Abstract
The bacterioplankton community structure in Moss Lake, a maritime Antarctic oligotrophic lake, was determined with vertical depth in the water column, during the ice-free period on Signy Island in the South Orkney Islands. Bacterioplankton community structure was determined using a combination of direct counting of 4′,6-diamidino-2-phenylindole (DAPI) stained cells, PCR amplification of 16S rRNA gene fragments, denaturing gradient gel electrophoresis (DGGE) and in situ hybridization with group-specific, fluorescently labeled oligonucleotide probes. Using PCR amplification of 16S rRNA gene fragments and DGGE, the bacterioplankton community composition was shown to be constant with vertical depth in the water column. Specific bacterioplankton species identified through cloning and sequencing the DGGE products obtained were Flavobacterium xinjiangensis (a Flavobacterium), Leptothrix discophora (a beta-Proteobacterium), and a number of uncultured groups: two beta-Proteobacteria, an unclassified Proteobacterium, three sequences from Actinobacteria, and a Cyanobacterium. Fluorescence in situ hybridization (FISH), however, demonstrated that there were minor but significant fluctuations in different groups of bacteria with vertical depth in the water column. It showed that the beta-Proteobacteria accounted for between 26.4 and 71.5%, the alpha-Proteobacteria 2.3–10.6%, the gamma-Proteobacteria 0–29.6%, and the Cytophaga–Flavobacterium group 1.8–23.5% of cells hybridizing to a universal probe. This study reports the first description of the community structure of an oligotrophic Antarctic freshwater lake as determined by PCR-dependent and PCR-independent molecular techniques. It also suggests that the bacterioplankton community of Moss Lake contains classes of bacteria known to be important in freshwater systems elsewhere in the world.
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References
A Alfreider J Pernthaler R Amman B Sattler FO Glöckner A Wille R Psenner (1996) ArticleTitleCommunity analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Appl Environ Microb 62 2138–2144 Occurrence Handle1:CAS:528:DyaK28XjtlGgsbw%3D
J Antón E Llobet-Brossa F Rodríguez-Valera R Amann (1999) ArticleTitleFluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds. Environ Microbiol 1 517–523 Occurrence Handle11207773
RI Amann BJ Binder R Olson SW Chisholm R Devereux D Stahl (1990) ArticleTitleCombination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microb 56 1919–1925 Occurrence Handle1:CAS:528:DyaK3cXkvFCgsrs%3D Occurrence Handle2200342
RI Amman W Ludwig K-H Schleifer (1995) ArticleTitlePhylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59 143–169 Occurrence Handle1:CAS:528:DyaK2MXkvVGmurk%3D Occurrence Handle7535888
R Amman J Snaidr M Wagner W Ludwig K-H Schleifer (1996) ArticleTitleIn situ visualization of high genetic diversity in a natural microbial community. J Bacteriol 178 3496–3500 Occurrence Handle1:CAS:528:DyaK28XjsFGls7Y%3D Occurrence Handle8655546
R Amann M Kühl (1998) ArticleTitleIn situ methods for assessment of microorganisms and their activities. Curr Opin Microbiol 1 352–358 Occurrence Handle1:STN:280:DyaK1M7osFagtA%3D%3D Occurrence Handle10066487
R Amann BM Fuchs S Behrens (2001) ArticleTitleThe identification of microorganisms by fluorescence in situ hybridization. Curr Opin Biotechnol 12 231–236 Occurrence Handle1:CAS:528:DC%2BD3MXkt12lu74%3D Occurrence Handle11404099
N Bano JT Hollibaugh (2000) ArticleTitleDiversity and distribution of DNA sequences with affinity to ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Arctic Ocean. Appl Environ Microb 66 1960–1969 Occurrence Handle10.1128/AEM.66.5.1960-1969.2000 Occurrence Handle1:CAS:528:DC%2BD3cXjtV2ltb4%3D Occurrence Handle10788367
