High Throughput Culturing of Coral Associated Microorganisms

The decline of coral reefs has led to an increasing search for strategies that could aid corals to cope with climate change and local impacts. Although the permanent solution to protect corals is the reduction of CO2 emissions, there is also an urgent need for the development of approaches that can protect native populations while we deal with the current consequences of global warming. The use of probiotics has been recently shown to ameliorate bleaching and disease impacts on coral in laboratory trials and more research is being conducted in order to evaluate the safety and efficiency of such an approach in the field. However, despite promising results, this strategy relies on the manipulation of culturable microorganisms, which can represent only ~1% of the total microbes associated with environmental samples. Once these microbial isolates are obtained from coral samples, the putative beneficial ones are selected and tested as probiotics. That means that only a very small portion of the total coral microbiome is being accessed and tested as potential health promoters, due to methodological limitations and hurdles associated with microbial culturing. Therefore, we used a microfabricated array based, high-throughput system to grow hundreds of colonies in parallel to rapidly and efficiently isolate microbes from coral samples. A total of 1054 isolates were recovered from replicated Montipora digitata fragments and preliminarily identified by 16S rDNA sequencing. The commonly coral associated genera were isolated, such as Vibrio sp., Alteromonas sp., and Bacillus sp, as well as some representatives of bacteria rarely or not yet cultured from corals, such as Azomonas sp., Phyllobacterium sp. and Hydrobacter sp. The rare or not yet isolated cells were then selected and glycerol stocked for ongoing genome analysis and deeper investigation about their identity and potential use as beneficial microorganisms for corals (BMC). The results indicated that the use of this high throughput system can allow the quick acquisition of high numbers of microbial cultures obtained from coral samples, including new and rare isolates, as well as facilitate the screening for specific functional traits or taxonomic identity.