进化基因组学实验室

利用计算生物学、遗传学和微生物学方法，以纤毛虫原生动物、细菌、酵母等为研究模式，研究微生物演化，聚焦生物的突变规律和生活史演化，具体研究主题如下：

A. 土壤原生动物的生物多样性和促进植物生长的机制

B. 土壤原生动物生物肥料研发

C. 原生动物生活史的调控与演化

D. 环境胁迫下的病原微生物的突变与演化

We are interested in evolution of prokaryotic and eukaryotic microbes, with a focus on mutation rate and life history evolution. The research models are quite broad, including ciliates, bacteria, yeast, etc. Our research strategy combines population genetics theory, experimental evolution, -omics sequencing, genetic techniques, and bioinformatic tools. The lab deems the training of independent researchers as our first task and research as the second. Graduate students would receive complete training of scientific research and multiple undergrad assistants are also provided for their research. We are now exploring the following topics:

A. Soil protozoa: biodiversity and mechanisms of plant growth promotion

B. Development of soil protozoa-based bio-fertilizers

C. Regulation and evolution of life history in protozoa

D. Mutation and evolution of pathogens under environmental stress

招聘：协助拟加入人员申请中国海洋大学“青年英才工程”（http://rsc.ouc.edu.cn/04/50/c1485a66640/page.htm）等各层次人才计划；定期招收实验室管理、技术等科研助理岗位。

招生：常年招收优秀本科生兼职助理、硕士生、博士生和博士后。

具体信息请邮件咨询（longhongan@ouc.edu.cn）

• 国家自然科学基金面上项目（2023.01-2026.12；2025.01-2028.12）

• 山东省“泰山学者”特聘教授项目（2025.01-2029.12）
  

• 国家自然科学基金国际（地区）合作项目（2019.10-2024.9）
  

• 国家海外高层次人才引进项目（2019-2021）

• 本科生课程：

• 《微生物学》理论（40课时，2.5学分；春季学期，水产学院；龙红岸独立讲授）

• 《统计建模与推断》（48课时，3学分；春季学期，海德学院；张俣独立讲授）

• 《模式生物的发育与进化》（32课时，2学分；春季学期，全校通识课，水产学院；龙红岸与其他5位老师合开）

• 研究生课程：

• 《生物大数据分析》（公益培训，48课时；负责人：龙红岸，授课团队：进化基因组学实验室全体师生、朱明壮、杨伟等老师）

• • https://mp.weixin.qq.com/s/WeMWf0kieXQbN8fGimlD1A

Recent publications

Pan, J.; Wang, Y.; Li, C.; Zhang, S.; Ye, Z.; Ni, J.; Li, H.; Li, Y.; Yue, H.; Ruan, C.; Zhao, D.; Jiang, Y.; Wu, X.; Shen, X.; Zufall, R.A.; Zhang, Y.; Li, W.; Lynch, M.; Long, H. 2024. Molecular basis of phenotypic plasticity in a marine ciliate. The ISME Journal 18: wrae136 [Pan et al. ISME J 2024.pdf]

Li, H.; Wu, K.; Feng, Y.; Gao, C.; Wang, Y.; Zhang, Y.; Pan, J.; Shen, X.; Zufall, R.A.; Zhang, Y.; Zhang, W.; Sun, J.; Ye, Z.;  Li, W.; Lynch, M.; Long, H. 2024. Integrative analyses on the ciliates Colpoda illuminate the life history evolution of soil microorganisms. mSystems 9: e01379-23 [Li et al. mSystems 2024.pdf]

Zhang, Y.; Li, H.; Wang, Y.; Nie, M.; Zhang, K.; Pan, J.; Zhang, Y.; Ye, Z.; Zufall, R.; Lynch, M.; Long, H. 2024. Mitogenomic architecture and evolution of the soil ciliates Colpoda. mSystems 9: e01161-23 [Zhang et al. mSystems 2024.pdf]

