Design of novel primer sets for easy detection of <i>Ruegeria</i> species from seawater

Some coral-associated bacteria show protective roles for corals against pathogens. However, the distribution of coral-protecting bacteria in seawater is not well known. In addition, compared with the methods for investigating coral pathogens, few methods have been developed to detect coral-protecting bacteria. Here we prepared a simple method for detecting <i>Ruegeria</i> spp., some strains of which inhibit growth of the coral pathogen <i>Vibrio coralliilyticus</i>. We successfully obtained two <i>Ruegeria</i>-targeting primer sets through <i>in silico</i> and <i>in vitro</i> screening. The primer sets r38F-r30R and r445F-r446R, in addition to the newly designed universal primer set U357′F-U515′R, were evaluated <i>in vitro</i> using environmental DNA extracted from seawater collected in Osaka. These methods and primers should contribute to revealing the distribution of <i>Ruegeria</i> spp. in marine environments. This study provides an easy way of detecting specific bacteria in seawater or in DNA mixtures.部分珊瑚相关细菌可对珊瑚发挥抵御病原微生物的保护作用。然而，目前对于这类具有珊瑚保护功能的细菌在海水中的分布情况仍不甚明晰。此外，相较于针对珊瑚病原微生物的研究方法，目前用于检测珊瑚保护细菌的检测手段仍较为匮乏。本研究开发了一种用于检测鲁杰氏菌属（Ruegeria）的简便方法，该属部分菌株可抑制珊瑚病原微生物珊瑚溶弧菌（Vibrio coralliilyticus）的生长。本研究通过计算机模拟（in silico）与体外（in vitro）筛选，成功获得了两套靶向鲁杰氏菌属的引物组。针对引物组r38F-r30R、r445F-r446R，以及新设计的通用引物组U357′F-U515′R，本研究采用从大阪采集的海水提取的环境DNA进行了体外评估。上述方法与引物将有助于阐明鲁杰氏菌属在海洋环境中的分布情况。本研究为海水或DNA混合物中特定细菌的检测提供了一种简便可行的方案。