Bacterial and Archaeal DNA Extracted from Inoculated Experiments: Implication for the Optimization of DNA Extraction from Deep-Sea Basalts

REFERENCES

• Biddle , J F , Lipp , J S , Lever , M , Lloyd , K , S⊘rensen , K , Anderson , R , Fredricks , H F , Elvert , M , Kelly , T J , Schrag , D P , Sogin , M L , Brenchley , J E , Teske , A , House , C H and Hinrichs , K-U . 2006 . Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru . Proc Natl Acad Sci USA , 103 : 3846 – 3851 .
   PubMed Web of Science ®Google Scholar
• Burgmann , H , Pesaro , M , Widmer , F and Zeyer , J . 2001 . A strategy for optimizing quality of DNA extracted from soil . J Microbiol Meth , 45 : 7 – 20 .
   PubMed Web of Science ®Google Scholar
• Cowen , J P , Giovannoni , S J , Kenig , F , Johnson , H P , Butterfield , D , Rappé , M S , Hutnak , M and Lam , P . 2003 . Fluids from aging ocean crust that support microbial life . Science , 299 : 120 – 123 .
   PubMed Web of Science ®Google Scholar
• DeLong , E F . 1992 . Archaea in coastal marine environments . Proc Natl Acad Sci USA , 89 : 5685 – 5689 .
   PubMed Web of Science ®Google Scholar
• Edwards , K J , Rogers , D R , Wirsen , C O and McCollom , T M . 2003 . Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic α - and γ -Proteobacteria from the deep sea . Appl Environ Microbiol. , 69 : 2906 – 2913 .
   PubMed Web of Science ®Google Scholar
• Fisk , M R , Giovannoni , S J and Thorseth , I H . 1998 . Alteration of volcanic glass: textural evidence of microbial activity . Science , 281 : 978 – 980 .
   PubMed Web of Science ®Google Scholar
• Frostegard , A , Courtois , S , Ramisse , V , Clerc , S , Bernillon , D , Le Gall , F , Jeannin , P , Nesme , X and Simonet , P . 1999 . Quantification of bias related to the extraction of DNA directly from soils . Appl Environ Microbiol , 65 : 5409 – 5420 .
   PubMed Web of Science ®Google Scholar
• Griffiths , R I , Whiteley , A S , O'Donnell , A G and Bailey , M J . 2000 . Rapid method for coextraction of DNA and RNA from natural environments for analysis of robosomal DNA- and rRNA-based microbial community composition . Appl Environ Microbiol , 66 : 5488 – 5491 .
   PubMed Web of Science ®Google Scholar
• He , Z , Wu , L , Li , X , Fields , M and Zhou , J . 2005 . Empirical establishment of oligonucleotide probe design criteria . Appl Environ Microbiol , 71 : 3753 – 3760 .
   PubMed Web of Science ®Google Scholar
• Herrera , A and Cockell , C S . 2007 . Exploring microbial diversity in volcanic environments: A review of methods in DNA extraction . J Microbiol Meth , 70 : 1 – 12 .
   PubMed Web of Science ®Google Scholar
• Hoshino , Y T and Matsumoto , N . 2004 . An improved DNA extraction method using skim milk from soils that strongly adsorb DNA . Microb Environ , 19 : 13 – 19 .
   Google Scholar
• Hoshino , Y T and Matsumoto , N . 2005 . Skim milk drastically improves the efficiency of DNA extraction from andisol, a volcanic soil . JPN Agr Res Quarterly , 39 : 247 – 252 .
   Google Scholar
• Huu , N B , Denner , E B , Ha , D T , Wanner , G and Stan-Lotter , H . 1999 . Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil-producing well . Intl J Syst Bacteriol , 49 : 367 – 375 .
   PubMedGoogle Scholar
• Inagaki , F , Nunoura , T , Nakagawa , S , Teske , A , Ever , 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 .
   PubMed Web of Science ®Google Scholar
• Karner , M B , DeLong , E F and Karl , D M . 2001 . Achaeal dominance in the mesopelagic zone of the Pacific Ocean . Nature , 409 : 507 – 510 .
   PubMed Web of Science ®Google Scholar
• Kuske , C R , Banton , K L , Adorada , D L , Stark , P C , Hill , K K and Jackson , P J . 1998 . Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil . Appl Environ Microbiol , 64 : 2463 – 2472 .
   PubMed Web of Science ®Google Scholar
• Lipp , J S , Morono , Y , Inagaki , F and Hinrichs , K-U . 2008 . Significant contribution of Archaea to extant biomass in marine subsurface sediments . Nature , 454 : 991 – 994 .