Long, H.; Johri, P.; Gout, J.F.; Ni, J.; Hao, Y.; Licknack, T.; Wang, Y.; Pan, J.; Berenice Jiménez-Marín; Lynch, M. 2023. Paramecium genetics, genomics and evolution. Annual Review of Genetics 57: 391-410 [Long et al. ARG 2023.pdf]

Lynch, M.; Ali, F.; Lin, T.; Wang, Y.; Ni, J.; Long, H. 2023 The divergence of mutation rates and spectra across the Tree of Life. EMBO Reports e57561 [Lynch et al. EMBO Reports 2023.pdf]

Ni, J.; Pan, J.; Wang, Y.; Chen, T.; Feng, X.; Li, Y.; Lin, T.; Lynch, M.; Long, H.; Li, W. 2023. An integrative protocol for one-step PCR amplicon library construction and accurate demultiplexing of pooled sequencing data. Marine Life Science and Technology 5:564-572. [Ni et al. MLST 2023.pdf]

Wu, K.; Li, H.; Cui, X.; Feng, R.; Chen, W.; Jiang, Y.; Tang, C.; Wang, Y.; Shen, X.; Liu, Y.; Lynch, M.; Long, H. 2022. Mutagenesis and resistance development of bacteria challenged by silver nanoparticles. Antimicrobial Agents and Chemotherapy [Wu et al. AAC 2022.pdf]

Pan, J.; Li, W.; Ni, J.; Wu, K.; Konigsberg, I.; Rivera, C.; Tincher, C.; Gregory, C.; Zhou, X.; Doak, T.; Lee, H.; Wang, Y.; Gao, X.; Lynch, M.; Long, H. 2022. Rates of mutations and transcript errors in the foodborne pathogen Salmonella enterica subsp. enterica. Molecular Biology and Evolution 39(4): msac081[Pan et al. MBE 2022.pdf]

Long, H.; Miller, S.F.; Williams, E.; Lynch, M. 2018. Specificity of the DNA mismatch repair system (MMR) and mutagenesis bias in bacteria. Molecular Biology and Evolution 35(10):2414-2421. [Long et al Mol Biol Evol 2018.pdf]    

Long, H.; Sung, W.; Kucukyildirim,S.; Williams,E.; Miller, S.;Guo, W.; Patterson, C.; Gregory, C.; Strauss, C.; Stone, C.; Berne, C.; Kysela, D.; Shoemaker, W.; Muscarella, M.; Luo, H.; Lennon, J.; Brun, Y.; Lynch, M. 2018. Evolutionary determinants of genome-wide nucleotide composition. Nature Ecology and Evolution 2: 237-240. [Long et al Nat Ecol Evol 2018.pdf]

Long, H.; Miller, S.F.; Strauss, C.; Zhao, C.; Cheng, L.; Ye, Z.; Griffin, K.; Te, R.; Lee, H.; Chen, C.; Lynch, M. 2016. Antibiotic treatment enhances the genome-wide mutation rate of target cells. PNAS 113(18): E2498-E2505. [Long et al. PNAS 2016.pdf]

Long, H.; Kucukyildirim#, S.; Sung, W.; Williams, E.; Lee, H.; Ackerman, M.; Doak, T.; Tang, H.; Lynch, M. 2015. Background mutational features of the radiation-resistant bacterium Deinococcus radiodurans. Molecular Biology and Evolution 32(9): 2383-2392. [Long et al. MBE 2015.pdf]

2024 山东省科普创作大赛一等奖

2021 中国海洋大学优秀教师

2019 中国海洋大学第21届天泰奖一等奖；中国海洋大学优秀班主任；中国海洋大学第20届五四青年奖

2018 李氏基金会杰出创新奖

2016 美国遗传学会DeLill Nasser遗传学职业发展奖

2018 Li Foundation Heritage Prize-Excellence in Creativity

2016 DeLill Nasser Award for Professional Development in Genetics, Genetics Society of America