Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria

Abstract

It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns. IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.

Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats

“…3D). The SAR202 group III has been previously shown to be one of the most dominant Chloro exi in the water column of the global deep ocean [17,28], and our result highlights the signi cance of these bacteria in both pelagic and sedimentary habitats of the deep ocean. Expansion of paralogous enzymes, such as avin-dependent monooxygenases, in SAR202 group III has been suggested to be important for their adaptation in different deep-sea habitats, by diversifying the range of organic molecules that the cells can utilize [16,17].…”

“…Currently, the knowledge on the metabolism of deep-sea Chloro exi mainly relies on metagenomic or single-cell genomic analysis, due to the lacking of cultivated representatives for dominant deep-sea lineages [15][16][17]. These studies revealed that Chloro exi from deep-sea waters harbor genes involved in organosulfur compounds degradation [8,15], sul te oxidation [8,15], and the metabolisms of recalcitrant compounds such as cyclic alkanes and aromatic compounds [15][16][17]. The analysis of deep-sea Chloro exi from anoxic subsea oor sediments suggest these bacteria have potential for reductive respiration of organohalogen compounds, and for the fermentation of OM combined with CO 2 xation via the Wood-Ljungdahl pathway [9,18].…”

Exploring the abundance, metabolic potential and gene expression of subseafloor Chloroflexi in million-year-old oxic and anoxic abyssal clay

“… 2017 ; Saw et al . 2020 ), peptidases (Mehrshad et al . 2018 ) and potentially haloalkane and haloacetate dehalogenases (Wasmund et al .…”

Temperature impacts community structure and function of phototrophic Chloroflexi and Cyanobacteria in two alkaline hot springs in Yellowstone National Park

“…For example, a sister clade to the Anaerolineae named WPS-2 (formerly 'subphylum I') contains strains that encode phototrophic machinery but lack carbon fixation machinery (Ward et al, 2019a, b). The non-phototrophic Chloroflexi comprise a larger proportion of the phylum, predominately in the class Anaerolineae that are are widespread in the environment, including strains recovered from activated sludge and wastewater (Nierychlo et al, 2019) and several metagenome assembled genomes from deep ocean environments (Saw et al, 2020), but the ecology of the class remains poorly understood in hot springs.…”