The upper parts of oil field structures may leak gas which is supposed to be indirectly detected by the soil bacterial populations. Such microorganisms are capable of consuming this gas, supporting the Microbial Prospection of Oil and Gas (MPOG) methodology. The goal of the present work was to characterize microbial communities involved in short-chain alkane metabolism, namely methane, ethane and propane, in samples from a petroliferous (P) soil through clone libraries of the 16S rRNA gene of the Domains Bacteria and Archaea and the catabolic gene coding for the soluble di-iron monooxygenase (SDIMO) enzyme alpha subunit. The microbial community presented high abundance of the bacterial phylum Actinobacteria, which represented 53% of total clones, and the Crenarchaeota group I.1b from the Archaea Domain. The analysis of the catabolic genes revealed the occurrence of seven Operational Protein Families (OPF) and higher richness (Chao = 7; Ace = 7.5) and diversity (Shannon = 1.09) in P soil when compared with a non-petroliferous (Np) soil (Chao = 2; Ace = 0, Shannon = 0.44). Clones related to the ethene monooxygenase (EtnC) and methane monooxygenase (MmoX) coding genes occurred only in P soil, which also presented higher levels of methane and lower levels of ethane and propane, revealed by short-chain hydrocarbon measures. Real-time PCR results suggested that the SDIMO genes occur in very low abundance in the soil samples under study. Further investigations on SDIMOs genes in natural environments are necessary to unravel their still uncharted diversity and to provide reliable tools for the prospection of degrading populations. © 2011 Miqueletto et al.11116Borin, S., Brusetti, L., Daffonchio, D., Delaney, E., Baldi, F., Biodiversity of prokaryotic communities in sediments of different sub-basins of the Venice lagoon (2009) Research In Microbiology, 160, pp. 307-314. , doi:10.1016/j.resmic.2009.04.005Bourne, D., Lida, Y., Uthicke, S., Smith-Keune, C., Changes in coral-associated microbial communities during a bleaching event (2008) The ISME Journal, 2, pp. 350-363. , doi:10.1038/ismej.2007.112Brazelton, W.J., Brazelton, W.J., Ludwig, K.A., Sogin, M.L., Andreishcheva, E.N., Kelley, D.S., Shen, C., Baross, J.A., Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys (2010) Proc Natl Acad Sci USA, 107, pp. 1612-1617. , doi:10.1073/pnas.0905369107Brochier-Armanet, C., Boussau, B., Gribaldo, S., Forterre, P., Mesophilic crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota (2008) Nature Reviews Microbiology, 6, pp. 245-252. , doi:10.1038/nrmicro1852Casamayor, E.O., Massana, R., Benlloch, S., Overeas, L., Diez, B., Goddard, V., Gasol, J.M., 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 (2002) Appl Environ Microbiol, 4, pp. 338-348Chakraborty, S., Mukherji, S., Mukherji, S., Surface hydrophobicity of petroleum hydrocarbon degrading Burkholderia strains and their interactions with NAPLs and surfaces Colloids and Surfaces B (2010) Biointerfaces, 78, pp. 101-108. , doi:10.1016/j.colsurfb.2010.02.019Chao, A., Non-parametric estimation of the number of classes in a population (1984) Scand J Stat, 11, pp. 783-791Chao, A.M.C., Ma, Yang, M.C.K., Stopping rules and estimation for recapture debugging with unequal failure rates (1993) Biometrika, 80, pp. 193-201. , doi:10.1093/biomet/80.1.193Chien, C.C., Chen, C.C., Choi, M.H., Kung, S.S., Wei, Y.H., Production of polyhydroxybutyrate (PHB) by Vibrio spp. isolated from marine environment (2007) Journal of Biotechnology, 132, pp. 259-263. , doi:10.1016/j.jbiotec.2007.03.002Coleman, N.V., Bui, N.B., Holmes, A.J., Soluble di-iron monooxygenase gene diversity in soils, sediments and ethane enrichments (2006) Environmental Microbiology, 8, pp. 1228-1239. , doi:10.1111/j.1462-2920.2006.01015.xCooley, R.B., Dubbels, B.L., Sayavedra-Soto, L.A., Bottomley, P.J., Arp, D.J., Kinetic