Microbial Scout Hypothesis and Microbial Discovery

Abstract

<jats:title>ABSTRACT</jats:title><jats:p>In this study, we examine the temporal pattern of colony appearance during cultivation experiments, and whether this pattern could inform on optimizing the process of microbial discovery. In a series of long-term cultivation experiments, we observed an expected gradual increase over time of the total number of microbial isolates, culminating in a 700-fold colony count increase at 18 months. Conventional thought suggests that long-term incubations result in a culture collection enriched with species that are slow growing or rare, may be unavailable from short-term experiments, and likely are novel. However, after we examined the phylogenetic novelty of the isolates as a function of the time of their isolation, we found no correlation between the two. The probability of discovering either a new or rare species late in the incubation matched that of species isolated earlier. These outcomes are especially notable because of their generality: observations were essentially identical for marine and soil bacteria as well as for spore formers and non-spore formers. These findings are consistent with the idea of the stochastic awakening of dormant cells, thus lending support to the scout model. The process of microbial discovery is central to the study of environmental microorganisms and the human microbiome. While long-term incubation does not appear to increase the probability of discovering novel species, the technology enabling such incubations, i.e., single-cell cultivation, may still be the method of choice. While it does not necessarily allow more species to grow from a given inoculum, it minimizes the overall isolation effort and supplies needed.</jats:p>

Fine-scale transition to lower bacterial diversity and altered community composition precedes shell disease in laboratory-reared juvenile American lobster

“…OTU 19, an important shell bacterium found on affected shell, was most similar to other bacteria found in association with sponges (99% sequence identity, Sipkema et al 2011). It is likely that this bacterium is 52 Feinman et al: Bacterial communities in lobster shell disease from the genus Lutimonas (96% sequence identity, Buerger et al 2012), which is part of the same family as Aquimarina and may represent another opportunistic colonizer of diseased lobster shell.…”

“…OTU 19, an important shell bacterium found on affected shell, was most similar to other bacteria found in association with sponges (99% sequence identity, Sipkema et al 2011). It is likely that this bacterium is 52 Feinman et al: Bacterial communities in lobster shell disease from the genus Lutimonas (96% sequence identity, Buerger et al 2012), which is part of the same family as Aquimarina and may represent another opportunistic colonizer of diseased lobster shell.In addition to these core microbiome members, which appear to be important due to their relative abundance on either the transitionary or affected shell, there were a number of other core microbiome OTUs that had identities similar to taxa identified in previous studies of epizootic shell disease. Several studies have reported Aquimarina 'homaria' as a potential causative agent in shell disease, including a bacterial challenge study that was able to recover this bacterium from lobsters with lesions (Quinn et al 2012a) and a next-generation sequencing study that examined healthy and diseased shell (Meres et al 2012).…”

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

“…Epstein hypothesized that dormant bacteria (named scout) would awaken stochastically, without implications of external and environmental signals (152). If these hypotheses provided partially microbiological explanations, including the existence of viable but nonculturable cells (153), then extremely long-term incubations (Ͼ3 months) would not increase the proportion of new species isolation (154). The results of these experiments strongly suggest that the success in culturing of new species depends on the amount of cultivation effort rather than on the length of incubation.…”

“…The results of these experiments strongly suggest that the success in culturing of new species depends on the amount of cultivation effort rather than on the length of incubation. Those authors concluded that the single-cell approach allows the recovery of many more colonies from the same inoculum, as does cultivation by dilution to extinction (154).…”

Causes and consequences of soil bacterial rarity

“…Importantly, cultivability is not restricted to abundant species. The same techniques also capture many rare species (Buerger et al 2012, Shade et al 2012a. Still, only few cultivation studies make the effort to assess the abundance of isolated bacterial species in the field.…”