Home LiteratureArticle Details
PMID: 11823184 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean.

Applied and environmental microbiology ·Vol. 68 ·No. 2 ·2002-02-00 ·Pages 505-18

Bano N, Hollibaugh JT

Abstract

We analyzed the phylogenetic composition of bacterioplankton assemblages in 11 Arctic Ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and the clone libraries. Sequences of 88 clones fell into seven major lineages of the domain Bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-Proteobacteria; Cytophaga-Flexibacter-Bacteroides spp. (9%); Verrucomicrobium spp. (6%); and green nonsulfur bacteria (2%). A total of 34% of the cloned sequences (excluding clones in the SAR11 and Roseobacter groups) had sequence similarities that were <94% compared to previously reported sequences, indicating the presence of novel sequences. DGGE fingerprints of the selected samples showed that most of the bands were common to all samples in all three seasons. However, additional bands representing sequences related to Cytophaga and Polaribacter species were found in samples collected during the summer and fall. Of the clones in a library generated from one sample collected in spring of 1995, 50% were the same and were most closely affiliated (99% similarity) with Alteromonas macleodii, while 50% of the clones in another sample were most closely affiliated (90 to 96% similarity) with Oceanospirillum sp. The majority of the cloned sequences were most closely related to uncultured, environmental sequences. Prominent among these were members of the SAR11 group. Differences between mixed-layer and halocline samples were apparent in DGGE fingerprints and clone libraries. Sequences related to alpha-Proteobacteria (dominated by SAR11) were abundant (52%) in samples from the mixed layer, while sequences related to gamma-proteobacteria were more abundant (44%) in halocline samples. Two bands corresponding to sequences related to SAR307 (common in deep water) and the high-G+C gram-positive bacteria were characteristic of the halocline samples.

