Triggering Growth via Growth Initiation Factors in Nature: A Putative Mechanism for in situ Cultivation of Previously Uncultivated Microorganisms

Dawoon Jung; Koshi Machida; Yoichi Nakao; Tomonori Kindaichi; Akiyoshi Ohashi; Yoshiteru Aoi

doi:10.3389/fmicb.2021.537194

Triggering Growth via Growth Initiation Factors in Nature: A Putative Mechanism for in situ Cultivation of Previously Uncultivated Microorganisms

Front Microbiol. 2021 May 4:12:537194. doi: 10.3389/fmicb.2021.537194. eCollection 2021.

Authors

Dawoon Jung¹, Koshi Machida², Yoichi Nakao^{2

3}, Tomonori Kindaichi⁴, Akiyoshi Ohashi⁴, Yoshiteru Aoi^{1

5}

Affiliations

¹ Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Japan.
² Research Institute for Science and Engineering, Waseda University, Tokyo, Japan.
³ Department of Chemistry and Biochemistry, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
⁴ Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University, Higashihiroshima, Japan.
⁵ Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Japan.

Abstract

Most microorganisms resist cultivation under standard laboratory conditions. On the other hand, cultivating microbes in a membrane-bound device incubated in nature (in situ cultivation) can be an effective approach to overcome this limitation. In the present study, we applied in situ cultivation to isolate diverse previously uncultivated marine sponge-associated microbes and comparatively analyzed this method's efficiencies with those of the conventional method. Then, we attempted to investigate the key and previously unidentified mechanism of growing uncultivated microorganisms by in situ cultivation focusing on growth triggering via growth initiation factor. Significantly more novel and diverse microbial types were isolated via in situ cultivation than by standard direct plating (SDP). We hypothesized that some of environmental microorganisms which resist cultivation are in a non-growing state and require growth initiation factors for the recovery and that these can be provided from the environment (in this study from marine sponge). According to the hypothesis, the effect of the sponge extract on recovery on agar medium was compared between strains derived from in situ and SDP cultivation. Adding small amounts of the sponge extracts to the medium elevated the colony-formation efficiencies of the in situ strains at the starvation recovery step, while it showed no positive effect on that of SDP strains. Conversely, specific growth rates or saturated cell densities of all tested strains were not positively affected. These results indicate that, (1) the sponge extract contains chemical compounds that facilitate recovery of non-growing microbes, (2) these substances worked on the in situ strains, and (3) growth initiation factor in the sponge extract did not continuously promote growth activity but worked as triggers for regrowth (resuscitation from non-growing state).

Keywords: cultivation; diffusion chamber; dormancy; non-growing; resuscitation; uncultured microbes.