Our ability to isolate and cultivate microorganisms has advanced our capacity to identify microbial pathogens, understand microbial physiology and allow the production of microbial products such as antibiotics. In recent years, culture-independent methods, including 16S rRNA gene-based diversity analysis and metagenomics, have started to reveal the abundance and functions of marine microbes that have not been cultured yet1,2. While marine microbes have been found to play an essential role in biogeochemical cycling and as key mediators in climate change3, only a minority of those (except from chemoorganotrophic representatives) have been cultured so far. A prominent example is Pelagibacter ubique (SAR11 clade), one of the most abundant free-living organisms in the oceans and whose cultivation in the early 2000s4 revolutionized the culturing strategies of marine microbiomes. However, cultivation is still necessary for understanding the ecological roles played by microorganisms in their natural habitats. For instance, anaerobic microorganisms dominate the composition of seafloor sediments and hydrothermal vents, but they cannot survive under atmospheric oxygen. Most of the current information on them is derived from culture-independent reports, with their metabolic and ecological adaptations being inferred following bioinformatic analyses. Consequently, it is only possible to predict that some of these anaerobes are fundamental in oceanic sulfur and carbon cycles. However, if they were successfully cultivated in the lab, researchers could further test whether the isolated strains truly can convert sulfur organic compounds and identify their released metabolic products, which could constitute climate-active gases and could have some impact on global warming.
In a recent study published in Nature Communications, Lim et al. presented the isolation and culturing conditions of the marine bacteria SAR202. This bacterial clade belongs to the Chloroflexota phylum, which was initially defined by its high abundance in various habitats, particularly, anaerobic ones. The biology of this phylum has mostly been inferred from molecular, metagenomic and genomic surveys. For cultivating SAR202, the authors used high-throughput culturing techniques, where they diluted epipelagic (surface) seawater samples of the Yellow Sea in minimal seawater media up to 5 cells per ml and distributed them into 48-well microplates. Following incubation into strictly controlled dark–light cycling conditions for 1 month, growth-positive wells were detected by flow cytometry coupled with fluorescence staining. A total of 24 SAR202 isolates were retrieved, which could solely be cultured in the dark. Interestingly, SAR202 is found throughout the water column; from the bright epipelagic zones to the dark abyssopelagic regions and the culturing conditions suggest that SAR202 holds features of photoadaptation. In addition, the isolates corresponded to 68% of the SAR202 clade that were detected in an abundance of between 0.7% and 1.0% in the microbial communities of surface water samples. The authors hypothesize a vertical distribution of these cultivable SAR202 bacteria in the water column, in which their highest cell concentrations are reached in the epipelagic regions, but their relative abundance increases in deeper, aphotic zones (regions reached by little or no sunlight) due to their specialized and unique metabolic features.
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