Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing

Da-Shuai Mu,Ming-Jing Shi,Guan-Jun Chen,Qi-Yun Liang,Zong-Jun Du,Xiao-Man Wang,De-Chen Lu

doi:10.1186/s40168-018-0613-2

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsConsidering 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.

Highlights

The pure culture of prokaryotes remains essential to elucidating the role of these organisms
Culturing the marine sediment microbiotas based on the enrichment method We developed an enrichment culture method using a low-nutrient medium containing 10 mM sodium pyruvate in the culture (Fig. 1) because low-nutrient media facilitated the cultivation of previously uncultured marine bacterioplankton [11]
Dormant and active taxa calculation, viable but non-culturable (VBNC) bacteria resuscitation analysis, combined with metatranscriptomic and comparative genomic analyses of the culturability mechanism during enrichment culture showed that the so-called enrichment method could isolate “recalcitrant” strains through enriching their abundance and through resuscitation

Summary

Introduction

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. 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. Key questions remain because most microbial species in the biosphere resist cultivation in the laboratory [3, 4]. Researchers have pointed out that if one could provide the chemical components of natural These have been great successes; many microbial species in the biosphere that would otherwise be “culturable” may fail to grow because of their growth state in nature, such as dormancy [11], which results in species that are referred to as viable but non-culturable (VBNC) [12]. If one could predict the metabolism of an organism and provide the preferred carbon/nutrient sources, one should be theoretically able to switch a dormant to a non-dormant microbe

Methods

Results

Conclusion