Peer Reviewed Papers

(68) H. Luo. 2025. How big is big? The effective population size of marine bacteria. Annual Review of Marine Science (invited review; in press)

(67) T. Liao, S. Wang, H. Zhang, E.E. Stüeken, and H. Luo. 2024. Dating ammonia-oxidizing bacteria with abundant eukaryotic fossils. Molecular Biology and Evolution (in press)

(66) H. Zhang, F.L. Hellweger, and H. Luo. 2024. Genome reduction occurred in early Prochlorococcus with an unusually low effective population size. The ISME Journal (in press)

(65) C.R. Voolstra, J.B. Raina, M. Dörr, A. Cárdenas, C. Pogoreutz, C.B. Silveira, A.R Mohamed, D.G Bourne, H. Luo, S.A. Amin, R.S. Peixoto. 2024. Coral bacterial microbiome in sickness, in health, and in a changing world. Nature Reviews Microbiology (in press)

(64) A. Camuel, A. Teulet, M. Carcagno, F. Haq, V. Pacquit, D. Gully, M. Pervent, C. Chaintreuil, J. Fardoux, N. Horta-Araujo, S. Okazaki, S.T.N. Ratu, F. Gueye, J. Zilli, N. Nouwen, J-F. Arrighi, H. Luo, P. Mergaert, L. Deslandes, and E. Giraud. 2023. Widespread Bradyrhizobium distribution of diverse Type III effectors that trigger legume nodulation in the absence of Nod factor. The ISME Journal 17(9): 1416–1429

(63) B. Nowinski, X. Feng, C.M. Preston, J.M. Birch, H. Luo, W.B. Whitman, and M.A. Moran. 2023. Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression. The ISME Journal 17(6): 813-822

(62) T. Liao, S. Wang, E.E. Stüeken, and H. Luo. 2022. Phylogenomic evidence for the origin of obligately anaerobic Anammox bacteria around the Great Oxidation Event. Molecular Biology and Evolution 39(8): msac170

(61) X. Chu, X. Wang, L.S. Cheung, X. Feng, P. Ang, S.Y. Lee, S.A. Crowe, and H. Luo. 2022. Coastal transient niches shape the microdiversity pattern of a bacterioplankton population with reduced genomes. mBio 13(4): e00571-22

(60) X. Lin, J. McNichol, X. Chu, Y. Qian, and H. Luo. 2022. Cryptic niche differentiation of novel sediment ecotypes of Ruegeria pomeroyi correlates with nitrate respiration. Environmental Microbiology 24(1): 390-403

(59)  Z. Chen, X. Wang, Y. Song, Q. Zeng, Y. Zhang, and H. Luo. 2022. Prochlorococcus have low global mutation rate and small effective population size. Nature Ecology & Evolution 6(2): 183-194

(58) H. Zhang, Y. Sun, Q. Zeng, S.A. Crowe, and H. Luo. 2021. Snowball Earth, population bottleneck and Prochlorococcus evolution. Proceedings of the Royal Society B 288(1963): 20211956

(57) H. Jian, G. Xu, Y. Yi, Y. Hao, Y. Wang, L. Xiong, S. Wang, S. Liu, C. Meng, J. Wang, Y. Zhang, C. Chen, X. Feng, H. Luo, H. Zhang, X. Zhang, L. Wang, Z. Wang, Z. Deng, F. Wang, X. Xiao. 2021. The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes. Nature Communications 12(1): 6382

(56) X. Feng, X. Chu, Y. Qian, M.W. Henson, V.C. Lanclos, F. Qin, S. Barnes, Y. Zhao, J.C. Thrash, and H. Luo. 2021. Mechanisms driving genome reduction of a novel Roseobacter lineage. The ISME Journal 15(12): 3576-3586

(55) S. Wang and H. Luo. 2021. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nature Communications 12: 3324

(54) D. Luo, X. Wang, X. Feng, M. Tian, S. Wang, S-L. Tang, P. Ang, A. Yan, and H. Luo. 2021. Population differentiation of Rhodobacteraceae along coral compartments. The ISME Journal 15(11): 3286-3302

(53) J. Tao, S. Wang, T. Liao, and H. Luo. 2021. Evolutionary origin and ecological implication of a unique nif island in free-living Bradyrhizobium lineages. The ISME Journal 15(11): 3195-3206

(52) J. Gu, X. Wang, X. Ma, Y. Sun, X. Xiao, and H. Luo. 2021. Unexpectedly high mutation rate of a deep-sea hyperthermophilic anaerobic archaeon. The ISME Journal 15(6): 1862-1869

