Characterization of the First Cultured Representative of " Candidatus Thermofonsia" Clade 2 within Chloroflexi Reveals Its Phototrophic Lifestyle

" Thermofonsia" represents a novel class within the phylum . Metagenomic analysis reveals " Thermofonsia" harbors phototrophs outside the classically phototrophic class. Unfortunately, the paucity of pure cultures limits further insights into their potential phototrophy. Here, we report the successful isolation of a " Thermofonsia" representative ( ZRK33) from a deep-sea cold seep. Using combined physiological, genomic, and transcriptomic methods, we further show the long-wavelength light (e.g., red and infrared light) could promote the growth of strain ZRK33 and upregulate the expression of genes associated with phototrophy. In particular, strain ZRK33 has a typical phototrophic lifestyle under both laboratory and deep-sea conditions. Strain ZRK33 also possesses the ability to fix inorganic carbon through the 3-hydroxypropionate bicycle in both laboratory and deep-sea environments, and the combined autotrophic, phototrophic, and heterotrophic capabilities endow strain ZRK33 with a photomixotrophic lifestyle. Notably, the predicted genes associated with phototrophy broadly exist in the metagenomes of 27 deep-sea members, strongly suggesting diverse phototrophic members are distributed in various unexplored deep biospheres. The deep ocean microbiota represents the unexplored majority of global ocean waters. The phylum is abundant and broadly distributed in various deep-sea ecosystems. It was reported that some members of " Thermofonsia" clade 2 might possess phototrophs; however, the absence of cultured representatives is a significant bottleneck toward understanding their phototrophic characteristics. In the present study, we successfully isolated a representative of the novel class " Thermofonsia" from a deep-sea cold seep by using an enrichment medium constantly supplemented with rifampicin, allowing researchers to isolate more members in the future. Importantly, outside the classically phototrophic class, we discover a novel phototrophic clade within the phylum and demonstrate the existence of phototrophic lifestyles in the deep sea. Thus, this study expands the range of phototrophic and provides a good model to study the mechanism of phototrophy performed in the deep biosphere.