Bacterial diversity in the active stage of a bioremediation system for mineral oil hydrocarbon-contaminated soils.

Soils contaminated with mineral oil hydrocarbons are often cleaned in off-site bioremediation systems. In order to find out which bacteria are active during the degradation phase in such systems, the diversity of the active microflora in a degrading soil remediation system was investigated by small-subunit (SSU) rRNA analysis. Two sequential RNA extracts from one soil sample were generated by a procedure incorporating bead beating. Both extracts were analysed separately by generating individual SSU rDNA clone libraries from cDNA of the two extracts. The sequencing results showed moderate diversity. The two clone libraries were dominated by Gammaproteobacteria, especially Pseudomonas spp. Alphaproteobacteria and Betaproteobacteria were two other large groups in the clone libraries. Actinobacteria, Firmicutes, Bacteroidetes and Epsilonproteobacteria were detected in lower numbers. The obtained sequences were predominantly related to genera for which cultivated representatives have been described, but were often clustered together in the phylogenetic tree, and the sequences that were most similar were originally obtained from soils and not from pure cultures. Most of the dominant genera in the clone libraries, e.g. Pseudomonas, Acinetobacter, Sphingomonas, Acidovorax and Thiobacillus, had already been detected in (mineral oil hydrocarbon) contaminated environmental samples. The occurrence of the genera Zymomonas and Rhodoferax was novel in mineral oil hydrocarbon-contaminated soil.

[1]  J. Handelsman,et al.  Introducing TreeClimber, a Test To Compare Microbial Community Structures , 2006, Applied and Environmental Microbiology.

[2]  G. La Rosa,et al.  Genetic diversity of bacterial strains isolated from soils, contaminated with polycyclic aromatic hydrocarbons, by 16S rRNA gene sequencing and amplified fragment length polymorphism fingerprinting. , 2006, Microbiological research.

[3]  S. Heiss-Blanquet,et al.  Assessing the role of alkane hydroxylase genotypes in environmental samples by competitive PCR , 2005, Journal of applied microbiology.

[4]  K. Timmis,et al.  Natural microbial diversity in superficial sediments of Milazzo Harbor (Sicily) and community successions during microcosm enrichment with various hydrocarbons. , 2005, Environmental microbiology.

[5]  K. Timmis,et al.  Effects of long-term benzene pollution on bacterial diversity and community structure in groundwater. , 2005, Environmental microbiology.

[6]  J. Aislabie,et al.  Hydrocarbon contamination changes the bacterial diversity of soil from around Scott Base, Antarctica. , 2005, FEMS microbiology ecology.

[7]  G. Dieckmann,et al.  Influence of crude oil on changes of bacterial communities in Arctic sea-ice. , 2005, FEMS microbiology ecology.

[8]  J. Handelsman,et al.  Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness , 2005, Applied and Environmental Microbiology.

[9]  M. Mau,et al.  Two unusual chlorocatechol catabolic gene clusters in Sphingomonas sp. TFD44 , 2005, Archives of Microbiology.

[10]  Laurent Excoffier,et al.  Arlequin (version 3.0): An integrated software package for population genetics data analysis , 2005, Evolutionary bioinformatics online.

[11]  Robert K. Colwell,et al.  A new statistical approach for assessing similarity of species composition with incidence and abundance data , 2004 .

[12]  G. Zylstra,et al.  Hydrocarboniphaga effusa gen. nov., sp. nov., a novel member of the gamma-Proteobacteria active in alkane and aromatic hydrocarbon degradation. , 2004, International journal of systematic and evolutionary microbiology.

[13]  W. Verstraete,et al.  Occurrence and Phylogenetic Diversity of Sphingomonas Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons , 2004, Applied and Environmental Microbiology.

[14]  K. Schleifer,et al.  ARB: a software environment for sequence data. , 2004, Nucleic acids research.

[15]  C. Kaplan,et al.  Bacterial Succession in a Petroleum Land Treatment Unit , 2004, Applied and Environmental Microbiology.

