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Molecular approaches to problems in biogeochemical cycling

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Summary

By using molecular probe techniques in combination with activity and expression measurements, it is possible to estimate bacterial populations in nature. This information can be expooited to study a number of important environmental problems. For instance, it will be possible to study ecosystem perturbation and microbial competition, by altering an ecosystem or a laboratory model of an ecosystem, and assessing corresponding changes in key activities and populations. In addition, regulation of activities in the laboratory can be compared to the response of activities and populations in situ, to develop an understanding of the key parameters that control these processes in nature. These types of approaches are important steps for determining the role of microorganisms in geochemical cycling, in both specific habitats and on a global basis.

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References

  • Anthony C (1986) Bacterial oxidation of methane and methanol. Adv. Microb. Physiol. 27: 113–209

    CAS  PubMed  Google Scholar 

  • Barkay T & Olson BH (1986) Phenotypic and genotypic adaptation of aerobic heterotrophic sediment bacterial communities to microbial stress. Appl. Environ. Microbiol. 52: 403–406

    CAS  PubMed  Google Scholar 

  • Barraquio WL, Dumont A & Knowles R (1988) Enumeration of free-living aerobic N2-fixing H2-oxidizing bacteria by using a heterotrophic semisolid medium and most-probable-number technique. Appl. Environ. Microbiol. 54: 1313–1317

    PubMed  Google Scholar 

  • Bergman B, Lindblad P & Rai AN (1986) Nitrogenase in free-living and symbiotic cyanobacteria; immunoelectron microscopic localization. FEMS Microbiol. Lett. 35: 75–78

    Article  CAS  Google Scholar 

  • Carlucci AF & Pramer D (1957) Factors influencing the plate method for determining the abundance of bacteria in sea water. Proc. Soc. Exp. Biol. Med. 96: 392–394

    CAS  PubMed  Google Scholar 

  • Cavanaugh CM, Abott MS & Veenhuis M (1988) Immunocytochemical localization of ribulose-1,5-bisphosphate carboxylase in the symbiont-containing gills ofSolemya velum (Bivalvia: Mollusca). Proc. Natl. Acad. Sci. USA (in press)

  • Colwell RR, Brayton PR, Grimes DJ, Roszak, DB, Huq SA & Palmer LM (1985) Viable but non-culturableVibrio cholerae and related pathogens in the environment: Implications for release of genetically engeneered microorganisms. Biotechnology 3: 817–820

    Google Scholar 

  • Distel DL, Lane DJ, Olsen GJ, Giovannoni SJ, Pace B, Stahl DA & Felbeck H (1988) Sulfur-oxidizing bacterial endosymbionts: analysis of phylogeny and specificity by 16S rRNA sequences. J. Bacteriol. 170: 2506–2510

    CAS  PubMed  Google Scholar 

  • Ferguson RL, Buckley EN & Palumbo AV (1984) Response of marine bacterioplankton to differential filtration and confinement. Appl. Environ. Microbiol. 47: 49–55

    CAS  PubMed  Google Scholar 

  • Fuhrman JA, Comeau DE, Hagstrom A & Chan AM (1988) Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl. Environ. Microbiol. 54: 1426–1429

    CAS  PubMed  Google Scholar 

  • Giovannoni SJ, DeLong EF, Olsen GJ & Pace NR (1988) Phylogenetic group-specific oligodeoxy-nucleotide probes for identification of single microbial cells. J. Bacteriol. 170: 720–726

    CAS  PubMed  Google Scholar 

  • Holben WE, Jannsson JK, Chelm BK & Tiedje JM (1988) DNA probe method for the detection of specific microorganisms in the soil bacterial community. Appl. Envir. Microbiol. 54: 703–711

    CAS  Google Scholar 

  • Jensen K, Hertz JB, Samra J, Magiar C, Larsen FS, Selmer J & Sompolinsky D (1985) A serological study with monoclonal antibodies to an antigen common to a wide range of bacteria. FEMS Microbiol. Lett. 19: 129–133

