Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome
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Strain HIMB11 is a planktonic marine bacterium isolated from coastal seawater in Kaneohe Bay, Oahu, Hawaii belonging to the ubiquitous and versatile Roseobacter clade of the alphaproteobacterial family Rhodobacteraceae. Here we describe the preliminary characteristics of strain HIMB11, including annotation of the draft genome sequence and comparative genomic analysis with other members of the Roseobacter lineage. The 3,098,747 bp draft genome is arranged in 34 contigs and contains 3,183 protein-coding genes and 54 RNA genes. Phylogenomic and 16S rRNA gene analyses indicate that HIMB11 represents a unique sublineage within the Roseobacter clade. Comparison with other publicly available genome sequences from members of the Roseobacter lineage reveals that strain HIMB11 has the genomic potential to utilize a wide variety of energy sources (e.g. organic matter, reduced inorganic sulfur, light, carbon monoxide), while possessing a reduced number of substrate transporters.
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The microorganisms that were more represented in the water samples were completely different and belonged to very common marine groups (HIMB11, SAR11, AEGEAN).
“Indeed, the microorganisms that were more represented in the water samples were completely different and belonged to very common marine groups (HIMB11, SAR11, AEGEAN) (Morris et al., 2002; Durham et al., 2014; Cram et al., 2015).”
From Potential lineage transmission within the active microbiota of the eggs and the nauplii of the shrimp <i>Litopenaeus stylirostris</i> : possible influence of the rearing water and more (2021) · cites this paper as Durham et al., 2014
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“Analysis of 5S, 16S, and 23S rRNA sequence identity showed that the most closely related species to RS1 and RS2 was the Rhodobacteraceae bacterium HIMB11 isolated from coastal seawater in the Kaneohe Bay [30], exhibiting >99.6% identity.”
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“The same result was also obtained for Rhodobacteraceae bacterium HIMB11 [50], another PRC member whose ecology and evolution has been studied.”
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“8% 16S rRNA gene identity with Roseobacter strain HIMB11 [57], and FZCC0089 belongs to a newly identified Roseobacter lineage located close to HIMB11 and SAG-019 lineages (Supplementary Fig.”
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“These characteristics indicated that HIMB11 may participate in the biogeochemical cycle of sulfur and carbon [38].”
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“Studies have shown that the HIMB11 strain typically functions as an opportunistic taxon in environmental settings, capable of persisting under oligotrophic conditions until the emergence of favorable conditions for rapid growth (e.g., phytoplankton blooms) [59].”
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“of the greenhouse gas carbon monoxide (54).”
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“Furthermore, as a unique sublineage within the Roseobacter clade (Durham et al. 2014), the HIMB11 strain might produce antimicrobial compounds such as tropodithietic acid to defend against pathogens (Raina et al. 2016).”
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“The elevated contribution of members such as HIMB11 and OM60 in warmer months could be attributed to their utilization of alternative energy supply pathways, such as bacterial chlorophylls and protein rhodopsins (Durham et al. 2014; Spring and Riedel 2013).”
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New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage
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“Pleomorphism and irregular morphology has been recorded in other Roseobacter group members, including HIMB11 [96].”
Wang, S., Shi, Y., Wang, H., Li, Z., & Zhao, M. (2023) · Bulletin of Environmental Contamination and Toxicology · doi:10.1007/s00128-023-03700-0 · Cited by 6 · see citing works
Tu, T., Lin, E.-J., Hung, C., Chou, W., & Shih, Y. (2024) · Estuarine Coastal and Shelf Science · doi:10.1016/j.ecss.2024.109080 · Cited by 5 · see citing works
González-Sánchez, J. M., Panagiotopoulos, C., Antich, C., Papillon, L., Garcia, N., Wambeke, F. V., & Misson, B. (2023) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2023.167770 · Cited by 4 · see citing works
Liu, Y., Brinkhoff, T., & Simon, M. (2025) · Microbiome · doi:10.1186/s40168-025-02259-8 · Cited by 3 · see citing works
“The COR cluster includes two isolates with fully sequenced genomes (HIMB11, SB2) [6, 61].”
How Big Is Big? The Effective Population Size of Marine Bacteria
Luo, H. (2024) · Annual Review of Marine Science · doi:10.1146/annurev-marine-050823-104415 · Cited by 3 · see citing works
Coupling between environmental drivers and microbial networks in shaping marine plankton dynamics
Choi, H. S., Kang, S. U., Park, N. Y., Chun, S.-J., & Lim, A. S. (2025) · Marine Environmental Research · doi:10.1016/j.marenvres.2025.107816 · Cited by 2 · see citing works
Pin, A. O., Clark, G. F., Burkart-Radtke, R. F., Quade, J., & Gardner, S. G. (2026) · PLoS ONE · doi:10.1371/journal.pone.0346135 · Cited by 2 · see citing works
“…of the family Rhodobacteraceae, and despite its comparatively more streamlined and smaller genome size (indicating a more specialised lifestyle [89]), it has been found to be capable of degrading dimethylsulfoniopropionate [90], a major source of organic sulfur found in significant…”
Microbial community respiration kinetics and their dynamics in coastal seawater
Cheung, H. L. S., Simister, R. L., Not, C., & Crowe, S. A. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.176119 · Cited by 1 · see citing works
Manna, V., Balestra, C., Banchi, E., Fonti, V., Kralj, M., & Celussi, M. (2025) · Ocean Microbiology · doi:10.1186/s44375-025-00002-0 · Cited by 1 · see citing works
“Both taxa are capable of photoheterotrophy, harbouring the genomic potential for proteorhodopsin-or bacteri-ochlorophyll-mediated energy production, as well as the metabolic repertoire to perform anaplerotic CO 2 fixation [82, 83].”