characterization of the soluble butane monooxygenase from Thauera butanivorans, formerly 'Pseudomonas butanovora' (2009) Microbiology, 155, pp. 2086-2096. , doi:10.1099/mic.0.028175-0Davis, J.B., Updegraff, D.M., Microbiology in the Petroleum Industry Magnolia Petroleum Company. Field Research Laboratories, Dallas, Texas, 18, pp. 215-238Dimitriu, P.A., Pinkart, H.C., Peyton, B.M., Mormile, M.R., Microbial diversity of a meromictic soda lake in Washington, USA: Spatial and temporal (2008) Applied and Environmental Microbiology, 74, pp. 4877-4888. , doi:10.1128/AEM.00455-08Ewing, B., Hillier, L.D., Wendl, M.C., Green, P., Basecalling of automated sequencer traces using phred. I. Accuracy assessment (1998) Genome Research, 8, pp. 175-185Fierer, N., Bradford, M.A., Jackson, R.B., Toward an Ecological Classification of Soil Bacteria (2007) Ecology, 88, pp. 1354-2136. , doi:10.1890/05-1839Galand, P.E., Casamayor, E.O., Kirchman, D.L., Lovejoy, C., Ecology of the rare microbial biosphere of the Arctic Ocean (2009) Proc Natl Acad Sci USA, 106, pp. 22427-22432. , doi:10.1073/pnas.0908284106Ginkel, C.G., Welten, H.G.J., de Bont, J.A.M., Oxidation of Gaseous and Volatile Hydrocarbons by Selected Alkene-Utilizing Bacteria (1987) Applied and Environmental Microbiology, 53, pp. 2903-2907Gomez-Leon, J., Villamil, L., Lemos, M.L., Novoa, B., Figueras, A., Isolation of Vibrio alginolyticus and Vibrio splendidus from Aquacultured Carpet Shell Clam (Ruditapes decussatus) Larvae Associated with Mass Mortalities (2005) Applied and Environmental Microbiology, 71, pp. 98-104. , doi:10.1128/AEM.71.1.98-104.2005Guan, T.W., Liu, Y., Zhao, K., Xia, Z.F., Zhang, X.P., Zhang, L.L., Actinopolyspora xinjiangensis sp. nov., a novel extremely halophilic actinomycete isolated from a salt lake in Xinjiang, China (2010) Antonie Van Leeuwenhoek, 98, pp. 447-453. , doi:10.1007/s10482-010-9458-9Hartman, M., Lee, S., Hallam, S.J., Mohn, W.W., Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands (2009) Environmental Microbiology, 11, pp. 3045-3062. , doi:10.1111/j.1462-2920.2009.02008.xHatzenpichler, R., Lebedeva, E.V., Spieck, E., Stoecker, K., Richter, A., Daims, H., Wagner, M., A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring (2007) PNAS, 105, pp. 2134-2139Hennessee, C.T., Seo, J.S., Alvarez, A.M., Li, Q.X., 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 (2009) Nov Int J Syst Evol Microbiol, 59, pp. 378-387. , doi:10.1099/ijs.0.65827-0Hitzman, D.C., Schumacher, D., Clavareau, L., Strategies for surface geochemical surveys in southeast Asia: Best practice designs and recent case studies (2009) Proceedings, Indonesian Petroleum Association, Thirty-Third Annual Convention & ExhibitionHolmes, A.J., Coleman, N.V., Evolutionary ecology and multidisciplinary approaches to prospecting for monooxygenases as biocatalysts (2008) Antonie Van Leeuwenhoek, 94, pp. 75-84. , doi:10.1007/s10482-008-9227-1Horvitz, L., Geochemical Exploration for Petroleum (1985) Science, 229, pp. 821-827. , doi:10.1126/science.229.4716.821Janssen, P.H., Identifying the Dominant Soil Bacterial taxa in Libraries. of 16S rRNA and 16S rRNA Genes (2006) Applied and Environmental Microbiology, 72, pp. 1719-1728. , doi:10.1128/AEM.72.3.1719-1728.2006Kao, C.M., Chen, C.S., Tsa, F.Y., Yang, K.H., Chien, C.C., Liang, S.H., Yang, C., Chen, S.C., 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 (2010) Journal of Hazardous Materials, 178, pp. 409-416. , doi:10.1016/j.jhazmat.2010.01.096Kimura, M., A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences (1980) Journal of Molecular Evolution, 16, pp. 111-120. , doi:10.1007/BF01731581Kniemeyer, O., Musat, F., Sievert, S.M., Knittel, K., Wilkes, H., Blumenberg, M., Michaelis, W., Widdel, F., Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria (2007) Nature, 449, pp. 