High-throughput sequencing covers greater nematode diversity than conventional morphotyping on natural cedar forests in Yakushima Island, Japan
High-throughput sequencing covers greater nematode diversity than conventional morphotyping on natural cedar forests in Yakushima Island, Japan
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DOI：
10.1016/j.ejsobi.2022.103432
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发表时间：
2022-08-28
影响因子：
4.2
通讯作者：
Matsuda, Yosuke
中科院分区：
文献类型：
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作者：
Kitagami, Yudai;Matsuda, Yosuke
通过高通量测序(HTS)方法获得的大量序列读数为广泛识别某些生境中的线虫提供了机会，从而能够产生描述自然生态系统中线虫群落的组装模式。然而，我们不知道HTS分析是否产生了类似于传统形态分析产生的线虫群落的组装模式。对日本南部屋久岛岛1000多年生的天然日本雪松(Cryptomeria Japan Onica)林地土壤线虫群落结构进行了HTS测定和形态分析比较。在Shiratani(SR)和Arakawa(AR)两个地点采集了土壤线虫，并在复合光学显微镜下进行了属水平的鉴定。线虫也进行了DNA序列分析，重点是部分小亚单位rRNA。形态分析将线虫划分为9目34科42属。509个扩增子序列变异体隶属于11目，45科，76属。根据Aphelenchoidae的系统发育分析，我们的序列被划分为12个独立分支，Bootstrap值大于70%。形态分析和HTS分析分别鉴定出SR和AR属77个和72个属，HTS分析分别占SR和AR样本线虫属总数的88%和85%。通过HTS分析得到的线虫丰度与Acrobeloides、Aphelenchoides、Helicotylichus、Rhabdolaimus和Wilsonema的形态丰度显著相关。非度量多维尺度散点图指数表明，无论采用何种方法，SR和AR之间的线虫群落结构存在显著差异。因此，HTS分析比形态分析更有助于识别自然生态系统中的线虫群落，以揭示隐藏的多样性。
Massive sequence reads obtained via high-throughput sequencing (HTS) methods have provided opportunities to extensively identify nematodes in certain habitats, thereby enabling the generation of assemblage patterns depicting nematode communities in natural ecosystems. However, we do not know whether HTS analysis yields assemblage patterns for nematode communities that are similar to those generated by conventional morpho-logical analyses. We compared the community structures of soil nematodes determined by HTS and morpho-logical analyses in natural Japanese cedar (Cryptomeria japonica) forests more than 1,000 years old on Yakushima Island, South Japan. Soil nematodes were collected at two sites, namely, Shiratani (SR) and Arakawa (AR), and identified to the genus level under a compound light microscope. Nematodes were also subjected to DNA sequence analysis, focusing on partial small subunit rRNA. Morphological analysis divided the nematodes into 9 orders, 34 families, and 42 genera. The 509 amplicon sequence variants were assigned to 11 orders, 45 families, and 76 genera. Based on the phylogenetic analysis of Aphelenchoides, our sequences were divided into 12 in-dependent clades with bootstrap values greater than 70%. From both morphological and HTS analyses, 77 and 72 genera were identified for SR and AR, respectively, and HTS analysis covered 88% and 85% of the total nematode genera in samples from SR and AR, respectively. The nematode abundance obtained via HTS analysis was significantly correlated with the morphological abundance of Acrobeloides, Aphelenchoides, Helicotylenchus, Rhabdolaimus, and Wilsonema. The non-metric multidimensional scaling scatter plot indices showed that nem-atode community structures were significantly different between SR and AR, regardless of the methodology. Thus, HTS analysis is more useful than morphological analysis for identifying the nematode communities of natural ecosystems to uncover hidden diversity.