Isolate-anchored comparisons reveal evolutionary and functional differentiation across SAR86 marine bacteria

Abstract

SAR86 is one of the most abundant groups of bacteria in the global surface ocean. However, since its discovery over 30 years ago, it has remained recalcitrant to isolation and many details regarding this group are still unknown. Here, we report the cellular characteristics from the first SAR86 isolate brought into culture, Magnimaribacter mokuoloeensis strain HIMB1674, and use its closed genome in concert with over 700 environmental genomes to assess the phylogenomic and functional characteristics of this order-level lineage of marine Gammaproteobacteria. The SAR86 order Magnimaribacterales invests significant genomic resources into the capacity for $\beta$-oxidation, which is present in most genomes with high gene copy numbers. This cyclical set of reactions appears to be fed by components of cell membranes that include lipids such as phosphatidylcholine, phosphatidylethanolamine, glycolipids, and sulfolipids. In addition to the widespread capacity to degrade the side chain of steroidal compounds via $\beta$-oxidation, several SAR86 sublineages also appear able to fully degrade the steroid polycyclic ring structure as well as other aromatic, polycyclic, and heterocyclic molecules. Read recruitment from publicly available metagenomes reveals that the Magnimaribacterales compose up to 6% of the global surface ocean microbial community. Only a subset of genera drives these high relative abundances, with some more globally dominant and others restricted to specific oceanic regions. This study provides an unprecedented foundation through which to understand this highly abundant yet poorly understood lineage of marine bacteria and charts a path to bring more representatives of this order into laboratory culture.

Keywords: Magnimaribacter; SAR86; marine bacteria; phylogenomics; proteorhodopsin.

Figure 1

Phylogenetic affiliations of strain HIMB1674. (A) Comparison between a 16S rRNA gene phylogeny (left) and a phylogenomic analysis using a concatenated alignment of 120 single-copy core genes (right). Magnimaribacter mokuoloeensis str. HIMB1674 diverges at the root of SAR86 within the SAR156 subclade, now the family Magnimaribacteraceae. Historical subgroups CHAB-I-7 and RedeBAC7D1 are shown, along with historical subgroups I-IV that together make up the family-level Suzuki lineage. “G” denotes genus-level groupings defined by phylogenomics and RED values. Solid circles indicate bootstrap values greater than 95%, whereas open circles indicate values over 80%. The 16S rRNA gene phylogeny was constructed from rRNA genes extracted from the SAR86 expanded genome dataset with historical sequences included for reference. Betaproteobacteria 16S rRNA gene sequences were used as an outgroup. The phylogenomic analysis included members of the gammaproteobacterial orders Burkholderiales and Pseudomonadales as an outgroup (GCF_000305785.2, GCF_003752585.1, GCF_003574215.1, GCF_006980785.1). For phylogenomic analysis, support value circles were removed from below genus nodes to maintain clarity on branching patterns. (B) Phylogenetic placement of the SAR86 order Magnimaribacterales within the Gammaproteobacteria. Genomes from 416 family-level lineages of Proteobacteria from GTDB release 202 and 75 genomes from the Magnimaribacterales order were included. The phylogeny is rooted in the internal node distinguishing the Gammaproteobacteria from the other three classes Alphaproteobacteria, Magnetococcia, and Zetaproteobacteria. Circles indicate ultrafast bootstrap support values ≥95% from 1000 replicates.

Figure 2

Characteristics of M. mokuoloeensis str. HIMB1674 and high-quality SAR86 environmental genomes. (A) TEM and SEM images reveal uniform small coccobacilli in a growing monoculture of strain HIMB1674. (B) Distribution of genome completeness based on the GTDB Gammaproteobacteria marker gene set compared with absolute genome length. HIMB1674 is indicated by a square. (C) The different families within the SAR86 order Magnimaribacterales harbor distinct %GC values. (D) The different families within the Magnimaribacterales also harbor distinct predicted genome lengths, calculated with the Gammaproteobacteria marker genes present in the complete HIMB1674 isolate genome as well as marker genes present within the high-quality genomes of each family. (E) Barchart showing the number of marker genes from the Gammaproteobacteria dataset present for different groupings. The SAR86 expanded genome dataset (n = 185) used in panels B–E includes 25 Magnimaribacteraceae, 57 RedeBAC7D11, 10 CHAB-I-7, and 93 Suzuki genomes.

Figure 3

Distribution of key metabolic features across the bacterial order Magnimaribacterales. The size of each circle indicates the average per genome abundance of each gene within a genus. A comprehensive table of this data is provided in Table S5.

Figure 4

Relative abundance of the bacterial order Magnimaribacterales across the global ocean. (A) Percent of reads recruited from TARA (n = 144) and GEOTRACES (n = 462) metagenomes originating from the uppermost 300 m of the water column were mapped to genomes from across the SAR86 species dataset, revealing maximum abundance within the surface layer (<100 m). This was mirrored by the abundance of three of four families, with only the Magnimaribacteraceae increasing in abundance with depth. (B) Genus-level view of the read recruitment shown in panel a, highlighting differences in the distribution of genera and the prevalence of Ma-G1 with depth. Relative abundance of Magnimaribacterales families (C) and genera (D) within the upper 100 m of the water column across the global ocean, using the read recruitment data shown in panel A. The numbers above each pie chart indicate the number of metagenomes utilized for the average relative abundance calculation from each region, whereas the size of the pie chart indicates the relative abundance of Magnimaribacterales in the particular oceanic region. Slices correspond to the relative abundance of each of the four families. Colored triangles indicate TARA oceans and GEOTRACEs metagenome sample locations, with fill color corresponding to their associated ocean region.