Laboratory of Nematology, Graduate School for Experimental Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands, Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus 'Las Lagunillas' s/n, Edificio B3, 23071 Jaén, Spain.
Mol Ecol Resour. 2008 Jan;8(1):23-34. doi: 10.1111/j.1471-8286.2007.01963.x.
Indigenous communities of soil-resident nematodes have a high potential for soil health assessment as nematodes are diverse, abundant, trophically heterogeneous and easily extractable from soil. The conserved morphology of nematodes is the main operational reason for their under-exploitation as soil health indicators, and a user-friendly biosensor system should preferably be based on nonmorphological traits. More than 80% of the most environmental stress-sensitive nematode families belong to the orders Mononchida and Dorylaimida. The phylogenetic resolution offered by full-length small subunit ribosomal DNA (SSU rDNA) sequences within these two orders is highly different. Notwithstanding several discrepancies between morphology and SSU rDNA-based systematics, Mononchida families (indicated here as M1-M5) are relatively well-supported and, consequently, family-specific DNA sequences signatures could be defined. Apart from Nygolaimidae and Longidoridae, the resolution among Dorylaimida families was poor. Therefore, a part of the more variable large subunit rDNA (≈ 1000 bp from the 5'-end) was sequenced for 72 Dorylaimida species. Sequence analysis revealed a subclade division among Dorylaimida (here defined as D1-D9, PP1-PP3) that shows only distant similarity with 'classical' Dorylaimid systematics. Most subclades were trophically homogeneous, and - in most cases - specific morphological characteristics could be pinpointed that support the proposed division. To illustrate the practicability of the proposed molecular framework, we designed primers for the detection of individual subclades within the order Mononchida in a complex DNA background (viz. in terrestrial or freshwater nematode communities) and tested them in quantitative assays (real-time polymerase chain reaction). Our results constitute proof-of-principle for the concept of DNA sequence signatures-based monitoring of stress sensitive nematode families in environmental samples.
土壤常驻线虫的土著群落具有很高的土壤健康评估潜力，因为线虫种类繁多、丰富、营养异质性强，且易于从土壤中提取。线虫形态的保守性是其作为土壤健康指标未被充分利用的主要原因，用户友好的生物传感器系统最好基于非形态特征。超过 80%的对环境压力最敏感的线虫科属于 Mononchida 和 Dorylaimida 目。这两个目中全长小亚基核糖体 DNA（SSU rDNA）序列提供的系统发育分辨率差异很大。尽管形态学和基于 SSU rDNA 的系统发育学之间存在一些差异，但 Mononchida 科（这里表示为 M1-M5）得到了较好的支持，因此可以定义特定科的 DNA 序列特征。除了 Nygolaimidae 和 Longidoridae 科外，Dorylaimida 科之间的分辨率较差。因此，对 72 种 Dorylaimida 种的较大亚基 rDNA（≈5'-端的 1000 bp 左右）的一部分进行了测序。序列分析揭示了 Dorylaimida 中的一个亚分支划分（这里定义为 D1-D9、PP1-PP3），与“经典”Dorylaimid 系统发育学仅有遥远的相似性。大多数亚分支是营养同质的，并且在大多数情况下，可以确定特定的形态特征，支持所提出的划分。为了说明所提出的分子框架的实用性，我们设计了用于在复杂 DNA 背景（即陆地或淡水线虫群落）中检测 Mononchida 目中个体亚分支的引物，并在定量测定（实时聚合酶链反应）中对其进行了测试。我们的结果为基于 DNA 序列特征的环境样本中应激敏感线虫科监测的概念提供了原理证明。
