Cultivation of marine bacteria of the SAR202 clade

Abstract

Bacteria 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.

Predicting microbial growth conditions from amino acid composition

“…7 ) 34,35 . Within the Chloroflexota class Dehalococcoidia , the model correctly identified the order Dehalococcoidales to be entirely anaerobic and orders Tepidiformales /OLB14 and SAR202/UBA1151 as containing aerobes, in agreement with previous reports 36–38 . Elevated optimal temperature was correctly predicted for phyla Hadarchaeota and Calescibacterota ( Fig.…”

A pilot study suggests the correspondence between SAR202 bacteria and dissolved organic matter in the late stage of a year-long microcosm incubation

“…Nonetheless, the powerful oxidative enzymes (e.g., FMNOs) that are encoded by deep-sea lineages of the SAR202 clade are also present in the surface subgroups in fewer copies ( Landry et al, 2017 ; Saw et al, 2020 ). Recently, several closely related strains of SAR202 bacteria in subgroup Ia were successfully cultivated ( Lim et al, 2023 ). Subsequent growth experiments showed that the subgroup Ia SAR202 did not reach the exponential phase until 50 days at 20°C and the growth responses to fucose and rhamnose were slow and did not reach the highest cell density until the late exponential phase, which coincided with our detection of increased SAR202 abundance in the treatment on day 60 ( Figure 1B ).…”

“…This suggests that SAR202 bacteria are specifically utilizing a unique niche of high-abundance unsaturated compounds that were either not consumed by other bacteria or produced by bacteria in phase 1. It has been postulated that SAR202 bacteria are capable of exploiting the DOM that other deep-sea bacterioplankton cannot degrade ( Varela et al, 2008 ; Lim et al, 2023 ). Through the ultrahigh-resolution FT-ICR-MS approach, our data provided first-hand evidence that the SAR202-MFs possess possibly aromatic but certainly unsaturated characteristics.…”

Crystal structure of l-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a α-furanosyl hemiketal of substrates

“…This metabolic fate is also hydrolyzed to pyruvate and l -lactate by the hydrolase (LRA6), which is phylogenetically close to FucG. Recently, non-phosphorylating l -fucose and/or l -rhamnose pathway(s) were shown to play important physiological roles in the gastrointestinal pathogen Campylobacter jejuni 6 and (previously unculturable) marine bacteria of the SAR202 clade 7 .…”