From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes
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REVIEW
From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes Nimaichand Salam1 · Wen‑Dong Xian1 · Mipeshwaree Devi Asem1 · Min Xiao1 · Wen‑Jun Li1,2 Received: 26 May 2020 / Accepted: 22 July 2020 © Ocean University of China 2020
Abstract Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities. Keywords Biofilms · Ecophysiology · Unculturability · Co-occurrence network · Reverse genomics
Introduction Bacterial cultivation was revolutionized with the accidental discovery of agar as a solidifying agent in the preparation of culture media in the late nineteenth century (Hesse 1992). Subsequently, plenty of bacterial and fungal strains have been brought into pure cultures in laboratory conditions for downstream investigation. As of April 2020, 16,529 bacterial and archaeal species have been described with valid nomenclature (https://lpsn.dsmz.de/text/numbers; accessed SPECIAL TOPIC: Cultivation of uncultured microorganisms. Edited by Chengchao Chen. * Wen‑Jun Li [email protected] 1
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Science and School of Ecology, Sun Yat-Sen University, Guangzhou 510275, China
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
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on 24 May 2020). These described species largely fall within the bacterial phyla of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes (Rinke et al. 2013). Bacterial diversity has been largely estimated on the basis of molecular markers, particularly the 16S rRNA gene sequence (Pace 1997). A systematic comparison between the described bacterial species and the global bacterial diversity indices indicated that most (> 99%) bacteria escaped cultivation, i.e., not-yet-cultured (Bernard et al. 2000; Hofer 20
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