520
Views
52
CrossRef citations to date
0
Altmetric
Original Articles

Bacterial Communities Inside and Surrounding Soil Iron-Manganese Nodules

, , , &
Pages 14-24 | Received 14 Sep 2007, Accepted 26 Nov 2007, Published online: 30 Jan 2008

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 .
  • Barns , S M , Cain , E C , Sommerville , L and Kuske , C R . 2007 . Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum . Appl Environ Microbiol , 73 : 3113 – 3116 .
  • Barns , S M , Takala , S L and Kuske , C R . 1999 . Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment . Appl Environ Microbiol , 65 : 1731 – 1737 .
  • Battaglia-Brunet , F , Itard , Y , Garrido , F , Delorme , F , Crouzet , C , Greffie , C and Joulian , C . 2006 . A simple biogeochemical process removing arsenic from a mine drainage water . Geomicrobiol J , 23 : 201 – 211 .
  • Brouwers , G J , de Vrind , J PM , Corstjens , P LAM , Cornelis , P , Baysse , C and de Vrind-de Jong , E W . 1999 . cumA, a gene encoding a multicopper oxidase, is involved in Mn2 + oxidation in pseudomonas putida GB-1 . Appl Environ Microbiol , 65 : 1762 – 1768 .
  • Burns , R G and Burns , V M . 1975 . Mechanisms for nucleation and growth of manganese nodules . Nature , 255 : 130 – 131 .
  • Chow , M L , Radomski , C C , McDermott , J M , Davies , J and Axelrood , P E . 2002 . Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source . FEMS Microbiol Ecol , 42 : 347 – 357 .
  • Chapnick , S D , Moore , W S and Nealson , K H . 1982 . Microbially mediated manganese oxidation in a freshwater lake . Limnol Oceanogr , 27 : 1004 – 1014 .
  • Cole , J R , Chai , B , Farris , R J , Wang , Q , Kulam-Syed-Mohideen , A S , McGarrell , D M , Bandela , A M , Cardenas , E , Garrity , G M and Tiedje , J M . 2007 . The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data . Nucleic Acids Res , 35 : D169 – D172 . (Database issue)
  • Cowen , J P , Massoth , G J and Baker , E T . 1986 . Bacterial scavenging of Mn and Fe in a mid- to far-field hydrothermal particle plume . Nature , 322 : 169 – 171 .
  • Crecchio , C , Ruggiero , P , Curci , M , Colombo , C , Palumbo , G and Stotzky , G . 2005 . Binding of DNA from Bacillus subtilis on montmorillonite-humic acids-aluminum or iron hydroxypolymers: effects on transformation and protection against DNase . Soil Sci Soc Am J , 69 : 834 – 841 .
  • Dick , G J , Lee , Y E and Tebo , B M . 2006 . Manganese (II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes . Appl Environ Microbiol , 72 : 3184 – 3190 .
  • Douka , C . 1977 . Study of bacteria from manganese concretions . Soil Biol Biochem , 9 : 89 – 97 .
  • Francis , C A , Co , E M and Tebo , B M . 2001 . Enzymatic manganese (II) oxidation by a marine alpha-Proteobacterium . Appl Environ Microbiol , 67 : 4024 – 4029 .
  • Hall , T A . 1999 . BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT . Nucl Acids Symp Ser , 41 : 95 – 98 .
  • Harvey , J W and Fuller , C C . 1998 . Effect of enhanced manganese oxidation in the hyporheic zone on basin-scale geochemical mass balance . Water Resour Res , 34 : 623 – 636 .
  • He , J Z , Xu , Z H and Hughes , J . 2005 . Pre-lysis washing improves DNA extraction from a forest soil . Soil Biol Biochem , 37 : 2337 – 2341 .
  • He , J Z , Xu , Z H and Hughes , J . 2006 . Molecular bacterial diversity of a forest soil under residue management regimes in subtropical Australia . FEMS Microbiol Ecol , 55 : 38 – 47 .