MeSH Terms
Arctic Regions Bacteria/classification,genetics Cloning, Molecular/methods DNA Fingerprinting/methods DNA, Bacterial/analysis,genetics DNA, Ribosomal/analysis,genetics Ecosystem Electrophoresis/methods Genes, rRNA Molecular Sequence Data Phylogeny RNA, Ribosomal, 16S/genetics Seawater/microbiology Sequence Analysis, DNA
Chemicals
DNA, Bacterial DNA, Ribosomal RNA, Ribosomal, 16S
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Bano Nasreen
Department of Marine Sciences, University of Georgia, Athens, GA 30602-3636, USA.
Hollibaugh James T
References (36)
36 references, click to expand
  1. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom.
    Appl Environ Microbiol. 2000 Feb;66(2):578-87 PMID: 10653721
  2. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity.
    Appl Environ Microbiol. 2000 Aug;66(8):3376-80 PMID: 10919794
  3. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli.
    Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801-5 PMID: 368799
  4. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes.
    Nature. 1998 Jun 4;393(6684):464-7 PMID: 9624000
  5. Proteorhodopsin phototrophy in the ocean.
    Nature. 2001 Jun 14;411(6839):786-9 PMID: 11459054
  6. Diversity of free-living and attached bacteria in offshore Western Mediterranean waters as depicted by analysis of genes encoding 16S rRNA.
    Appl Environ Microbiol. 1999 Feb;65(2):514-22 PMID: 9925576
  7. Polymerase chain reaction reveals cloning artefacts.
    Nature. 1988 Aug 4;334(6181):387-8 PMID: 2841606
  8. Successional changes in the genetic diversity of a marine bacterial assemblage during confinement.
    Arch Microbiol. 2000 Feb;173(2):138-45 PMID: 10795685
  9. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans.
    Appl Environ Microbiol. 1993 May;59(5):1294-302 PMID: 7685997
  10. Culturability and In situ abundance of pelagic bacteria from the North Sea.
    Appl Environ Microbiol. 2000 Jul;66(7):3044-51 PMID: 10877804
  11. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.
    Int J Syst Bacteriol. 1999 Apr;49 Pt 2:705-24 PMID: 10319494
  12. Diversity 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 Microbiol. 2000 May;66(5):1960-9 PMID: 10788367
  13. A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer.
    Appl Environ Microbiol. 1997 Apr;63(4):1441-8 PMID: 9097442
  14. Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria.
    J Bacteriol. 1994 Nov;176(21):6623-30 PMID: 7961414
  15. High bacterial diversity in permanently cold marine sediments.
    Appl Environ Microbiol. 1999 Sep;65(9):3982-9 PMID: 10473405
  16. Microvariation artifacts introduced by PCR and cloning of closely related 16S rRNA gene sequences.
    Appl Environ Microbiol. 2001 Jan;67(1):469-72 PMID: 11133483
  17. Seasonal and spatial variability of bacterial and archaeal assemblages in the coastal waters near Anvers Island, Antarctica.
    Appl Environ Microbiol. 1998 Jul;64(7):2585-95 PMID: 9647834
  18. Nearly all single base substitutions in DNA fragments joined to a GC-clamp can be detected by denaturing gradient gel electrophoresis.
    Nucleic Acids Res. 1985 May 10;13(9):3131-45 PMID: 4000972
  19. Fluorometric determination of DNA in aquatic microorganisms by use of hoechst 33258.
    Appl Environ Microbiol. 1982 Jun;43(6):1393-9 PMID: 16346035
  20. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria.
    Appl Environ Microbiol. 1997 Jan;63(1):63-70 PMID: 8979340
  21. Phylogenetic compositions of bacterioplankton from two California estuaries compared by denaturing gradient gel electrophoresis of 16S rDNA fragments.
    Appl Environ Microbiol. 1996 Jul;62(7):2676-80 PMID: 8779608
  22. Biodiversity of gas vacuolate bacteria from Antarctic sea ice and water.
    Appl Environ Microbiol. 1995 Sep;61(9):3486-9 PMID: 7574660
  23. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  24. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of 'Flectobacillus glomeratus' as Polaribacter glomeratus comb. nov.
    Int J Syst Bacteriol. 1998 Jan;48 Pt 1:223-35 PMID: 9542092
  25. 16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria.
    Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7979-84 PMID: 8755588
  26. Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium.
    Int J Syst Bacteriol. 1998 Apr;48 Pt 2:339-48 PMID: 9731272
  27. Fundibacter jadensis gen. nov., sp. nov., a new slightly halophilic bacterium, isolated from intertidal sediment.
    Int J Syst Bacteriol. 1999 Apr;49 Pt 2:441-8 PMID: 10319463
  28. Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I.
    Mol Ecol. 2000 Jul;9(7):935-48 PMID: 10886656
  29. Poles apart: biodiversity and biogeography of sea ice bacteria.
    Annu Rev Microbiol. 1999;53:189-215 PMID: 10547690
  30. Effect of iron supply on Southern Ocean CO2 uptake and implications for glacial atmospheric CO2.
    Nature. 2000 Oct 12;407(6805):730-3 PMID: 11048716
  31. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis.
    FEMS Microbiol Rev. 1997 Nov;21(3):213-29 PMID: 9451814
  32. Distribution and diversity of sulfur-oxidizing Thiomicrospira spp. at a shallow-water hydrothermal vent in the Aegean Sea (Milos, Greece).
    Appl Environ Microbiol. 1999 Sep;65(9):3843-9 PMID: 10473384
  33. Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing.
    Appl Environ Microbiol. 1991 Jun;57(6):1707-13 PMID: 1714704
  34. Environmental diversity of bacteria and archaea.
    Syst Biol. 2001 Aug;50(4):470-8 PMID: 12116647
  35. Bacterial community structure associated with a dimethylsulfoniopropionate-producing North Atlantic algal bloom.
    Appl Environ Microbiol. 2000 Oct;66(10):4237-46 PMID: 11010865
  36. Gas vesicles.
    Microbiol Rev. 1994 Mar;58(1):94-144 PMID: 8177173
Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
DOI
10.1128/AEM.68.2.505-518.2002
Published
2002-02-00
Pages
505-18
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC126663
Subset
IM
Databases
GENBANK
AF353208, AF353209, AF353210, AF353212, AF353213, AF353214, AF353215, AF353216, AF353217, AF353218, AF353219, AF353220, AF353221, AF353222, AF353223, AF353224, AF353225, AF353226, AF353227, AF353228, AF353229, AF353230, AF353231, AF353232, AF353233, AF353234, AF353235, AF353237, AF353238, AF353239, AF353240, AF353241, AF353242, AF354595, AF354596, AF354597, AF354598, AF354599, AF354600, AF354601, AF354602, AF354603, AF354604, AF354605, AF354606, AF354607, AF354609, AF354610, AF354611, AF354612, AF354613, AF354615, AF354616, AF354617, AF355044
External Links
PubMed source DOI: 10.1128/AEM.68.2.505-518.2002 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2