Cabrol Léa, Delleuze Mélanie, Szylit Arthur, Schwob Guillaume, Quéméneur Marianne, Misson Benjamin
Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO, Marseille, France; Millennium Institute BASE "Biodiversity of Antarctic and Subantarctic Ecosystems", Las Palmeras, 3425, Santiago, Chile; Instituto de Ecologia y Biodiversidad, Santiago, Chile.
Millennium Institute BASE "Biodiversity of Antarctic and Subantarctic Ecosystems", Las Palmeras, 3425, Santiago, Chile; Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
Mar Pollut Bull. 2023 Oct 27;197:115688. doi: 10.1016/j.marpolbul.2023.115688.
Marine free-living (FL) and plankton-associated prokaryotes (plankton-microbiota) are at the basis of trophic webs and play crucial roles in the transfer and cycling of nutrients, organic matter, and contaminants. Different ecological niches exist along the plankton size fraction gradient. Despite its relevant ecological role, the plankton-microbiota has rarely been investigated with a sufficient level of size-fraction resolution, and it can be challenging to study because of overwhelming eukaryotic DNA. Here we compared the prokaryotic diversity obtained by 16S rRNA gene sequencing from six plankton size fractions (from FL to mesoplankton), through three DNA recovery methods: direct extraction, desorption pretreatment, enrichment post-treatment. The plankton microbiota differed strongly according to the plankton size-fraction and methodological approach. Prokaryotic taxa specific to each size fraction, and methodology used, were identified. Vibrionaceae were over-represented by cell desorption pretreatment, while prokaryotic DNA enrichment had taxon-specific effects, indicating that direct DNA extraction was the most appropriate method.
海洋自由生活（FL）原核生物和与浮游生物相关的原核生物（浮游生物微生物群）是营养网的基础，在营养物质、有机物和污染物的转移与循环中发挥着关键作用。沿着浮游生物大小分级梯度存在不同的生态位。尽管浮游生物微生物群具有重要的生态作用，但很少以足够的大小分级分辨率进行研究，并且由于真核生物DNA过多，研究起来可能具有挑战性。在这里，我们通过三种DNA回收方法，比较了从六个浮游生物大小分级（从FL到中型浮游生物）中通过16S rRNA基因测序获得的原核生物多样性：直接提取、解吸预处理、富集后处理。浮游生物微生物群根据浮游生物大小分级和方法学方法有很大差异。确定了每个大小分级和所用方法特有的原核生物分类群。弧菌科在细胞解吸预处理中占比过高，而原核生物DNA富集具有分类群特异性效应，表明直接DNA提取是最合适的方法。