  • Hedlund , B P , Gosink , J J and Staley , J T . 1997 . Verrucomicrobia div. nov., a new division of the Bacteria containing three new species of Prosthecobacter . Antonie Leeuwenkoek , 72 : 29 – 38 .
  • Hiraishi , A , Kishimoto , N , Kosako , Y , Wakao , N and Tano , T . 1995 . Phylogenetic position of the menaquinone-containing acidophilic chemo-organotroph Acidobacterium capsulatum . FEMS Microbiol Lett , 132 : 91 – 94 .
  • Hugenholtz , P , Goebel , B M and Pace , N R . 1998 . Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity . J Bacteriol , 180 : 4765 – 4774 .
  • Kay , J T , Conklin , M H , Fuller , C C and O'Day , P A . 2001 . Processes of nickel and cobalt uptake by a manganese oxide forming sediment in Pinal Creek, globe mining district, Arizona . Environ Sci Technol , 35 : 4719 – 4725 .
  • Khanna , M and Stotzky , G . 1992 . Transformation of Bacillus subtilis by DNA bound on montmorillonite and effect of DNase on the transforming ability of bound DNA . Appl Environ Microbiol , 58 : 1930 – 1939 .
  • Kim , H S , Pasten , P A , Gaillard , J F and Stair , P C . 2003 . Nanocrystalline todorokite-like manganese oxide produced by bacterial catalysis . J Am Chem Soc , 125 : 14284 – 14285 .
  • Kumar , S , Tamura , K and Nei , M . 2004 . MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment . Briefings Bioinfor , 5 : 150 – 163 .
  • Lane , D J . 1991 . “ 16S/23S rRNA sequencing ” . In Nucleic Acid Techniques in Bacterial Systematics , Edited by: Stackebrandt , E and Goodfellow , M . 115 – 175 . Chichester, , England : John Wiley & Sons .
  • Lin , L H , Hall , J , Onstott , T C , Gihring , T , Lollar , B S , Boice , E , Pratt , L , Lippmann-Pipke , J and Bellamy , R ES . 2006 . Planktonic microbial communities associated with fracture-derived groundwater in a deep gold mine of South Africa . Geomicrobiol J , 23 : 475 – 497 .
  • Liu , F , Colombo , C , Adamo , P , He , J Z and Violante , A . 2002 . Trace elements in manganese-iron nodules from a Chinese alfisol . Soil Sci Soc Am J , 66 : 661 – 670 .
  • Nazina , T N , Kosareva , I M , Davydov , A S , Turova , T P , Novikova , E V , Khafizov , R R and Poltaraus , A B . 2000 . Physico-chemical and microbiological characteristics of groundwater from observation boreholes of a deep radioactive liquid waste repository . Mikrobiologiia , 69 : 105 – 112 .
  • Nealson , K H , Tebo , B M and Rosson , R A . 1988 . Occurrence and mechanisms of microbial oxidation of manganese . Adv Appl Microbiol , 33 : 279 – 318 .
  • Northup , D E , Barns , S M , Yu , L E , Spilde , M N , Schelble , R T , Dano , K E , Crossey , L J , Connolly , C A , Boston , P J , Natvig , D O and Dahm , C N . 2003 . Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves . Environ Microbiol , 5 : 1071 – 1086 .
  • Okamoto , T , Maruyama , A , Imura , S , Takeyama , H and Naganuma , T . 2004 . Comparative phylogenetic analyses of Halomonas variabilis and related organisms based on sequences 16S rRNA, gyrB and ectBC gene sequences . Syst Appl Microbiol , 27 : 323 – 333 .
  • Pace , N R . 1997 . A molecular view of microbial diversity and the biosphere . Science , 276 : 734 – 740 .
  • 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 : 6037 – 6046 .
  • Selenska-Pobell , S , Kampf , G , Hemming , K , Radeva , G and Satchanska , G . 2001 . Bacterial diversity in soil samples from two uranium waste piles as determined by rep-APD, RISA and 16S rDNA retrieval . Anton Leeuw Int J G , 79 : 149 – 161 .