J Brosius TL Dull DD Sleeter HF Noller (1981) ArticleTitleGene organization and primary structure of a ribosomal operon from Escherichia coli. J Mol Biol 148 107–127 Occurrence Handle1:CAS:528:DyaL3MXltFSgtro%3D Occurrence Handle7028991
IHM Brümmer W Fehr I Wagner-Döbler (2000) ArticleTitleBiofilm community structure in polluted rivers: abundance of dominant phylogenetic groups over a complete annual cycle. Appl Environ Microb 66 3078–3082 Occurrence Handle10877809
AT Bull M Goodfellow JH Slater (1992) ArticleTitleBiodiversity as a source of innovation in biotechnology. Annu Rev Microbiol 46 219–252 Occurrence Handle10.1146/annurev.micro.46.1.219 Occurrence Handle1:CAS:528:DyaK3sXhtVSgu7s%3D Occurrence Handle1444255
EO Casamayor H Schafer L Baneras C Pedros-Alio G Muyzer (2000) ArticleTitleIdentification of and spatio-temporal differences between microbial assemblages from two neighbouring sulfurous lakes: Comparison by microscopy and denaturing gradient gel electrophoresis. Appl Environ Microb 66 499–508 Occurrence Handle1:CAS:528:DC%2BD3cXhtFerur0%3D Occurrence Handle10653710
MT Cottrell DL Kirchman (2000) ArticleTitleCommunity composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl Environ Microb 66 5116–5122 Occurrence Handle1:CAS:528:DC%2BD3MXjsVyhtLs%3D
E Cytryn D Minz RS Oremland Y Cohen (2000) ArticleTitleDistribution and diversity of archaea corresponding to the limnological cycle of a hypersaline stratified lake (Solar lake, Sinai, Egypt) Appl Environ Microb 66 3269–3276 Occurrence Handle1:CAS:528:DC%2BD3cXlsFaku7o%3D Occurrence Handle10919780
H Daims A Brühl R Amann K-H Schleifer M Wagner (1999) ArticleTitleThe 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 Occurrence Handle1:CAS:528:DyaK1MXmvVentrw%3D Occurrence Handle10553296
CF D’Elia PA Steudler N Corwin (1977) ArticleTitleDetermination of total nitrogen in aqueous samples using persulphate digestion. Limnol Oceanogr 22 760–764 Occurrence Handle1:CAS:528:DyaE2sXlslamtbc%3D
JC Ellis-Evans (1982) ArticleTitleSeasonal microbial activity in Antarctic freshwater lake sediments. Polar Biol 1 129–140
JC Ellis-Evans (1996) ArticleTitleMicrobial diversity and function in Antarctic freshwater ecosystems. Biodivers Conserv 5 1395–1431
FO Glöckner R Amann A Alfreider J Pernthaler R Psenner K Trebesius K-H Schleifer (1996) ArticleTitleAn in situ hybridization protocol for detection and identification of planktonic bacteria. Syst Appl Microbiol 19 403–406
FO Glöckner BM Fuchs R Amann (1999) ArticleTitleBacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl Environ Microb 65 3721–3726
HJM Harmsen D Prieur C Jeanthon (1997) ArticleTitleGroup-specific 16S rRNA-targeted oligonucleotide probes to identify thermophilic bacteria in marine hydrothermal vents. Appl Environ Microb 63 4061–4068 Occurrence Handle1:CAS:528:DyaK2sXms1Sgt7g%3D
IM Head JR Saunders RW Pickup (1998) ArticleTitleMicrobial evolution, diversity, and ecology: A decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol 35 1–21 Occurrence Handle9459655
Helms C (1990) Method: Denaturing gradient gel electrophoresis (DGGE) http://hdklab.wustl.edu/lab_manual/dgge/dgge1.html%25
RB Heywood HJG Dartnall J Priddle (1980) ArticleTitleCharacteristics and classification of the lakes of Signy Island, South Orkney Islands, Antarctica. Freshwater Biol 10 47–59
CR Jackson PF Churchill EE Roden (2001) ArticleTitleSuccessional changes in bacterial assemblage structure during epilithic biofilm development. Ecology 82 555–566
K Jürgens J Pernthaler S Schalla R Amann (1999) ArticleTitleMorphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing. Appl Environ Microb 65 1241–1250
E Llobet-Brossa R Rosselló-Mora R Amann (1998) ArticleTitleMicrobial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl Environ Microb 64 2691–2696 Occurrence Handle9647850
