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Original Articles

Mineralogical, Chemical and Biological Characterization of an Anaerobic Biofilm Collected from a Borehole in a Deep Gold Mine in South Africa

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Pages 491-504 | Received 15 Sep 2006, Accepted 30 May 2007, Published online: 01 Oct 2007

REFERENCES

  • Abulencia , C B , Wyborski , D L , Garcia , J A , Podar , M , Chen , W , Chang , S H , Chang , H W , Watson , D , Brodie , E L , Hazen , T C and Keller , M . 2006 . Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl . Environ Microbiol , 72 : 3291 – 3301 .
  • Banfield , J F , Welch , S A , Zhang , H , Ebert , T T and Penn , R L . 2000 . Aggregation-based crystal growth and microstructure development in natural iron oxyhydroxide biomineralization products . Science , 289 : 751 – 754 .
  • Banfield , J F , Moreau , J W , Chan , C S , Welch , S A and Little , B . 2001 . Mineralogical biosignatures and the search for life on Mars . Astrobiol , 1 : 447 – 467 .
  • Beller , H R , Chain , P SG , Letain , T E , Chakicherla , A , Latimer , F W , Richardson , P M , Coleman , M A , Wood , A P and Kelly , D P . 2006 . The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. . J Bacteriol , 188 : 1473 – 1488 .
  • Benzerara , K , Menguy , N , Lopez-Garcia , P , Yoon , T H , Kazmierczak , J , Tyliszczak , T , Guyot , F and Brown , G E . 2006 . Nanoscale detection of organic signatures in carbonate microbialites . Proc Natl Acad Sci USA , 103 : 9440 – 9445 .
  • Berner , R A . 1969 . The synthesis of frambiodal pyrite . Econ Geol , 64 : 383 – 384 .
  • Berner , R A . 1970 . Sedimentary pyrite formation . Amer J Sci , 268 : 1 – 23 .
  • Bodrossy , L , Holmes , E M , Holmes , A J , Kovacs , K L and Murrell , J C . 1997 . Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, Methylocaldum gen. nov. Arch . Microbiol , 168 : 493 – 503 .
  • Bonin , A S . 2005 . Deep subsurface microbiology of the south African gold mines , Ph.D. Dissertation 116 Portland State University .
  • Bowman , J P and McCuaig , R D . 2003 . Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic Continental Shelf sediment . Appl Environ Microbiol , 69 : 2463 – 2483 .
  • Brodie , E L , De Santis , T Z , Joyner , D C , Baek , S M , Larsen , J T , Andersen , G L , Hazen , T C , Richardson , P M , Herman , D J , Tokunaga , T K , Wan , J M and Firestone , M K . 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 .
  • Butler , I B and Rickard , D T . 2000a . The origin of framboids . Lithos , 3 : 269 – 293 .
  • Butler , I B and Rickard , D . 2000b . Framboidal pyrite formation via the oxidation of iron (II) monosulphide by hydrogen sulphide . Geochim Cosmochim Acta , 64 : 2665 – 2672 .
  • Cady , S L , Farmer , J D , Grotzinger , J P , Schopf , J W and Steele , A . 2003 . Morphological biosignatures and the search for life on Mars . Astrobiol , 3 : 351 – 368 .
  • Chao , A . 1984 . Non-parametric estimation of the number of classes in a population . Scand J Stat , 11 : 265 – 270 .
  • Chen , X G , Geng , A L , Yan , R , Gould , W D , Ng , Y L and Liang , D T . 2004a . Isolation and characterization of sulphur-oxidizing Thiomonas sp. and its potential application in biological deodorization . Lett Appl Microbiol , 39 : 95 – 503 .
  • Chen , C L , Macarie , H , Ramirez , I , Olmos , A , Ong , S L , Monroy , O and Liu , W T . 2004b . Microbial community structure in a thermophilic anaerobic hybrid reactor degrading terephthalate . Microbiology (Reading, Engl.) , 150 : 3429 – 3440 .
  • Dedysh , S N , Ricke , P and Liesack , W . 2004 . NifH and NifD phylogenies: an evolutionary basis for understanding nitrogen fixation capabilities of methanotrophic bacteria . Microbiology (Reading, Engl.) , 150 : 1301 – 1313 .
  • Dedysh , S N , Pankratov , T A , Belova , S E , Kulichevskaya , I S and Liesack , W . 2006 . Phylogenetic analysis and in situ identification of bacteria community composition in an acidic Sphagnum peat bog . Appl Environ Microbiol , 72 : 2110 – 2117 .
  • Donald , R and Southam , G . 1999 . Low temperature anaerobic bacterial diagenesis of ferrous monosulfide to pyrite . Geochim Cosmochim Acta , 63 : 2019 – 2023 .
