The Red Sea's Microbial Bounty
The Marine Microbial Ecology group, led by Assistant Professor of Marine Science, Uli Stingl, is ideally positioned at King Abdullah University of Science and Technology to investigate and utilize the microbial diversity of the Red Sea.
The Red Sea's combination of environmental extremes resembles the worst case effects of global warming in temperate oceans. By studying adaptations to therma stress and high salinity of the most prominent photo- and heterotrophs in marine waters worldwide, the Cyanobacteria Prochlorococcus sp. and the Proteobacteria 'SAR11', the Marine Microbial Ecology researchers are trying to understand the consequences of global warming for marine bacteria and their impact on the marine food web.
Because the Red Sea has many salinity, temperature, and nutrient gradients, samples are being collected from many areas to create a complete inventory of Red Sea microbial communities. Utilizing metagenomic analyses, the group has already identified several genetic features involved in microbes' adaptive response to high temperatures. Marine Microbial Ecology researchers are also sequencing genomes of single bacteria that are not possible to be cultivated in laboratory conditions.
These sequences will lead to discoveries of environment-specific genomic regions — for example, genes that help microbes survive in the high temperatures of the Red Sea. Regular sampling of microbial populations at a fixed location on the Red Sea will offer a view into long-term changes in the microbial community and the effects that temperature and other physical parameters have. These samples will be characterized by pyrosequencing of the highly conserved 16S rRNA gene.
A collection of microbes will be maintained for in-depth physiological and genomic studies and will be made available as a resource beyond KAUST.
The Marine Microbiology Ecology group's forays into characterization of extremophilic microorganisms from deep-sea anoxic brine pools in the Red Sea have already yielded isolation of previously unknown microbes and identification of entirely new groups of microbes. Stingl's group expects that the microbes possess novel metabolic pathways, enzymes, and chemicals that may have use in biotechnology applications.
Halophiles, such as those isolated by the researchers, may offer valuable new proteins and enzymes for production of food additives; bioplastics; and bacteriorhodopsin, which has wide use including in holography, neural networks, and optical computing. These microbes may also aid bioremediation of contaminated soils and waters, enhance oil-recovery processes, and recover saline soils for agriculture.
In another research project, with a focus on a single, macroscopic microorganism, the Marine Microbial Ecology group is working to demystify the enigmatic Epulopiscium sp. bacterium, which lives symbiotically within intestinal tracts of surgeonfish.
This microbe is one of the largest prokaryotes and is, in fact, so big (700 μm) that it can be seen without a microscope. Despite its monumental size (in relation to its microscopic relatives, which are almost ten orders of magnitude smaller in volume), Epulopiscium is not well studied. Stingl's group believes the microbe might have unconventional intracellular molecules and pathways to control local gene regulation and expression—molecules that could be useful for the biotechnology industry.
To cultivate this little-studied microbe in the lab, the group intends to determine oxygen, hydrogen, pH, and redox profiles, as well as the chemical composition of fatty acids, of the gut of surgeonfish, where the microbes live. With these data, the researchers can develop a cultivation approach that will allow Epulopiscium to be grown in the lab.
The group is also obtaining data on the genome of different Epulopiscium species, their diversity and distribution in surgeonfishes and similar coral reef fishes through pyrosequencing of the 16S rRNA gene, and investigating the phylogenetic diversity of all symbiotic bacteria together with the host fish to determine whether the symbionts coevolved with their hosts.