Comparison of the microbiota recovered from surface and deep subsurface rock, water, and soil along an elevational gradient

Haldeman, Dana L.; Pitonzo, Beth J.; Story, Sandra P.; Amy, Penny S.

doi:10.1080/01490459409377976

Cited by 14 publications

(2 citation statements)

References 25 publications

(17 reference statements)

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“…During the last 10 years, the U.S. Department of Energy's (DOE) Subsurface Science Program has sponsored numerous geomicrobiological investigations of subsurface environments. This effort has revealed surprising microbial and metabolic diversity at depths previously thought to be devoid of microbial life [1–6]. Most of these investigations have relied upon traditional culture‐based methods to assess the presence, abundance, diversity, spatial distribution and phylogenetic traits of subsurface microbes.…”

Section: Introductionmentioning

confidence: 99%

A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment

Chandler

Spadoni

et al. 2006

FEMS Microbiology Ecology

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Culture‐based techniques have traditionally been the primary tools utilized for studying the microbiology of terrestrial subsurface environments. Recently, nucleic acid‐based methods have been employed to further characterize the microbial diversity in subsurface sediments and rocks, but the results have not been related to individual bacteria cultivated from the same environment. Restriction fragment length profiles of 16S rRNA genes derived from bulk community DNA or bacterial isolates were compared to determine the efficacy of PCR‐based methods for studying microbial diversity and phylogeny in a deep (188 m) subsurface environment. The phylogenetic relatedness between 16S rRNA genes of enrichment cultures and individual clones was also determined through DNA sequence analysis of 16S rRNA genes. Restriction fragment length profiles from PCR clone libraries accounted for 64% of recovered isolates and 55% of the estimated culturable diversity based upon their 16S rDNA RFLP signatures. DNA sequence comparisons between the 16S rDNA of the most commonly occurring isolates and clones confirmed that similar DNA sequences were contained within the RFLP groups used to categorize the isolates and clones. For 7 of 8 RFLP groups for which DNA sequences were obtained, nearest neighbor assignments corresponded at the genus level but suggested that 16S rDNA sequences from multiple genera were contained within single RFLP profiles. Phylogenetic analysis of 16S rRNA sequences supported the nearest neighbor inferences and indicated that 16S rDNA clones derived from bulk sediment were specifically related to isolates recovered on enrichment plates. This study has shown that a majority of the cultivated aerobic heterotrophic bacteria in a subsurface sediment could be described by 16S rDNA clones obtained from directly extracted DNA, but that PCR‐based methods cannot account for all organisms from a given sample. Consequently, a more comprehensive assessment of microbial diversity in subsurface (and probably other) environments can be obtained by using a combination of culture‐ and molecular‐based techniques than by using either method alone.

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Section: Introductionmentioning

confidence: 99%

A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment

Chandler

Spadoni

et al. 2006

FEMS Microbiology Ecology

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“…One would expect to find native subsurface microbes in the repository environment. Microbial communities have been isolated from a variety of deep subsurface environments, and ongoing work has already identified some of the native microbiota in the Yucca Mountain region (Russell et al, 1994;Haldeman et al, 1994;.…”

Section: Preliminary Evidence Shows That Bacteria May Promote Dissolumentioning

confidence: 99%

Microbial activity at Yucca Mountain

Horn¹,

Meike²

1995

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Volcanic Tuffs: Deep Subsurface Microbiology of

Haldeman

Amy

2003

Encyclopedia of Environmental Microbiology

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Comparison of the microbiota recovered from surface and deep subsurface rock, water, and soil along an elevational gradient

Cited by 14 publications

References 25 publications

A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment

A molecular comparison of culturable aerobic heterotrophic bacteria and 16S rDNA clones derived from a deep subsurface sediment

Microbial activity at Yucca Mountain

Volcanic Tuffs: Deep Subsurface Microbiology of

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