DOI: 10.1128/aem.65.4.1662-1669.1999. Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning

Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning

10.1128/aem.65.4.1662-1669.1999

Crossref journal-article

American Society for Microbiology

Applied and Environmental Microbiology (235)

Abstract

ABSTRACT Techniques based on amplification of 16S rRNA genes for comparing bacterial communities are now widely used in microbial ecology, but calibration of these techniques with traditional tools, such as cultivation, has been conspicuously absent. In this study, we compared levels of bacterial community diversity in two pinyon rhizosphere soil samples and two between-tree (interspace) soil samples by analyzing 179 cultivated bacterial isolates and 801 16S rRNA genes amplified from extracted soil DNA. Phylotypes were defined by performing a restriction fragment length polymorphism analysis of 16S rRNA gene sequences with the enzymes Rsa I and Bst UI. The average level of 16S rRNA gene sequence similarity of members of a phylotype was 86.6% based on an analysis of partial sequences. A total of 498 phylotypes were identified among the 16S ribosomal DNA (rDNA) clones, while 34 phylotypes occurred among the cultivated isolates. Analysis of sequences from a subset of the phylotypes showed that at least seven bacterial divisions were represented in the clone libraries, whereas the isolates represented only three. The phylotype richness, frequency distribution (evenness), and composition of the four culture collections and the four clone libraries were investigated by using a variety of diversity indices. Although cultivation and 16S rRNA cloning analyses gave contradictory descriptions of the relative phylotype richness for one of the four environments, the two methods identified qualitatively consistent relationships when levels of evenness were compared. The levels of phylotype similarity between communities were uniformly low (15 to 31%). Both methods consistently indicated that one environment was distinct from the other three. Our data illustrate that while 16S rDNA cloning and cultivation generally describe similar relationships between soil microbial communities, significant discrepancies can occur.

Bibliography

Dunbar, J., Takala, S., Barns, S. M., Davis, J. A., & Kuske, C. R. (1999). Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning. Applied and Environmental Microbiology, 65(4), 1662â1669.

Authors 5

John Dunbar (first)
Shannon Takala (additional)
Susan M. Barns (additional)
Jody A. Davis (additional)
Cheryl R. Kuske (additional)

References 51 Referenced 332

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Dates

Type	When
Created	5 years, 8 months ago (Dec. 19, 2019, 2:49 p.m.)
Deposited	3 years, 6 months ago (Feb. 23, 2022, 3:33 a.m.)
Indexed	2 months ago (July 2, 2025, 4:15 p.m.)
Issued	26 years, 5 months ago (April 1, 1999)
Published	26 years, 5 months ago (April 1, 1999)
Published Print	26 years, 5 months ago (April 1, 1999)

Funders 0

None

BibTeX

@article{Dunbar_1999, title={Levels of Bacterial Community Diversity in Four Arid Soils Compared by Cultivation and 16S rRNA Gene Cloning}, volume={65}, ISSN={1098-5336}, url={http://dx.doi.org/10.1128/aem.65.4.1662-1669.1999}, DOI={10.1128/aem.65.4.1662-1669.1999}, number={4}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Dunbar, John and Takala, Shannon and Barns, Susan M. and Davis, Jody A. and Kuske, Cheryl R.}, year={1999}, month=apr, pages={1662–1669} }

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      "value": "1998-09-04",
      "order": 0,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "1999-01-04",
      "order": 1,
      "name": "accepted",
      "label": "Accepted",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "1999-04-01",
      "order": 2,
      "name": "published",
      "label": "Published",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    }
  ]
}