Submitted Papers

X. Wang^, K. Uematsu^, A. O’Rourke, T. Akita, K. Kimura, Y. Tomaru, C.R. Voolstra, H. Innan*, and H. Luo*. 2022. A novel bacterial speciation process observed in a symbiotic marine population. (on bioRxiv).

L. Qu^+, X. Feng^, Y. Chen, L. Li, X. Wang, Z. Hu, H. Wang, and H. Luo*. 2021. Metapopulation structure of diatom-associated marine bacteria. (on bioRxiv)

Peer Reviewed Papers

(*Corresponding Author; ^equal contribution; lab members; +visiting student)

(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. FengX. ChuY. 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. ChuH. 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). pii: 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. SunY. HuangX. 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