FJH Mackereth J Heron JF Talling (1989) Water analysis: Some revised methods for limnologists. Freshwater Biological Association Ambleside, Cumbria, UK
W Manz R Amann W Ludwig M Wagner K-H Schleifer (1992) ArticleTitlePhylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst Appl Microbiol 15 593–600
W Manz R Amann W Ludwig M Vancanneyt K-H Schleifer (1996) ArticleTitleApplication 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
AE Murray CM Preston R Massana LT Taylor A Blakis K Wu EF Delong (1998) ArticleTitleSeasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica. Appl Environ Microb 64 2585–2595 Occurrence Handle1:CAS:528:DyaK1cXkt1Ogsrw%3D Occurrence Handle9647834
G Muyzer EC de Waal AG Uitterlinden (1993) ArticleTitleProfiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction–amplified genes coding for 16S rRNA. Appl Environ Microb 59 695–700 Occurrence Handle7683183
G Muyzer A Teske CO Wirsen HW Jannasch (1995) ArticleTitlePhylogenetic 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 Occurrence Handle10.1007/s002030050250 Occurrence Handle1:CAS:528:DyaK2MXovFyjsrk%3D Occurrence Handle7545384
J Overmann MJL Coolen C Tuschak (1999) ArticleTitleSpecific detection of different phylogenetic groups of chemocline bacteria based on PCR and denaturing gradient gel electrophoresis of 16S rRNA gene fragments. Arch Microbiol 172 83–94 Occurrence Handle10415169
L Øvreås L Forney FL Daae V Torsvik (1997) ArticleTitleDistribution of bacterioplankton in meromictic lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microb 63 3367–3373 Occurrence Handle9292986
DA Pearce (2000) ArticleTitleA rapid, sensitive method for monitoring bacterioplankton community dynamics, applied to Antarctic freshwater lakes. Polar Biol 23 352–356
J Pernthaler A Alfreider T Posch S Andreatta R Psenner (1997) ArticleTitleIn situ classification and image cytometry of pelagic bacteria from a high mountain lake (Gossenköllesee, Austria) Appl Environ Microb 63 4778–4783 Occurrence Handle1:CAS:528:DyaK2sXnvV2rt7o%3D
J Pernthaler FO Glöckner S Unterholzner A Alfreider R Psenner R Amann (1998) ArticleTitleSeasonal community and population dynamics of pelagic bacteria and archaea in a high mountain lake. Appl Environ Microb 64 4299–4306 Occurrence Handle9797280
KG Porter YS Feig (1980) ArticleTitleThe use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25 943–948
NB Ramsing H Fossing TG Ferdelman F Andersen B Thamdrup (1996) ArticleTitleDistribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl Environ Microb 62 1391–1404 Occurrence Handle1:CAS:528:DyaK28XitFektL0%3D
H Sass E Wieringa H Cypionka HD Babenzien J Overmann (1998) ArticleTitleHigh genetic and physiological diversity of sulfate-reducing bacteria isolated from an oligotrophic lake sediment. Arch Microbiol 170 243–251 Occurrence Handle10.1007/s002030050639 Occurrence Handle1:CAS:528:DyaK1cXms1Gjt7o%3D Occurrence Handle9732438
M Simon FO Glöckner R Amann (1999) ArticleTitleDifferent community structure and temperature optima of heterotrophic picoplankton in various regions of the Southern Ocean. Aquat Microb Ecol 18 275–284
J Snaidr R Amann I Huber W Ludwig K-H Schleifer (1997) ArticleTitlePhylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63 2884–2896 Occurrence Handle1:CAS:528:DyaK2sXktlekt7Y%3D Occurrence Handle9212435
PL Southwick LA Ernst EW Tauriello SR Parker RB Mujumdar SR Mujumdar HA Clever AS Waggoner (1990) ArticleTitleCyanine dye labeling reagents—carboxymethylindocyanine succinimidyl esters. Cytometry 11 418–430 Occurrence Handle1:CAS:528:DyaK3MXit1Crtbw%3D Occurrence Handle2340776
E Stackebrandt MF Goodfellow (1991) Nucleic Acid Techniques in Bacterial Systematics. Modern Microbiological Methods series. Wiley and Sons New York
DA Stahl R Amann (1991) Development and application of nucleic acid probes. E Stackebrandt M Goodfellow (Eds) Nucleic Acid Techniques in Bacterial Systematics. John Wiley and Sons Chichester, UK 205–248