(51) B-B. Xie, J-C. Rong, B-L. Tang, S. Wang, G. Liu, Q-L. Qin, X-Y. Zhang, W. Zhang, Q. She, Y. Chen, F. Li, S. Li, X-L. Chen, H. Luo, and Y-Z. Zhang. 2021. Evolutionary trajectory of the replication mode of bacterial replicons. mBio 12(1): e02745-20

(50) Z. Zhang, F. Qin, F. Chen, X. Chu, H. Luo, R. Zhang, S. Du, Z. Tian, and Y. Zhao. 2021. Culturing novel and abundant pelagiphages in the ocean. Environmental Microbiology 23(2): 1145-1161

(49) X. Chu, S. Li, S. Wang, D. Luo, and H. Luo. 2021. Gene loss through pseudogenization contributes to the ecological diversification of a generalist Roseobacter lineage. The ISME Journal 15(2): 489-502

(48) X. Wang, Y. Zhang, M. Ren, T. Xia, X. Chu, C. Liu, X. Lin, Y. Huang, Z. Chen, A. Yan, and H. Luo. 2020. Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites. The ISME Journal 14(12): 3106-3119

(47) S. Wang, A. Meade, H-M. Lam, and H. Luo. 2020. Evolutionary timeline and genomic plasticity underlying the lifestyle diversity in Rhizobiales. mSystems 5(4): e00438-20

(46) C-X. Xue, H. Zhang, H-Y. Lin, Y. Sun, D. Luo, Y. Huang, X-H. Zhang, and H. Luo. 2020. Ancestral niche separation and evolutionary rate differentiation between sister marine flavobacteria lineages. Environmental Microbiology 22(8): 3234-3247

(45) Z. Zhang, F. Chen, X. Chu, H. Zhang, H. Luo, F. Qin, Z. Zhai, M. Yang, J. Sun, and Y. Zhao. 2019. Diverse, abundant and novel viruses infecting the marine abundant Roseobacter RCA lineage. mSystems 4(6): e00494-19

(44) M. Ren, X. Feng, Y. Huang, H. Wang, Z. Hu, S. Clingenpeel, B.K. Swan, M.M. Fonseca, D. Posada, R. Stepanauskas, J.T. Hollibaugh, P.G. Foster, T. Woyke, and H. Luo. 2019. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. The ISME Journal 13(9): 2150-2161

(43) H. Zhang, S. Yoshizawa, Y. Sun, Y. Huang, X. Chu, J.M. González, J. Pinhassi, and H. Luo. 2019. Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats. Environmental Microbiology 21(2): 648-666

(42) H. Cao, T. Xia, Y. Li, Z. Xu, S. Bougouffa, Y.K. Lo, V.B. Bajic, H. Luo, P.C.Y. Woo, and A. Yan. 2019. A multidrug resistant clinical P. aeruginosa isolate with a distinctive MLST genotype: uncoupled quorum sensing modulates the interplay of virulence and resistance. Antimicrobial Agents and Chemotherapy 63(4): e01944-18

(41) G. Yu, Y. Jiang, J. Wang, H. Zhang, and H. Luo. 2018. BMC3C: Binning Metagenomic Contigs using Codon usage, sequence Composition and read Coverage. Bioinformatics 34(24): 4172-4179

(40) Y. Sun and H. Luo. 2018. Homologous recombination in core genomes facilitates marine bacterial adaptation. Applied and Environmental Microbiology 84(11): e02545-17 (selected as a “Spotlight” article by the journal)

(39) F.L. Hellweger, Y. Huang, and H. Luo. 2018. Carbon limitation drives GC content evolution of a marine bacterium in an individual-based genome-scale model. The ISME Journal 12(5): 1180-1187

(38) W. Xie, H. Luo, S.K. Murugapiran, J.A. Dodsworth, S. Chen, Y. Sun, B.P. Hedlund, P. Wang, H. Fang, M. Deng, and C. Zhang. 2018. Localized high abundance of Marine group II archaea in the subtropical Pearl River Estuary: implications for their niche adaptation. Environmental Microbiology 20(2): 734-754

(37) H. Long, W. Sung, S. Kucukyildirim, E. Williams, S. Miller, W. Guo, C. Patterson, C. Gregory, C. Strauss, C. Stone, C. Berne, D. Kysela, W.R. Shoemaker, M. Muscarella, H. Luo, J.T. Lennon, Y.V. Brun, and M. Lynch. 2018. Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology & Evolution 2(2): 237-240

