Desulfotomaculum genus-and subgenus-specific 16S rRNA hybridization probes for environmental studies

Krassimira R. Hristova, Margit Mau, Dandan Zheng, Rustam I. Aminov, Roderick I. Mackie, H. Rex Gaskins, Lutgarde Raskin

Research output: Contribution to journalArticle

Abstract

Based on comparative analysis of 16S rRNA sequences and the recently established phylogeny of the genus Desulfotomaculum, a set of phylogenetically nested hybridization probes was developed and characterized. A genus-specific probe targets all known Desulfotomaculum species (with the exception of Desulfotomaculum acetoxidans), and five specific probes target subclusters within the Desulfotomaculum genus. The dissociation temperature of each probe was determined experimentally. Probe specificities were verified through hybridizations with pure culture rRNA isolated from a wide variety of target and non-target organisms and through an evaluation of probe 'nesting' using samples obtained from four different environments. Fixation and hybridization conditions for fluorescence in situ hybridizations were also optimized. The probes were used in quantitative membrane hybridizations to determine the abundance of Desulfotomaculum species in thermophilic anaerobic digesters, in soil, in human faeces and in pig colon samples. Desulfotomaculum rRNA accounted for 0.3-2.1% of the total rRNA in the digesters, 2.6-6.6% in soil, 1.5-3.3% in human faeces and 2.5-6.2% in pig colon samples.

Original languageEnglish (US)
Pages (from-to)143-159
Number of pages17
JournalEnvironmental Microbiology
Volume2
Issue number2
DOIs
StatePublished - Jan 1 2000

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Desulfotomaculum
probes (equipment)
probe
ribosomal RNA
hybridization
Desulfotomaculum acetoxidans
Feces
colon
pig
Colon
feces
Swine
Soil
anaerobic digesters
swine
nontarget organisms
nontarget organism
Phylogeny
fluorescence in situ hybridization
Fluorescence In Situ Hybridization

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Desulfotomaculum genus-and subgenus-specific 16S rRNA hybridization probes for environmental studies. / Hristova, Krassimira R.; Mau, Margit; Zheng, Dandan; Aminov, Rustam I.; Mackie, Roderick I.; Gaskins, H. Rex; Raskin, Lutgarde.

In: Environmental Microbiology, Vol. 2, No. 2, 01.01.2000, p. 143-159.

Research output: Contribution to journalArticle

Hristova, Krassimira R. ; Mau, Margit ; Zheng, Dandan ; Aminov, Rustam I. ; Mackie, Roderick I. ; Gaskins, H. Rex ; Raskin, Lutgarde. / Desulfotomaculum genus-and subgenus-specific 16S rRNA hybridization probes for environmental studies. In: Environmental Microbiology. 2000 ; Vol. 2, No. 2. pp. 143-159.
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