Strategies for culturing active/dormant marine microbes

Abstract

Microorganisms are ubiquitous in the ocean environment and they play key roles in marine ecosystem function and service. However, many of their functions and phenotypes remain unknown because indigenous marine bacteria are mostly difficult to culture. Although many novel techniques have brought previously uncultured microbes into laboratory culture, there are still many most-wanted or key players that need to be cultured from marine environments. This review discusses possible reasons for 'unculturable microbes' and categorizes uncultured bacteria into three groups: dominant active bacteria, rare active bacteria, and dormant bacteria. This review also summarizes advances in cultivation techniques for culturing each group of unculturable bacteria. Simulating the natural environment is an effective strategy for isolating dominant active bacteria, whereas culturomics and enrichment culture methods are proposed for isolating rare active bacteria. For dormant bacteria, resuscitation culture is an appropriate strategy. Furthermore, the review provides a list of the most-wanted bacteria and proposes potential strategies for culturing these bacteria in marine environments. The review provides new insight into the development of strategies for the cultivation of specific groups of uncultured bacteria and therefore paves the way for the detection of novel microbes and their functions in marine ecosystems.

What do we mean by viability in terms of ‘viable but non‐culturable’ cells?

“…If VBNC cells are unable to go into the lag phase in an appropriate time period (Fig. 1), they may well maintain dormancy or even lose viability on the media (Mu et al ., 2021; Zhang et al ., 2021). This is a major difference between VBNC and persister cells, which pertains to resuscitation dynamics.…”

Diversity and Distribution of Uncultured and Cultured Gaiellales and Rubrobacterales in South China Sea Sediments

“…Further results showed that marine Gaiellales strains were hygrophilous and halophilic, different from the species G. occulta. Therefore, simulating the natural environment, especially its potential key factors, is an effective strategy for isolating novel, rare, or uncultured bacteria (Mu et al, 2020).…”

Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories

“…However, these antifungal compounds have not always proven to be effective and fungicides like pevaryl (econazole nitrate; 1%) and benlate (benomyl, or methyl l-(butylcarbamoyl)-2-benzimidazole carbamate;4 mg•ml −1 ) appear to be more adequate in inhibiting fungal growth (Lage and Bondoso, 2011). Futhermore, when the targated strains belong from marine sample, the authors commonly use filtired marine water or artificial seawater in order to complement the medium and to reach the bacterial natural environment (Schlesner, 1994;Mu et al, 2020;Wiegand et al, 2020). This was especially relevant for marine aquatic Planctomycetes.…”