Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans - PubMed (original) (raw)

Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans

J A Fuhrman et al. Appl Environ Microbiol. 1993 May.

Erratum in

Appl Environ Microbiol 1995 Dec;61(12):4517

Abstract

The extent of the diversity of marine prokaryotes is not well known, primarily because of poor cultivability. However, new techniques permit the characterization of such organisms without culturing, via 16S rRNA sequences obtained directly from biomass. We performed such an analysis by polymerase chain reaction amplification with universal primers on five oligotrophic open-ocean samples: from 100-m (three samples) and 500-m depths in the western California Current (Pacific Ocean) and from a 10-m depth in the Atlantic Ocean near Bermuda. Of 61 clones, 90% were in clusters of two or more related marine clones obtained by ourselves or others. We report 15 clones related to clone SAR 11 found earlier near Bermuda (S. J. Giovannoni, T. B. Britschgi, C. L. Moyer, and K. G. Field, Nature [London] 345:60-63, 1990), 11 related to marine cyanobacteria, 9 clustered in a group affiliated with gram-positive bacteria, 9 in an archaeal cluster we recently described (mostly from the 500-m sample), 4 in a novel gamma-proteobacterial cluster, and 6 in three two-membered clusters (including other archaea). One clone was related to flavobacteria. Only the cyanobacteria plus one other clone, related to Roseobacter denitrificans (formerly Erythrobacter longus Och114), were within 10% sequence identity to any previously sequenced cultured organism in a major data base. We never found more than two occurrences of the same sequence in a sample, although four times we found identical sequences between samples, two of which were between oceans; one of these sequences was also identical to SAR 11.(ABSTRACT TRUNCATED AT 250 WORDS)

PubMed Disclaimer

Cited by

Assessing the global phylum level diversity within the bacterial domain: A review.
Youssef NH, Couger MB, McCully AL, Criado AE, Elshahed MS. Youssef NH, et al. J Adv Res. 2015 May;6(3):269-82. doi: 10.1016/j.jare.2014.10.005. Epub 2014 Nov 4. J Adv Res. 2015. PMID: 26257925 Free PMC article. Review.
Microbial Composition and Variability of Natural Marine Planktonic and Biofouling Communities From the Bay of Bengal.
Angelova AG, Ellis GA, Wijesekera HW, Vora GJ. Angelova AG, et al. Front Microbiol. 2019 Dec 6;10:2738. doi: 10.3389/fmicb.2019.02738. eCollection 2019. Front Microbiol. 2019. PMID: 31866960 Free PMC article.
Ether lipids of planktonic archaea in the marine water column.
Hoefs M, Schouten S, De Leeuw JW, King LL, Wakeham SG, Damste J. Hoefs M, et al. Appl Environ Microbiol. 1997 Aug;63(8):3090-5. doi: 10.1128/aem.63.8.3090-3095.1997. Appl Environ Microbiol. 1997. PMID: 16535669 Free PMC article.
Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators.
Wu CH, Sercu B, Van de Werfhorst LC, Wong J, DeSantis TZ, Brodie EL, Hazen TC, Holden PA, Andersen GL. Wu CH, et al. PLoS One. 2010 Jun 23;5(6):e11285. doi: 10.1371/journal.pone.0011285. PLoS One. 2010. PMID: 20585654 Free PMC article.
Response of Archaeal communities in beach sediments to spilled oil and bioremediation.
Röling WF, de Brito Couto IR, Swannell RP, Head IM. Röling WF, et al. Appl Environ Microbiol. 2004 May;70(5):2614-20. doi: 10.1128/AEM.70.5.2614-2620.2004. Appl Environ Microbiol. 2004. PMID: 15128510 Free PMC article.

References

1. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5685-9 - PubMed
1. Nucleic Acids Res. 1988 Mar 11;16(5):1861-3 - PubMed
1. Nature. 1992 Jan 16;355(6357):267-70 - PubMed
1. Nature. 1990 May 3;345(6270):60-3 - PubMed
1. Methods Enzymol. 1988;164:793-812 - PubMed

Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans - PubMed (original) (raw)