Award: OCE-2129823

This project studied how low oxygen availability influences the biodiversity and ecological role of bacteria of the SAR11 clade, one of the most abundant microbial groups in the ocean. Using a combination of genomic, microbiological, and biogeochemical methods, the overarching aims of the project were to identify the mechanisms by which SAR11 strains diversify into separate niches and species (if any), and how these strains contribute biochemically to the ecosystem through the nitrogen cycling pathways. The work involved oceanographic sampling across a range of oxygen and nutrient levels in the Eastern Tropical North Pacific (ETNP) Ocean and elsewhere. 

Summary of results on intellectual merit: In genomic surveys of bacteria to reveal species-level clusters, the aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria) are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, the team analyzed high-quality, single-cell amplified genomes (SAGs), and companion metagenomes from an oxygen minimum zone (OMZ) in the ETNP, where the SAR11 make up ~20% of the total microbial community. Their results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86% and 91% (vs. 84-96% in most other bacterial species), with intra-species ANI ranging between 91% and 100%. Measuring recent gene exchange among these genomes based on a recently developed methodology (Conrad et al., Nat. Comms. 2024) revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR11 appears to be more promiscuous compared to other prokaryotic species, likely due to the deletion of universal genes involved in the mismatch repair, and has facilitated the spreading of adaptive mutations within the species (gene sweeps), further promoting the high intraspecies diversity observed (Zhao et al., ISME 2025). More recent work has shown that each of the sequence-discrete species identified may carry unique (species-specific) functional gene content that is differentially tuned to the physicochemical gradient across the OMZ (Zhao et al., in preparation). Collectively, these results implicated rampant, genome-wide homologous recombination as the mechanism of cohesion for distinct SAR11 species and largely addressed the research objectives of the project. We also leveraged the methods developed as part of this project for several related projects. These projects involved the quantification of the sources of pollution of waterbodies based on the microbial species recovered by short-read metagenomes (Linder et al., ES&T 2024), comparison of the species-level patterns of SAR11 bacteria to those of viral genomes (Aldeguer-Rikelme et al., mBio 2024), and the mechanisms of diversity generation in Salinibacter ruber, the bacterial group dominating coastal salterns (Viver et al., SAM 2023 & Nat. Comms. 2024). We have also made our bioinformatics pipelines, tools and data available to our collaborators at Montana State U. (Prof. Frank Stewart and his team) to facilitate their work as part of this project.

Brief summary of results on broader impacts: The team has conducted substantial outreach and educational activities to make bioinformatics more accessible to undergraduate students and the public and provide an overview of the importance of microbiome research and the new employment opportunities in this sector. Specifically, the bioinformatics tools developed such as the read-recruitment plots and the approach to identify strains within species have been made freely available for download (e.g., https://github.com/rotheconrad/F100_Prok_Recombination and https://doi.org/10.5281/zenodo.13922077), as well as for online analysis using our webserver (available through https://enveomics.scigap.org/). Further, the team delivered a short, 2-day workshop at the University of Puerto Rico system on microbiome technologies and associated career opportunities, and hosted one of the undergraduate participants of the workshop for a research experience for ~10 weeks in the summer of 2024. The student was trained on metagenomic techniques and the bioinformatics pipelines, and he subsequently applied this knowledge on samples collected at Puerto Rico. In addition, the PI (Konstantinidis) included hands-on laboratory sessions using bioinformatic tools from this project in the undergraduate and graduate level courses he taught at Georgia Tech as well as during invited contributions to prestigious short summer courses and workshops organized across the country and abroad such as the annual meeting of the American Society for Microbiology, and the congress of the International Society for Microbial Ecology (ISME-19) in summer of 2024. Metagenomic, metatranscriptomics, SAG and oceanographic data have been deposited to NCBI’s SRA and the BCO-DMO databases (i.e., https://www.bco-dmo.org/project/885604). In total, the project trained four PhD students, one post-doctoral research associate, and four undergraduate students, and resulted in 12 peer-reviewed publications (all available at NSF’s Public Access Repository; PAR), while three additional manuscripts are in preparation for publication at the time of this writing. 

 

Last Modified: 03/07/2026
Modified by: Konstantinos T Konstantinidis