Wang, F., Peng, Z., Liu, Q., He, Y., Ghonimy, A., & Zhang, X. (2025) · Marine Environmental Research · doi:10.1016/j.marenvres.2025.107692 · Cited by 1 · see citing works
Zhu, L., Zhang, L., Wang, Z., Zhao, L., Gu, B., Lin, J., Wang, M., & Zhang, H. (2025) · Environmental Research · doi:10.1016/j.envres.2025.123502 · Cited by 1 · see citing works
Gu, J., Foley, K., Huber, L., Hunt, D. E., & Johnson, Z. I. (2026) · Frontiers in Marine Science · doi:10.3389/fmars.2025.1687609 · Cited by 1 · see citing works
Advancements in Bioinformatics and Role in Marine Genomics and Metagenomics
Nathani, N. M., Mitra, A., Chandrashekar, M., & Kothari, R. K. (2020) · Encyclopedia of Marine Biotechnology · doi:10.1002/9781119143802.ch76
Characterization of microbial communities in carbonate sediments
Hoyningen-Huene, A. V. (2021) · doi:10.53846/goediss-8975
Effects of coastal shellfish farming and hypoxic stress on DMS productionPreprint
Zhang, S., Sun, J. M., Zhang, X., Yao, C. L., Zhao, M., Zhao, W., Zhang, H., Yang, G.-P., & Zhao, J.-M. (2022) · Research Square · doi:10.21203/rs.3.rs-1800042/v1
Microbial and environmental interactions of the 2021 mucilage event in the Sea of Marmara
Karahan, A., Deliceirmak, S., Esti, M., Kalkan, E., Öztürk, E., & Örek, H. (2025) · Regional Studies in Marine Science · doi:10.1016/j.rsma.2025.104619
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Solís-Marín, F. A., Vergara-Ovando, C., Rojas-Oropeza, M., Gutiérrez, F. C., Medina-Tanco, G., & Cabirol, N. (2026) · Scientific Reports · doi:10.1038/s41598-026-36065-5
“Lastly, HIMB11 has a sox gene cluster which could reflect metabolic potential for sulfur oxidation 44 .”
Gao, S., Zhao, W., Jiang, J., Guan, X., Pan, Y., Zhao, Z., Wang, B., Xiao, Y., Zhang, G., Zhao, D., et al. (2026) · Environmental Microbiology Reports · doi:10.1111/1758-2229.70357
“HIMB11 plays a crucial role in marine biogeochemical cycles, which are essential for maintaining ecological balance and nutrient cycling (Durham et al. 2014).”
Wei, J., Gao, M., Fan, Y., Ai, S., Zhang, M., Zhang, Y., Wu, H., & Hu, Z. (2026) · Microorganisms · doi:10.3390/microorganisms14061359
“Additionally, members of the Roseobacter clade contribute substantially to heterotrophic processing of organic matter and to sulfur and DOM transformations [46].”
Alcorta, J., Ramos‐Barbero, M. D., Santos, F., & Antón, J. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.18.733169
“Dominant bacterial genera varied across samples: genus HIMB11, closely related to the marine Roseobacter clade [84], dominated in LAGOLA; genus HIMB30, within the marine Gammaproteobacteria family Litorivicinaceae [85] in TERMET; and the moderately halophilic bacterium Spiribacter [86] and the…”
- Authors
- Durham, B. P., Grote, J., Whittaker, K. A., Bender, S. J., Luo, H., Grim, S. L., Brown, J. M., Casey, J. R., Dron, A., Florez-Leiva, L., Krupke, A., Luria, C. M., Mine, A. H., Nigro, O. D., Pather, S., Talarmin, A., Wear, E. K., Weber, T. S., Wilson, J. M., Church, M. J., DeLong, E. F., Karl, D. M., Steward, G. F., Eppley, J. M., Kyrpides, N. C., Schuster, S., & Rappé, M. S.
- Affiliations
- University of Hawaiʻi at Mānoa (US)
- University of Georgia (US)
- University of Massachusetts Dartmouth (US)
- Corresponding author
- Rappé, Michael S.
- ORCID
- Venue
- Standards in Genomic Sciences
- Published
- 2014-03-15
- Volume
- 9
- Issue
- 3
- Pages
- 632-645
- ISSN
- 1944-3277 (ISSN-L)
- PMC
- PMC4148974
- OpenAlex
- W2082434558
- Cited by
- 62
- References
- 51
- Citations by year
- 2026: 6 · 2025: 10 · 2024: 7 · 2023: 5 · 2022: 6 · 2021: 11 · 2020: 9 · 2019: 4 · 2018: 1 · 2016: 3
- FWCI
- 0.87
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Standards in Genomic Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Journal of Media Literacy Education (submittedVersion, cc-by-sa)
- Open Access Server of the Woods Hole Scientific Community (Woods Hole Scientific Community) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- Funders
- National Science Foundation (0424599)
- Gordon and Betty Moore Foundation (EF0424599)
- University of Georgia
- Agouron Institute
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Roseobacter clade, Rhodobacteraceae, Alphaproteobacteria, draft genome sequence, genome annotation, comparative genomics, phylogenomics, 16S rRNA gene, small genomes, energy sources, Kaneohe Bay
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