J Syst Evol

• Research Article •     Next Articles

A simple Liquid-Medium-Dilution (LMD) method recovers high phylogenetic novelty: isolation of a novel order (Poseidonivirgales ord. nov.) within Alphaproteobacteria

Hong-Chuan Wangb, c, Osama Abdalla Abdelshafy Mohamadd, g, h*, Kai Lib, Dan-Yuan Guob, Meng-Han Huangc, Zi-Qi Pengb, Pan-Deng Wangb, e, Dao-Feng Zhangc, Jia-Ling Lib, f, Wen-Jun Lib, c, d *, Zi-Wen Yanga, b*   

  1. aGuangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
    bState Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
    cJiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, China
    dState Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
    eSchool of Pharmacy (Shenzhen University Medical School), and Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
    fSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
    gDepartment of Biological, Marine Sciences and Environmental Agriculture, Institute for Post Graduate Environmental Studies, Arish University, Al-Arish 45511, Egypt
    hDepartment of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish 45511, Egypt
    These authors contributed equally to this work.
    *Corresponding authors: Zi-Wen Yang, E-mail: yangziwen@m.scnu.edu.cn
    Wen-Jun Li, E-mail: liwenjun3@mail.sysu.edu.cn
    Osama Abdalla Abdelshafy Mohamad, E-mail: osama@aru.edu.eg
  • Received:2026-04-07 Accepted:2026-08-03
  • Supported by:
    This work was supported by the National Natural Science Foundation of China (Grant No. 32400003).

Abstract: Although microbial isolation techniques have been developed for over a century, conventional methods often fail to capture the vast majority of environmental microbial diversity, largely because slow-growing bacteria are outcompeted by fast-growing taxa. To address this limitation, we developed a simple Liquid-Medium-Dilution (LMD) method that physically isolates single cells in liquid microcultures using limiting dilution and the Poisson distribution, without requiring specialized equipment. Comparative analysis of 787 bacterial strains isolated from estuarine sediments of the Qiantang River, China, showed that LMD recovered 72 putative novel species (19.2%), a significantly higher proportion than the Traditional-Solid-Culture (TSC) method (47 strains, 11.4%; P < 0.01). Importantly, LMD uniquely accessed rare and slow-growing lineages, including members of the phylum Verrucomicrobiota and most notably two novel species, Poseidonivirga lenticrescens gen. nov., sp. nov., and Poseidonivirga cretacea sp. nov. These strains exhibit low 16S rRNA gene sequence similarities (90.37% and 90.51%) to known taxa and represent a novel order, Poseidonivirgales, within the class Alphaproteobacteria. Our findings demonstrate that the LMD method effectively minimizes competitive exclusion, enabling the cultivation of previously unculturable, slow-growing, and phylogenetically deep bacterial lineages using standard laboratory conditions.