Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Carl von Ossietzky Str. 9-11, D-26129 Oldenburg, Germany.
Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
Syst Appl Microbiol. 2019 Sep;42(5):126000. doi: 10.1016/j.syapm.2019.06.005. Epub 2019 Jul 4.
Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) and amplicon sequencing of the total (16S rRNA gene) and potentially active (16S rRNA transcripts), community are the major state of the art approaches for assessing the composition of bacterial communities in marine pelagic and other ecosystems. However, CARD-FISH and amplicon sequencing methods have not yet been directly compared to assess the composition of bacterioplankton communities. Therefore, these approaches were used to study the composition of bacterial communities in two North Sea seawater mesocosm experiments supplemented with diatom-derived organic matter (OM). All approaches revealed Proteobacteria and Bacteroidetes as major components of the bacterioplankton communities. The Roseobacter group and its RCA cluster, as well as Bacteroidetes and Gammaproteobacteria, responded most strongly to OM addition, whereas the SAR11 clade responded in only one of the two mesocosms. A correlation analysis showed that CARD-FISH and amplicon sequencing data of the SAR11 clade and the Roseobacter group, together with its RCA cluster, were highly significantly correlated, whereas Bacteroidetes did not yield any significant correlation and Gammaproteobacteria was only correlated with the potentially active fraction. However, subgroups of these phylogenetic groups, the SAR92 clade, the genera Pseudoalteromonas and Polaribacter, exhibited significant correlations in one of the two mesocosms. Correlations of CARD-FISH with amplicon sequencing data from the total and potentially active fractions of these lineages exhibited distinct differences. The study showed that CARD-FISH and amplicon sequencing data of distinct bacterioplankton groups and especially the phylogenetic lineages at a higher taxonomic level were correlated but reflected different aspects of their growth dynamics.
催化报告分子沉积荧光原位杂交（CARD-FISH）和扩增子测序的总（16S rRNA 基因）和潜在活性（16S rRNA 转录物），是评估海洋浮游生物和其他生态系统中细菌群落组成的主要最新方法。然而，CARD-FISH 和扩增子测序方法尚未直接进行比较，以评估细菌浮游生物群落的组成。因此，这些方法被用于研究两个北海海水中培养实验中细菌群落的组成，这些实验中添加了硅藻衍生的有机物（OM）。所有方法都揭示了变形菌门和拟杆菌门是浮游细菌群落的主要组成部分。玫瑰杆菌群及其 RCA 簇，以及拟杆菌门和γ-变形菌门，对 OM 添加的反应最为强烈，而 SAR11 分支在两个中培养实验中仅在一个中做出反应。相关性分析表明，CARD-FISH 和扩增子测序数据的 SAR11 分支和玫瑰杆菌群及其 RCA 簇高度显著相关，而拟杆菌门没有产生任何显著相关性，γ-变形菌门仅与潜在活性部分相关。然而，这些系统发育群的亚群，SAR92 分支，假交替单胞菌属和极地杆菌属，在两个中培养实验中的一个中表现出显著相关性。CARD-FISH 与这些谱系的总和潜在活性部分的扩增子测序数据的相关性存在明显差异。该研究表明，CARD-FISH 和扩增子测序数据的不同浮游细菌群，特别是在更高的分类水平上的系统发育谱系相关，但反映了它们生长动态的不同方面。
