Metabarcoding as a tool for investigating arthropod diversity in Nepenthes pitcher plants
Metabarcoding as a tool for investigating arthropod diversity in Nepenthes pitcher plants
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DOI：
10.1111/aec.12271
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发表时间：
2016-04-01
期刊：
影响因子：
1.5
通讯作者：
Pierce, Naomi E.
中科院分区：
文献类型：
--
作者：
Bittleston, Leonora S.;Baker, Christopher C. M.;Pierce, Naomi E.
热带森林的生物多样性主要由难以检测和表征的小生物组成。下一代测序（NGS）方法可以促进对这些节肢动物和微生物群落的分析，从而更好地了解现有的多样性和影响群落组装的因素。肉食性猪笼草的捕虫笼通常容纳着令人惊讶的离散群落，并为使用 NGS 方法进行分析提供了理想的系统。这些植物在贫瘠的土壤中生长时会消化昆虫以获得必需的营养；然而，这些捕虫笼也是被称为“inquilines”的生物群落的家园。某些节肢动物似乎与它们的猪笼草宿主共同进化，并且在其他环境中没有发现。我们使用 Illumina 的 18S rDNA 扩增子测序来表征新加坡三个不同公园中三种猪笼草（猪笼草科）猪笼草（猪笼草、莱佛士猪笼草和壶腹猪笼草）的真核生物特征。这些数据揭示了真核生物意想不到的多样性、宿主物种之间群落多样性的显着差异、inquilines宿主特异性的变化以及聚居寄生虫的存在。第一个收集年的整个鸡翅节肢动物的计数与按比例缩放的 18S 序列丰度大致相关，表明扩增子测序是衡量群落结构的有效手段。我们使用 COI 引物对双翅目幼虫的子集进行条形码标记，得到的系统发育树与使用 18S 基因座发现的系统发育树基本一致，但五个形态种之一除外。对于许多 18S 和 COI 序列，最佳 BLASTn 匹配显示出较低的序列同一性，这说明需要更好的东南亚双翅目数据库。最后，核心节肢动物及其宿主物种的网络被用来研究多个宿主之间的宿主特异性程度，这揭示了某些节肢动物区系的显着特化。
The biodiversity of tropical forests consists primarily of small organisms that are difficult to detect and characterize. Next-generation sequencing (NGS) methods can facilitate analyses of these arthropod and microbial communities, leading to a better understanding of existing diversity and factors influencing community assembly. The pitchers of carnivorous pitcher plants often house surprisingly discrete communities and provide ideal systems for analysis using an NGS approach. The plants digest insects in order to access essential nutrients while growing in poor soils; however, the pitchers are also home to communities of living organisms, called inquilines. Certain arthropods appear to have coevolved with their pitcher plant hosts and are not found in other environments. We used Illumina amplicon sequencing of 18S rDNA to characterize the eukaryotes in three species of Nepenthes (Nepenthaceae) pitcher plants - N.gracilis, N.rafflesiana and N.ampullaria - in each of three different parks in Singapore. The data reveal an unexpected diversity of eukaryotes, significant differences in community diversity among host species, variation in host specificity of inquilines and the presence of gregarine parasites. Counts of whole inquiline arthropods from the first collection year were roughly correlated with scaled 18S sequence abundances, indicating that amplicon sequencing is an effective means of gauging community structure. We barcoded a subset of the dipteran larvae using COI primers, and the resulting phylogenetic tree is mostly congruent with that found using the 18S locus, with the exception of one of five morphospecies. For many 18S and COI sequences, the best BLASTn matches showed low sequence identity, illustrating the need for better databases of Southeast Asian dipterans. Finally, networks of core arthropods and their host species were used to investigate degree of host specificity across multiple hosts, and this revealed significant specialization of certain arthropod fauna.