Kang, Ilnam

AbstractBacteria of the SAR202 clade, within the phylum Chloroflexota, are ubiquitously distributed in the ocean but have not yet been cultivated in the lab. It has been proposed that ancient expansions of catabolic enzyme paralogs broadened the spectrum of organic compounds that SAR202 bacteria could oxidize, leading to transformations of the Earth’s carbon cycle. Here, we report the successful cultivation of SAR202 bacteria from surface seawater using dilution-to-extinction culturing. The growth of these strains is very slow (0.18–0.24 day−1) and is inhibited by exposure to light. The genomes, of ca. 3.08 Mbp, encode archaella (archaeal motility structures) and multiple sets of enzyme paralogs, including 80 genes coding for enolase superfamily enzymes and 44 genes encoding NAD(P)-dependent dehydrogenases. We propose that these enzyme paralogs participate in multiple parallel pathways for non-phosphorylative catabolism of sugars and sugar acids. Indeed, we demonstrate that SAR202 strains can utilize several substrates that are metabolized through the predicted pathways, such as sugars ʟ-fucose and ʟ-rhamnose, as well as their lactone and acid forms.

Significance Heme is essential for respiration. As a cofactor of cytochromes, heme functions as a main electron carrier in all respiratory electron transport chains. Therefore, it is natural to expect all respiring and free-living microorganisms to make heme. Against this expectation, here we show that the acI lineage, one of the most abundant bacterial groups in freshwater environments, is unable to biosynthesize heme and requires exogenous heme. Furthermore, we provide genomic evidence for putative heme auxotrophy among many not-yet-cultured aquatic microbial groups. Heme should be the focus of future research on the metabolic dependency among microorganisms and the role of exchangeable metabolites in structuring diverse ecosystems, and would also be a media component that must be considered when cultivating novel microbes.

Abstract The actinobacterial acI lineage is among the most successful and ubiquitous freshwater bacterioplankton found on all continents, often representing more than half of all microbial cells in the lacustrine environment and constituting multiple ecotypes. However, stably growing pure cultures of the acI lineage have not been established despite various cultivation efforts based on ecological and genomic studies on the lineage, which is in contrast to the ocean from which abundant microorganisms such as Prochlorococcus, Pelagibacter, and Nitrosopumilus have been isolated. Here, we report the first two pure cultures of the acI lineage successfully maintained by supplementing the growth media with catalase. Catalase was critical for stabilizing the growth of acI strains irrespective of the genomic presence of the catalase-peroxidase (katG) gene. The two strains, representing two novel species, displayed differential phenotypes and distinct preferences for reduced sulfurs and carbohydrates, some of which were difficult to predict based on genomic information. Our results suggest that culture of previously uncultured freshwater bacteria can be facilitated by a simple catalase-supplement method and indicate that genome-based metabolic prediction can be complemented by physiological analyses.

ABSTRACT The complete genome sequence of “ Candidatus Puniceispirillum marinum” IMCC1322, the first cultured representative of the SAR116 clade in the Alphaproteobacteria , is reported here. The genome contains genes for proteorhodopsin, aerobic-type carbon monoxide dehydrogenase, dimethylsulfoniopropionate demethylase, and C 1 compound metabolism. The genome information proposes the SAR116 group to be metabolic generalists in ocean nutrient cycling.