  • Drobner , E , Huber , H , Rachel , R and Stetter , K O . 1992 . Thiobacillus plumbophilus sp. nov., a novel galena and hydrogen oxidizer . Arch Microbiol , 157 : 213 – 217 .
  • Druschel , G K , Labrenz , M , Thomsen-Ebert , T , Fowle , D A and Banfield , J F . 2002 . Geochemical modeling of ZnS in biofilms: An example of ore depositional processes . Econ Geol , 97 : 1319 – 1329 .
  • Eder , W , Ludwig , W and Huber , R . 1999 . Novel 16S rRNA gene sequences retrieved from highly saline brine sediments of Kebrit Deep, Red Sea . Arch Microbiol , 172 : 213 – 218 .
  • Finneran , K T , Forbush , H M , Van Praagh , C V and Lovley , D R . 2002 . Desulfitobacterium metallireducens sp. nov., an anaerobic bacterium that couples growth to the reduction of metals and humic acids as well as chlorinated compounds . Int J Syst Evol Microbiol , 52 : 1929 – 1935 .
  • Fortin , D , Davis , B , Southam , G and Beveridge , T J . 1995 . Biogeochemical phenomena induced by bacteria within sulfidic mine tailings . J Indust Microbiol , 14 : 178 – 185 .
  • Fredrickson , J K and Onstott , T C . 1996 . Microbes deep inside the Earth . Sci Amer , 275 : 68 – 73 .
  • Geesey , G G . 2001 . Bacterial behavior at surfaces . Curr Op Microbiol , 4 : 296 – 300 .
  • Gihring , T M , Moser , D P , Lin , L-H , Davidson , M , Onstott , T C , Morgan , L , Milleson , M , Kieft , T , Trimarco , E , Balkwill , D L and Dollhopf , M . 2006 . The distribution of microbial taxa in the subsurface water of the Kalahari Shield, South Africa . Geomicrobiol J , 23 : 415 – 430 .
  • Giovannoni , S J . 1991 . “ The polymerase chain reaction ” . In Nucleic acid techniques in bacterial systematics , Edited by: Stackebrandt , E and Goodfellow , M . 177 – 203 . New York : John Wiley & Sons .
  • Inagaki , F , Nunoura , T , Nakagawa , S , Teske , A , Lever , M , Lauer , A , Suzuki , M , Takai , K , Delwiche , M , Colwell , F S , Nealson , K H , Horikoshi , K , D'Hondt , S and Jorgensen , B B . 2006 . Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin . Proc Natl Acad Sci USA , 103 : 2815 – 2820 .
  • Inagaki , F , Suzuki , M , Takai , K , Oida , H , Sakamoto , T , Aoki , K , Nealson , K H and Horikoshi , K . 2003 . Microbial communities associated with geological horizons in coastal subseafloor sediments from the sea of Okhotsk . Appl Environ Microbiol , 69 : 7224 – 7235 .
  • Kaksonen , A H , Plumb , J J , Robertson , W J , Franzmann , P D , Gibson , J AE and Puhakka , J A . 2004 . Culturable diversity and community fatty acid profiling of sulfate-reducing fluidized-bed reactors treating acidic, metal-containing wastewater . Geomicrobiol J , 2 : 469 – 480 .
  • Kasai , Y , Takahata , Y , Hoaki , T and Watanabe , K . 2005 . Physiological and molecular characterization of a microbial community established in unsaturated, petroleum-contaminated soil . Environ Microbiol , 7 : 806 – 818 .
  • Labrenz , M , Druchel , G , Thomsen-Ebert , T , Gilbert , B , Welch , S A , Kemner , K M , Logan , G A , Summons , R E , De Stasio , G , Bond , P L , Lai , B , Kelly , S D and Banfield , J F . 2000 . Formation of sphalerite (ZnS) deposits in natural biofilms of sulfate-reducing bacteria . Science , 290 : 1744 – 1747 .
  • Lane , D J . 1991 . “ Nucleic acid techniques in bacterial systematics ” . In Nucleic Acid Techniques in Bacterial Systematics , Edited by: Stackebrandt , E and Goodfellow , M . 115 – 175 . New York : Wiley .
  • Ley , R E , Harris , J K , Wilcox , J , Spear , J R , Miller , S R , Bebout , B M , Maresca , J A , Bryant , D A , Sogin , M L and Pace , N R . 2006 . Unexpected diversity and complexity of the guerrero negro hypersaline microbial mat . Appl Environ Microbiol , 72 : 3685 – 3695 .
  • Lin , L-H. , Gihring , T. M. , Sherwood Lollar , B , Boice , E , Pratt , L M , Lippmann-Pipke , J , Bellamy , R ES , Hall , J and Onstott , T C . 2006 . Planktonic microbial communities associated with fracture-derived groundwater in a deep gold mine of South Africa . Geomicrobiol J , 23 : 474 – 497 .
