cohesin-dockerin complex . PNAS , 103 ( 2 ) : 305 – 310 .
  • Altschul , S F , Gish , W , Miller , W , Miers , W and Lipman , D J . 1990 . Basic local alignment search tool . J Mol Biol , 215 : 403 – 410 .
  • Anderson , M J . 2001 . A new method for non-parametric multivariate analysis of variance . Austral Ecol , 26 ( 1 ) : 32 – 46 .
  • Anderson , M J and Willis , T J . 2003 . Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology . Ecology , 84 ( 2 ) : 511 – 525 .
  • Aouad , G , Crovisier , J L , Damidot , D , Stille , P , Hutchens , E , Mutterer , J , Meyer , J M and Geoffroy , V . 2008 . Interactions between MSWI bottom ash and Pseudomonas aeruginosa. . Sci Total Environ , 393 ( 2–3 ) : 385 – 393 .
  • Banfield , J F and Hammers , R . 1997 . “ Processes at minerals and surfaces with relevance to microorganisms and prebiotic synthesis ” . In Geomicrobiology: Interactions between Microbes and Minerals , Edited by: Banfield , J F and Nealson , K H . 81 – 119 . Washington, DC : Mineralogical Society of America . Reviews in Mineralogy, 35
  • Barker , W W and Banfield , J F . 1996 . Biologically versus inorganically mediated weathering reactions: relationships between minerals and extracellular microbial polymers in lithobiontic communities . Chem Geol , 132 : 55 – 69 .
  • Barker , W W , Welch , S A and Banfield , J F . 1997 . “ Biochemical weathering of silicate minerals ” . In Geomicrobiology: Interactions between Microbes and Minerals , Reviews in Mineralogy, 35 Edited by: Banfield , J F and Nealson , K H . 391 – 428 . Washington, DC : Mineralogical Society of America .
  • Bennett , P C , Rogers , J R and Choi , W J . 2001 . Silicates, silicate weathering, and microbial ecology . Geomicrobiol J , 18 : 3 – 19 .
  • Beveridge , T , Makin , S A , Kadurugamuwa , J L and Li , Z . 1997 . Interactions between biofilms and the environment . FEMS Microbiol Rev , 20 : 291 – 303 .
  • Bintrim , S B , Donohue , T J , Handelsman , J , Roberts , J P and Goodman , R M . 1997 . Molecular phylogeny of Archaea from soil . PNAS , 94 : 277 – 282 .
  • Boivin-Jahns , V , Ruimy , R , Bianchi , A , Dacmas , S and Christen , R . 1996 . Bacterial diversity in a deep-subsurface clay environment . Appl Environ Microbiol , 62 : 3405 – 3412 .
  • Boyd , E S , Cummings , D E and Geesey , G G . 2007 . Mineralogy influences structure and diversity of bacterial communities associated with geological substrata in a pristine aquifer . Microb Ecol , 54 : 170 – 182 .
  • Brodie , E , Edwards , S and Clipson , N . 2002 . Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem . Microb Ecol , 44 : 260 – 270 .
  • Chaturvedi , P , Reddy , G N and Shivaji , S . 2005 . Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India . Int J Syst Evol Microbiol , 55 : 2113 – 2117 .
  • Cooper , E L and DeVere Burton , L . 2000 . Agroscience: Fundamentals and Applications, , 3rd Edition , 773 Cengage Learning .
  • Davey , M L and Currah , S R . 2006 . A new species of Cladophialophora (hyphomycetes) from boreal and montane bryophytes . Mycologycal Res , 111 ( 1 ) : 106 – 116 .
  • de la Torre , B M Jr , Goebel , E I , Friedmann , N and Pace , R . 2003 . Microbial diversity of cryptoendolithic communities from the McMurdo Dry Valleys, Antarctica . Appl Environ Microbiol , 69 : 3858 – 3867 .
  • Dragan-Bularda , M . 2000 . Microbiologie Generala. Lucrari Practice , 232 Cluj-Napoca (Romania) : Universitatea Babes-Boliay . Editia 3
  • Duff , R B , Webley , D M and Scott , R O . 1962 . Solubilization of minerals and related materials by 2-ketogluconic acid-producing bacteria . Soil Sci , 95 : 105 – 114 .
