The prevalence and diversity of mobile genetic elements in bacterial communities of different environmental habitats: insights gained from different methodological approaches

Abstract

The pool of mobile genetic elements (MGE) in microbial communities consists of plasmids, bacteriophages and other elements that are either self-transmissible or use mobile plasmids and phages as vehicles for their dissemination. By facilitating horizontal gene exchange, the horizontal gene pool (HGP) promotes the evolution and adaptation of microbial communities. Efforts to characterise MGE from bacterial populations resident in a variety of ecological habitats have revealed a surprisingly vast and seemingly untapped diversity. MGE, conferring such selectable traits as mercury or antibiotic resistance and degradative functions, have been readily acquired from diverse microbial communities. To circumvent the need to isolate microbial hosts, polymerase chain reaction (PCR)-based detection methods have frequently been used to assess the prevalence of MGE-specific sequences resident in the 'microbial community' HGP. As studies continue to reveal novel and distinct MGE, sequencing of newly isolated MGE from diverse habitats is essential for the continued development of DNA probes, PCR primers as well as for gene array and proteomics-based approaches. This minireview highlights insight gained from different methodological approaches, biased albeit largely toward plasmids in Gram-negative bacteria, used to study the HGP of naturally occurring microbial communities from various aquatic and terrestrial habitats.

Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities

“…Several studies have detected MGEs including plasmids, transposons and integrons across a wide variety of habitats (for example, Sobecky, 1999;Smalla and Sobecky, 2002;van Elsas and Bailey, 2002;Frost et al, 2005), but rarely in a quantitative manner due to previous methodological constraints. In those studies that did quantify MGE abundance in bacterial communities, class 1 integrase (intI1) genes were shown to be abundant in Gram-positive and Gram-negative bacteria in poultry litter obtained from farms with varying antibiotic usage regimes regardless of antibiotic usage (Nandi et al, 2004), while mercury exposure was recently demonstrated to increase the abundance of IncP-1 plasmids (Smalla et al, 2006).…”

Safety Assessment of Transgenic Organisms, Volume 4

“…Approximately 18% of bacterial isolates from the phytosphere of sugar beets were found to contain plasmids (Powell et al, 1993) and a large proportion of these plasmids were able to mobilise non-self-transferable but mobilisable IncQ plasmids . To whatever extent environmental samples have been used, recipients functioning as a genetic sink and introduced under laboratory or in situ conditions have acquired MGEs conferring selectable traits such as mercury or antibiotic resistance (Smalla and Sobecky, 2002). In several of the studies increased transfer frequencies were observed when the environmental samples were stressed with pollutants.…”

“…A clear limitation of the endogenous plasmid isolation technique is the dependence on culturability of the plasmid host. Another disadvantage of endogenous plasmid isolations is that nothing is known about the relevance of such plasmids to in situ gene transfer processes Smalla and Sobecky, 2002). Plasmids with a high transfer potential might be overlooked when their hosts are less dominant or belong to the majority of bacteria which are not accessible by the cultivation techniques used.…”

Horizontal gene transfer between bacteria

“…Approximately 18% of bacterial isolates from the phytosphere of sugar beets were found to contain plasmids (Powell et al, 1993), and a large proportion of these plasmids were able to mobilize non-selftransferable but mobilizable IncQ plasmids (Kobayashi and Bailey, 1994). The exogenous isolation of MGEs, which was originally used to retrieve plasmids from river epilithon (Bale et al, 1988), was also successfully used to capture MGEs from soil or phytosphere communities (Smalla and Sobecky, 2002). Recipients functioning as a genetic sink, and introduced under laboratory or in situ conditions, have acquired MGEs conferring selectable traits such as mercury or antibiotic resistance from the bacterial fraction of bulk or rhizosphere soil (Drønen et al, 1998;Heuer and Smalla, 2007;Heuer et al, 2002;van Overbeek et al, 2002).…”