skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample

Abstract

Numerous investigations applying the cloning and sequencing of rRNA genes (rDNAs) to the study of marine bacterioplankton diversity have shown that the sequences of genes cloned directly from environmental DNA do not correspond to the genes of cultured marine taxa. These results have been interpreted as support for the hypothesis that the most abundant heterotrophic marine bacterioplankton species are not readily culturable by commonly used methods. However, an alternative explanation is that marine bacterioplankton can be easily cultured but are not well represented in sequence databases. To further examine this question, we compared the small-subunit (SSU) rDNAs of 127 cellular clones isolated from a water sample collected off the Oregon coast to 58 bacterial SSU rDNAs cloned from environmental DNAs from the same water sample. The results revealed little overlap between partial SSU rDNA sequences from the cellular clones and the environmental clone library. An exception was the SSU rDNA sequence recovered from a cellular clone belonging to the Pseudomonas subgroup of the {gamma} subclass of the class Proteobacteria, which was related to a single gene cloned directly from the same water sample (OCS181) (similarity, 94.6%). In addition, partial SSU rDNA sequences from three of the cultured strains matched amore » novel rDNA clone related to the {gamma} subclass of the Proteobacteria found previously in an environmental clone library from marine aggregates (AGG53) (similarity, 94.3 to 99.6%). Our results support the hypothesis that many of the most abundant bacterioplankton species are not readily culturable by standard methods but also show that heterotrophic bacterioplankton that are culturable on media with high organic contents include many strains for which SSU rDNA sequences are not available in sequence databases. 34 refs., 4 figs., 3 tabs.« less

Authors:
; ;  [1]
  1. Oregon State Univ., Corvallis, OR (United States); and others
Publication Date:
OSTI Identifier:
518323
DOE Contract Number:  
FG06-93ER61697
Resource Type:
Journal Article
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 63; Journal Issue: 3; Other Information: PBD: Mar 1997
Country of Publication:
United States
Language:
English
Subject:
55 BIOLOGY AND MEDICINE, BASIC STUDIES; BACTERIA; GENETIC VARIABILITY; SEAWATER; AQUATIC ORGANISMS

Citation Formats

Suzuki, M T, Rappe, M S, and Haimberger, Z W. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. United States: N. p., 1997. Web.
Suzuki, M T, Rappe, M S, & Haimberger, Z W. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. United States.
Suzuki, M T, Rappe, M S, and Haimberger, Z W. 1997. "Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample". United States.
@article{osti_518323,
title = {Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample},
author = {Suzuki, M T and Rappe, M S and Haimberger, Z W},
abstractNote = {Numerous investigations applying the cloning and sequencing of rRNA genes (rDNAs) to the study of marine bacterioplankton diversity have shown that the sequences of genes cloned directly from environmental DNA do not correspond to the genes of cultured marine taxa. These results have been interpreted as support for the hypothesis that the most abundant heterotrophic marine bacterioplankton species are not readily culturable by commonly used methods. However, an alternative explanation is that marine bacterioplankton can be easily cultured but are not well represented in sequence databases. To further examine this question, we compared the small-subunit (SSU) rDNAs of 127 cellular clones isolated from a water sample collected off the Oregon coast to 58 bacterial SSU rDNAs cloned from environmental DNAs from the same water sample. The results revealed little overlap between partial SSU rDNA sequences from the cellular clones and the environmental clone library. An exception was the SSU rDNA sequence recovered from a cellular clone belonging to the Pseudomonas subgroup of the {gamma} subclass of the class Proteobacteria, which was related to a single gene cloned directly from the same water sample (OCS181) (similarity, 94.6%). In addition, partial SSU rDNA sequences from three of the cultured strains matched a novel rDNA clone related to the {gamma} subclass of the Proteobacteria found previously in an environmental clone library from marine aggregates (AGG53) (similarity, 94.3 to 99.6%). Our results support the hypothesis that many of the most abundant bacterioplankton species are not readily culturable by standard methods but also show that heterotrophic bacterioplankton that are culturable on media with high organic contents include many strains for which SSU rDNA sequences are not available in sequence databases. 34 refs., 4 figs., 3 tabs.},
doi = {},
url = {https://www.osti.gov/biblio/518323}, journal = {Applied and Environmental Microbiology},
number = 3,
volume = 63,
place = {United States},
year = {Sat Mar 01 00:00:00 EST 1997},
month = {Sat Mar 01 00:00:00 EST 1997}
}