  • Little , B J , Wagner , P A and Lewandowski , Z . 1997 . “ Spatial relations between bacteria and metal surfaces ” . In Geomicrobiology: Interactions between microbes and minerals , Edited by: Banfield , J F and Nealson , K H . Vol. 35 , 123 – 159 . Mineral Geochem .
  • Lovley , D R and Klug , M J . 1983 . Sulfate reducers can outcompete methanogens at freshwater sulfate concentrations . Appl Environ Microbiol , 45 : 187 – 192 .
  • Mills , H J , Hodges , C , Wilson , K , MacDonald , I R and Sobecky , P A . 2003 . Microbial diversity in sediments associated with surface-breaching gas hydrate mounds in the Gulf of Mexico . FEMS Microbiol Ecol , 46 : 39 – 52 .
  • Miyoshi , T , Iwatsuki , T and Naganuma , T . 2005 . Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters . Appl Environ Microbiol , 71 : 1084 – 1088 .
  • Moser , D P , Onstott , T C , Fredrickson , J K , Brockman , F J , Takai , K , Balkwill , D L , Drake , G , Pfiffner , S , White , D C , Baker , B J , Pratt , L M , Fong , J , Sherwood Lollar , B , Slater , G , Phelps , T J , Spoelstra , N , DeFlaun , M , Southam , G , Welty , A T and Hoek , J . 2003 . Evolution of microbial community structure and geochemistry in an ultradeep south african gold mine borehole . Geomicrobiol J , 20 : 517 – 548 .
  • Nakagawa , S , Inagaki , F , Suzuki , Y , Steinsbu , B O , Lever , M A , Takai , K , Engelen , B , Sako , Y , Wheat , C G and Horikoshi , K . 2006 . Microbial community in black rust exposed to hot ridge flank crustal fluids. Appl. Environ . Microbiol , 72 : 6789 – 6799 .
  • Onstott , T C , Moser , D P , Fredrickson , J K , Brockman , F J , Pfiffner , S M , Phelps , T J , White , D C , Peacock , A , Balkwill , D , Hoover , R , Krumholz , L R , Borscik , M , Kieft , T L and Wilson , R B . 2003 . Indigenous versus contaminant microbes in ultradeep mines . Env Microbiol , 5 : 1168 – 1191 .
  • Onstott , T C , Lin , L-H , Davidson , M , Mislowack , B , Borcsik , M , Hall , J , Slater , G , Ward , J , Sherwood Lollar , B , Lippmann-Pipke , J , Boice , E , Pratt , L M , Pfiffner , S M , Moser , D P , Gihring , T M , Kieft , T , Phelps , T J , van Heerden , E , Litthaur , D , De Flaun , M , Rothmel , R , Wanger , G and Southam , G . 2006 . The origin and age of biogeochemical trends in deep fracture water of the Witwatersrand Basin, South Africa . Geomicrobiol J , 23 : 369 – 414 .
  • Pedersen , K , Hallbeck , L , Arlinger , J , Erlandson , A C and Jahromi , N . 1997 . Investigation of the potential for microbial contamination of deep granitic aquifers during drilling using 16S rRNA gene sequencing and culturing methods . J Microbiol Meth , 30 : 179 – 192 .
  • Penn , R L and Banfield , J F . 1998 . Imperfect oriented attachment: a mechanism for dislocation generation in defect-free nanocrystals . Science , 281 : 969 – 971 .
  • Pudry , K J , Munson , M A , Nedwell , D B and Embley , T M . 2002 . Comparison of the molecular diversity of the methanogenic community at the brackish and marine ends of a UK estuary . FEMS Microbiol Ecol , 39 : 17 – 21 .
  • Raghoebarsing , A A , Pol , A , van de Pas-Schoonen , K T , Smolders , A JP , Ettwig , K F , Rijpstra , I C , Schouten , S , Sinninghe Damste , J S , Op den Camp , H JM , Jetten , M SM and Strous , M . 2006 . A microbial consortium couples anaerobic methane oxidation to denitrification . Nature , 440 : 918 – 921 .
  • Rickard , D . 1975 . Kinetics and mechanism of pyrite formation at low temperatures . Amer J Sci , 275 : 636 – 652 .
  • Rickard , D . 1997 . Kinetics of pyrite formation by the H2S oxidation of iron (II) monosulfide in aqueous solutions between 25 and 125°C: The rate equation . Geochim Cosmochim Acta , 61 : 115 – 134 .
  • Rickard , D and Luther , G W III . 1997 . Kinetics of pyrite formation by the H2S oxidation of iron (II) monosulfide in aqueous solutions between 25 and 125°C: The mechanism . Geochim Cosmochim Acta , 61 : 135 – 147 .
