Ecophysiology of the Cosmopolitan OM252 Bacterioplankton (
            <i>Gammaproteobacteria</i>
            )

Savoie, Emily R.; Lanclos, V. Celeste; Henson, Michael W.; Cheng, Chuankai; Getz, Eric W.; Barnes, Shelby J; LaRowe, Douglas E.; Rappé, Michael S.; Thrash, J. Cameron

doi:10.1128/msystems.00276-21

Cited by 6 publications

(5 citation statements)

References 109 publications

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“…Subclades within SAR11 were delineated using phylogenetic branching ( Supplementary Text ) [ 37 – 39 ], 16S rRNA gene BLAST identity, average nucleotide identity (ANI) [ 40 ], and average amino acid identity (AAI) ( https://github.com/dparks1134/CompareM , default settings). Comparative genomics was completed using Anvi’o version 7.1 [ 41 , 42 ] with the pangenomics workflow ( https://merenlab.org/2016/11/08/pangenomics-v2 ) as previously reported [ 43 ] using the following annotation sources from Interproscan [ 44 ] and anvi-estimate-metabolism : SMART, PRINTS, MobiDBLite, KEGG_Class, KOfam, Gene3D, ProSiteProfiles, SUPERFAMILY, Pfam, CDD, Coils, Hamap, ProSitePatterns, PANTHER, SFLD, KEGG_Module, PIRSF, and TIGRFAM. Pfam and KOfam were primarily used for detailed gene searches.…”

Section: Methodsmentioning

confidence: 99%

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

et al. 2023

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The Order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacterioplankton in global oceans and comprises multiple subclades with unique spatiotemporal distributions. Subclade IIIa is the primary SAR11 group in brackish waters and shares a common ancestor with the dominant freshwater IIIb (LD12) subclade. Despite its dominance in brackish environments, subclade IIIa lacks systematic genomic or ecological studies. Here, we combine closed genomes from new IIIa isolates, new IIIa MAGS from San Francisco Bay (SFB), and 460 highly complete publicly available SAR11 genomes for the most comprehensive pangenomic study of subclade IIIa to date. Subclade IIIa represents a taxonomic family containing three genera (denoted as subgroups IIIa.1, IIIa.2, and IIIa.3) that had distinct ecological distributions related to salinity. The expansion of taxon selection within subclade IIIa also established previously noted metabolic differentiation in subclade IIIa compared to other SAR11 subclades such as glycine/serine prototrophy, mosaic glyoxylate shunt presence, and polyhydroxyalkanoate synthesis potential. Our analysis further shows metabolic flexibility among subgroups within IIIa. Additionally, we find that subclade IIIa.3 bridges the marine and freshwater clades based on its potential for compatible solute transport, iron utilization, and bicarbonate management potential. Pure culture experimentation validated differential salinity ranges in IIIa.1 and IIIa.3 and provided detailed IIIa cell size and volume data. This study is an important step forward for understanding the genomic, ecological, and physiological differentiation of subclade IIIa and the overall evolutionary history of SAR11.

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Section: Methodsmentioning

confidence: 99%

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

et al. 2023

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“…Genomes from AEGEAN-169 and SAR11 clade members were used for phylogenomics with conserved single-copy protein sequences as described previously ( 57 ). Briefly, 70 single-copy orthologs were selected from the Anvi’o pangenomics output and all amino acid sequence sets were aligned and trimmed using Muscle v3.8.1551 and Trimal v1.4.1 with the “-automated1” flag ( 43 , 58 ).…”

Section: Methodsmentioning

confidence: 99%

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

et al. 2023

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Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning order-level divergence ( Pelagibacterales ). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to the Pelagibacterales is highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to the Pelagibacterales . We used a new isolate genome, recently released single-amplified genomes and metagenome-assembled genomes, and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with the recruitment of metagenomes spanning the open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade and support the contention that this group represents a taxonomic family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in the transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa. IMPORTANCE One goal of marine microbiologists is to uncover the roles various microorganisms are playing in biogeochemical cycles. Success in this endeavor relies on differentiating groups of microbes and circumscribing their relationships. An early-diverging group (subclade V) of the most abundant bacterioplankton, SAR11, has recently been proposed as a separate lineage that does not share a most recent common ancestor. But beyond phylogenetics, little has been done to evaluate how these organisms compare with SAR11. Our work leverages dozens of new genomes to demonstrate the similarities and differences between subclade V and SAR11. In our analysis, we also establish that subclade V is synonymous with a group of bacteria established from 16S rRNA gene sequences, AEGEAN-169. Subclade V/AEGEAN-169 has clear metabolic distinctions from SAR11 and their shared traits point to remarkable convergent evolution if they do not share a most recent common ancestor.

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“…Genomes from AEGEAN-169 and SAR11 clade members were used for phylogenomics with conserved single-copy protein sequences as described previously (57). Briefly, single-copy orthologs were selected from the Anvi’o pangenomics output and all amino acid sequences were aligned and trimmed using Muscle v3.8.1551 and Trimal v1.4.1 with the “-automated1” flag, (43, 58).…”

Section: Methodsmentioning

confidence: 99%

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

Getz

Lanclos

Kojima

et al. 2023

Preprint

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Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning Order level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to thePelagibacteralesis highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to thePelagibacterales. We used a new isolate genome, recently released single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with recruitment of metagenomes spanning open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade, and support the contention that this group represents a taxonomic Family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa.

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Ecophysiology of the Cosmopolitan OM252 Bacterioplankton ( Gammaproteobacteria )

Cited by 6 publications

References 109 publications

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

Ecophysiology and genomics of the brackish water adapted SAR11 subclade IIIa

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct

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