Cultivation of uncultured marine microorganisms

Alongi DM (2014) Carbon cycling and storage in mangrove forests. Ann Rev Mar Sci 6:195–219

Asem MD, Shi L, Jiao JY, Wang D, Han MX, Dong L, Liu F, Salam N, Li WJ (2018) Desertimonas flava gen. nov., sp. nov., isolated from a desert soil, and proposal of Ilumatobacteraceae fam. nov. Int J Syst Evol Microbiol 68:3593–3599

Baker BJ, De Anda V, Seitz KW, Dombrowski N, Santoro AE, Lloyd KG (2020) Diversity, ecology and evolution of Archaea. Nat Microbiol 5:887–900

Castelle CJ, Banfield JF (2018) Major new microbial groups expand diversity and alter our understanding of the tree of life. Cell 172:1181–1197

Cui H-L, Dyall-Smith ML (2021) Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments. Mar Life Sci Technol 3:243–251

Ding L, Xu P, Zhang W, Yuan Y, He X, Su D, Shi Y, Naman CB, Yan X, Wu B, Lazaro JEH, Li S, He S (2020) Three new diketopiperazines from the previously uncultivable marine bacterium Gallaecimonas mangrovi HK-28 cultivated by iChip. Chem Biodiv 17:e2000221

Gutleben J, Chaib De Mares M, van Elsas JD, Smidt H, Overmann J, Sipkema D (2018) The multi-omics promise in context: from sequence to microbial isolate. Crit Rev Microbiol 44:212–229

Hofer U (2018) The majority is uncultured. Nat Rev Microbiol 16:716–717

Hu B, Xu B, Yun J, Wang J, Xie B, Li C, Yu Y, Lan Y, Zhu Y, Dai X, Huang Y, Huang L, Pan J, Du W (2020) High-throughput single-cell cultivation reveals the underexplored rare biosphere in deep-sea sediments along the Southwest Indian Ridge. Lab Chip 20:363–372

Hu B, Xu P, Ma L, Chen D, Wang J, Dai X, Huang L, Du W (2021a) One cell at a time: droplet-based microbial cultivation, screening and sequencing. Mar Life Sci Technol 3:169–188

Hu H, Natarajan VP, Wang F (2021b) Towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods. Mar Life Sci Technol 3:231–242

Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF (2016) A new view of the tree of life. Nat Microbiol 1:16048

Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, Takano Y, Uematsu K, Ikuta T, Ito M, Matsui Y, Miyazaki M, Murata K, Saito Y, Sakai S, Song C, Tasumi E, Yamanaka Y, Yamaguchi T, Kamagata Y et al (2020) Isolation of an archaeon at the prokaryote–eukaryote interface. Nature 577:519–525

Jiang C, Dong L, Zhao J, Hu X, Shen C, Qiao Y, Zhang X, Wang Y, Ismagilov RF, Liu S, Du W (2016) High-throughput single-cell cultivation on microluidic streak plates. Appl Environ Microbiol 82:2210–2218

Jiao JY, Liu L, Hua ZS, Fang BZ, Zhou EM, Salam N, Hedlund BP, Li WJ (2020) Microbial dark matter coming to light: challenges and opportunities. Natl Sci Rev. https://doi.org/10.1093/nsr/nwaa280

Jung D, Liu L, He S (2021) Application of in situ cultivation in marine microbial resource mining. Mar Life Sci Technol 3:148–161

Liu H, Xue R, Wang Y, Stirling E, Ye S, Xu J, Ma B (2021) FACS-iChip: a high-efficient iChip system for microbial ‘dark matter’ mining in sediments. Mar Life Sci Technol 3:162–168

Lok C (2015) Mining the microbial dark matter. Nature 522:270–273

Lyu L, Wang Q, Wang G (2021) Cultivation and diversity analysis of novel marine thraustochytrids. Mar Life Sci Technol 3:263–275

Mu D-S, Liang Q-Y, Wang X-M, Lu D-C, Shi M-J, Chen G-J, Du Z-J (2018) Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. Microbiome 6:230

