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PMID: 16332756 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Microbial diversity in coastal subsurface sediments: a cultivation approach using various electron acceptors and substrate gradients.

Applied and environmental microbiology ·Vol. 71 ·No. 12 ·2005-12-00 ·Pages 7819-30

Köpke B, Wilms R, Engelen B, Cypionka H, Sass H

Abstract

Microbial communities in coastal subsurface sediments are scarcely investigated and have escaped attention so far. But since they are likely to play an important role in biogeochemical cycles, knowledge of their composition and ecological adaptations is important. Microbial communities in tidal sediments were investigated along the geochemical gradients from the surface down to a depth of 5.5 m. Most-probable-number (MPN) series were prepared with a variety of different carbon substrates, each at a low concentration, in combination with different electron acceptors such as iron and manganese oxides. These achieved remarkably high cultivation efficiencies (up to 23% of the total cell counts) along the upper 200 cm. In the deeper sediment layers, MPN counts dropped significantly. Parallel to the liquid enrichment cultures in the MPN series, gradient cultures with embedded sediment subcores were prepared as an additional enrichment approach. In total, 112 pure cultures were isolated; they could be grouped into 53 different operational taxonomic units (OTU). The isolates belonged to the Proteobacteria, "Bacteroidetes," "Fusobacteria," Actinobacteria, and "Firmicutes." Each cultivation approach yielded a specific set of isolates that in general were restricted to this single isolation procedure. Analysis of the enrichment cultures by PCR and denaturing gradient gel electrophoresis revealed an even higher diversity in the primary enrichments that was only partially reflected by the culture collection. The majority of the isolates grew well under anoxic conditions, by fermentation, or by anaerobic respiration with nitrate, sulfate, ferrihydrite, or manganese oxides as electron acceptors.