898-901. , doi:10.1038/nature06200Kotani, 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 (2006) Journal of Bioscience and Bioengineering, 102, pp. 184-192. , doi:10.1263/jbb.102.184Krause, L., Diaz, N.N., Edwards, R.A., Gartemann, K.H., Krömeke, H., Neuweger, H., Pühler, A., Goesmann, A., Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas (2008) Journal of Biotechnology, 136, pp. 91-101. , doi:10.1016/j.jbiotec.2008.06.003Krober, M., Bekel, T., Diaz, N.N., Goesmann, A., Jaenicke, S., Krause, L., Millera, D., Schlütera, A., Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing (2009) Journal of Biotechnology, 142, pp. 38-49. , doi:10.1016/j.jbiotec.2009.02.010Kudo, Y., Nakajima, T., Miyaki, T., Oyazu, H., Methanogen Flora of Paddy Soils in Japan (1997) FEMS Microbiology Ecology, 22, pp. 39-48. , doi:10.1111/j.1574-6941.1997.tb00354.xKumar, S., Tamura, K., Jakobsen, I.B., Nei, M., MEGA2: Molecular Evolutionary Genetics Analysis software (2001) Bioinformatics, 17, pp. 1244-1245. , doi:10.1093/bioinformatics/17.12.1244Lacoste, A., Jalabert, F., Malham, S.K., Cueff, A., Poulet, S.A., Stress and Stress-Induced Neuroendocrine Changes Increase the Susceptibility of Juvenile Oysters (Crassostrea gigas) to Vibrio splendidus (2001) Applied and Environmental Microbiology, pp. 2304-2309Lane, D.J., 16S/23S rRNA sequencing (1991) Nucleic Acid Techniques In Bacterial Systematics, pp. 115-175. , Stackebrandt E, Goodfellow M (ed), John Willey & Sons, ChinchesterLeahy, J.G., Batchelor, P.J., Morcomb, S.M., Evolution of the soluble diiron monooxygenases (2003) FEMS Microbiology Reviews, 27, pp. 449-479. , doi:10.1016/S0168-6445(03)00023-8Li, H., Yang, S.Z., Mu, B.Z., Rong, Z.F., Zhang, J., Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield (2007) FEMS Microbiology Ecology, 60, pp. 74-84. , doi:10.1111/j.1574-6941.2006.00266.xLovatini, A., Myers, K., Watterson, P., Campbell, T., An integrated approach to exploration data in the Potiguar basin, offshore Brazil (2010) First Break, 28, pp. 55-59Magurran, A.E., (2004) Measuring Biological Diversity, , Blackwell Publishing, OxfordMendez, M.O., Neilson, J.W., Maier, R.M., Characterization of a Bacterial Community in an Abandoned Semiarid Lead-Zinc Mine Tailing Site (2008) Applied and Environmental Microbiology, 74, pp. 3899-3907. , doi:10.1128/AEM.02883-07Pimentel-Elardo, S.M., Tiro, L.P., Grozdanov, L., Hentschel, U., Saccharopolyspora cebuensis sp. nov., a novel actinomycete isolated from a Philippine sponge (Porifera) (2008) International Journal of Systematic and Evolutionary Microbiology, 58, pp. 628-632. , doi:10.1099/ijs.0.64971-0Pukall, R., Gehrich-Schröter, G., Lapidus, A., Nolan, M., Del Rio, T.G., Lucas, S., Chen, F., Han, C., Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134T) (2009) Standards In Genomic Sciences, 1, p. 3. , doi:10.4056/sigs.492Qin, S., Chen, H.H., Klenk, H.P., Kim, C.J., Xu, L.H., Li, W.J., Saccharopolyspora gloriosae sp. nov., an endophytic actinomycete isolated from the stem of Gloriosa superba L (2010) Int J Syst Evol Microbiol, 60, pp. 1147-1151. , doi:10.1099/ijs.0.015792-0Quaiser, A., Ochsenreiter, T., Lanz, C., Schuster, S.C., Treusch, A.H., Eck, J., Schleper, C., Acidobacteria form a coherent but highly diverse group within the bacterial domain: Evidence from environmental genomics (2003) Molecular Microbiology, 50, pp. 563-575. , doi:10.1046/j.1365-2958.2003.03707.xRasheed, M.A., Prasanna, M.V., Kumar, T.S., Patil, D.J., Dayal, A.M., Geo-microbial prospecting method for hydrocarbon exploration in Vengannapalli Village, Cuddapah Basin, India (2008) Current Science, 95, pp. 361-366Schloss, P.D., Handelsman, J., Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness (2005) Applied and Environmental Microbiology, 71, pp. 1501-1506. , doi:10.1128/AEM.71.3.1501-1506.2005Schumacher, D., Surface geochemical exploration for oil