References
- Acinas, S. G., V. Klepac-Ceraj, D. E. Hunt, C. Pharino, I. Ceraj, D. L. Distel, and M. F. Polz. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554 https://doi.org/10.1038/nature02649
- Alain, K., M. Zbinden, N. Le Bris, F. Lesongeur, J. Querellou, F. Gaill, and M. A. Cambon-Bonavita. 2004. Early steps in microbial colonization processes at deep-sea hydrothermal vents. Environ. Microbiol. 6: 227-241 https://doi.org/10.1111/j.1462-2920.2003.00557.x
- Bahr, M., B. C. Crump, V. Klepac-Ceraj, A. Teske, M. L. Sogin, and J. E. Hobbie. 2005. Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environ. Microbiol. 7: 1175-1185 https://doi.org/10.1111/j.1462-2920.2005.00796.x
- Buchan, A., S. Y. Newell, M. Butler, E. J. Biers, J. T. Hollibaugh, and M. A. Moran. 2003. Dynamics of bacterial and fungal communities on decaying salt marsh grass. Appl. Environ. Microbiol. 69: 6676-6687 https://doi.org/10.1128/AEM.69.11.6676-6687.2003
- Felsenstein, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22: 521-565 https://doi.org/10.1146/annurev.ge.22.120188.002513
- Hines, M. E., R. S. Evans, B. R. S. Genthner, S. G. Willis, S. Friedman, J. N. Rooney-Varga, and R. Devereux. 1999. Molecular phylogenetic and biogeochemical studies of sulfate-reducing bacteria in the rhizosphere of Spartina alterniflora. Appl. Environ. Microbiol. 65: 2209-2216
- Hold, G. L., E. A. Smith, M. S. Rappe, E. W. Maas, E. R. B. Moore, C. Stroempl, J. R. Stephen, J. I. Prosser, T. H. Birkbeck, and S. Gallacher. 2001. Characterization of bacterial communities associated with toxic and non-toxic dinoflagellates: Alexandrium spp. and Scrippsiella trochoidea. FEMS Microbiol. Ecol. 37: 161-173 https://doi.org/10.1111/j.1574-6941.2001.tb00864.x
- Hugenholtz, P., C. Pitulle, K. L. Hershberger, and N. R. Pace. 1998. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366-376
- Hurt, R. A., X. Qiu, L. Wu, Y. Roh, A. V. Palumbo, J. M. Tiedje, and J. Zhou. 2001. Simultaneous recovery of RNA and DNA from soils and sediments. Appl. Environ. Microbiol. 67: 4495-4503 https://doi.org/10.1128/AEM.67.10.4495-4503.2001
- Juretschko, S., A. Loy, A. Lehner, and M. Wagner. 2002. The microbial community composition of a nitrifyingdenitrifying activated sludge from an industrial sewage treatment plant analyzed by the full-cycle rRNA approach. Syst. Appl. Microbiol. 25: 84-99 https://doi.org/10.1078/0723-2020-00093
- Kim, B. S., H. M. Oh, H. Kang, S. S. Park, and J. Chun. 2004. Remarkable bacterial diversity in the tidal sediment as revealed by 16S rDNA analysis. J. Microbiol. Biotechnol. 14: 205-211
- Klepac-Ceraj, V., M. Bahr, B. C. Crump, A. P. Teske, J. E. Hobbie, and M. F. Polz. 2004. High overall diversity and dominance of microdiverse relationships in salt marsh sulphate-reducing bacteria. Environ. Microbiol. 6: 686-698 https://doi.org/10.1111/j.1462-2920.2004.00600.x
- Li, L., C. Kato, and K. Horikoshi. 1999. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan Trench. Mar. Biotechnol. 1: 391-400 https://doi.org/10.1007/PL00011793
- Lowe, M., E. L. Madsen, K. Schindler, C. Smith, S. Emrich, F. Robb, and R. U. Halden. 2002. Geochemistry and microbial diversity of a trichloroethene-contaminated Superfund site undergoing intrinsic in situ reductive dechlorination. FEMS Microbiol. Ecol. 40: 123-134 https://doi.org/10.1111/j.1574-6941.2002.tb00944.x
- Lueders, T., B. Pommerenke, and M. W. Friedrich. 2004. Stable-isotope probing of microorganisms thriving at thermodynamic limits: Syntrophic propionate oxidation in flooded soil. Appl. Environ. Microbiol. 70: 5778-5786 https://doi.org/10.1128/AEM.70.10.5778-5786.2004
- Lydell, C., L. Dowell, M. Sikaroodi, P. Gillevet, and D. Emerson. 2004. A population survey of members of the phylum Bacteroidetes isolated from salt marsh sediments along the east coast of the United States. Microb. Ecol. 48: 263-273 https://doi.org/10.1007/s00248-003-1068-x
