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

Abstract

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.

Topographic effects of coastal seas on the composition of the culturable bacterial communities in marine sediments

“…However, the study of the composition of the culturable bacteria in the analysis of entire bacterial communities in the environment has been proven to be beneficial by Ellis et al (2003) who demonstrated that in soils, culturable bacteria are the most active prokaryotes in environmental samples and provide a rapid assessment of biological responses to pollution. Furthermore, Chandler et al (1997) also previously reported that the majority of the data on marine sediment bacteria detected by culture-based methods can match and closely complement data obtained from culture-independent approaches. Therefore the differences in the compositions of the culturable strains from the open and the enclosed coastal seas in this study are considered to reflect their topographic differences.…”

Fungal diversity associated with Brazilian energy transmission towers

“…Conversely, enrichment cultures recovered a higher number of yeast isolates in comparison with filamentous fungi isolates. The observed differences in the microbial community composition revealed by the two strategies was already reported in other studies regarding soil and sediments (Chandler et al 1997;Stephen et al 1996) and petroleum reservoir (Sette et al 2007), suggesting that using a combined technique allow for a more comprehensive assessment of the microbial diversity from environmental samples.…”

“…Culture-based techniques have traditionally been the primary tools used for studying how microbes are structured in their environments (Chandler et al 1997). These approaches do not necessarily provide comprehensive information on the composition of microbial communities (van Hamme et al 2003).…”

Analysis of the composition of bacterial communities in oil reservoirs from a southern offshore Brazilian basin

“…Theses discrepancies between microbial groups recovered using the two strategies were also observed by other authors in different environments, such as soil and sediment (Chandler et al 1997;Stephen et al 1996), suggesting that a more comprehensive assessment of microbial diversity in oil, and probably other environments, can be obtained by using a combination of culture-and molecular-based techniques than by using either method alone.…”

“…Culture-based techniques have traditionally been the primary tools used for studying the microbiology of different environments (Chandler et al 1997). These approaches, while extremely important for understanding the physiological potential of isolated organisms, do not necessarily provide comprehensive information on the composition of microbial communities (van Hamme et al 2003).…”