Final Report Summary - PARASOL (The Paradox of Sulfur Bacteria in Soda Lakes)
Soda lakes are extreme environments with pH values between 9 and 11, and salt concentrations up to saturation. The sulfur cycle, driven by halo-alkaliphilic sulfur-oxidizing bacteria and sulfidogens, is one of the most active element cycles in these lakes. The overall goal of the project is to obtain a comprehensive understanding of the diversity and ecophysiology of sulfur bacteria in soda lakes, their niche differentiation, and the molecular mechanisms by which they adapt to extreme halo-alkaline conditions. To achieve this goal, we studied the sulfur bacteria at the molecular level, the strain level and the community level. We performed comparative analysis of the genomes of more than 70 Thioalkalivibrio strains and found 15 novel 'genomic' species next to the 10 already describes species. In addition, we found that the genus is not monophyletic, but separated by species from other genera into two groups. Pan-genome analysis showed that the genome was an open pan-genome consisting of 10.221 Orthologous Groups (OGs). The core genome consisted of 1.353 OGs that are involved in house-keeping, core-metabolism, and information storage. The accessory genome consisting of dispensable and strain-specific genes comprised 8.868 OGs that were mainly involved in signal transduction and cell wall biogenesis. To study the cause of this large diversity within the genus Thioalkalivibrio we started experiments to test the hypothesis that environmental stress stimulates diversity. Addition of sub-lethal concentrations of the antibiotic ampicillin created hypermutants with more than 55.000 mutations.
The genomes of three Thioalkalivibrio species that are able to use thiocyanate as an energy and nitrogen source were analysed in more detail. Substantial differences were found in the carbon, nitrogen and sulfur metabolic pathways. To obtain more insight in thiocyanate oxidation, we studied the ecophysiology of one of these strains, Thioalkalivibiro thiocyanoxidans, under controlled conditions in replicate chemostats with thiocyanate or thiosulfate as a substrate. Transcriptomic analysis showed the expression of thiocyanate dehydrogenase and adjacent genes in cells grown with thiocyanate, and genes involved in cell wall and cell membrane synthesis in cells grown with thiosulfate as substrate.
Apart from sulfur-oxidizing bacteria, sulfidogens play an important role in the reductive part of the sulfur cycle in soda lakes. We analysed the genomes of three species that are able to disproportionate, whereby a single sulfur compound is split into a more reduced and a more oxidized compound. Subsequently, one of these sulfidogens, Desulfonatronospira thiodismutants, was grown in chemostats under autotrophic (sulfite/CO2) and heterotrophic (sulfite/lactate or sulfate/lactate) conditions. We found that genes involved in the reduction of sulfate to sulfide were equally expressed in all setups, whilst genes for heterotrophic lactate oxidation and Wood Ljungdahl carbon fixation were differentially expressed. A membrane electron transfer cluster was highly upregulated during sulfite disproportionation.
At the community level we analysed the metagenomes of microbial communities from brines and sediments of different soda lakes from the Kulunda Steppe (Altaï, Russia) that had salt concentrations between 170 and 400 g/L. Both 16S amplicon and metagenomic sequencing showed the dominance of member of the Bacteroidetes, Alpha- and Gammaproteobacteria at salinities below 250 g/L and Euryarchaeota at salinities above 250 g/L. From the metagenomes of sediment communities we reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Analysis of the reconstructed genomes of several community members showed the ability to degrade recalcitrant substrates, such as cellulose and chitin, as well as the presence of xenorhodopsins. In addition, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducing and methanogens.
The research from this project has been published in different scientific journals, and has been presented at different conferences and meetings.
The results can be used to improve the sustainable removal of noxious sulfur compounds from wastewater. In addition, proteins that have been identified in novel organisms can be used for neurobiology or for pre-treatment of agricultural waste that is used for the production for biofuels. Moreover, the results can us insight into possible life on other planets.
The genomes of three Thioalkalivibrio species that are able to use thiocyanate as an energy and nitrogen source were analysed in more detail. Substantial differences were found in the carbon, nitrogen and sulfur metabolic pathways. To obtain more insight in thiocyanate oxidation, we studied the ecophysiology of one of these strains, Thioalkalivibiro thiocyanoxidans, under controlled conditions in replicate chemostats with thiocyanate or thiosulfate as a substrate. Transcriptomic analysis showed the expression of thiocyanate dehydrogenase and adjacent genes in cells grown with thiocyanate, and genes involved in cell wall and cell membrane synthesis in cells grown with thiosulfate as substrate.
Apart from sulfur-oxidizing bacteria, sulfidogens play an important role in the reductive part of the sulfur cycle in soda lakes. We analysed the genomes of three species that are able to disproportionate, whereby a single sulfur compound is split into a more reduced and a more oxidized compound. Subsequently, one of these sulfidogens, Desulfonatronospira thiodismutants, was grown in chemostats under autotrophic (sulfite/CO2) and heterotrophic (sulfite/lactate or sulfate/lactate) conditions. We found that genes involved in the reduction of sulfate to sulfide were equally expressed in all setups, whilst genes for heterotrophic lactate oxidation and Wood Ljungdahl carbon fixation were differentially expressed. A membrane electron transfer cluster was highly upregulated during sulfite disproportionation.
At the community level we analysed the metagenomes of microbial communities from brines and sediments of different soda lakes from the Kulunda Steppe (Altaï, Russia) that had salt concentrations between 170 and 400 g/L. Both 16S amplicon and metagenomic sequencing showed the dominance of member of the Bacteroidetes, Alpha- and Gammaproteobacteria at salinities below 250 g/L and Euryarchaeota at salinities above 250 g/L. From the metagenomes of sediment communities we reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Analysis of the reconstructed genomes of several community members showed the ability to degrade recalcitrant substrates, such as cellulose and chitin, as well as the presence of xenorhodopsins. In addition, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducing and methanogens.
The research from this project has been published in different scientific journals, and has been presented at different conferences and meetings.
The results can be used to improve the sustainable removal of noxious sulfur compounds from wastewater. In addition, proteins that have been identified in novel organisms can be used for neurobiology or for pre-treatment of agricultural waste that is used for the production for biofuels. Moreover, the results can us insight into possible life on other planets.