- Macbeth, T. W., D. E. Cummings, S. Spring, L. M. Petzke, and K. S. Sorenson Jr. 2004. Molecular characterization of a dechlorinating community resulting from in situ biostimulation in a trichloroethene-contaminated deep, fractured basalt aquifer and comparison to a derivative laboratory culture. Appl. Environ. Microbiol. 70: 7329- 7341 https://doi.org/10.1128/AEM.70.12.7329-7341.2004
- Mussmann, M., K. Ishii, R. Rabus, and R. Amann. 2005. Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea. Environ. Microbiol. 7: 405-418 https://doi.org/10.1111/j.1462-2920.2005.00708.x
- Nakagawa, S., K. Takai, F. Inagaki, H. Chiba, J. Ishibashi, S. Kataoka, H. Hirayama, T. Nunoura, K. Horikoshi, and Y. Sako. 2005. Variability in microbial community and venting chemistry in a sediment-hosted backarc hydrothermal system: Impacts of subseafloor phase-separation. FEMS Microbiol. Ecol. 54: 141-155 https://doi.org/10.1016/j.femsec.2005.03.007
- Nercessian, O., Y. Fouquet, C. Pierre, D. Prieur, and C. Jeanthon. 2005. Diversity of bacteria and Archaea associated with a carbonate-rich metalliferous sediment sample from the Rainbow vent field on the Mid-Atlantic Ridge. Environ. Microbiol. 7: 698-714 https://doi.org/10.1111/j.1462-2920.2005.00744.x
- Nesbo, C. L., Y. Boucher, M. Dlutek, and F. W. Doolittle. 2005. Lateral gene transfer and phylogenetic assignment of environmental fosmid clones. Environ. Microbiol. 7: 2011- 2026 https://doi.org/10.1111/j.1462-2920.2005.00918.x
- Okabe, S., T. Ito, K. Sugita, and H. Satoh. 2005. Succession of internal sulfur cycles and sulfur-oxidizing bacterial communities in microaerophilic wastewater biofilms. Appl. Environ. Microbiol. 71: 2520-2529 https://doi.org/10.1128/AEM.71.5.2520-2529.2005
- Purdy, K. J., D. B. Nedwell, and T. M. Embley. 2003. Analysis of the sulfate-reducing bacterial and methanogenic Archaeal populations in contrasting Antarctic sediments. Appl. Environ. Microbiol. 69: 3181-3191 https://doi.org/10.1128/AEM.69.6.3181-3191.2003
- Ravenschlag, K., K. Sahm, J. Pernthaler, and R. Amann. 1999. High bacterial diversity in permanently cold marine sediments. Appl. Environ. Microbiol. 65: 3982-3989
- Saiki, R. K., D. H. Gelfand, S. Stoffel, S. J. Scharf, R. Higuchi, G. T. Horn, K. B. Mullis, and H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491 https://doi.org/10.1126/science.2448875
- Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425
- Schloetelburg, C., C. von Wintzingerode, R. Hauck, F. von Wintzingerode, W. Hegemann, and U. B. Goebel. 2002. Microbial structure of an anaerobic bioreactor population that continuously dechlorinates 1,2-dichloropropane. FEMS Microbiol. Ecol. 39: 229-237 https://doi.org/10.1111/j.1574-6941.2002.tb00925.x
- Selenska-Pobell, S., G. Kampf, K. Hemming, G. Radeva, and G. Satchanska. 2001. Bacterial diversity in soil samples from two uranium waste piles as determined by rep-APD, RISA and 16S rDNA retrieval. Antonie Van Leeuwenhoek 79: 149-161 https://doi.org/10.1023/A:1010237711077
- Singleton, D. R., M. A. Furlong, S. L. Rathbun, and W. W. B. 2001. Quantitative comparisons of 16S rDNA sequence libraries from environmental samples. Appl. Environ. Microbiol. 67: 4373-4376
- Stubner, S., T. Wind, and R. Conrad. 1998. Sulfur oxidation in rice field soil: Activity, enumeration, isolation and characterization of thiosulfate-oxidizing bacteria. Syst. Appl. Microbiol. 21: 569-578 https://doi.org/10.1016/S0723-2020(98)80069-6
- Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680 https://doi.org/10.1093/nar/22.22.4673
- Volossiouk, T., E. J. Robb, and R. N. Nazar. 1995. Direct DNA extraction for PCR-mediated assays of soil organisms. Appl. Environ. Microbiol. 61: 3972-3976
- Watanabe, K., Y. Kodama, K. Syutsubo, and S. Harayama. 2000. Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities. Appl. Environ. Microbiol. 66: 4803-4809 https://doi.org/10.1128/AEM.66.11.4803-4809.2000
- Yanagibayashi, M., Y. Nogi, L. Li, and C. Kato. 1999. Changes in the microbial community in Japan Trench sediment from a depth of 6292 m during cultivation without decompression. FEMS Microbiol. Lett. 170: 271-279 https://doi.org/10.1111/j.1574-6968.1999.tb13384.x
- Zhou, J., M. A. Bruns, and J. M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62: 316-322