Borin S, Brusetti L, Daffonchio D, Delaney E, Baldi F: Biodiversity of prokaryotic communities in sediments of different sub-basins of the Venice lagoon. Research in Microbiology 2009, 160: 307–314. 10.1016/j.resmic.2009.04.005
Article
PubMed
Google Scholar
Bourne D, Lida Y, Uthicke S, Smith-Keune C: Changes in coral-associated microbial communities during a bleaching event. The ISME Journal 2008, 2: 350–363. 10.1038/ismej.2007.112
Article
CAS
PubMed
Google Scholar
Brazelton WJ, Brazelton WJ, Ludwig KA, Sogin ML, Andreishcheva EN, Kelley DS, Shen C, Edwards RL, Baross JA: Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys. Proc Natl Acad Sci USA 2010, 107: 1612–1617. 10.1073/pnas.0905369107
Article
CAS
PubMed Central
PubMed
Google Scholar
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P: Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology 2008, 6: 245–252. 10.1038/nrmicro1852
Article
CAS
PubMed
Google Scholar
Casamayor EO, Massana R, Benlloch S, Overeas L, Diez B, Goddard V, Gasol JM, Joint I, Rodríguez-Valera F, Pedrós-Alió C: Changes in archaeal, bacterial, and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern scaling plots. Appl Environ Microbiol 2002, 4: 338–348.
Google Scholar
Chakraborty S, Mukherji S, Mukherji S: Surface hydrophobicity of petroleum hydrocarbon degrading Burkholderia strains and their interactions with NAPLs and surfaces Colloids and Surfaces B. Biointerfaces 2010, 78: 101–108. 10.1016/j.colsurfb.2010.02.019
Article
CAS
PubMed
Google Scholar
Chao A: Non-parametric estimation of the number of classes in a population. Scand J Stat 1984, 11: 783–791.
Google Scholar
Chao AMC, Ma , Yang MCK: Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika 1993, 80: 193–201. 10.1093/biomet/80.1.193
Article
Google Scholar
Chien CC, Chen CC, Choi MH, Kung SS, Wei YH: Production of poly-hydroxybutyrate (PHB) by Vibrio spp. isolated from marine environment. Journal of Biotechnology 2007, 132: 259–263. 10.1016/j.jbiotec.2007.03.002
Article
CAS
PubMed
Google Scholar
Coleman NV, Bui NB, Holmes AJ: Soluble di-iron monooxygenase gene diversity in soils, sediments and ethane enrichments. Environmental Microbiology 2006, 8: 1228–1239. 10.1111/j.1462-2920.2006.01015.x
Article
CAS
PubMed
Google Scholar
Cooley RB, Dubbels BL, Sayavedra-Soto LA, Bottomley PJ, Arp DJ: Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans , formerly ' Pseudomonas butanovora' . Microbiology 2009, 155: 2086–2096. 10.1099/mic.0.028175-0
Article
CAS
PubMed Central
PubMed
Google Scholar
Davis JB, Updegraff DM: Microbiology in the Petroleum Industry. Magnolia Petroleum Company. Volume 18. Field Research Laboratories, Dallas, Texas; 215–238.
Dimitriu PA, Pinkart HC, Peyton BM, Mormile MR: Microbial diversity of a meromictic soda lake in Washington, USA: spatial and temporal. Applied and Environmental Microbiology 2008, 74: 4877–4888. 10.1128/AEM.00455-08
Article
CAS
PubMed Central
PubMed
Google Scholar
Ewing B, Hillier LD, Wendl MC, Green P: Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research 1998, 8: 175–185.
Article
CAS
PubMed
Google Scholar
Fierer N, Bradford MA, Jackson RB: Toward an Ecological Classification of Soil Bacteria. Ecology 2007, 88: 1354–136. 10.1890/05-1839
Article
PubMed
Google Scholar
Galand PE, Casamayor EO, Kirchman DL, Lovejoy C: Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci USA 2009, 106: 22427–22432. 10.1073/pnas.0908284106
Article
CAS
PubMed Central
PubMed
Google Scholar
Ginkel CG, Welten HGJ, De Bont JAM: Oxidation of Gaseous and Volatile Hydrocarbons by Selected Alkene-Utilizing Bacteria. Applied and Environmental Microbiology 1987, 53: 2903–2907.