Mu D-S, Zhou L-Y, Liang Q-Y, Chen G-J, Du Z-J (2020a) Tichowtungia aerotolerans gen. nov., sp. nov., a novel representative of the phylum Kiritimatiellaeota and proposal of Tichowtungiaceae fam. nov., Tichowtungiales ord. nov. and Tichowtungiia class. nov. Int J Syst Evol Microbiol 70:5001–5011

Mu D-S, Wang S, Liang Q-Y, Du Z-Z, Tian R, Ouyang Y, Wang X-P, Zhou A, Gong Y, Chen G-J, Nostrand JV, Yang Y, Zhou J, Du Z-J (2020b) Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. Microbiome 8:126

Mu D-S, Ouyang Y, Chen G-J, Du Z-J (2021) Strategies for culturing active/dormant marine microbes. Mar Life Sci Technol 3:121–131

Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen I-M, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP et al (2020) A genomic catalog of Earth’s microbiomes. Nat Biotechnol. https://doi.org/10.1038/s41587-020-0718-6

Oliver JD (2016) The viable but nonculturable state for bacteria: status update. Microbe 11:159–164

Oren A (2014) The family Halobacteriaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes: other major lineages of bacteria and the archaea. Springer, Berlin, pp 41–121

Overmann J, Lepleux C (2016) Marine bacteria and archaea: diversity, adaptations, and culturability. In: Stal LJ, Cretoiu MS (eds) The marine microbiome: an untapped source of biodiversity and biotechnological potential. Springer International Publishing, Cham, pp 21–56

Pinto D, Santos MA, Chambel L (2015) Thirty years of viable but nonculturable state research: unsolved molecular mechanisms. Crit Rev Microbiol 41:61–76

Qin S, Li J, Chen HH, Zhao GZ, Zhu WY, Jiang CL, Xu LH, Li WJ (2009) Isolation, diversity and antimicrobial activity of rare actinobacteria from medicinal plants of tropical rainforests, Xishuangbanna. Appl Environ Microbiol 75:6176–6186

Rappé MS, Connon SA, Vergin KL, Giovannoni SJ (2002) Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630–633

Salam N, Xian W-D, Asem MD, Xiao M, Li W-J (2021) From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes. Mar Life Sci Technol 3:132–147

Spang A, Caceres EF, Ettema TJG (2017) Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 357:eaaf3883

Wang W, Li Z, Zeng L, Shao Z (2020) The oxidation of hydrocarbons by diverse heterotrophic and mixotrophic bacteria that inhabit deep-sea hydrothermal ecosystems. ISME J 14:1994–2006

Xian W-D, Salam N, Li M-M, Zhou E-M, Yin Y-R, Liu Z-T, Ming Y-Z, Zhang X-T, Wu G, Liu L, Xiao M, Jiang H-C, Li W-J (2020) Network-directed efficient isolation of previously uncultivated Chloroflexi and related bacteria in hot spring microbial mats. NPJ Biofilms Microb 6:20

Xu H-S, Roberts N, Singleton FL, Attwell RW, Grimes DJ, Colwell RR (1982) Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb Ecol 8:313–323

Zeng X, Alain K, Shao Z (2021) Microorganisms from deep-sea hydrothermal vents. Mar Life Sci Technol 3:204–230

Zhang C-J, Pan J, Duan C-H, Wang Y-M, Liu Y, Sun J, Zhou H-C, Song X, Li M (2019) Prokaryotic diversity in mangrove sediments across Southeastern China fundamentally differs from that in other biomes. mSystems 4:e00442–e519

Zhang C-J, Chen Y-L, Sun Y-H, Pan J, Cai M-W, Li M (2021a) Diversity, metabolism and cultivation of archaea in mangrove ecosystems. Mar Life Sci Technol 3:252–262

Zhang X-H, Ahmad W, Zhu X-Y, Chen J, Austin B (2021b) Viable but nonculturable bacteria and their resuscitation: implications for cultivating uncultured marine microorganisms. Mar Life Sci Technol 3:189–203