  • Dunbar , J , Ticknor , L O and Kuske , C R . 2001 . Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities . Appl Environ Microbiol , 67 : 190 – 197 .
  • Erlich , H L . 1996 . Geomicrobiology , 719 New York : Marcel Dekker .
  • Erlich , H L . 2006 . “ Geomicrobiology: relative roles of bacteria and fungi as geomicrobial agents ” . In Fungi in biogeochemical cycles , Edited by: Gadd , G M . 1 – 28 . New York : Cambridge University Press .
  • Fisk , M R , Giovannoni , S J and Thorseth , I H . 1998 . Alteration of volcanic glass: textural evidence of microbial activity . Science , 281 : 978 – 980 .
  • Fletcher , M and Marshall , K C . 1982 . Bubble contact angle method for evaluating substratum interfacial characteristics and its relevance to bacterial attachment . Appl Environ Microbiol , 44 ( 1 ) : 184 – 192 .
  • Frisvad , J C . 2007 . “ Fungi in cold ecosystems ” . In Psychrophiles: From Biodiversity to Biotechnology , Edited by: Margesin , R , Schinner , F , Marx , J-C and Gerday , C . 137 – 156 . Berlin Heidelberg : Springer .
  • Gadd , G M . 2007 . Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation . Mycological Res , 111 : 3 – 49 .
  • Gleeson , D B , Clipson , N , Melville , K , Gadd , G M and McDermott , F P . 2005 . Mineralogical control of fungal community structure in a weathered pegmatitic granite . Microb Ecol , 50 : 360 – 368 .
  • Gleeson , B G , Kennedy , N M , Clipson , N , Melville , K , Gadd , G M and McDermott , P F . 2006b . Characterization of bacterial community structure on a weathered pegmatitic granite . Microb Ecol , 51 ( 4 ) : 526 – 534 .
  • Gleeson , D , McDermott , F and Clipson , N . 2006a . Structural diversity of bacterial communities in a heavy metal mineralized granite outcrop . Environ Microbiol , 8 ( 3 ) : 383 – 393 .
  • Gorbushina , A A . 2007 . Life on the rocks . Environ Microbiol , 9 ( 7 ) : 1613 – 1631 .
  • Gorbushina , A A and Krumbein , W E . 2000a . “ Subaerial microbial mats and their effects on soil and rock ” . In Microbial Sediments , Edited by: Riding , R and Awramik , S . 161 – 170 . Berlin : Springer .
  • Gorbushina , A A and Krumbein , W E . 2000b . “ Rock Dwelling Fungal Communities: Diversity of Life Styles and Colony Structure ” . In Journey to Diverse Microbial Worlds. Adaptation to Exotic Environments , Edited by: Seckbach , J . 317 – 334 . Dordrecht : Kluwer .
  • Gorbushina , A A , Heyrman , J , Dornieden , T , Gonzalez-Delvalle , M , Krumbein , W E , Laiz , L , Petersen , K , Saiz-Jimenez , C and Swings , J . 2004 . Bacterial and fungal diversity and biodeterioration problems in mural painting environments of St. Martins church (Greene-Kreiensen, Germany) . Int Biodeterior Biodegrad , 53 ( 1 ) : 13 – 24 .
  • Haldeman , D L , Amy , P S , White , D C and Ringelberg , D B . 1994 . Changes in bacteria recoverable from subsurface volcanic rock samples during storage at 4°C . Appl Envion Microbiol , 60 ( 8 ) : 2697 – 2703 .
  • Hansen , S K , Rainey , P B , Haagensen , J A and Molin , S . 2007 . Evolution of species in a biofilm community . Nature , 445 : 533 – 536 .
  • Hatzenpichler , R , Lebedeva , E V , Spieck , E , Stoecker , K , Richter , A , Daims , H and Wagner , M . 2008 . A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring . PNAS , 105 ( 6 ) : 2134 – 2139 .
  • Hilley , G E and Porder , S . 2008 . A framework for predicting global silicate weathering and CO2 drawdown rates over geologic time-scales . PNAS , 105 ( 44 ) : 16855 – 16859 .
  • Hirsch , P , Eckhardt , F EW and Palmer , R J Jr . 1995 . Fungi active in weathering rock and stone monuments . Can J Bot , 73 : 1384 – 1390 .