  • Rozanova , E P , Tourova , T P , Kolganova , T V , Lysenko , A M , Mityushina , L L , Yusupov , S K and Belyaev , S S . 2001 . Desulfacinum subterraneum sp. nov., a new thermophilic sulfate-reducing bacteria isolated from a high-temperature oil field . Microbiol , 70 : 466 – 471 .
  • Sait , M , Hugenholtz , P and Janssen , P H . 2002 . Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys . Environ Microbiol , 4 : 654 – 666 .
  • Sanford , R A , Cole , J R and Tiedje , J M . 2002 . Characterization and description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an aryl-halorespiring facultative anaerobic myxobacterium . Appl Environ Microbiol , 68 : 893 – 900 .
  • Schoonen , M AA . 2004 . Mechanisms of sedimentary pyrite formation. In: Sulfur Biogeochemistry—Past and present (Amend J.P., Edwards K.J., Lyons T.W., eds) . GSA Special Paper , 379 : 117 – 134 .
  • Schrenk , M O , Kelley , D S , Delaney , J R and Baross , J A . 2003 . Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney . Appl Environ Microbiol , 69 : 3580 – 3592 .
  • Sherwood Lollar , B , Lacrampe-Couloume , G , Slater , G F , Ward , J A , Moser , D P , Gihring , T M , Lin , L-H and Onstott , T C . 2006 . Unravelling abiogenic and biogenic sources of methane in the Earth's deep subsurface . Chem Geol , 226 : 328 – 339 .
  • Shigematsu , T , Tang , Y , Mizuno , Y , Kawaguchi , H , Morimura , S and Kida , K . 2006 . Microbial diversity of mesophilic methanogenic consortium that can degrade long-chain fatty acids in chemostat cultivation . J Biosci Bioeng , 102 : 535 – 544 .
  • Tringe , S G , von Mering , C , Kobayashi , A , Salamov , A A , Chen , K , Chang , H W , Podar , M , Short , J M , Mathur , E J , Detter , J C , Bork , P , Hugenholtz , P and Rubin , E M . 2005 . Comparative metagenomics of microbial communities . Science , 308 : 554 – 557 .
  • Trudinger , P A , Chambers , L A and Smith , J W . 1985 . Low-temperature sulphate reduction: biological versus abiological . Can J Earth Sci , 22 : 1910 – 1918 .
  • Tuttle , J H , Dugan , C B and Randles , C I . 1969 . Microbial sulfate reduction and its potential utility as an acid mine water pollution abatement procedure . Appl Microbiol , 17 : 297 – 302 .
  • Tweedie , E B . 1981 . The geology of the Evander Basin, Southeastern Transvaal, Republic of South Africa , M.Sc. thesis 221 Univ. of the Witswatersrand, Jhb .
  • Vetriani , C , Tran , H V and Kerkhof , L J . 2003 . Fingerprinting Microbial Assemblages from the Oxic/Anoxic Chemocline of the Black Sea . Appl Environ Microbiol , 69 : 6481 – 6488 .
  • Weber , K A , Urrutia , M M , Churchill , P F , Kukkadapu , R K and Roden , E E . 2006 . Anaerobic redox cycling of iron by freshwater sediment microorganisms . Environ Microbiol , 8 : 100 – 113 .
  • Wilkin , R T and Barnes , H L . 1997 . Formation processes of framboidal pyrite . Geochim Cosmochim Acta , 61 : 323 – 339 .
  • Wilson , A JC . 1963 . Mathematical Theory of X-ray Powder Diffraction , Eindhoven, , The Netherlands : Philips Technical Library .
  • Xie , C H and Yokota , A . 2006 . Zoogloea oryzae sp. nov., a nitrogen-fixing bacterium isolated from rice paddy soil, and reclassification of the strain ATCC 19623 as Crabtreella saccharophila gen. nov., sp. nov . Int J Syst Evol Microbiol , 56 : 19 – 624 .
  • Yamada , T , Sekiguchi , Y , Imachi , H , Kamagata , Y , Ohashi , A and Harada , H . 2005 . Diversity, localization, and physiological properties of filamentous microbes belonging to Chloroflexi subphylum I in mesophilic and thermophilic methanogenic sludge granules . Appl Environ Microbiol , 71 : 7493 – 7503 .
  • Yoshida , N , Takahashi , N and Hiraishi , A . 2005 . Phylogenetic characterization of a polychlorinated-dioxin-dechlorinating microbial community by use of microcosm studies . Appl Environ Microbiol , 71 : 4325 – 4334 .
  • Zhang , H , Sekiguchi , Y , Hanada , S , Hugenholtz , P , Kim , H , Kamagata , Y and Nakamura , K . 2003 . Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov . Int J Syst Evol Microbiol , 53 : 1155 – 1163 .
  • Zobell , C E . 1946 . Studies of redox potential of marine sediments . Bull Am Assoc Petrol Geol , 30 : 477 – 513 .

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