Bacterioplankton community diversity in a maritime Antarctic lake, determined by culture-dependent and culture-independent techniques

FEMS Microbiology Ecology

Volumn 45, Issue 1, 2003, Pages 59-70

  Pearce, D A ^a   Van Der Gast, C J ^b   Lawley, B ^a   Ellis Evans, J C ^a  

^a BRITISH ANTARCTIC SURVEY   (United Kingdom)

^b CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

16S rRNA; Antarctic freshwater lake; Bacterioplankton; Cloning; Community structure; Fatty acid methyl ester

Indexed keywords

BACTERIAL RNA; DNA 16S; FATTY ACID ESTER; PIGMENT; RNA 16S;

BACTERIOPLANKTON; COMMUNITY STRUCTURE; LAKE ECOSYSTEM; SPECIES DIVERSITY;

ANTARCTICA; ARTICLE; BACTERIAL FLORA; BACTERIOPLANKTON; BACTERIUM; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BIODIVERSITY; COMMUNITY STRUCTURE; CONTROLLED STUDY; CORYNEBACTERIUM; CULTURE TECHNIQUE; DENATURING GRADIENT GEL ELECTROPHORESIS; ECOLOGY; FLAVOBACTERIUM; FLEXIBACTERACEAE; FLUORESCENCE; FRESHWATER ENVIRONMENT; GENE SEQUENCE; IN SITU HYBRIDIZATION; INTERMETHOD COMPARISON; LAKE; MICROBIAL DIVERSITY; MICROBIAL POPULATION DYNAMICS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PELAGIC ZONE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOMONAS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

ANTARCTICA;

BACTERIA (MICROORGANISMS); CORYNEBACTERIUM; CYTOPHAGA; FLAVOBACTERIUM; JANTHINOBACTERIUM; PSEUDOMONAS;

EID: 0038542819     PISSN: 01686496     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-6496(03)00110-7     Document Type: Article

References (64)

