Cultivation-success of rare soil bacteria is not influenced by incubation time and growth medium

• Published in: PloS one 2019-01, Vol.14 (1), p.e0210073-e0210073
• Main Authors: Kurm, Viola, van der Putten, Wim H, Hol, W H Gera
• Format: Article
• Language: English
• Subjects: Abundance; Analysis; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - growth & development; Bacteriological Techniques - methods; Biodiversity; Biointeractions and Plant Health; Biology and Life Sciences; Computer and Information Sciences; Cultivation; Culture media; Culture Media - chemistry; Culture Media - pharmacology; Ecology; Ecology and Environmental Sciences; EPS; Incubation; Laboratories; Laboratorium voor Nematologie; Laboratory of Nematology; Legislative bodies; Media (culture); Medicine and Health Sciences; Netherlands; Oligotrophs; PE&RC; Phylogenetics; Phylogeny; PPO/PRI Biointeracties en plantgezondheid; PPO/PRI Biointeractions and Plant Health; Rare species; Relative abundance; Research and Analysis Methods; RNA, Ribosomal, 16S - genetics; Soil - chemistry; Soil bacteria; Soil investigations; Soil Microbiology; Soil microorganisms; Soils; Species Specificity; Studies; Taxa; Time Factors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0210073

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) 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.