PubMed Central
PubMed
Google Scholar
Gomez-Leon J, Villamil L, Lemos ML, Novoa B, Figueras A: Isolation of Vibrio alginolyticus and Vibrio splendidus from Aquacultured Carpet Shell Clam ( Ruditapes decussatus ) Larvae Associated with Mass Mortalities. Applied and Environmental Microbiology 2005, 71: 98–104. 10.1128/AEM.71.1.98-104.2005
Article
CAS
PubMed Central
PubMed
Google Scholar
Guan TW, Liu Y, Zhao K, Xia ZF, Zhang XP, Zhang LL: Actinopolyspora xinjiangensis sp. nov., a novel extremely halophilic actinomycete isolated from a salt lake in Xinjiang, China. Antonie van Leeuwenhoek 2010, 98: 447–453. 10.1007/s10482-010-9458-9
Article
CAS
PubMed
Google Scholar
Hartman M, Lee S, Hallam SJ, Mohn WW: Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands. Environmental Microbiology 2009, 11: 3045–3062. 10.1111/j.1462-2920.2009.02008.x
Article
Google Scholar
Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M: A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. PNAS 2007, 105: 2134–2139.
Article
Google Scholar
Hennessee CT, Seo JS, Alvarez AM, Li QX: Polycyclic aromatic hydrocarbon-degrading species isolated from Hawaiian soils: Mycobacterium crocinum sp. nov., Mycobacterium pallens sp. nov., Mycobacterium rutilum sp. nov., Mycobacterium rufum sp. nov. and Mycobacterium aromaticivorans sp. Nov Int J Syst Evol Microbiol 2009, 59: 378–387. 10.1099/ijs.0.65827-0
Article
CAS
PubMed
Google Scholar
Hitzman DC, Schumacher D, Clavareau L: Strategies for surface geochemical surveys in southeast Asia: Best practice designs and recent case studies. Proceedings, Indonesian Petroleum Association, Thirty-Third Annual Convention & Exhibition 2009.
Google Scholar
Holmes AJ, Coleman NV: Evolutionary ecology and multidisciplinary approaches to prospecting for monooxygenases as biocatalysts. Antonie van Leeuwenhoek 2008, 94: 75–84. 10.1007/s10482-008-9227-1
Article
CAS
PubMed
Google Scholar
Horvitz L: Geochemical Exploration for Petroleum. Science 1985, 229: 821–827. 10.1126/science.229.4716.821
Article
CAS
PubMed
Google Scholar
Janssen PH: Identifying the Dominant Soil Bacterial taxa in Libraries. of 16S rRNA and 16S rRNA Genes. Applied and Environmental Microbiology 2006, 72: 1719–1728. 10.1128/AEM.72.3.1719-1728.2006
Article
CAS
PubMed Central
PubMed
Google Scholar
Kao CM, Chen CS, Tsa FY, Yang KH, Chien CC, Liang SH, Yang C, Chen SC: Application of real-time PCR, DGGE fingerprinting, and culture-based method to evaluate the effectiveness of intrinsic bioremediation on the control of petroleum-hydrocarbon plume. Journal of Hazardous Materials 2010, 178: 409–416. 10.1016/j.jhazmat.2010.01.096
Article
CAS
PubMed
Google Scholar
Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 1980, 16: 111–20. 10.1007/BF01731581
Article
CAS
PubMed
Google Scholar
Kniemeyer O, Musat F, Sievert SM, Knittel K, Wilkes H, Blumenberg M, Michaelis W, Classen A, Bolm C, Joye SB, Widdel F: Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature 2007, 449: 898–901. 10.1038/nature06200
Article
CAS
PubMed
Google Scholar
Kotani T, Kawashima Y, Yurimoto H, Kato N, Sakai Y: Gene structure and regulation of alkane monooxygenases in propane-utilizing Mycobacterium sp. TY-6 and Pseudonocardia sp. TY-7. Journal of Bioscience and Bioengineering 2006, 102: 184–192. 10.1263/jbb.102.184
Article
CAS
PubMed
Google Scholar
Krause L, Diaz NN, Edwards RA, Gartemann KH, Krömeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A: Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas. Journal of Biotechnology 2008, 136: 91–101. 10.1016/j.jbiotec.2008.06.003
Article
CAS
PubMed
Google Scholar
Krober M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Millera D, Runte KJ, Viehöverc P, Pühlera A, Schlütera A: Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. Journal of Biotechnology 2009, 142: 38–49. 10.1016/j.jbiotec.2009.02.010
Article
PubMed
Google Scholar
Kudo Y, Nakajima T, Miyaki T, Oyazu H: Methanogen Flora of Paddy Soils in Japan. FEMS Microbiology Ecology 1997, 22: 39–48. 10.1111/j.1574-6941.1997.tb00354.x
Article
CAS
Google Scholar
Kumar S, Tamura K, Jakobsen IB, Nei M: MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 2001, 17: 1244–1245. 10.1093/bioinformatics/17.12.1244
Article
CAS
PubMed
Google Scholar
Lacoste A, Jalabert F, Malham SK, Cueff A, Poulet SA: Stress and Stress-Induced Neuroendocrine Changes Increase the Susceptibility of Juvenile Oysters ( Crassostrea gigas ) to Vibrio splendidus . Applied and Environmental Microbiology 2001, 2304–2309.