1. White P.L., Wynn-Williams D.D., Russell N.J. Diversity of thermal responses of lipid composition in the membranes of the dominant culturable members of an Antarctic fellfield soil bacterial community. Antarct. Sci. 12:2000;386-393.
2. Buffan-Dubau E., Pringault O., de Wit R. Artificial cold-adapted microbial mats cultured from Antarctic lake samples. 1. Formation and structure. Aquat. Microb. Ecol. 26:2001;115-125.
3. Mazumder R., Pinkart H.C., Alban P.S., Phelps T.J., Benoit R.E. Low-substrate regulated microaerophilic behavior as a stress response of aquatic and soil bacteria. Curr. Microbiol. 41:2000;79-83.
4. Bharathi P.A.L., Nair S., De Souza M.J., Chandramohan D. Truce with oxygen - Anaerobiosis outcompete aerobiosis in the Antarctic lacustrine bacteria. Curr. Sci. 76:1999;1585-1587.
5. McMeekin T.A., Franzmann P.D. Effect of temperature on the growth-rates of halotolerant and halophilic bacteria isolated from Antarctic saline lakes. Polar Biol. 8:1988;281-285.
6. Dobson S.J., James S.R., Franzmann P.D., McMeekin T.A. A numerical taxanomic study of some pigmented bacteria isolated from Organic Lake, and Antarctic hypersaline lake. Arch. Microbiol. 156:1991;56-61.
7. Ellis-Evans J.C. Microbial diversity and function in Antarctic freshwater ecosystems. Biodivers. Conserv. 5:1996;1395-1431.
8. Wynn-Williams D.D. Antarctic microbial diversity: The basis of polar ecosystem processes. Biodivers. Conserv. 5:1996;1271-1293.
9. Zwart G., Crump B.C., Kampst-van Agterveld M.P., Hagen F., Han S.-K. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28:2002;141-155.
10. Orphan V.J., Taylor L.T., Hafenbradl D., DeLong E.F. Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl. Environ. Microbiol. 66:2000;700-711.
11. Ward D.M., Weller R., Bateson M.M. 16S ribosomal RNA sequences reveal numerous uncultured microorganisms in a natural community. Nature. 345:1990;63-65.
12. Chandler D.P., Brockman F.J., Fredrickson J.K. Use of 16S rDNA clone libraries to study changes in a microbial community resulting from ex situ perturbation of a subsurface sediment. FEMS Microbiol. Rev. 20:1997;217-230.
13. Chandler D.P., Li S.M., Spadoni C.M., Drake G.R., Balkwill D.L., Fredrickson J.K., Brockman F.J. A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment. FEMS Microbiol. Ecol. 23:1997;131-144.
14. Ward, N., Rainey, F.A., Goebel, B. and Stakebrandt, E. (1995) Identification and culturing the 'unculuturables': a challenge for microbiologists. In: Microbial Diversity and Ecosystem Function (Allsopp, D., Colwell, R.R. and Hawksworth, D.L., Eds.), pp. 89-110. CAB International, Wallingford.
15. Chattopadhyay M.K. Cold-adaptation of Antarctic microorganisms - possible involvement of viable but nonculturable state. Polar Biol. 23:2002;223-224.
16. Dunbar J., Takala S., Barns S.M., Davis J.A., Kuske C.R. Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Appl. Environ. Microbiol. 65:1999;1662-1669.
17. Blackall L.L., Burrell P.C., Gwilliam H., Bradford D., Bond P.L., Hugenholtz P. The use of 16S rDNA clone libraries to describe the microbial diversity of activated sludge processes. Water Sci. Technol. 37:1998;451-454.
18. Amman R., Glockner F.O., Neef A. Modern methods in subsurface microbiology: in situ identification of microorganisms with nucleic acid probes. FEMS Microbiol. Rev. 20:1997;191-200.
19. Ercolini D., Moschetti G., Blaiotta G., Coppola S. The potential of a polyphasic PCR-DGGE approach in evaluating microbial diversity of natural whey cultures for water buffalo mozzarella cheese production: bias of culture-dependent and culture-independent analyses. Syst. Appl. Microbiol. 24:2001;610-617.
20. Roling W.F.M., van Breukelen B.M., Braster M., Goeltom M.T., Groen J., van Verseveld H.W. Analysis of microbial communities in a landfill leachate polluted aquifer using a new method for anaerobic physiological profiling and 16S rDNA fingerprinting. Microb. Ecol. 40:2000;177-188.
21. Dees P.M., Ghiorse W.C. Microbial diversity in hot synthetic compost as revealed by PCR amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol. Ecol. 35:2001;207-216.
22. Klib B., Kuhlmann B., Eschweiler B., Preuss G., Ziemann E., Schottler U. Community structures of groundwater habitats investigated using methods of molecular biology. Acta Hydrochem. Hydrobiol. 26:1998;349-354.
23. Yang C.H., Crowley D.E., Borneman J., Keen N.T. Microbial phyllosphere populations are more complex than previously realized. Proc. Natl. Acad. Sci. USA. 98:2001;3889-3894.
24. Kowalchuk G.A., Stienstra A.W., Heilig G.H.J., Stephen J.R., Woldendorp J.W. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands. Environ. Microbiol. 2:2000;99-110.
25. Bauer S., Tholen A., Overmann J., Brune A. Characterization of abundance and diversity of lactic acid bacteria in the hindgut of wood- and soil-feeding termites by molecular and culture-dependent techniques. Arch. Microbiol. 173:2000;126-137.
26. Vainio E.J., Moilanen A., Koivula T.T., Bamford D.H., Hantula J. Comparison of partial 16S rRNA gene sequences obtained from activated sludge bacteria. Appl. Microbiol. Biot. 48:1997;73-79.
27. Teske A., Wawer C., Muyzer G., Ramsing N.B. Distribution of sulphate-reducing bacteria in a stratified fjord (Mariager fjord, Denmark) as evaluated by most probable number counts and denaturing gradient gel electrophoresis of PCR amplified ribosomal DNA fragments. Appl. Environ. Microbiol. 62:1996;1405-1415.
28. Wagner M., Amman R., Lemmer H., Schleifer K.H. Probing activated sludge with oligonucleotides specific for proteobacteria - inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59:1993;1520-1525.
29. Bakken L.R., Olsen R.A. The relationship between cell size and viability of soil bacteria. Microb. Ecol. 13:1987;103-114.
