Metapangenomics reveals depth-dependent shifts in metabolic potential for the ubiquitous marine bacterial SAR324 lineage

Abstract

Background Oceanic microbiomes play a pivotal role in the global carbon cycle and are central to the transformation and recycling of carbon and energy in the ocean’s interior. SAR324 is a ubiquitous but poorly understood uncultivated clade of Deltaproteobacteria that inhabits the entire water column, from ocean surface waters to its deep interior. Although some progress has been made in elucidating potential metabolic traits of SAR324 in the dark ocean, very little is known about the ecology and the metabolic capabilities of this group in the euphotic and twilight zones. To investigate the comparative genomics, ecology, and physiological potential of the SAR324 clade, we examined the distribution and variability of key genomic features and metabolic pathways in this group from surface waters to the abyss in the North Pacific Subtropical Gyre, one of the largest biomes on Earth. Results We leveraged a pangenomic ecological approach, combining spatio-temporally resolved single-amplified genome, metagenomic, and metatranscriptomic datasets. The data revealed substantial genomic diversity throughout the SAR324 clade, with distinct depth and temporal distributions that clearly differentiated ecotypes. Phylogenomic subclade delineation, environmental distributions, genomic feature similarities, and metabolic capacities revealed strong congruence. The four SAR324 ecotypes delineated in this study revealed striking divergence from one another with respect to their habitat-specific metabolic potentials. The ecotypes living in the dark or twilight oceans shared genomic features and metabolic capabilities consistent with a sulfur-based chemolithoautotrophic lifestyle. In contrast, those inhabiting the sunlit ocean displayed higher plasticity energy-related metabolic pathways, supporting a presumptive photoheterotrophic lifestyle. In epipelagic SAR324 ecotypes, we observed the presence of two types of proton-pumping rhodopsins, as well as genomic, transcriptomic, and ecological evidence for active photoheterotrophy, based on xanthorhodopsin-like light-harvesting proteins. Conclusions Combining pangenomic and both metagenomic and metatranscriptomic profiling revealed a striking divergence in the vertical distribution, genomic composition, metabolic potential, and predicted lifestyle strategies of geographically co-located members of the SAR324 bacterial clade. The results highlight the utility of metapangenomic approaches employed across environmental gradients, to decipher the properties and variation in function and ecological traits of specific phylogenetic clades within complex microbiomes.

Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf

“…Taxonomic assignments at the order level ( Fig. 1C ) indicate that the SAR11 ( 42 ), SUP05 ( 19 , 43 , 44 ), and SAR324 ( 45 , 46 ) clades among Alpha -, Gamma - and Deltaproteobacteria , respectively, are predominant in the surface ocean and OMZ waters but nearly absent in the sediment. The SWI displays a clearly increased abundance of Gammaproteobacteria , such as Halioglobus ( 47 ), but overall, the relative abundance of Gammaproteobacteria decreases gradually with sediment depth.…”

“…These two cosmopolitan planktonic clades display genomic and metabolic streamlining with predicted advantages in dissolved OM assimilation ( 69 ). In OMZ waters, the gammaproteobacterial SUP05 ( 19 , 44 ) and deltaproteobacterial SAR324 clades ( 45 , 46 ) predominate in the taxonomic assemblages. These two clades display metabolic potential for sulfur oxidation via reverse dsr and apr genes ( Fig.…”

“…Instead, the data show high activity by sulfur and sulfide oxidizing Gammaproteobacteria (SUP05 clade) and Deltaproteobacteria (SAR324 clade) (e.g., expressing the rDsr and reverse apr genes) and support prior studies of the Namibian ( 24 , 25 ), Arabian ( 9 , 90 ), and Peruvian ( 23 , 71 ) OMZs that reported sulfide oxidation in the water column as a key process tightly coupled with benthic fluxes ( 10 ). Although not precluding a cryptic sulfur cycle, the deltaproteobacterial SAR324 clade ( 46 ), which was found most abundantly in deep offshore waters ( Fig. 1C ), only expressed r DsrA and aprA genes ( Fig.…”

Phylogeny and Metabolic Potential of the Candidate Phylum SAR324

“…Additionally, SAR324 was recently identified as a potential major contributor to both carbon fixation and incorporation in the North Atlantic Deep Water [24]. A recent pangenomic study shed light on SAR324 in the different depth layers of the North Pacific Subtropical Gyre, revealing a depth-dependent shift in their metabolic potential [25]. It appears that SAR324 is split into different eco-groups, showing characteristic features depending on the depth of their occurrence, such as the presence of proteorhodopsin in surface-associated SAR324 and the CBB cycle in the deep ocean [25].…”

“…A recent pangenomic study shed light on SAR324 in the different depth layers of the North Pacific Subtropical Gyre, revealing a depth-dependent shift in their metabolic potential [25]. It appears that SAR324 is split into different eco-groups, showing characteristic features depending on the depth of their occurrence, such as the presence of proteorhodopsin in surface-associated SAR324 and the CBB cycle in the deep ocean [25]. Still, very little is known about the functional diversity of SAR324 in other marine regions and how they compare to non-marine environments, precluding a deeper understanding of the role of this phylum from a global perspective.…”