[16]  S. Hsu,et al.  Response of the soil bacterial community to the addition of toluene and toluene-degrading bacteria , 2004 .

[17]  S. Kjelleberg,et al.  Influence of petroleum contamination and biostimulation treatment on the diversity of Pseudomonas spp. in soil microcosms as evaluated by 16S rRNA based‐PCR and DGGE , 2004, Letters in applied microbiology.

[18]  T. W. Jeffries,et al.  Bacteria engineered for fuel ethanol production: current status , 2003, Applied Microbiology and Biotechnology.

[19]  H. Aldrich,et al.  Alkanindiges illinoisensis gen. nov., sp. nov., an obligately hydrocarbonoclastic, aerobic squalane-degrading bacterium isolated from oilfield soils. , 2003, International journal of systematic and evolutionary microbiology.

[20]  C. Litchfield,et al.  A comparison of DNA profiling techniques for monitoring nutrient impact on microbial community composition during bioremediation of petroleum-contaminated soils. , 2003, Journal of microbiological methods.

[21]  K. Witzel,et al.  Wide Geographic Distribution of Bacteriophages That Lyse the Same Indigenous Freshwater Isolate (Sphingomonas sp. Strain B18) , 2003, Applied and Environmental Microbiology.

[22]  J. Baross,et al.  Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption. , 2003, FEMS microbiology ecology.

[23]  M. Eriksson,et al.  Degradation of Polycyclic Aromatic Hydrocarbons at Low Temperature under Aerobic and Nitrate-Reducing Conditions in Enrichment Cultures from Northern Soils , 2003, Applied and Environmental Microbiology.

[24]  Kazuya Watanabe,et al.  Isolation and Characterization of a Sulfur-Oxidizing Chemolithotroph Growing on Crude Oil under Anaerobic Conditions , 2003, Applied and Environmental Microbiology.

[25]  T. Reichenauer,et al.  Bacterial rhizosphere populations of black poplar and herbal plants to be used for phytoremediation of diesel fuel , 2002 .

[26]  Kazuya Watanabe,et al.  Diversity and abundance of bacteria in an underground oil-storage cavity , 2002, BMC Microbiology.

[27]  Andrew P. Martin.  Phylogenetic Approaches for Describing and Comparing the Diversity of Microbial Communities , 2002, Applied and Environmental Microbiology.

[28]  E. Madsen,et al.  Diversity of 16S rDNA and Naphthalene Dioxygenase Genes from Coal-Tar-Waste-Contaminated Aquifer Waters , 2002, Microbial Ecology.

[29]  A. Konopka,et al.  Analyses of microbial activity in biomass-recycle reactors using denaturing gradient gel electrophoresis of 16S rDNA and 16S rRNA PCR products. , 2002, Canadian journal of microbiology.

[30]  W. Whitman,et al.  Molecular and Culture-Based Analyses of Prokaryotic Communities from an Agricultural Soil and the Burrows and Casts of the Earthworm Lumbricus rubellus , 2002, Applied and Environmental Microbiology.

[31]  T. Kudo,et al.  Isolation and Characterization of Dibenzofuran-degrading Actinomycetes: Analysis of Multiple Extradiol Dioxygenase Genes in Dibenzofuran-degrading Rhodococcus Species , 2002, Bioscience, biotechnology, and biochemistry.

[32]  J. Fry,et al.  New Degenerate Cytophaga-Flexibacter-Bacteroides-Specific 16S Ribosomal DNA-Targeted Oligonucleotide Probes Reveal High Bacterial Diversity in River Taff Epilithon , 2002, Applied and Environmental Microbiology.

[33]  L. Ranjard,et al.  Quantitative and qualitative microscale distribution of bacteria in soil. , 2001, Research in microbiology.

[34]  W. Wade,et al.  Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov. , 2001, International journal of systematic and evolutionary microbiology.

[35]  Wolfgang Eder,et al.  Microbial Diversity of the Brine-Seawater Interface of the Kebrit Deep, Red Sea, Studied via 16S rRNA Gene Sequences and Cultivation Methods , 2001, Applied and Environmental Microbiology.

