Cultivation gives context to the microbial ecologist

Abstract

The posed debate asks whether cultivation has a place in contemporary environmental microbial ecology. Approximately two decades ago, cultivation-independent methods experienced an advance (Olsen et al. , 1986) concurrent with the establishment in the literature of the following sentence: ‘It is well known that 99.9% of all organisms are unculturable’ (Rothschild, 2006). While technical advancements have been made in sequence-based and cultivation-based microbial ecology, the ‘uncultivability’ of environmental microorganisms has stood as a beacon to the molecular community of the futility of cultivation. The same phenomenon has served as a welcome challenge to others, leading to the development of novel cultivation approaches and technologies. It appears now that microbial cultivation is an emerging frontier in environmental microbiology, in part because it provides information about communities that cannot be obtained directly from sequencing efforts alone (Ellis et al. , 2003). As the barriers to cultivation are reduced, the complications of undertaking microbial ecology in its absence are becoming more apparent. Sequence collection efforts may appear, at first glance, far superior to cultivation because they bypass the discrepancy between the number of microbial cells present in a sample and the number of colonies produced in vitro (Schloss & Handelsman, 2005). The promise of genomes without cultivation has made metagenomics a popular cultivation-independent approach to microbial community assessment (Handelsman, 2004; DeLong, 2005). Isolation and sequencing of microbial DNA from mixed communities en masse, rather than focusing on select phylogenetic markers, potentially provides access to the full complement of microbial genes and the opportunity to reassemble genomes without the requirement of environmental isolates (Handelsman et al. , 1998). However, closing genomes from these efforts proves exceedingly difficult, apparently owing to genomic micro-heterogeneity (Tringe & Rubin, 2005), compounded by species diversity within samples (Venter et al. , 2004). Even with closure, typically 40% or …