  • Spilde , M N , Northup , D E , Boston , P J , Schelble , R T , Dano , K E , Crossey , L J and Dahm , C N . 2005 . Geomicrobiology of cave ferromanganese deposits: A field and laboratory investigation . Geomicrobiol J , 22 : 99 – 116 .
  • Stein , L Y , La Duc , M T , Grundl , T J and Nealson , K H . 2001 . Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments . Environ Microbiol , 3 : 10 – 18 .
  • Stokstad , E . 2003 . Paleontology—Ancient DNA pulled from soil . Science , 300 : 407 – 407 .
  • Sullivan , L A and Koppi , A J . 1992 . Manganese oxide accumulations associated with some soil structural pores. I. Morphology, composition and genesis . Aust J Soil Res , 30 : 409 – 427 .
  • Tan , W F , Liu , F , Li , Y H , Hu , H Q and Huang , Q Y . 2006 . Elemental composition and geochemical characteristics of iron-manganese nodules in main soils of China . Pedosphere , 16 : 72 – 81 .
  • Tebo , B M and Emerson , S . 1985 . The effect of oxygen tension, Mn(II) concentration and temperature on the microbially catalyzed Mn(II) oxidation rate in a marine fjord . Appl Environ Microbiol , 50 : 1268 – 1273 .
  • Tebo , B M , Bargar , J R , Clement , B G , Dick , G J , Murray , K J , Parker , D , Verity , R and Webb , S M . 2004 . Biogenic manganese oxides: Properties and mechanisms of formation . Annu Rev Earth Pl Sc , 32 : 287 – 328 .
  • Tebo , B M , Ghiorse , W C , Waasbergen van , L G , Siering , P L and Caspi , R . 1997 . “ Bacterially-mediated mineral formation: Insights into manganese(II) oxidation from molecular genetic and biochemical studies ” . In Geomicrobiology: Interactions between Microbes and Minerals , Edited by: Banfield , J F and Nealson , K H . 225 – 266 . Washington, DC : Mineralogical Society of America .
  • Templeton , A S , Staudigel , H and Tebo , B M . 2005 . Diverse Mn(II)-oxidizing bacteria isolated from submarine basalts at Loihi Seamount . Geomicrobiol J , 22 : 127 – 139 .
  • van Cappellen , P , Viollier , E , Roychoudhury , A , Clark , L , Ingall , E , Lowe , K and Dichristina , T . 1998 . Biogeochemical cycles of manganese and iron at the oxic-anoxic transition of a stratified marine basin (Orca Basin, Gulf of Mexico) . Environ Sci Technol , 32 : 2931 – 2939 .
  • Weber , K A , Pollock , J , Cole , K A , O'connor , S M , Achenbach , L A and Coates , J D . 2006 . Anaerobic nitrate-dependent iron (II) bio-oxidation by a novel Lithoautotrophic Betaproteobacterium, Strain 2002 . Appl Environ Microbiol , 72 : 686 – 694 .
  • Wehrli , B , Friedl , G and Manceau , A . 1995 . Reaction rates and products of manganese oxidation at the sediment-water interface . Aquatic Chem , 244 : 111 – 134 .
  • Zhang , G X , Dong , H L , Xu , Z Q , Zhao , D G and Zhang , C L . 2005 . Microbial diversity in ultra-high-pressure rocks and fluids from the Chinese continental scientific drilling project in China . Appl Environ Microbiol , 71 : 3213 – 3227 .
  • Zhang , L M , Liu , F , Tan , W F , Feng , X H , Zhu , Y G and He , J Z . 2007 . Microbial DNA extraction and analyses of soil iron-manganese nodules . Soil Biol Biochem , doi:10.1016/j.soilbio.2007.01.004
  • Zimmermann , J , Gonzalez , J M , Saiz-Jimenez , C and Ludwig , W . 2005 . Detection and phylogenetic relationships of highly diverse uncultured acidobacterial communities in altamira cave using 23S rRNA sequence analyses . Geomicrobiol J , 22 : 379 – 388 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.