Application of in situ cultivation in marine microbial resource mining
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REVIEW
Application of in situ cultivation in marine microbial resource mining Dawoon Jung1 · Liwei Liu1 · Shan He1 Received: 23 April 2020 / Accepted: 28 June 2020 © Ocean University of China 2020
Abstract Microbial communities in marine habitats are regarded as underexplored reservoirs for discovering new natural products with potential application. However, only a few microbes in nature can be cultivated in the laboratory. This has led to the development of a variety of isolation and cultivation methods, and in situ cultivation is one of the most popular. Diverse in situ cultivation methods, with the same basic principle, have been applied to a variety of environmental samples. Compared with conventional approaches, these new methods are able to cultivate previously uncultured and phylogenetically novel microbes, many with biotechnological potential. This review introduces the various in situ cultivation methods for the isolation of previously uncultured microbial species and their potential for marine microbial resource mining. Furthermore, studies that investigated the key and previously unidentified mechanisms of growing uncultivated microorganisms by in situ cultivation, which will shed light on the understanding of microbial uncultivability, were also reviewed. Keywords Uncultured microorganism · Marine microbial resource · In situ cultivation · Microbial diversity
Introduction Microorganisms from marine environments are regarded as a major source for natural products discovery. These represent a wide diversity of biological activities, including antimicrobial, anti-inflammatory and anti-tumor activities (Blunt et al. 2018; Liu et al. 2010; Srilekha et al. 2017; Xiong et al. 2012, 2013). Pure cultivation of microorganisms is essential to enable efficient discovery of novel natural products with industrial and biotechnological potential, especially for new antibiotics. Despite the availability of culture-independent molecular tools for analysis of microbial communities in natural environments (Wang et al. 2012) and heterologous expression of biosynthetic gene clusters (Gomez-Escribano and Bibb 2014; Nah et al. 2017; Ongley et al. 2013), culture-dependent approaches are still necessary, because SPECIAL TOPIC: Cultivation of uncultured microorganisms. Edited by Chengchao Chen. * Shan He [email protected] 1
Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315832, China
a comprehensive physiological characterization and a full assessment of application potential can only be performed through the isolation of individual bacterial strains in pure culture (Vartoukian et al. 2010). Most marine microbial species, however, are unculturable and cannot grow under regular laboratory conditions (Rinke et al. 2013). Only a few of these (generally about 1%) can grow into colonies on standard agar media, thus leading to the ‘great plate count anomaly’, a feature for more than 120 years (Amann 1911; Amann et al. 1995; S
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