Bacterial diversity of metagenomic and PCR libraries from the Delaware River

Environmental Microbiology

Volumn 7, Issue 12, 2005, Pages 1883-1895

  Cottrell, Matthew T ^a   Waidner, Lisa A ^a   Yu, Liying ^a   Kirchman, David L ^a  

^a UNIVERSITY OF DELAWARE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; FRESH WATER; RNA 16S;

ACTINOBACTERIA; ARTICLE; BACTERIUM; BETAPROTEOBACTERIA; BIODIVERSITY; BURKHOLDERIACEAE; COMPARATIVE STUDY; CYTOPHAGA; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LIBRARY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE; UNITED STATES;

ACTINOBACTERIA; BACTERIA; BETAPROTEOBACTERIA; BIODIVERSITY; BURKHOLDERIACEAE; CYTOPHAGA; DELAWARE; FRESH WATER; GENOMIC LIBRARY; IN SITU HYBRIDIZATION, FLUORESCENCE; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY; WATER MICROBIOLOGY;

ACTINOBACTERIA; BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; CYTOPHAGA; POLYNUCLEOBACTER NECESSARIUS; RHODOFERAX SP.;

EID: 28644449327     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00762.x     Document Type: Article

References (59)

1. Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R., and Stahl, D.A. (1990) Combination of 16S ribosomal-RNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56: 1919-1925.
2. Amon, R.M.W., and Benner, R. (1996) Photochemical and microbial consumption of dissolved organic carbon and dissolved oxygen in the Amazon River system. Geochim Cosmochim Ac 60: 1783-1792.
3. Beja, O., Aravind, L., Koonin, E.V., Suzuki, M.T., Hadd, A., Nguyen, L.P., et al. (2000a) Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289: 1902-1906.
4. Beja, O., Suzuki, M.T., Koonin, E.V., Aravind, L., Hadd, A., Nguyen, L.P., et al. (2000b) Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2: 516-529.
5. Beja, O., Spudich, E.N., Spudich, J.L., Leclerc, M., and DeLong, E.F. (2001) Proteorhodopsin phototrophy in the ocean. Nature 411: 786-789.
6. Button, D.K., and Robertson, B.R. (2001) Determination of DNA content of aquatic bacteria by flow cytometry. Appl Environ Microbiol 67: 1636-1645.
7. Button, D.K., Robertson, B.R., Lepp, P.W., and Schmidt, T.M. (1998) A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater. Appl Environ Microbiol 64: 4467-4476.
8. Castle, D., and Kirchman, D.L. (2004) Composition of estuarine bacterial communities assessed by denaturing gradient gel electrophoresis and fluorescence in situ hybridization. Limnol Oceanogr 2: 303-314.
9. Cottrell, M.T., and Kirchman, D.L. (2000) Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microbiol 66: 5116-5122.
10. Cottrell, M.T., and Kirchman, D.L. (2003) Contribution of major bacterial groups to bacterial biomass production (thymidine and leucine incorporation) in the Delaware estuary. Limnol Oceanogr 48: 168-178.
11. Cottrell, M.T., Moore, J.A., and Kirchman, D.L. (1999) Chitinases from uncultured marine microorganisms. Appl Environ Microbiol 65: 2553-2557.
12. Covert, J.S., and Moran, M.A. (2001) Molecular characterization of estuarine bacterial communities that use high- and low-molecular weight fractions of dissolved organic carbon. Aquat Microb Ecol 25: 127-139.
13. Daims, H., Bruhl, A., Amann, R., Schleifer, K.H., and Wagner, M. (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: Development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22: 434-444.
14. Dunbar, J., Takala, S., Barns, S.M., Davis, J.A., and Kuske, C.R. (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl Environ Microbiol 65: 1662-1669.
15. Fegatella, F., Lim, J., Kjelleberg, S., and Cavicchioli, R. (1998) Implications of rRNA operon copy number and ribosome content in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256. Appl Environ Microbiol 64: 4433-4438.