  • Hirsch , P , Ludwig , W , Hethke , C , Sittig , M , Hoffmann , B and Gallikowski , C A . 1998 . Hymenobacter roseosalivarius gen. nov., sp. nov. from Continental Antarctic soils and sandstone: Bacteria of the Cytophaga/Flavobacterium/ Bacteroides line of phylogenetic descent . System Appl Microbiol , 21 ( 3 ) : 374 – 383 .
  • Hutchens , E , Valsami-Jones , E , Harouyia , N , Chaïrat , C , McEldoney , S and Oelkers , E . 2006 . How do microorganisms enhance mineral dissolution rates? An experimental investigation of the effect of Bacillus megaterium on apatite dissolution rates . Geomicrobiol J , 23 ( 3 ) : 177 – 182 .
  • Hutchens , E , Valsami-Jones , E and McEldowney , S . 2003 . The role of heterotrophic bacteria in feldspar dissolution—an experimental approach . Min Mag , 67 ( 6 ) : 1157 – 1170 .
  • Jeon , S-O , Ahn , T-S and Hong , S-H . 2008 . A novel archaeal group in the phylum Crenarchaeota found unexpectedly in an eukaryotic survey in the Cariaco basin . J Microbiol , 46 ( 1 ) : 34 – 39 .
  • Könneke , M , Bernhard Anne , E R , de la Torre , J , Walker , C B , Waterbury , J B and Stahl , D A . 2005 . Isolation of an autotrophic ammonia-oxidizing marine archaeon . Nature , 437 : 543 – 546 .
  • Kubátová , A and Váňová , M . . Soil micromycetes in selected localities in the Krkonoše Mts. (Giant Mountain, Czech Republic) . Geoekologiczne Problemy Karkonoszy Symposium . October 3–5 2006 , Vrchlabí, Czech Republic.
  • Kuhlman , K R , Fusco , W G , La Duc , M T , Allenbach , L B , Ball , C L , Kuhlman , G M , Anderson , R C , Erickson , I K , Stuecker , T , Benardini , J , Strap , J L and Crawford , R L . 2006 . Diversity of microorganisms within rock varnish in the Whipple Mountains, California . Appl Environ Microbiol , 72 ( 2 ) : 1708 – 1715 .
  • Laiz , L , Hermosin , B , Caballero , B and Saiz-Jimenez , S . 2000 . Bacteria isolated from the rocks supporting prehistoric paintings in two shelters from Sierra de Cazorla, Jaen, Spain . Aerobiologia , 16 ( 1 ) : 119 – 124 .
  • Laiz , L , Miller , A , Jurado , V , Akatova , E , Sanchez-Moral , S , Gonzales , J , Dionísio , A , Macedo , M and Saiz-Jimenez , S . 2008 . Isolation of five Rubrobacter strains from biodeteriorated monuments . Naturwissenschaften , DOI 10.1007/s00114-008-0452-2
  • Lane , D J . 1991 . “ 16S/23S rRNA sequencing ” . In Nucleic acid techniques in bacterial systematics , Edited by: Stackebrandt , E and Goodfellow , M . 115 – 175 . New York : John Wiley and Sons .
  • Leadbetter , J and Greenberg , E P . 2000 . Metabolism of acyl-homoserine lactone quorum-sensing signals by Variovorax paradoxus. . J Bacteriol , 182 ( 24 ) : 6921 – 6926 .
  • Leininger , S , Urich , T , Schloter , M , Schwark , L , Qi , J , Nicol , G W , Prosser , J I , Schuster , S C and Schleper , C . 2006 . Archaea predominate among ammonia-oxidizing prokaryotes in soils . Nature , 442 : 806 – 809 .
  • Liermann , L J , Barnes , A S , Kalinowski , B E , Zhou , X and Brantley , S . 2000 . Microenvironments of pH in biofilms grown on dissolving silicate surfaces . Chem Geol , 171 : 1 – 16 .
  • López , M A , Díaz de la Serna , F JZ , Jan-Roblero , J , Romero , J M and Hernández-Rodríguez , C . 2006 . Phylogenetic analysis of a biofilm bacterial population in a water pipeline in the Gulf of Mexico . FEMS Microbiol Ecol , 58 ( 1 ) : 145 – 154 .