Google Scholar
Lane DJ: 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Edited by: Stackebrandt E, Goodfellow M. John Willey & Sons, Chinchester; 1991:115–175.
Google Scholar
Leahy JG, Batchelor PJ, Morcomb SM: Evolution of the soluble diiron monooxygenases. FEMS Microbiology Reviews 2003, 27: 449–479. 10.1016/S0168-6445(03)00023-8
Article
CAS
PubMed
Google Scholar
Li H, Yang SZ, Mu BZ, Rong ZF, Zhang J: Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield. FEMS Microbiology Ecology 2007, 60: 74–84. 10.1111/j.1574-6941.2006.00266.x
Article
CAS
PubMed
Google Scholar
Lovatini A, Myers K, Watterson P, Campbell T: An integrated approach to exploration data in the Potiguar basin, offshore Brazil. First Break 2010, 28: 55–59.
Google Scholar
Magurran AE: Measuring Biological Diversity. Blackwell Publishing, Oxford; 2004.
Google Scholar
Mendez MO, Neilson JW, Maier RM: Characterization of a Bacterial Community in an Abandoned Semiarid Lead-Zinc Mine Tailing Site. Applied and Environmental Microbiology 2008, 74: 3899–3907. 10.1128/AEM.02883-07
Article
CAS
PubMed Central
PubMed
Google Scholar
Pimentel-Elardo SM, Tiro LP, Grozdanov L, Hentschel U: Saccharopolyspora cebuensis sp. nov., a novel actinomycete isolated from a Philippine sponge (Porifera). International Journal of Systematic and Evolutionary Microbiology 2008, 58: 628–632. 10.1099/ijs.0.64971-0
Article
CAS
PubMed
Google Scholar
Pukall R, Gehrich-Schröter G, Lapidus A, Nolan M, Del Rio TG, Lucas S, Chen F, Tice H, Pitluck S, Cheng JF, Copeland A, Saunders E, Brettin T, Detter JC, Bruce D, Goodwin L, Pati A, Ivanova N, Mavromatis K, Ovchinnikova G, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Han C: Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T
). Standards in Genomic Sciences 2009, 1: 3. 10.4056/sigs.492
Article
PubMed Central
PubMed
Google Scholar
Qin S, Chen HH, Klenk HP, Kim CJ, Xu LH, Li WJ: Saccharopolyspora gloriosae sp. nov., an endophytic actinomycete isolated from the stem of Gloriosa superba L. Int J Syst Evol Microbiol 2010, 60: 1147–1151. 10.1099/ijs.0.015792-0
Article
CAS
PubMed
Google Scholar
Quaiser A, Ochsenreiter T, Lanz C, Schuster SC, Treusch AH, Eck J, Schleper C: Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Molecular Microbiology 2003, 50: 563–575. 10.1046/j.1365-2958.2003.03707.x
Article
CAS
PubMed
Google Scholar
Rasheed MA, Prasanna MV, Kumar TS, Patil DJ, Dayal AM: Geo-microbial prospecting method for hydrocarbon exploration in Vengannapalli Village, Cuddapah Basin, India. Current Science 2008, 95: 361–366.
CAS
Google Scholar
Schloss PD, Handelsman J: Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness. Applied and Environmental Microbiology 2005, 71: 1501–1506. 10.1128/AEM.71.3.1501-1506.2005
Article
CAS
PubMed Central
PubMed
Google Scholar
Schumacher D: Surface geochemical exploration for oil and gas: New life for an old technology. In Geo-Microbial Technologies. The Leading Edge; 2000:258–261.
