PCR-based detection of non-indigenous microorganisms in ‘pristine’ environments

Abstract

PCR-based technologies are widely employed for the detection of specific microorganisms, and may be applied to the identification of non-indigenous microorganisms in 'pristine' environments. For 'pristine' environments such as those found on the Antarctic continent, the application of these methods to the assessment of environmental contamination from human activities must be treated with caution. Issues such as the possibility of non-human dispersal of organisms, stability and survival of non-indigenous organisms in vivo, the sensitivity, reproducibility and specificity of the PCR process (and particularly primer design) and the sampling regime employed must all be considered in detail. We conclude that despite these limitations, PCR and related technologies offer enormous scope for assessment of both natural and non-indigenous microbial distributions.

Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river

“…The bulk community DNA sequences were amplified with nine pairs of primers (Table 1) covering the different regions of the SSU ribosomal genes: two pairs of universal primers were used for both eukaryotes and prokaryotes (U1 and U2), one pair was used to detect archaea (A), four pairs were specific for prokaryotes (B1, B2, B3, and B4), and two pairs were specific for eukaryotes (Euc1 and Euc2). Primers were chosen according to previous analyses showing that biodiversity richness is linked to the primer sequences (Medlin et al 1988;Reysenbach et al 1994;Dassarma and Fleischmann 1995;Vetriani et al 1999;Baker et al 2003;Huse et al 2008). Only one primer was adapted for this study (343FB) (Hansen et al 1998).…”

Dissemination and survival of non-indigenous bacterial genomes in pristine Antarctic environments

“…Microbial contamination has been detected at both the macroscopic (Eckford et al 2002) and microscopic levels. For example, there are numerous reports on the isolation or detection of non-indigenous enteric bacteria derived from human faecal waste (McFeters et al 1993;Edwards et al 1998;Sjoling and Cowan 2000;Bruni et al 1997;Baker et al 2003). Here we show that non-enteric human commensal microbiota are rapidly disseminated into the Antarctic Dry Valley mineral soils tested, and that although cell viability is rapidly lost, non-viable cells and/or naked DNA persist for long periods.…”

Exploring the Last Continent

“…Molecular approaches can also be used to target specific microbial 'indicators' of human activity (Baker et al 2003).…”