  • Lovejoy , C , Massana , R and Pedrós-Alió , C . 2006 . Diversity and distribution of marine microbial eukaryotes in the arctic ocean and adjacent seas . Appl Environ Microbiol , 72 : 3085 – 3095 .
  • Männistö , M K , Tiirola , M and Häggblom , M M . 2007 . Bacterial communities in Arctic fields of Finnish Lapland are stable but highly pH-dependent . FEMS Microbiol Ecol , 59 ( 2 ) : 452 – 465 .
  • Mason , O U , Stingl , U , Wilhelm , L J , Moeseneder , M M , Meo-Savoie , C A , Fisk , M R and Giovannoni , S J . 2007 . The phylogeny of endolithic microbes associated with marine basalts . Environ Microbiol , 9 : 2539 – 2550 .
  • Mauck , B S and Roberts , J . 2007 . Mineralogic control on abundance and diversity of surface-adherent microbial communities . Geomicrobiol J , 24 : 167 – 177 .
  • McArdle , B H and Anderson , M J . 2001 . Fitting multivariate models to community data, a comment on a distance-based redundancy analysis . Ecology , 82 : 290 – 297 .
  • McEldowney , S and Fletcher , M . 1986 . Effect of growth conditions and surface characteristics of aquatic bacteria on their attachment to solid surfaces . J Gen Microbiol , 132 : 513 – 523 .
  • Normand , P , Ponsonnet , C , Nesme , X , Neyra , M and Simonet , P . 1996 . “ ITS analysis of procariotes ” . In Molecular Microbial Ecology Manual , Edited by: Akkermans , D L , van Elsas , J D and De Bruijn , E L . 1 – 12 . Amsterdam, , the Netherlands : Kluwer Academic Publishers .
  • Northup , D E and Lavoie , K H . 2001 . Geomicrobiology of caves: a review . Geomicrobiol J , 19 : 199 – 222 .
  • Peacock , A D , Chang , Y-J , Istok , J D , Krumholz , L , Geyer , R , Kinsall , B , Watson , D , Sublette , K L and White , D C . 2004 . Utilization of microbial biofilms as monitors of bioremediation . Microb Ecolol , 47 : 284 – 292 .
  • Pringle , J H , Fletcher , M and Ellwood , D C . 1983 . Selection of attachment mutants during the continuous culture of Pseudomonas fluorescence and relationship between attachment ability and surface composition . J Gen Microbiol , 129 : 2557 – 2569 .
  • Pratt , J E , Gibbs , J N and Webber , J F . 1999 . Registration of Phlebiopsis gigantea as a Forest biocontrol agent in the UK: Recent experience . Biocontrol Sci Technol , 9 ( 1 ) : 113 – 118 . (6)
  • Quaiser , A T , Ochsenreiter , H P , Klenk , A , Kletzin , A H , Treusch , G , Meurer , J , Eck , C W , Sensen , C and Schleper , S . 2002 . First insight into the genome of an uncultivated crenarchaeote from soil . Environ Microbiol , 4 : 603 – 611 .
  • Ramsey , M H , Potts , P J , Webb , P C , Watkins , P , Watson , J S and Coles , B J . 1995 . An objective assessment of analytical method precision: comparison of ICP-AES and XRF for the analysis of silicate rocks . Chem Geol , 124 : 1 – 19 .
  • Ranjard , L , Poly , F , Lata , J-C , Mougel , C , Thioulouse , J and Nazaret , S . 2001 . Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability . Appl Environ Microbiol , 67 ( 10 ) : 4479 – 4487 .
  • Reading , N C and Sperandio , V . 2006 . Quorum sensing: The many languages of bacteria . FEMS Microbiol Lett , 254 : 1 – 11 .
  • Reardon , C L , Cummings , D E , Petzke , L M , Kinsall , B L , Watson , D B , Peyton , B M and Geesey , G G . 2004 . Composition and diversity of microbial communities recovered from surrogate minerals incubated in an acidic uranium-contaminated aquifer . Appl Environ Microbiol , 70 ( 10 ) : 6037 – 6046 .
  • Redfield , R J . 2002 . Is quorum sensing a side effect of diffusion sensing? . Trends Microbiol , 10 : 365 – 370 .