    Google Scholar 

  • Kirby R & Rybicki EP (1986) Enzyme-linked immunosorbent assay (ELISA) as a means of taxonomic analysis ofStreptomyces and related organisms. J. Gen. Microbiol. 132: 1891–1984

    CAS  PubMed  Google Scholar 

  • Kirchman D, Sigda J, Kapuscinski R & Mitchell R (1982) Statistical analysis of the direct count method for enumerating bacteria. Appl. Environ. Microbiol. 44: 376–383

    CAS  PubMed  Google Scholar 

  • Mah RA, Ward DM, Baresi L & Glass TL (1977) Biogenesis of methane. Ann. Rev. Microbiol. 31: 309–341

    CAS  Google Scholar 

  • Matthews JA & Kricka LJ (1988) Analytical strategies for the use of DNA probes. Anal. Biochem. 169: 1–25

    Article  CAS  PubMed  Google Scholar 

  • Muyzer G, De Bruyn AC, Schmedding DJM, Bos P, Westbroek P & Kuenen GJ (1987) Combined immunofluorescence-DNA-fluorescence staining technique for enumeration ofThiobacillus ferrooxidans in a population of acidophilic bacteria. Appl. Envir. Microbiol. 53: 660–664

    Google Scholar 

  • Ogram A, Sayler GS & Barklay T (1987) The extraction and purification of microbial DNA from sediments. J. Microbiol. Meth. 7: 57–66

    Article  CAS  Google Scholar 

  • Olsen Gary J, Lane David J, Giovannoni Stephen J, Pace Norman R & Stahl David A (1986) Microbial ecology and evolution: A ribosomal approach. Ann. Rev. Microbiol. 40: 337–365

    Google Scholar 

  • Pace NR, Stahl DA, Lane DJ & Olsen GJ (1986) The use of rRNA sequences to characterize natural microbial populations. Adv. Microb. Ecol. 9: 1–55

    CAS  Google Scholar 

  • Rudd JWM & Taylor DD (1980) Methane cycling in aquatic environments. Adv. Aquat. Microbiol. 2: 77–150

    CAS  Google Scholar 

  • Saiki RK, Gelfand DH, Stoffel B, Scharf SJ, Higuchi R, Horn GT, Mullis KB & Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487–490

    CAS  PubMed  Google Scholar 

  • Schmidt E (1974) Quantitative autecological study of microorganisms in soil by immunofluorescence. Soil Sci. 118: 141–149

    Google Scholar 

  • Stahl A, Lane DJ, Olsen GJ & Pace NR (1985) Characterization of a Yellowstone hot spring microbial community by 5S ribosomal RNA sequences. Appl. Environ. Microbiol. 49: 1379–1384

    CAS  PubMed  Google Scholar 

  • Stahl A, Lane DJ, Olsen GJ & Pace NR (1984) Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224: 409–411

    CAS  Google Scholar 

  • Ward BB & Carlucci AF (1985) Marine ammonia- and nitrite-oxidizing bacteria: Serological diversity determined by immunofluorescence in culture and in the environment. Appl. Env. Microbiol. 50: 194–201

    Google Scholar 

  • Williams CA, Nelson DC, Farah BA, Jannasch HW & Shively JM (1988) Ribulose bisphosphate carboxylase of the procarbotic symbiont of a hydrothermal vent tube worm: kinetics, activity and gene hybridization. FEMS Microbiol. Lett. 50: 107–112

    CAS  Google Scholar 

  • Zwadyk Peter Jr, Cooksey Robert C & Thornsberry Clyde (1986) Commercial detection methods for biotinylated gene probes: Comparison with32P-labelled DNA probes. Curr. Microbiol. 14: 95–99

    Google Scholar 

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  1. Keck Laboratories 138-78, California Institute of Technology, 91125, Pasadena, CA, USA

    Mary E. Lidstrom

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  1. Mary E. Lidstrom
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Lidstrom, M.E. Molecular approaches to problems in biogeochemical cycling. Antonie van Leeuwenhoek 55, 7–14 (1989). https://doi.org/10.1007/BF02309614

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  • DOI: https://doi.org/10.1007/BF02309614

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