[36]  F. Dewhirst,et al.  Bacterial Diversity in Human Subgingival Plaque , 2001, Journal of bacteriology.

[37]  R. Samson,et al.  Clogging of a limestone fracture by stimulating groundwater microbes. , 2001, Water research.

[38]  Kazuya Watanabe,et al.  Microorganisms relevant to bioremediation. , 2001, Current opinion in biotechnology.

[39]  L. Young,et al.  Unusual bacterioplankton community structure in ultra‐oligotrophic Crater Lake , 2001 .

[40]  J. P. Del’Arco,et al.  Influence of oil contamination levels on hydrocarbon biodegradation in sandy sediment. , 2001, Environmental pollution.

[41]  E. Smit,et al.  Diversity and Seasonal Fluctuations of the Dominant Members of the Bacterial Soil Community in a Wheat Field as Determined by Cultivation and Molecular Methods , 2001, Applied and Environmental Microbiology.

[42]  H. Bürgmann,et al.  A strategy for optimizing quality and quantity of DNA extracted from soil. , 2001, Journal of microbiological methods.

[43]  B. Lal,et al.  Evaluation of Inoculum Addition To Stimulate In Situ Bioremediation of Oily-Sludge-Contaminated Soil , 2001, Applied and Environmental Microbiology.

[44]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[45]  Zhongtang Yu,et al.  Apparent Contradiction: Psychrotolerant Bacteria from Hydrocarbon-Contaminated Arctic Tundra Soils That Degrade Diterpenoids Synthesized by Trees , 2000, Applied and Environmental Microbiology.

[46]  Gerrit Voordouw,et al.  Composition of Soil Microbial Communities Enriched on a Mixture of Aromatic Hydrocarbons , 2000, Applied and Environmental Microbiology.

[47]  Rudolf Amann,et al.  Comparative 16S rRNA Analysis of Lake Bacterioplankton Reveals Globally Distributed Phylogenetic Clusters Including an Abundant Group of Actinobacteria , 2000, Applied and Environmental Microbiology.

[48]  Trevor C. Charles,et al.  Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities. , 2000, FEMS microbiology ecology.

[49]  U. Klinner,et al.  Distribution of alkB genes within n‐alkane‐degrading bacteria , 2000, Journal of applied microbiology.

[50]  D. M. Ward,et al.  Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Molecular Analysis of Enrichments and Isolates Suggests Selection Based on Bioavailability , 2000, Applied and Environmental Microbiology.

[51]  D. M. Ward,et al.  Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Different Enrichment Conditions Influence Bioavailability and Selection of Phenanthrene-Degrading Isolates , 2000, Applied and Environmental Microbiology.

[52]  W. Liesack,et al.  Spatial Changes in the Bacterial Community Structure along a Vertical Oxygen Gradient in Flooded Paddy Soil Cores , 2000, Applied and Environmental Microbiology.

[53]  M. Aragno,et al.  Phylogenetic diversity of bacterial communities differing in degree of proximity of Lolium perenne and Trifolium repens roots , 1999 .

[54]  A. Felske,et al.  Searching for predominant soil bacteria: 16S rDNA cloning versus strain cultivation. , 1999, FEMS microbiology ecology.

[55]  K. Timmis,et al.  Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. , 1999, Environmental microbiology.

[56]  C. Kuske,et al.  Phylogeny, ribosomal RNA gene typing and relative abundance of new Pseudomonas species (sensu stricto) isolated from two pinyon-juniper woodland soils of the arid southwest U.S. , 1999, Systematic and applied microbiology.

[57]  J. Prosser,et al.  Molecular Analysis of Bacterial Community Structure and Diversity in Unimproved and Improved Upland Grass Pastures , 1999, Applied and Environmental Microbiology.

[58]  J. Puhakka,et al.  Diversity of chlorophenol-degrading bacteria isolated from contaminated boreal groundwater , 1999, Archives of Microbiology.