(36) H. Luo, Y. Huang, R. Stepanauskas, and J. Tang. 2017. Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes. Nature Microbiology 2: 17091

(35) H.A. Bullock, H. Luo, and W.B. Whitman. 2017. Evolution of dimethylsulfoniopropionate metabolism in marine phytoplankton and bacteria. Frontiers in Microbiology 8: 637

(34) Y. Sun, Y. Zhang, J.T. Hollibaugh, and H. Luo. 2017. Ecotype diversification of an abundant Roseobacter lineage. Environmental Microbiology 19(4): 1625-1638

(33) Y. Sun, K.E. Powell, W. Sung, M. Lynch, M.A. Moran, and H. Luo. 2017. Spontaneous mutations of a model heterotrophic marine bacterium. The ISME Journal 11(7): 1713-1718

(32) W. Zhang, W. Ding, B. Yang, R. Tian, S. Gu, H. Luo, and P-Y. Qian. 2016. Genomic and transcriptomic evidence for carbohydrate consumption among microorganisms in a cold seep brine pool. Frontiers in Microbiology 7: 1825

(31) H. Luo, Y. Sun, J.T. Hollibaugh, and M.A. Moran. 2016. Low genome content diversity of marine planktonic Thaumarchaeota. Environmental Microbiology Reports 8(4): 501-507

(30) Y. Zhang, Y. Sun, N. Jiao, R. Stepanauskas, and H. Luo. 2016. Ecological genomics of the uncultivated marine Roseobacter lineage CHAB-I-5. Applied and Environmental Microbiology 82(7): 2100-2111

(29) H. Luo, L. Thompson, U. Stingl, and A.L. Hughes. 2015. Selection maintains low genomic GC content in marine SAR11 lineages. Molecular Biology and Evolution 32(10): 2738-2748

(28) H. Luo and M.A. Moran. 2015. How do divergent ecological strategies emerge among marine bacterioplankton lineages? Trends in Microbiology 23(9): 577-584

(27) J.M. Labonté, B.K. Swan, B. Poulos, H. Luo, S. Koren, S.J. Hallam, M.B. Sullivan, T. Woyke, K.E. Wommack, and R. Stepanauskas. 2015. Single cell genomics-based analysis of virus-host interactions in marine surfacebacterioplankton. The ISME Journal 9(11): 2386-2399

(26) H. Luo. 2015. The use of evolutionary approaches to understand single cell genomes. Frontiers in Microbiology 6: 191

(25) H. Luo. 2015. Evolutionary origin of a streamlined marine bacterioplankton lineage. The ISME Journal 9(6): 1423-1433

Before CUHK

(24) B.P. Durham, S. Sharma, H. Luo, C.B. Smith, S.A. Amin, S.J. Bender, S.P. Dearth, B.A.S. Van Mooy, S.R. Campagna, E.B. Kujawinski, E.V. Armbrust, and M.A. Moran. 2015. Cryptic carbon and sulfur cycling between surface ocean plankton. Proc. Natl. Acad. Sci. USA 112 (2): 453-457

(23) H. Luo and M.A. Moran. 2014. Evolutionary ecology of the marine Roseobacter clade. Microbiology and Molecular Biology Reviews 78 (4): 573-587

(22) M. Lin, M.V. Kitahara, H. Luo, D. Tracey, J. Geller, F. Hironobu, D.J. Miller, and C.A. Chen. 2014. Mitochondrial genome rearrangements in the Scleractinia / Corallimorpharia complex: implications for coral phylogeny. Genome Biology and Evolution 6 (5): 1086-1095

(21) B.P. Durham, J. Grote, K.A. Whittaker, S.J. Bender, H. Luo, S.L. Grim, J.M. Brown, J.R. Casey, A. Dron, L. Florez-Leiva, A. Krupke, C.M. Luria, A.H. Mine, S. Pather, A. Talarmin, E.K. Wear, T.S. Weber, J.M. Wilson, M.J. Church, E.F. DeLong, D.M. Karl, G.F. Steward, J.M. Eppley, N.C.Kyrpides, S. Schuster, and M.S. Rappe. 2014. 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. Standards in Genomic Sciences 9: 632-645

(20) H. Luo, B.K. Swan, R. Stepanauskas, A.L. Hughes, and M.A. Moran. 2014. Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. The ISME Journal 8: 1428-1439

(19) H. Luo, B.K. Swan, R. Stepanauskas, A.L. Hughes, and M.A. Moran. 2014. Comparing effective population sizes of dominant marine Alphaproteobacteria lineages. Environmental Microbiology Reports 6 (2): 167-172

