Abstract
Rare bacterial species have recently attracted interest due to their many potential beneficial functions. However, only little is known about their cultivability. In this study we test the hypotheses that the use of flow cell-sorting for cultivation results in a high proportion of rare soil bacterial isolates relative to bacterial taxa that are abundant in soil. Moreover, we investigate whether different oligotrophic cultivation media and a prolonged incubation time increase the number of cultivated rare species. In a cultivation study we used flow cell sorting to select for small cells and to separate single cells, and grew bacteria on different oligotrophic media with prolonged incubation times. The abundance of the isolates in the field was assessed by comparing them to a 454-sequencing dataset from the same soil. Consequentially, all bacterial isolates were classified as either rare (<0.01% relative abundance) or abundant (>0.01% relative abundance) in the field soil. We found more bacterial taxa among the isolates that were abundant in soil than would be expected by the proportion of abundant species in the field. Neither incubation time nor growth medium had an influence on the recovery of rare species. However, we did find differences in time until visible growth on the plate between different phylogenetic classes of the isolates. These results indicate that rare cultivable species are active and not more likely to be dormant than abundant species, as has been suggested as a reason for their rarity. Moreover, future studies should be aware of the influence incubation time might have on the phylogenetic composition of the isolate collection.
Highlights
IntroductionSpecies traits that might be related to causes of species rarity, such as slow growth rates, the sensitivity to environmental conditions, competition or predation, have mostly been studied by analysing general changes in community composition or by other molecular techniques, such as stable isotope probing [4, 5]
The invention and improvement of high-throughput sequencing techniques has led to the discovery of a large proportion of previously undetected rare species in bacterial communities and multiple studies indicated the importance of rare soil bacterial species for various ecosystem functions [1, 2]
The species abundance distribution of the sequenced field community shows a high number of rare species, but bacterial isolates were found to rank relatively high within this abundance distribution (Fig 1)
Summary
Species traits that might be related to causes of species rarity, such as slow growth rates, the sensitivity to environmental conditions, competition or predation, have mostly been studied by analysing general changes in community composition or by other molecular techniques, such as stable isotope probing [4, 5]. These potential traits will have to be verified in vitro. There is a clear need for more informed cultivation approaches to increase the chances of capturing bacteria of interest for subsequent studies both with respect to species abundance and to other traits, such as phylogeny
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