16. Fogel, G.B., Collins, C.R., Li, J., and Brunk, C.F. (1999) Prokaryotic genome size and SSU rDNA copy number: Estimation of microbial relative abundance from a mixed population. Microb Ecol 38: 93-113.
17. Fuhrman, J.A., McCallum, K., and Davis, A.A. (1992) Novel major Archaebacterial group from marine plankton. Nature 356: 148-149.
18. Gillespie, D.E., Brady, S.F., Bettermann, A.D., Cianciotto, N.P., Liles, M.R., Rondon, M.R., et al. (2002) Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 68: 4301-4306.
19. Giovannoni, S.J., and Rappé, M.S. (2000) Evolution, diversity and molecular ecology of marine prokaryotes. In Microbial Ecology of the Oceans. Kirchman, D.L. (ed.). New York, USA: Wiley-Liss, pp. 47-84.
20. Glöckner, F.O., Fuchs, B.M., and Amann, R. (1999) Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microbiol 65: 3721-3726.
21. Glöckner, F.O., Zaichikov, E., Belkova, N., Denissova, L., Pernthaler, J., Pernthaler, A., and Amann, R. (2000) Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl Environ Microbiol 66: 5053-5065.
22. Gonzalez, J.M., and Moran, M.A. (1997) Numerical dominance of a group of marine bacteria in the alpha- subclass of the class Proteobacteria in coastal seawater. Appl Environ Microbiol 63: 4237-4242.
23. Hernes, P.J., and Benner, R. (2002) Transport and diagenesis of dissolved and particulate terrigenous organic matter in the North Pacific Ocean. Deep-Sea Res Part II - Top Stud Oceanogr 49: 2119-2132.
24. Karner, M., and Fuhrman, J.A. (1997) Determination of active marine bacterioplankton: a comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining. Appl Environ Microbiol 63: 1208-1213.
25. Karner, M.B., DeLong, E.F., and Karl, D.M. (2001) Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409: 507-510.
26. Kirchman, D.L. (2002) The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol Ecol 39: 91-100.
27. Kirchman, D.L., Yu, L.Y., and Cottrell, M.T. (2003) Diversity and abundance of uncultured Cytophagia-like bacteria in the Delaware Estuary. Appl Environ Microbiol 69: 6587-6596.
28. Klappenbach, J.A., Dunbar, J.M., and Schmidt, T.M. (2000) rRNA operon copy number reflects ecological strategies of bacteria. Appl Environ Microbiol 66: 1328-1333.
29. Knietsch, A., Waschkowitz, T., Bowien, S., Henne, A., and Daniel, R. (2003) Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli. J Mol Microbiol Biotechnol 5: 46-56.
30. Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E. and Goodfellow, M. (eds). Chichester, UK: Wiley and Sons, pp. 115-175.
31. Liles, M.R., Manske, B.F., Bintrim, S.B., Handelsman, J., and Goodman, R.M. (2003) A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 69: 2684-2691.
32. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
33. Manz, W., Amann, R., Ludwig, W., Wagner, M., and Schleifer, K.H. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria - problems and solutions. Syst Appl Microbiol 15: 593-600.
34. Manz, W., Amann, R., Ludwig, W., Vancanneyt, M., and Schleifer, K.H. (1996) Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum Cytophaga-Flavobacter-Bacteroides in the natural environment. Microbiology 142: 1097-1106.
35. Massana, R., Taylor, L.J., Murray, A.E., Wu, K.Y., Jeffrey, W.H., and DeLong, E.F. (1998) Vertical distribution and temporal variation of marine planktonic archaea in the Gerlache Strait, Antarctica, during early spring. Limnol Oceanogr 43: 607-617.
36. Massana, R., DeLong, E.F., and Pedros-Alio, C. (2000) A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces. Appl Environ Microbiol 66: 1777-1787.
37. Morris, R.M., Rappé, M.S., Connon, S.A., Vergin, K.L., Siebold, W.A., Carlson, C.A., and Giovannoni, S.J. (2002) SAR11 clade dominates ocean surface bacterioplankton communities. Nature 420: 806-810.
