New approaches for bringing the uncultured into culture

Abstract

It took more than 23 years to propose a defined medium to culture “Pelagibacter ubique” HTCC1062, one of the most dominant clades in the ocean. Although it was first identified in the 1990s by culture-independent approaches based on rRNA gene cloning and sequencing, an artificial seawater enrichment medium has only recently been proposed for this isolate. This success story is a result of the improvement of culture methods, better sensitivity of growth detection, and knowledge of metabolic activities predicted from genome sequences. The new approaches now offer a fraction of 14-40 % that can be cultured. From an optimistic point of view, all uncultured marine microorganisms could now simply be regarded as “not yet cultured”. Culturing is no longer an “old fashioned” technique but an innovative and fast-moving area of research. Technological developments include micro-engineering of ichips, manipulation of single cells, community culture, high-throughput culturing (HTC) processes, and new methods for low biomass detection or targeting specific microorganisms. Culture remains a prerequisite for microbiological studies, as we need to grow microorganisms in the laboratory in order to identify their functions and validate hypotheses deduced from their genomes. The development, improvement, and combination of innovative culture techniques based on information deduced from omics will undoubtedly lead to the isolation and study of presently uncultured marine microorganisms.