   PubMed Web of Science ®Google Scholar
• Lysnes , K , Thorseth , I H , Steinsbu , B O , Øreås , L , Torsvik , T and Pedersen , R B . 2004 . Microbial community diversity in seafloor basalt from the Arctic spreading ridges . FEMS Microbiol Ecol , 50 : 213 – 230 .
   PubMed Web of Science ®Google Scholar
• Mauclaire , L , Zepp , K , Meister , P and McKenzie , J . 2004 . Direct in situ detection of cells in deep-sea sediment cores from the Peru Margin (ODP Leg 201, Site 1229) . Geobiology , 2 : 217 – 223 .
   Web of Science ®Google Scholar
• Miller , D N , Bryant , J E , Madsen , E L and Ghiorse , W C . 1999 . Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples . Appl Environ Microbiol , 65 : 4715 – 4724 .
   PubMed Web of Science ®Google Scholar
• More , M I , Herrich , J B , Silva , M C , Ghiorse , W C and Madsen , E L . 1994 . Quantitative cell lysis of indifenous microorganisms and rapid extraction of microbial DNA from sediment . Appl Environ Microbiol , 60 : 1572 – 1580 .
   PubMed Web of Science ®Google Scholar
• Mumy , K L and Findlay , R H . 2004 . Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR . J Micro Meth , 57 : 259 – 268 .
   PubMed Web of Science ®Google Scholar
• Ogram , A V , Mathot , M L , Harsh , J B , Boyle , J and Pettigrew , C A . 1994 . Effects of DNA polymer length on its adsorption to soils . Appl Environ Microbiol , 60 : 393 – 396 .
   PubMed Web of Science ®Google Scholar
• Oren , A , Gurevich , P , Gemmell , R E and Teske , A . 1995 . Halobaculum gomorrense gen. nov., sp. nov., a novel extremely halophilic Archaeon from the Dead Sea . Int J Syst Bacteriol , 45 : 747 – 754 .
   PubMedGoogle Scholar
• Purdy , K J , Embley , T M , Takii , S and Nedwell , D B . 1996 . Rapid extraction of DNA and rRNA from sediments by a novel hydroxyapatite spin-column method . Appl Environ Microbiol , 62 : 3905 – 3907 .
   PubMed Web of Science ®Google Scholar
• Rochelle , P A , Cragg , B A , Fry , J C , Parkes , R J and Weightman , A J . 1994 . Effect of sample handling on estimation of bacterial diversity in marine sediments by 16S rDNA gene sequence analysis . FEMS Microbiol Ecol , 15 : 215 – 226 .
   Web of Science ®Google Scholar
• Santelle , C M , Orcutt , B N , Banning Bach , E W , Moyer , C L , Sogin , M L , Staudigel , H and Edwards , K J . 2008 . Abundance and diversity of microbial life in ocean crust . Nature , 453 : 653 – 656 .
   PubMedGoogle Scholar
• Schippers , A . 2005 . Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria . Nature , 433 : 861 – 864 .
   PubMed Web of Science ®Google Scholar
• Schwertmann , U and Cornell , R M . 2000 . Iron Oxides in the Laboratory: Preparation and Characterization , 103 – 112 . Hoboken, NJ : Wiley .
   Google Scholar
• Thoresth , I H , Torsvik , T , Torsvik , V , Daae , F L , Pedersen , R B and Kekdysh-98 Scientific Party . 2001 . Diversity of life in ocean floor basalt . Earth Planet Sci Lett , 194 : 31 – 37 .
   Google Scholar
• Tsai , Y L and Olson , B H . 1992 . Detection of low numbers of bacterial cells in soils and sediments by polymerase chain reaction . Appl Environ Microbiol , 61 : 754 – 757 .
   Google Scholar
• Volossiouk , T , Robb , E J and Zazar , R N . 1995 . Direct DNA extraction fro PCR-mediated assays of soil organisms . Appl Environ Microbiol , 61 : 3972 – 3976 .
   PubMed Web of Science ®Google Scholar
• Wikstrom , K P , Wiklund , A , Anderson , A and Forsman , M . 1996 . DNA recovery and PCR quantification of catechol 2,3-dioxygenase genes from different soil types . J Biotechnol , 52 : 107 – 120 .
   PubMed Web of Science ®Google Scholar
• Zhou , J , Bruns , M A and Tiedje , J M . 1996 . DNA recovery from soils of diverse composition . J Biotechnol , 62 : 316 – 322 .
   Google Scholar