[59]  W. Hillen,et al.  Expression of Alkane Hydroxylase fromAcinetobacter sp. Strain ADP1 Is Induced by a Broad Range of n- Alkanes and Requires the Transcriptional Activator AlkR , 1998, Journal of bacteriology.

[60]  Philip Hugenholtz,et al.  Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity , 1998, Journal of bacteriology.

[61]  S. Macnaughton,et al.  Microbial Population Changes during Bioremediation of an Experimental Oil Spill , 1998, Applied and Environmental Microbiology.

[62]  W. Rulkens,et al.  Microbiological aspects of surfactant use for biological soil remediation , 1997, Biodegradation.

[63]  M. Bouchez,et al.  Kinetic studies of biodegradation of insoluble compounds by continuous determination of oxygen consumption , 1997, Journal of applied microbiology.

[64]  M. Forsman,et al.  DNA recovery and PCR quantification of catechol 2,3-dioxygenase genes from different soil types. , 1996, Journal of biotechnology.

[65]  J. Trevors.  DNA in soil: adsorption, genetic transformation, molecular evolution and genetic microchip , 1996, Antonie van Leeuwenhoek.

[66]  J. Borneman,et al.  Molecular microbial diversity of an agricultural soil in Wisconsin , 1996, Applied and environmental microbiology.

[67]  S. Radwan,et al.  Soil management enhancing hydrocarbon biodegradation in the polluted Kuwaiti desert , 1995, Applied Microbiology and Biotechnology.

[68]  K. Schleifer,et al.  Phylogenetic identification and in situ detection of individual microbial cells without cultivation. , 1995, Microbiological reviews.

[69]  D. Moore.  Purification and Concentration of DNA from Aqueous Solutions , 1993, Current protocols in immunology.

[70]  M. Slatkin.  Inbreeding coefficients and coalescence times. , 1991, Genetical research.

[71]  F. Collins,et al.  Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. , 1991, Nucleic acids research.

[72]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[73]  V. Torsvik,et al.  High diversity in DNA of soil bacteria , 1990, Applied and environmental microbiology.

[74]  M. Slatkin.  Inbreeding coefficients and coalescence times. , 2007, Genetical research.

[75]  J. T. Staley,et al.  The alpha-, beta-, delta-, and epsilonproteobacteria , 2005 .

[76]  F. Lépine,et al.  Improving the Biotreatment of Hydrocarbons-Contaminated Soils by Addition of Activated Sludge taken from the Wastewater Treatment Facilities of an Oil Refinery , 2004, Biodegradation.

[77]  Jorge Loredo,et al.  Bioremediation of diesel-contaminated soils: Evaluation of potential in situ techniques by study of bacterial degradation , 2004, Biodegradation.

[78]  D. A. Barry,et al.  Field trial of a new aeration system for enhancing biodegradation in a biopile. , 2004, Waste management.

[79]  G. Płaza,et al.  Relationship between soil microbial diversity and bioremediation process at an oil refinery. , 2003, Acta microbiologica Polonica.

[80]  James R. Cole,et al.  The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy , 2003, Nucleic Acids Res..

[81]  W. Babel,et al.  Microbial diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosomal DNA analysis. , 2002, Systematic and applied microbiology.

[82]  G. Zaikov,et al.  Research of kinetic parameters of growth of the bacterial strain Rhodococcus luteus on different substrates , 2002 .

[83]  H. Flint,et al.  Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. , 2002, FEMS microbiology ecology.

[84]  F. Choy,et al.  Large-scale colony screening and insert orientation determination using PCR. , 2001, BioTechniques.

[85]  Kazuya Watanabe,et al.  Molecular Characterization of Bacterial Populations in Petroleum-Contaminated Groundwater Discharged from Underground Crude Oil Storage Cavities , 2000 .

[86]  D. Lane.  16S/23S rRNA sequencing , 1991 .

[87]  S. Kaplan,et al.  Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides. , 1990, Nucleic acids research.