38. Muyzer, G., Teske, A., Wirsen, C.O., and Jannasch, H.W. (1995) Phylogenetic-relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel-electrophoresis of 16S rDNA fragments. Arch Microbiol 164: 165-172.
39. Neef, A. (1997) Anwendung der in situ-Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in Komplexen Mikrobiellen Biozonosen. Munich, Germany: Technische Universitat Munchen.
40. Opsahl, S., Benner, R., and Amon, R.M.W. (1999) Major flux of terrigenous dissolved organic matter through the Arctic Ocean. Limnol Oceanogr 44: 2017-2023.
41. O'Sullivan, L.A., Weightman, A.J., and Fry, J.C. (2002) New degenerate Cytophaga-Flexibacter-Bacteroides-specific 16S ribosomal DNA-targeted oligonucleotide probes reveal high bacterial diversity in River Taff epilithon. Appl Environ Microbiol 68: 201-210.
42. Pettit, A.N. (1982) Cramer-von Misess statistic. In Encyclopedia of Statistical Sciences. Kotz, S., Johnson, N.L., and Read, C.B. (eds). New York, USA: Wiley, pp. 220-221.
43. Quaiser, A., Ochsenreiter. T., Klenk, H.P., Kletzin, A., Treusch, A.H., Meurer, G., et al. (2002) First insight into the genome of an uncultivated crenarchaeote from soil. Environ Microbiol 4: 603-611.
44. Rappé, M.S., and Giovannoni, S.J. (2003) The uncultured microbial majority. Annu Rev Microbiol 57: 369-394.
45. Rappé, M.S., Gordon, D.A., Vergin, K.L., and Giovannoni, S.J. (1999) Phylogeny of Actinobacteria small subunit (SSU) rRNA gene clones recovered from marine bacterioplankton. Syst Appl Microbiol 22: 106-112.
46. Rappé, M.S., Connon, S.A., Vergin, K.L., and Giovannoni, S.J. (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418: 630-633.
47. Roller, C., Wagner, M., Amann, R., Ludwig, W., and Schleifer, K.H. (1994) In-situ probing of Gram-positive bacteria with high DNA G+C content using 23S-ribosomal-RNA-targeted oligonucleotides. Microbiology 140: 2849-2858.
48. Rondon, M.R., August, P.R., Bettermann, A.D., Brady, S.F., Grossman, T.H., Liles, M.R., et al. (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66: 2541-2547.
49. Sabehi, G., Massana, R., Bielawski, J.P., Rosenberg, M., Delong, E.F., and Beja, O. (2003) Novel proteorhodopsin variants from the Mediterranean and Red Seas. Environ Microbiol 5: 842-849.
50. Singleton, D.R., Furlong, M.A., Rathbun, S.L., and Whitman, W.B. (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374-4376.
51. Stackebrandt, E., and Goebel, B.M. (1994) A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence-analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44: 846-849.
52. Stein, J.L., Marsh, T.L., Wu, K.Y., Shizuya, H., and DeLong, E.F. (1996) Characterization of uncultivated prokaryotes: Isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 178: 591-599.
53. Thompson, J.R., Marcelino, L.A., and Polz, M.F. (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30: 2083-2088.
54. Topp, E. (2003) Bacteria in agricultural soils: Diversity, role and future perspectives. Can J Soil Sci 83: 303-309.
55. Weller, R., Glöckner, F.O., and Amann, R. (2000) 16S rRNA-targeted oligonucleotide probes for the in situ detection of members of the phylum Cytophaga-Flavobacterium-Bacteroides. Syst Appl Microbiol 23: 107-114.
56. von Wintzingerode, F., Gobel, U.B., and Stackebrandt, E. (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21: 213-229.
57. Zaitlin, B., Watson, S.B., Dixon, J., and Steel, D. (2003) Actinomycetes in the Elbow River Basin, Alberta. Can Water Quality Res J Can 38: 115-125.
58. Zwart, G., Hiorns, W.D., Methe, B.A., Van Agterveld, M.P., Huismans, R., Nold, S.C., et al. (1998) Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria. Syst Appl Microbiol 21: 546-556.
59. Zwart, G., Crump, B.C., Agterveld, M., Hagen, F., and Han, S.K. (2002) Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol 28: 141-155.