Kerrigan Zak, Kirkpatrick John B, D'Hondt Steven
Graduate School of Oceanography, The University of Rhode Island, Narragansett, RI, United States.
The Evergreen State College, Olympia, WA, United States.
Front Microbiol. 2019 Jul 16;10:1640. doi: 10.3389/fmicb.2019.01640. eCollection 2019.
To assess the influence of 16S ribosomal RNA (rRNA) tag choice on estimates of microbial diversity and/or community composition in seawater and marine sediment, we examined bacterial diversity and community composition from a site in the Central North Atlantic and a site in the Equatorial Pacific. For each site, we analyzed samples from four zones in the water column, a seafloor sediment sample, and two subseafloor sediment horizons (with stratigraphic ages of 1.5 and 5.5 million years old). We amplified both the V4 and V6 hypervariable regions of the 16S rRNA gene and clustered the sequences into operational taxonomic units (OTUs) of 97% similarity to analyze for diversity and community composition. OTU richness is much higher with the V6 tag than with the V4 tag, and subsequently OTU-level community composition is quite different between the two tags. Vertical patterns of relative diversity are broadly the same for both tags, with maximum taxonomic richness in seafloor sediment and lowest richness in subseafloor sediment at both geographic locations. Genetic dissimilarity between sample locations is also broadly the same for both tags. Community composition is very similar for both tags at the class level, but very different at the level of 97% similar OTUs. Class-level diversity and community composition of water-column samples are very similar at each water depth between the Atlantic and Pacific. However, sediment communities differ greatly from the Atlantic site to the Pacific site. Finally, for relative patterns of diversity and class-level community composition, deep sequencing and shallow sequencing provide similar results.
为评估16S核糖体RNA（rRNA）标签选择对海水和海洋沉积物中微生物多样性和/或群落组成估计值的影响，我们研究了北大西洋中部一个站点和赤道太平洋一个站点的细菌多样性及群落组成。对于每个站点，我们分析了水柱中四个区域的样本、一个海底沉积物样本以及两个海底以下沉积物层（地层年龄分别为150万年和550万年）。我们扩增了16S rRNA基因的V4和V6高变区，并将序列聚类为相似度为97%的操作分类单元（OTU），以分析多样性和群落组成。与V4标签相比，V6标签的OTU丰富度要高得多，因此两个标签之间的OTU水平群落组成差异很大。两个标签的相对多样性垂直模式大致相同，在两个地理位置的海底沉积物中分类丰富度最高，在海底以下沉积物中丰富度最低。两个标签在样本位置之间的遗传差异也大致相同。两个标签在纲水平上的群落组成非常相似，但在相似度为97%的OTU水平上差异很大。在大西洋和太平洋的每个水深，水柱样本的纲水平多样性和群落组成非常相似。然而，从大西洋站点到太平洋站点，沉积物群落差异很大。最后，对于多样性的相对模式和纲水平群落组成，深度测序和浅层测序提供了相似的结果。
