Roager Line, Sonnenschein Eva C, Gram Lone
Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
Microbiol Spectr. 2023 Mar 28;11(2):e0340822. doi: 10.1128/spectrum.03408-22.
The bacterial communities associated with microalgae are vital for the growth and health of the host, and engineering algal microbiomes can enhance the fitness of the algae. Characterization of these microbiomes mostly relies on sequencing of DNA, which can be extracted with an array of protocols that potentially impact DNA quantity and quality and thus potentially affect subsequent analyses of microbiome composition. Here, we extracted DNA from Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii microbiomes using four different protocols. DNA yield and quality was greatly impacted by the choice of extraction protocol, whereas microbiome composition determined by 16S rRNA gene amplicon sequencing was only impacted to a minor degree, with microalgal host species being the main determinant of microbiome composition. The microbiome was dominated by the genus , whereas the microbiome associated with T. suecica was dominated by and family members. While these two families were also prevalent in the microbiome associated with , and were also highly dominant. Phenol-chloroform extraction resulted in higher DNA quality and quantity compared to commercial kits; however, because they have other advantages such as high throughput and low toxicity, commercial kits can be employed to great benefit for the characterization of microalgal microbiomes. Microalgae are very important as primary producers in the ocean, but also as forthcoming sustainable producers of biotechnologically interesting compounds. Accordingly, the bacterial microbiomes associated with microalgae are attracting increasing attention due to their effects on the growth and health of microalgae. Since most members of these microbiomes cannot be cultured, knowledge about community composition is best obtained using sequencing-based methods. This study evaluates the impact of DNA extraction methods on DNA quantity and quality along with sequence-based characterization of the bacterial microbiome composition of three microalgae: Isochrysis galbana, Tetraselmis suecica, and Conticribra weissflogii.
与微藻相关的细菌群落对宿主的生长和健康至关重要，工程化藻类微生物组可以提高藻类的适应性。这些微生物组的表征主要依赖于DNA测序，DNA可以通过一系列协议提取，这些协议可能会影响DNA的数量和质量，从而可能影响随后对微生物组组成的分析。在这里，我们使用四种不同的协议从等鞭金藻、小新月菱形藻和威氏海链藻微生物组中提取DNA。DNA产量和质量受到提取协议选择的极大影响，而通过16S rRNA基因扩增子测序确定的微生物组组成仅受到轻微影响，微藻宿主物种是微生物组组成的主要决定因素。 微生物组以 属为主，而与小新月菱形藻相关的微生物组以 和 家族成员为主。虽然这两个家族在与 相关的微生物组中也很普遍，但 和 也高度占主导地位。与商业试剂盒相比，酚氯仿提取产生的DNA质量和数量更高；然而，由于商业试剂盒具有高通量和低毒性等其他优点，因此可以非常有益地用于表征微藻微生物组。微藻作为海洋中的初级生产者非常重要，同时也是即将出现的生物技术感兴趣化合物的可持续生产者。因此，与微藻相关的细菌微生物组因其对微藻生长和健康的影响而受到越来越多的关注。由于这些微生物组的大多数成员无法培养，因此最好使用基于测序的方法来获取有关群落组成的知识。本研究评估了DNA提取方法对DNA数量和质量的影响，以及对三种微藻（等鞭金藻、小新月菱形藻和威氏海链藻）细菌微生物组组成的基于序列的表征。