30. Tiedje, J.M. and Stein, J.L. (1999) Microbial biodiversity: Strategies for its recovery. In: Manual of Industrial Microbiology and Biotechnology (Demain, A.L. and Davies, J.E., Eds.), pp. 682-692. ASM Press, Washington, DC.
31. Suzuki M.T., Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62:1996;625-630.
32. Bharathi P.A.L., Nair S., De Souza M.J., Chandramohan D. Truce with oxygen - anaerobiosis outcompete aerobiosis in the Antarctic lacustrine bacteria. Curr. Sci. 76:1999;1585-1587.
33. Farrelly V., Rainey F.A., Stackenbrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61:1995;2798-2801.
34. Staley J.T., Konopka A. Measurement of in situ activities of non-photosynthetic organisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39:1985;321-346.
35. Heywood R.B., Dartnall H.J.G., Priddle J. Characteristics and classification of the lakes of Signy Island, South Orkney Islands, Antarctica. Freshw. Biol. 10:1980;47-59.
36. Ellis-Evans J.C. Seasonal microbial activity in Antarctic freshwater lake sediments. Polar Biol. 1:1982;129-140.
37. Jones J.G. Studies on freshwater bacteria: effect of medium composition on methods of estimation of bacterial populations. J. Appl. Bacteriol. 33:1970;679-687.
38. Thompson I.P., Bailey M.J., Ellis R.J., Purdy K.J. Subgrouping of bacterial populations by cellular fatty acid composition. FEMS Microbiol. Ecol. 102:1993;75-84.
39. van der Gast C.J., Knowles C.J., Wright M.A., Thompson I.P. Identification and characterisation of bacterial populations of an in-use metal-working fluid by phenotypic and genotypic methodology. Int. Biodeter. Biodegr. 47:2001;113-123.
40. Pearce D.A. A rapid, sensitive method for monitoring bacterioplankton community dynamics, applied to Antarctic freshwater lakes. Polar Biol. 23:2000;352-356.
41. Pearce D.A., Butler H.B. Short term stability of the microbial community structure in a maritime Antarctic lake. Polar Biol. 25:2002;479-487.
42. Altschul S.F., Madden T., Schäffer A.A., Zhang J., Zhang Z.W., Miller W. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
43. Porter K.G., Feig Y.S. The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25:1980;943-948.
44. Brosius J., Dull T.L., Sleeter D.D., Noller H.F. Gene organization and primary structure of a ribosomal operon from Escherichia coli. J. Mol. Biol. 148:1981;107-127.
45. Amann R.I., Binder B.J., Olson R., Chisholm S.W., Devereux R., Stahl D. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1990;1919-1925.
46. Manz W., Amann R., Ludwig W., Wagner M., Schleifer K.-H. Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst. Appl. Microbiol. 15:1992;593-600.
47. Manz W., Amann R., Ludwig W., Vancanneyt M., Schleifer K.-H. 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. 142:1996;1097-1106.
48. Southwick P.L., Ernst L.A., Tauriello E.W., Parker S.R., Mujumdar R.B., Mujumdar S.R., Clever H.A., Waggoner A.S. Cyanine dye labeling reagents - carboxymethylindocyanine succinimidyl esters. Cytometry. 11:1990;418-430.
49. Helms, C. (1990) Method: Denaturing gradient gel electrophoresis (DGGE) http://hdklab.wustl.edu/lab_manual/dgge/dgge1.html%25 .
50. Ellis-Evans J.C. Freshwater biology in the Antarctic: I Microbial numbers and activity in oligotrophic Moss Lake, Signy Island. Br. Antarct. Surv. Bull. 54:1981;85-104.
51. Ellis-Evans, J.C. (1985) Decomposition processes in maritime Antarctic lakes. In: Antarctic Nutrient Cycles and Food Webs (Siegfried, W.R., Condy, P.R. and Laws, R.M., Eds.), pp. 253-260. Springer-Verlag, Heidelberg.
52. Edwards M.L., Lilley A.K., Timms-Wilson T.H., Thompson I.P., Cooper I. Characterisation of the culturable heterotrophic bacterial community in a small eutrophic lake (Priest Pot). FEMS Microbiol. Ecol. 35:2001;295-304.
53. James S.R., Burton H.R., McMeekin T.A., Mancuso C.A. Seasonal abundance of Halomonas meridiana, Halomonas subglaciescola, Flavobacterium gondwanense and Flavobacterium salegens in 4 Antarctic lakes. Antarct. Sci. 6:1994;325-332.
54. Bowman J.P., McCammon C., Rea S.M., McMeekin T.A. The microbial composition of three limnologically disparate hypersaline lakes. FEMS Microbiol. Lett. 183:2000;81-88.
55. Zwart G., Hiorns W.D., Methé B.A., Van Agterveld M.P., Huismans R., Nold S.C., Zehr J.P., Laanbroek H.J. 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. 21:1998;546-556.
56. Glöckner F.O., Fuchs B.M., Amann R. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65:1999;3721-3726.
57. Methé B.A., Hiorns W.D., Zehr J.P. Contrasts between marine and freshwater bacterial community composition: analysis of communities in Lake George and six other Adirondak lakes. Limnol. Oceanogr. 43:1998;368-374.
58. Kaiser O., Puhler A., Selbitschka W. Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation dependent and cultivation independent approaches. Microb. Ecol. 42:2001;136-149.
59. Reysenbach A.L., Giver L.J., Wickham G.S., Pace N.R. Differential amplification of ribosomal-RNA genes by polymerase chain-reaction. Appl. Environ. Microbiol. 58:1992;3417-3418.
60. Ellis R.J., Thompson I.P., Bailey M.J. Temporal fluctuations in the pseudomonad population associated with sugar beet leaves. FEMS Microbiol. Ecol. 28:1999;345-356.
61. Stackebrandt E., Liesack W., Goebel B.M. Bacterial diversity in a soil sample from a sub-tropical Australian environment as determined by 16S rDNA analysis. FASEB J. 7:1993;232-236.
62. Cottrell M.T., Kirchman D.L. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66:2000;1692-1697.
63. Franzmann P.D., Dobson S.J. The phylogeny of bacteria from a modern Antarctic refuge. Antarct. Sci. 5:1993;267-270.
64. Liesack W., Weyland H., Stackebrandt E. Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microbial Ecology. 21:1993;191-198.