Showing papers by "Slava S. Epstein published in 2009"
TL;DR: The combined use of multiple PCR primer sets, multiple DNA extraction techniques, and deep community sequencing will minimize the biases and recover substantially more species than prior studies, but it is cautioned that this—yet to be used—approach may still leave an unknown number of species and higher taxa undetected.
Abstract: The rRNA approach is the principal tool to study microbial diversity, but it has important biases. These include polymerase chain reaction (PCR) primers bias, and relative inefficiency of DNA extraction techniques. Such sources of potential undersampling of microbial diversity are well known, but the scale of the undersampling has not been quantified. Using a marine tidal flat bacterial community as a model, we show that even with unlimited sampling and sequencing effort, a single combination of PCR primers/DNA extraction technique enables theoretical recovery of only half of the richness recoverable with three such combinations. This shows that different combinations of PCR primers/DNA extraction techniques recover in principle different species, as well as higher taxa. The majority of earlier estimates of microbial richness seem to be underestimates. The combined use of multiple PCR primer sets, multiple DNA extraction techniques, and deep community sequencing will minimize the biases and recover substantially more species than prior studies, but we caution that even this—yet to be used—approach may still leave an unknown number of species and higher taxa undetected.
262 citations
TL;DR: The protistan communities from the basins’ brine and brine/seawater interface appear to be particularly enriched with dinoflagellates, ciliates and other alveolates, as well as fungi, and are conspicuously poor in stramenopiles.
Abstract: Environmental factors restrict the distribution of microbial eukaryotes but the exact boundaries for eukaryotic life are not known. Here, we examine protistan communities at the extremes of salinity and osmotic pressure, and report rich assemblages inhabiting Bannock and Discovery, two deep-sea superhaline anoxic basins in the Mediterranean. Using a rRNA-based approach, we detected 1,538 protistan rRNA gene sequences from water samples with total salinity ranging from 39 to 280 g/Kg, and obtained evidence that this DNA was endogenous to the extreme habitat sampled. Statistical analyses indicate that the discovered phylotypes represent only a fraction of species actually inhabiting both the brine and the brine-seawater interface, with as much as 82% of the actual richness missed by our survey. Jaccard indices (e.g., for a comparison of community membership) suggest that the brine/interface protistan communities are unique to Bannock and Discovery basins, and share little (0.8-2.8%) in species composition with overlying waters with typical marine salinity and oxygen tension. The protistan communities from the basins' brine and brine/seawater interface appear to be particularly enriched with dinoflagellates, ciliates and other alveolates, as well as fungi, and are conspicuously poor in stramenopiles. The uniqueness and diversity of brine and brine-interface protistan communities make them promising targets for protistan discovery.
93 citations
01 Jan 2009
TL;DR: If microbial behavior in vivo conforms to the scout model, this will by necessity manifest itself in vitro as the Great Plate Count Anomaly, and this leads to a novel model of the microbial life cycle in nature, termed the “scout model.”
Abstract: It has been known for over a century that only a small percent of cells from environmental samples form colonies on standard media (Great Plate Count Anomaly, Staley and Konopka (Annu Rev Microbiol 39:321–346, 1985). This chapter focuses on the causes of this disparity, and describes new cultivation technologies aiming to close the gap. It summarizes the original and literature data on the biology of “uncultivable” species\uncultivable\ species is summarized, and the nature of the restrictions likely limiting the growth of these species is discussed. This analysis leads to a novel model of the microbial life cycle in nature, termed the “scout model.” We argue that if microbial behavior in vivo conforms to the scout model, this will by necessity manifest itself in vitro as the Great Plate Count Anomaly. The scout model also draws connections to other aspects of microbial behavior, such as viability – but not cultivability – of some cells, an apparent slow growth of certain species, seeming ability of microbes to persist in the presence of unfavorable factors, including antibiotics, and latent infections.
34 citations