EJ Van Hannen W Mooij MP van Agterveld HJ Gons HJ Laanbroek (1999) ArticleTitleDetritus-dependent development of the microbial community in an experimental system: Qualitative analysis by denaturing gradient gel electrophoresis. Appl Environ Microbiol 65 2478–2484 Occurrence Handle1:CAS:528:DyaK1MXjs12gsb8%3D Occurrence Handle10347030
EJ Van Hannen G Zwart MP van Agterveld HJ Gons J Ebert HJ Laanbroek (1999) ArticleTitleChanges in bacterial and eukaryotic community structure after mass lysis of filamentous cyanobacteria associated with viruses. Appl Environ Microb 65 795–801 Occurrence Handle9925618
MA Voytek TL Nadeau LJ Kerkof (2000) Assessing microbial genetic diversity in freshwater Antarctic ponds using two PCR-based techniques. CR Bell M Brylinsky P Johnson-Green (Eds) Microbial Biosystems: New Frontiers. Proceedings of the 8th International Symposium on Microbial Ecology, Halifax Nova Scotia
M Wagner R Amann H Lemmer K-H Schleifer (1993) ArticleTitleProbing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependant methods for describing community structure. Appl Environ Microbiol 59 1520–1525 Occurrence Handle1:CAS:528:DyaK3sXktlels7s%3D Occurrence Handle8517747
M Wagner R Amann P Kämpfer B Assamus A Hartmann P Hutzler N Springer K-H Schleifer (1994) ArticleTitleIdentification and in situ detection of gram-negative filamentous bacteria in activated sludge. Syst Appl Microbiol 17 405–417
DM Ward MM Bateson R Weller AL Ruff-Roberts (1992) ArticleTitleRibosomal RNA analysis of microorganisms as they occur in nature. Adv Microb Ecol 12 219–286 Occurrence Handle1:CAS:528:DyaK3sXlsFGmtLo%3D
P Weiss B Schweitzer R Amann M Simon (1996) ArticleTitleIdentification in situ and dynamics of bacteria on limnetic organic aggregates (lake snow) Appl Environ Microbiol 62 1998–2005
NA Welschmeyer (1994) ArticleTitleFluorimetric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol Oceanogr 39 1985–1992 Occurrence Handle1:CAS:528:DyaK2MXks1Sru70%3D
FV Wintzingerode UB Göbel E Stackebrandt (1997) ArticleTitleDetermination of microbial diversity in environmental samples: pitfalls of PCR based rRNA analysis. FEMS Microbiol Rev 21 213–229 Occurrence Handle9451814
G Zwart WD Hiorns B Methe MP Van Agterveld R Huismans SC Nold JP Zehr HJ Laanbroek (1998) ArticleTitleNearly 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 Occurrence Handle1:STN:280:DyaK1M7itlyqug%3D%3D Occurrence Handle9924823
W Zwisler M Simon (2000) Analysis of the structural composition and function of aquatic bacteria communities in a mesotrophic lake. CR Bell M Brylinsky P Johnson-Green (Eds) Microbial Biosystems: New Frontiers. Proceedings of the 8th International Symposium on Microbial Ecology, Halifax Nova Scotia
Acknowledgements
I thank the Natural Environment Research Council through the British Antacrtic Survey for providing funding and facilities for this work, TAFB for time to process the data, and all the members of Signy Island research station for their assistance and support. I also thank in particular Matt Edworthy, who helped with the collection of samples in the field and who undertook the chemical analysis of the lake water, and Dr. J.C. Ellis-Evans, Dr. Alex D. Rogers, and each of the referees for helpful comments on the manuscript.
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Pearce, D. Bacterioplankton Community Structure in a Maritime Antarctic Oligotrophic Lake during a Period of Holomixis, as Determined by Denaturing Gradient Gel Electrophoresis (DGGE) and Fluorescence in Situ Hybridization (FISH) . Microb Ecol 46, 92–105 (2003). https://doi.org/10.1007/s00248-002-2039-3
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DOI: https://doi.org/10.1007/s00248-002-2039-3