Exploration of sulfur-cycling microorganisms from anoxic Black Sea waters and sediment

All forms of life, from bacteria to humans, require sulfur as essential nutrient. Furthermore, many bacteria and archaea interact with sulfur compounds to obtain the energy they need for growth. Some of these sulfur microbes – for instance sulfate-reducing microorganisms – produce sulfide (H2S), which has the smell of rotten eggs and can create ‘dead zones’ in the ocean because of its toxicity. However, other sulfur microbes do the opposite and consume H2S, using it as electron donor for energy. Sulfur microbes thus have a big impact on the marine environment, and even on the global climate. As microbiologists, we want to find out who are these sulfur microbes, and what else do they do?

To answer these questions, we focused on the Black Sea, the world’s largest anoxic basin. It is home to many different sulfur microbes which cannot tolerate oxygen and are yet to be studied. As tools, we used metagenomics and anaerobic cultivation. Metagenome-assembled-genomes (MAGs) were obtained from a cross-assembly of 15 metagenomes sampled at different water column depths. MAGs were then taxonomically classified, screened for functional marker genes to hypothesize their energy metabolism, and their relative abundance was profiled over depth to refine these hypotheses. We obtained medium-to-high-quality MAGs of various putative sulfur-oxidizing and sulfate-reducing bacteria, including known ones and novel ones. Specifically sulfate-reducing bacteria were surprisingly diverse and novel, meaning much is still to be learned about their role in the Black Sea and other marine waters with low oxygen levels.

With anaerobic cultivation, we have brought new and exciting sulfur microbes from Black Sea samples into pure culture, allowing us to study their metabolism in detail. For instance, we isolated two strains of a novel bacterial family which cleave sulfate ester groups from polysaccharides to digest their food. Their genomes contain more genes for sulfate-cleaving enzymes (sulfatases) than any other known organism. We narrowed down the complete enzymatic pathway used for degrading sulfated polysaccharides using transcriptomics, and along the way we found evidence for a novel pathway for degradation of the sugar molecule L-fucose. What's also exciting is that we observed other interesting features - these bacteria produce slimy extracellular biopolymers, part of which is structurally similar to specific polysaccharides found only in animals.