(18) H. Luo, B.B. Tolar, B.K. Swan, C.L. Zhang, R. Stepanauskas, M.A. Moran, and J.T. Hollibaugh. 2014. Single cell genomics shedding light on marine Thaumarchaeota diversification. The ISME Journal 8: 732-736

(17) H. Luo, M. Csuros, A.L. Hughes, and M.A. Moran. 2013. Evolution of divergent life history strategies in marine Alphaproteobacteria. mBio 4 (4): e00373-13

(16) B.K. Swan, B. Tupper, A. Sczyrba, F.M. Lauro, M. Martinez-Garcia, J.M. Gonzalez, H. Luo, J.J. Wright, Z. C. Landry, N.W. Hanson, B. Thompson, N.J. Poulton, P. Schwientek, S.G. Acinas, S.J. Giovannoni, M.A. Moran, S.J. Hallam, R.Cavicchioli, T. Woyke, and R. Stepanauskas. 2013. Prevalent genome streamlining and latitudinal divergence of marine bacteria in the surface ocean. Proc. Natl. Acad. Sci. USA 110 (28): 11463-11468

(15) H. Luo and M.A. Moran. 2013 Assembly-free metagenomic analysis reveals new metabolic capabilities in surface ocean bacterioplankton. Environmental Microbiology Reports 5 (5): 686-696

(14) N. Akram, J. Palovaara, J. Forsberg, M.V. Lindh, D.L. Milton, H. Luo, J.M. Gonzalez, and J. Pinhassi. 2013. Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp. AND4. Environmental Microbiology 15 (5): 1400-1415

(13) M.A. Moran, B. Satinsky, S.M. Gifford, H. Luo, A. Rivers, L. Chan, J. Meng, B.P. Durham, C. Shen, V.A.Varaljay, C.B. Smith, P.L. Yager, and B.M. Hopkinson. 2013. Sizing up metatranscriptomics. The ISME Journal 7: 237-243

(12) H. Luo and A.L. Hughes. 2012. dN/dS does not show positive selection drives separation of polar-tropical SAR11 populations. Molecular Systems Biology 8: 625

(11) H. Luo. 2012. Predicted protein subcellular localization in dominant surface ocean bacterioplankton. Applied and Environmental Microbiology 78 (18): 6550-6557

(10) H. Luo, W. Arndt, Y. Zhang, G. Shi, M. Alekseyev, J. Tang, A.L. Hughes, and R. Friedman. 2012. Phylogenetic analysis of genome rearrangements among five mammalian orders. Molecular Phylogenetics and Evolution 65 (3): 871-882

(9) H. Luo, A. Loytynoja, and M.A. Moran. 2012. Genome content of uncultivated marine roseobacters in the surface ocean. Environmental Microbiology 14 (1): 41-51

(8) H. Luo, R. Friedman, J. Tang, and A.L. Hughes. 2011. Genome reduction by deletion of paralogs in the marine cyanobacterium Prochlorococcus. Molecular Biology and Evolution 28 (10): 2751-2760

(7) H. Luo, H. Zhang, R.A. Long, and R. Benner. 2011. Depth distributions of alkaline phosphatase and phosphonate utilization genes in the North Pacific Subtropical Gyre. Aquatic Microbial Ecology 62: 61-69 (recommended by Faculty of 1000,

(6) H. Luo, J. Tang, R. Friedman, and A.L. Hughes. 2011. Ongoing purifying selection on the intergenic spacers in the Group A Streptococcus. Infection, Genetics and Evolution 11 (2): 343-348

(5) J. Shi, Y. Zhang, H. Luo, and J. Tang. 2010. Using jackknife to assess the quality of gene order phylogenies. BMC Bioinformatics 11: 168

(4) H. Luo, R. Benner, R. A. Long, and J. Hu. 2009. Subcellular localization of marine bacterial alkaline phosphatases. Proc. Natl. Acad. Sci. USA 106 (50): 21219-21223

(3) H. Luo, Z. Sun, W. Arndt, J. Shi, R. Friedman, and J. Tang. 2009. Gene order phylogeny and the evolution of methanogens. PLoS ONE 4 (6): e6069

(2) H. Luo, J. Shi, W. Arndt, J. Tang, and R. Friedman. 2008. Gene order phylogeny of the genus Prochlorococcus. PLoS ONE 3 (12): e3837

(1) B. Huang, L. Ou, H. Hong, H. Luo, and D. Wang. 2005. Bioavailability of dissolved organic phosphorus compounds to typical harmful dinoflagellate Prorocentrum donghaiense Lu. Marine Pollution Bulletin 51: 838-844