Google Scholar
Shennan JL: Utilisation of C2-C4 gaseous hydrocarbons and isoprene by microorganisms. Journal of Chemical Technology and Biotechnology 2006, 81: 237–256. 10.1002/jctb.1388
Article
CAS
Google Scholar
Silva CC, Ederson CJ, Torres APR, Sousa MP, Santiago VMJ, Oliveira VM: Investigation of Bacterial Diversity in Membrane Bioreactor and Conventional Activated Sludge Processes from Petroleum Refineries Using Phylogenetic and Statistical Approaches. J Microbiol Biotechnol 2010, 20: 447–459.
CAS
PubMed
Google Scholar
Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ: Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 2006, 103: 12115–12120. 10.1073/pnas.0605127103
Article
CAS
PubMed Central
PubMed
Google Scholar
Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C: Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends in Microbiology 2010, 18: 331–340. 10.1016/j.tim.2010.06.003
Article
CAS
PubMed
Google Scholar
Suthindhiran K, Kannabiran K: Cytotoxic and Antimicrobial Potential of Actinomycete Species Saccharopolyspora salina VITSDK4 isolated from the Bay of Bengal Coast of India. American Journal of Infectious Diseases 2009, 5: 90–98.
Article
CAS
Google Scholar
Tang SK, Wang Y, Cai M, Zhi XY, Lou K, Xu LH, Jiang CL, Li WJ: Saccharopolyspora halophila sp. nov., a novel halophilic actinomycete isolated from a saline lake in China. Int J Syst Evol Microbiol 2009, 59: 555–558. 10.1099/ijs.0.65705-0
Article
CAS
PubMed
Google Scholar
Thomas SH, Wagner RD, Arakaki AK, Skolnick J, Kirby JR, Shimkets LJ, Sanford RA, Löffler FE: The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria. PLoS One 2008, 3: e2103. 10.1371/journal.pone.0002103
Article
PubMed Central
PubMed
Google Scholar
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 1997, 24: 4876–4882.
Article
Google Scholar
Tucker J, Hitzman D: Long-term and seasonal trends in the response of hydrocarbon-utilizing microbes to light hydrocarbon gases in shallow soils. In Hydrocarbon migration and its near-surface expression: AAPG Memoir Edited by: Schumacher D, Abrams MA. 1996, 66: 353–357.
Google Scholar
Venier P, Varotto L, Rosani U, Millino C, Celegato C, Bernante F, Lanfranchi G, Novoa B, Roch P, Figueras A, Pallavicini A: Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis . BMC Genomics 2011, 12: 69. 10.1186/1471-2164-12-69
Article
CAS
PubMed Central
PubMed
Google Scholar
Vomberg A, Klinner U: Distribution of alkB genes within n-alkane-degrading bacteria. Journal of Applied Microbiology 2000, 89: 339–348. 10.1046/j.1365-2672.2000.01121.x
Article
CAS
PubMed
Google Scholar
Wagner : Case Histories of Microbial Prospection for Oil and Gas, Onshore and offshore in Northwest Europe, in Surface exploration case histories: Applications of geochemistry, magnetics, and remote sensing. SEG Geophysical References Series 2002, 11: 453–479.
Google Scholar
Yassin AF: Saccharopolyspora rosea sp. nov., isolated from a patient with bronchial carcinoma. Int J Syst Evol Microbiol 2009, 59: 1148–1152. 10.1099/ijs.0.005249-0
Article
CAS
PubMed
Google Scholar
Yi H, Chun J: Nocardioides aestuarii sp. nov., isolated from tidal flat sediment. International Journal of Systematic and Evolutionary Microbiology 2004, 54: 2151–2154. 10.1099/ijs.0.63192-0
Article
CAS
PubMed
Google Scholar
Youssef N, Elshahed MS: Diversity rankings among bacterial lineages in soil. The ISME Journal 2009, 3: 305–313. 10.1038/ismej.2008.106
Article
CAS
PubMed
Google Scholar
Yuan LJ, Zhang YQ, Guan Y, Wei YZ, Li QP, Yu LY, Li WJ, Zhang YQ: Saccharopolyspora antimicrobica sp. nov., an actinomycete from soil. Int J Syst Evol Microbiol 2008, 58: 1180–1185. 10.1099/ijs.0.65532-0
Article
CAS
PubMed
Google Scholar
Zhang F, She Y, Zheng Y, Zhou Z, Kong S, Hou D: Molecular biologic techniques applied to the microbial prospecting of oil and gas in the Ban 876 gas and oil field in China. Applied Microbiology and Biotechnology 2010, 86: 1183–1194. 10.1007/s00253-009-2426-5
Article
CAS
PubMed
Google Scholar