MeSH Terms
Actinobacteria/classification,isolation & purification,metabolism Bacteria, Anaerobic/classification,isolation & purification,metabolism Bacteroidetes/classification,isolation & purification,metabolism Base Sequence Biodiversity Carbon/metabolism Chlorides/metabolism DNA Primers Electron Transport Fusobacterium/classification,isolation & purification,metabolism Geologic Sediments/microbiology Germany Molecular Sequence Data Phylogeny Polymerase Chain Reaction Proteobacteria/classification,isolation & purification,metabolism RNA/genetics RNA, Bacterial/genetics RNA, Ribosomal, 16S/genetics,isolation & purification Seawater/microbiology Sulfates/metabolism
Chemicals
Chlorides DNA Primers RNA, Bacterial RNA, Ribosomal, 16S Sulfates RNA Carbon
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Köpke Beate
Institut für Chemie und Biologie des Meeres, Universität Oldenburg, Carl-von-Ossietzky Strasse 9-11, D-26111 Oldenburg, Germany.
Wilms Reinhard
Engelen Bert
Cypionka Heribert
Sass Henrik
References (38)
38 references, click to expand
  1. Effect of anoxia and high sulphide concentrations on heterotrophic microbial communities in reduced surface sediments (Black Spots) in sandy intertidal flats of the German Wadden Sea.
    FEMS Microbiol Ecol. 2003 Jun 1;44(3):291-301 PMID: 19719610
  2. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology.
    Int J Syst Evol Microbiol. 2002 May;52(Pt 3):1043-7 PMID: 12054223
  3. Deep sub-seafloor prokaryotes stimulated at interfaces over geological time.
    Nature. 2005 Jul 21;436(7049):390-4 PMID: 16034418
  4. The anaerobic degradation of organic matter in Danish coastal sediments: iron reduction, manganese reduction, and sulfate reduction.
    Geochim Cosmochim Acta. 1993 Aug;57(16):3867-83 PMID: 11537734
  5. Aging in bacteria.
    Curr Opin Microbiol. 2002 Dec;5(6):596-601 PMID: 12457704
  6. Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania basin, Mediterranean Sea).
    Appl Environ Microbiol. 2001 Dec;67(12):5392-402 PMID: 11722884
  7. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter.
    Appl Environ Microbiol. 2000 Apr;66(4):1692-7 PMID: 10742262
  8. Energetics of syntrophic propionate oxidation in defined batch and chemostat cocultures.
    Appl Environ Microbiol. 2000 Jul;66(7):2934-42 PMID: 10877789
  9. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys.
    Environ Microbiol. 2002 Nov;4(11):654-66 PMID: 12460273
  10. Prokaryotes: the unseen majority.
    Proc Natl Acad Sci U S A. 1998 Jun 9;95(12):6578-83 PMID: 9618454
  11. Decrease in culturability of Vibrio cholerae caused by glucose.
    Appl Environ Microbiol. 1995 Jul;61(7):2583-8 PMID: 7618870
  12. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia.
    Appl Environ Microbiol. 2002 May;68(5):2391-6 PMID: 11976113
  13. Methanogens: reevaluation of a unique biological group.
    Microbiol Rev. 1979 Jun;43(2):260-96 PMID: 390357
  14. Succession of pelagic marine bacteria during enrichment: a close look at cultivation-induced shifts.
    Appl Environ Microbiol. 2000 Nov;66(11):4634-40 PMID: 11055904
  15. New techniques for isolation of single prokaryotic cells.
    FEMS Microbiol Rev. 2000 Dec;24(5):567-72 PMID: 11077150
  16. Ferrihydrite-dependent growth of Sulfurospirillum deleyianum through electron transfer via sulfur cycling.
    Appl Environ Microbiol. 2004 Oct;70(10):5744-9 PMID: 15466509
  17. Anaerobic microflora of everglades sediments: effects of nutrients on population profiles and activities.
    Appl Environ Microbiol. 1996 Feb;62(2):486-93 PMID: 16535236
  18. Detection of abundant sulphate-reducing bacteria in marine oxic sediment layers by a combined cultivation and molecular approach.
    Environ Microbiol. 2000 Aug;2(4):417-27 PMID: 11234930
  19. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
    Nucleic Acids Res. 1997 Dec 15;25(24):4876-82 PMID: 9396791
  20. Phylogenetic identification and in situ detection of individual microbial cells without cultivation.
    Microbiol Rev. 1995 Mar;59(1):143-69 PMID: 7535888
  21. Sensitive determination of microbial growth by nucleic acid staining in aqueous suspension.
    Appl Environ Microbiol. 2006 Jan;72(1):87-95 PMID: 16391029
  22. Cultivating the uncultured.
    Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15681-6 PMID: 12438682
  23. Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria.
    Appl Environ Microbiol. 2005 Feb;71(2):826-34 PMID: 15691937
  24. Ongoing modification of Mediterranean Pleistocene sapropels mediated by prokaryotes.
    Science. 2002 Jun 28;296(5577):2407-10 PMID: 12089447
  25. Dissimilatory Fe(III) and Mn(IV) reduction.
    Microbiol Rev. 1991 Jun;55(2):259-87 PMID: 1886521
  26. Stable-isotope probing as a tool in microbial ecology.
    Nature. 2000 Feb 10;403(6770):646-9 PMID: 10688198
  27. Distributions of microbial activities in deep subseafloor sediments.
    Science. 2004 Dec 24;306(5705):2216-21 PMID: 15618510
  28. Oligotrophic bacterioplankton with a novel single-cell life strategy.
    Appl Environ Microbiol. 2004 Apr;70(4):2445-51 PMID: 15066843
  29. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment.
    Science. 2002 May 10;296(5570):1127-9 PMID: 12004133
  30. New strategies for cultivation and detection of previously uncultured microbes.
    Appl Environ Microbiol. 2004 Aug;70(8):4748-55 PMID: 15294811
  31. Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology.
    Appl Environ Microbiol. 1999 Mar;65(3):1289-97 PMID: 10049895
  32. Searching for predominant soil bacteria: 16S rDNA cloning versus strain cultivation.
    FEMS Microbiol Ecol. 1999 Oct 1;30(2):137-145 PMID: 10508938
  33. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates.
    Appl Environ Microbiol. 2002 Aug;68(8):3878-85 PMID: 12147485
  34. Large fraction of dead and inactive bacteria in coastal marine sediments: comparison of protocols for determination and ecological significance.
    Appl Environ Microbiol. 2002 Jul;68(7):3509-13 PMID: 12089035
  35. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample.
    Appl Environ Microbiol. 1997 Mar;63(3):983-9 PMID: 9055415
  36. Quantitative analysis of bacterial communities from Mediterranean sapropels based on cultivation-dependent methods.
    FEMS Microbiol Ecol. 2004 Dec 27;51(1):109-21 PMID: 16329860
  37. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 PMID: 9254694
  38. Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms.
    Appl Environ Microbiol. 1999 Nov;65(11):5042-9 PMID: 10543821
Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
DOI
10.1128/AEM.71.12.7819-7830.2005
Published
2005-12-00
Pages
7819-30
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC1317335
Subset
IM
Databases
GENBANK
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External Links
PubMed source DOI: 10.1128/AEM.71.12.7819-7830.2005 PMC Full Text View journal details
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