Burgunter-Delamare Bertille, Tanguy Gwenn, Legeay Erwan, Boyen Catherine, Dittami Simon M
CNRS, Sorbonne Université, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, 29680 Roscoff, France.
CNRS, Sorbonne Université, FR2424 Station Biologique de Roscoff, 29680 Roscoff, France.
Mar Genomics. 2022 Jun;63:100944. doi: 10.1016/j.margen.2022.100944. Epub 2022 Mar 14.
Brown macroalgae, including the kelp Saccharina latissima, are of both ecological and increasing economic interest. Together with their microbiota, these organisms form a singular entity, the holobiont. Sampling campaigns are required to study the microbiome of algae in natural populations, but freezing samples in liquid nitrogen is complex in the field, particularly at remote locations. Here we tested two simple alternative methods for sampling the microbial diversity associated with the kelp S. latissima: silica gel conservation of tissue and swab samples preserved in DNA/RNA shield solution. We used these techniques to compare apex and meristem samples from Roscoff (Brittany, France) and evaluated their impact on the results of 16S rDNA metabarcoding experiments. Both methods were able to separate apex and meristem microbiomes, and the results were concordant with results obtained for flash-frozen samples. However, differences were observed for several rare genera and ASVs, and the detection of contaminant sequences in the silica gel-preserved samples underline the importance of including blank samples for this method. Globally, our results confirm that the silica gel technique and swabbing combined with DNA/RNA shield preservation are valid alternatives to liquid nitrogen preservation when sampling brown macroalgae in the field. However, they also underline that, regardless of the method, caution should be taken when interpreting data on rare sequences.
包括海带（Saccharina latissima）在内的褐藻，在生态和经济方面都具有重要意义，且其重要性与日俱增。这些生物体与其微生物群共同构成了一个独特的实体——共生功能体。为了研究自然种群中藻类的微生物组，需要进行采样活动，但在野外，尤其是在偏远地区，将样本冷冻在液氮中操作复杂。在此，我们测试了两种简单的替代方法来采样与海带S. latissima相关的微生物多样性：用硅胶保存组织样本以及将拭子样本保存在DNA/RNA保护液中。我们运用这些技术比较了来自法国布列塔尼罗斯科夫的藻尖和分生组织样本，并评估了它们对16S rDNA宏条形码实验结果的影响。这两种方法都能够区分藻尖和分生组织的微生物组，且结果与速冻样本所得结果一致。然而，在几个稀有属和扩增子序列变体（ASV）方面观察到了差异，并且在硅胶保存样本中检测到污染序列这一情况凸显了该方法中包含空白样本的重要性。总体而言，我们的结果证实，在野外对褐藻进行采样时，硅胶技术以及结合DNA/RNA保护液保存的拭子采样法是液氮保存法的有效替代方法。不过，研究结果也强调，无论采用哪种方法，在解释稀有序列数据时都应谨慎。
