State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
College of Marine Science, Shandong University, Weihai, 264209, People's Republic of China.
Microbiome. 2018 Dec 26;6(1):230. doi: 10.1186/s40168-018-0613-2.
The pure culture of prokaryotes remains essential to elucidating the role of these organisms. Scientists have reasoned that hard to cultivate microorganisms might grow in pure culture if provided with the chemical components of their natural environment. However, most microbial species in the biosphere that would otherwise be "culturable" may fail to grow because of their growth state in nature, such as dormancy. That means even if scientist would provide microorganisms with the natural environment, such dormant microorganisms probably still remain in a dormant state.
We constructed an enrichment culture system for high-efficiency isolation of uncultured strains from marine sediment. Degree of enrichment analysis, dormant and active taxa calculation, viable but non-culturable bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the interactions between microbial communications during enrichment culture showed that the so-called enrichment method could culture the "uncultured" not only through enriching the abundance of "uncultured," but also through the resuscitation mechanism. In addition, the enrichment culture was a complicated mixed culture system, which contains the competition, cooperation, or coordination among bacterial communities, compared with pure cultures.
Considering that cultivation techniques must evolve further-from axenic to mixed cultures-for us to fully understand the microbial world, we should redevelop an understanding of the classic enrichment culture method. Enrichment culture methods can be developed and used to construct a model for analyzing mixed cultures and exploring microbial dark matter. This study provides a new train of thought to mining marine microbial dark matter based on mixed cultures.
原核生物的纯培养仍然是阐明这些生物作用的关键。科学家推断，如果提供其天然环境的化学组成部分，那些难以培养的微生物可能会在纯培养中生长。然而，由于其在自然界中的生长状态，如休眠，生物圈中大多数原本“可培养”的微生物物种可能无法生长。这意味着，即使科学家为微生物提供了天然环境，这些休眠的微生物可能仍然处于休眠状态。
我们构建了一种从海洋沉积物中高效分离未培养菌株的富集培养系统。通过对富集度分析、休眠和活性分类群计算、可培养但不可培养细菌复苏分析，结合富集培养过程中微生物间相互作用的宏转录组学和比较基因组学分析表明，所谓的富集方法不仅可以通过富集“未培养”的丰度来培养“未培养”的微生物，还可以通过复苏机制来培养。此外，与纯培养相比，富集培养是一个复杂的混合培养系统，其中包含细菌群落之间的竞争、合作或协调。
鉴于培养技术必须进一步从纯培养发展到混合培养，我们才能充分了解微生物世界，我们应该重新认识经典的富集培养方法。可以开发和利用富集培养方法来构建分析混合培养和探索微生物暗物质的模型。本研究为基于混合培养挖掘海洋微生物暗物质提供了新的思路。