and gas: New life for an old technology. Geo-Microbial Technologies (2000) The Leading Edge, pp. 258-261Shennan, J.L., Utilisation of C2-C4 gaseous hydrocarbons and isoprene by microorganisms (2006) Journal of Chemical Technology and Biotechnology, 81, pp. 237-256. , doi:10.1002/jctb.1388Silva, C.C., Ederson, C.J., Torres, A.P.R., Sousa, M.P., Santiago, V.M.J., Oliveira, V.M., Investigation of Bacterial Diversity in Membrane Bioreactor and Conventional Activated Sludge Processes from Petroleum Refineries Using Phylogenetic and Statistical Approaches (2010) J Microbiol Biotechnol, 20, pp. 447-459Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., Arrieta, J.M., Herndl, G.J., Microbial diversity in the deep sea and the underexplored "rare biosphere" (2006) Proc Natl Acad Sci USA, 103, pp. 12115-12120. , doi:10.1073/pnas.0605127103Spang, A., Hatzenpichler, R., Brochier-Armanet, C., Rattei, T., Tischler, P., Spieck, E., Streit, W., Schleper, C., Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota (2010) Trends In Microbiology, 18, pp. 331-340. , doi:10.1016/j.tim.2010.06.003Suthindhiran, K., Kannabiran, K., Cytotoxic and Antimicrobial Potential of Actinomycete Species Saccharopolyspora salina VITSDK4 isolated from the Bay of Bengal Coast of India (2009) American Journal of Infectious Diseases, 5, pp. 90-98Tang, S.K., Wang, Y., Cai, M., Zhi, X.Y., Lou, K., Xu, L.H., Jiang, C.L., Li, W.J., Saccharopolyspora halophila sp. nov., a novel halophilic actinomycete isolated from a saline lake in China (2009) Int J Syst Evol Microbiol, 59, pp. 555-558. , doi:10.1099/ijs.0.65705-0Thomas, S.H., Wagner, R.D., Arakaki, A.K., Skolnick, J., Kirby, J.R., Shimkets, L.J., Sanford, R.A., Löffler, F.E., The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the deltaproteobacteria (2008) PLoS One, 3, pp. e2103. , doi:10.1371/journal.pone.0002103Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools (1997) Nucleic Acids Research, 24, pp. 4876-4882Tucker, J., Hitzman, D., Long-term and seasonal trends in the response of hydrocarbon-utilizing microbes to light hydrocarbon gases in shallow soils (1996) Hydrocarbon Migration and Its Nearsurface Expression: AAPG Memoir, 66, pp. 353-357. , Schumacher D, Abrams MA (ed)Venier, P., Varotto, L., Rosani, U., Millino, C., Celegato, C., Bernante, F., Lanfranchi, G., Pallavicini, A., Insights into the innate immunity of the Mediterranean mussel Mytilus galloprovincialis (2011) BMC Genomics, 12, p. 69. , doi:10.1186/1471-2164-12-69Vomberg, A., Klinner, U., Distribution of alkB genes within n-alkanedegrading bacteria (2000) Journal of Applied Microbiology, 89, pp. 339-348. , doi:10.1046/j.1365-2672.2000.01121.xWagner, Case Histories of Microbial Prospection for Oil and Gas, Onshore and offshore in Northwest Europe (2002) Surface Exploration Case Histories: Applications of Geochemistry, Magnetics, and Remote Sensing. SEG Geophysical References Series, 11, pp. 453-479Yassin, A.F., Saccharopolyspora rosea sp. nov., isolated from a patient with bronchial carcinoma (2009) Int J Syst Evol Microbiol, 59, pp. 1148-1152. , doi:10.1099/ijs.0.005249-0Yi, H., Chun, J., Nocardioides aestuarii sp. nov., isolated from tidal flat sediment (2004) International Journal of Systematic and Evolutionary Microbiology, 54, pp. 2151-2154. , doi:10.1099/ijs.0.63192-0Youssef, N., Elshahed, M.S., Diversity rankings among bacterial lineages in soil (2009) The ISME Journal, 3, pp. 305-313. , doi:10.1038/ismej.2008.106Yuan, L.J., Zhang, Y.Q., Guan, Y., Wei, Y.Z., Li, Q.P., Yu, L.Y., Li, W.J., Zhang, Y.Q., Saccharopolyspora antimicrobica sp. nov., an actinomycete from soil (2008) Int J Syst Evol Microbiol, 58, pp. 1180-1185. , doi:10.1099/ijs.0.65532-0Zhang, 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 (2010) Applied Microbiology and Biotechnology, 86, pp. 1183-1194. , doi:10.1007/s00253-009-2426-5