  • Roberts , J . 2004 . Inhibition and enhancement of microbial surface colonization: the role of silicate composition . Chem Geol , 212 ( 304 ) : 313 – 327 .
  • Rogers , J R and Bennett , P C . 2004 . Mineral stimulation of subsurface microorganisms: release of limiting nutrients from silicates . Chem Geol , 203 : 91 – 108 .
  • Sakai , S H , Imachi , Y , Sekiguchi , A , Ohashi , H , Harada , Y and Kamagata , Y . 2007 . Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster rice cluster I . Appl Environ Microbiol , 73 : 4326 – 4331 .
  • Sambrook , J , Fritsh , E F and Maniatis , T . 1989 . A laboratory manual, , 2nd Ed. , Vol. 2 , Cold Spring Harbor, NY : Cold Spring Harbor Laboratory Press .
  • Schleper , C , Jurgens , G and Jonuscheit , M . 2005 . Genomic studies of uncultivated archaea . Nat Rev Microbiol , 3 : 479 – 488 .
  • Schmalenberger , A , Schwieger , F and Tebbe , C C . 2001 . Effect of primers hybridizing to different evolutionary conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling . Appl Environ Microbiol , 67 : 3557 – 3563 .
  • Sonjak , S , Frisvad , J C and Gunde-Cimerman , N . 2007 . Genetic variation among Penicillium crustosum isolates from arctic and other ecological niches . Microb Ecol , 54 ( 2 ) : 298 – 305 .
  • Sparks , D L , Hlemke , P A , Loeppert , R H , Soltanpour , P N and Tabatabai , M A . 1996 . Methods of Soil Analysis: Chemical Methods, Part 3 , Madison, WI, , USA : Soil Science Society of America .
  • Thorseth , I H , Furnes , H and Tumyr , O . 1995 . Textural and chemical effects of bacterial activity on basaltic glass: an experimental approach . Chem Geol , 119 : 139 – 160 .
  • Torsvik , V and Lise , O . 2002 . Microbial diversity and function in soil: from genes to ecosystems . Curr Opin Microbiol , 5 : 240 – 245 .
  • Turovskiy , Y , Kashtanov , D , Parkhover , B and Chikindas , M L . 2007 . “ Quorum sensing: Fact, fiction and everything in between ” . In Advances in Applied Microbiology, Vol. 62 , Edited by: Laskin , A I , Sariaslani , S and Gadd , G M . 191 – 228 . Academic Press Elsevier .
  • Ullman , W J , Kirchman , D L , Welch , S A and Vandevievere , P . 1996 . Laboratory evidence for microbially mediated silicate mineral dissolution in nature . Chem Geol , 132 : 11 – 17 .
  • Valsami-Jones , E and McEldowney , S . 2000 . “ Mineral dissolution by heterotrophic bacteria: principles and methodologies ” . In Environmental Mineralogy: Microbial Interactions, Anthropogenic Influences, Contaminated Land and Waste Management , Edited by: Cotter-Howells , J D , Campbell , L S , Valsami-Jones , E and Batchelder , M . 27 – 55 . Mineralogical Society of Great Britain & Ireland . Special Series, 9
  • van De , P Y and De Wachter , R . 1994 . TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment . Comput Appl Biosci , 10 : 569 – 570 .
  • Walker , J and Pace , N . 2007a . Phylogenetic composition of Rocky Mountain endolithic microbial ecosystems . Appl Environ Microbiol , 73 ( 11 ) : 3497 – 3504 .
  • Walker , J and Pace , N . 2007b . Geobiology of a microbial endolithic community in the Yellowstone geothermal ecosystem . Nature , 434 : 1011 – 1014 .
  • White , T J , Bruns , T , Lee , S and Taylor , J . 1990 . “ Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics ” . In PCR Protocols: A Guide to Methods and Applications , Edited by: Innis , M A , Gelfand , D H , Sninsky , J J and White , T J . 315 – 322 . New York : Academic Press .
  • Wilms , R , Sass , H , Köpke , B , Köster , J , Cypionka , H and Engelen , B . 2006 . Specific bacterial, archaeal and eukaryotic communities in tidal-flat sediments along a vertical profile of several meters . Appl Environ Microbiol , 72 : 2756 – 2764 .

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