Document Detail


A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats.
MedLine Citation:
PMID:  21585715     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
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.
Authors:
Martijn Holterman; Katarzyna Rybarczyk; Sven VAN DEN Elsen; Hanny VAN Megen; Paul Mooyman; Reyes Peña Santiago; Tom Bongers; Jaap Bakker; Johannes Helder
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Molecular ecology resources     Volume:  8     ISSN:  1755-098X     ISO Abbreviation:  Mol Ecol Resour     Publication Date:  2008 Jan 
Date Detail:
Created Date:  2011-05-18     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101465604     Medline TA:  Mol Ecol Resour     Country:  England    
Other Details:
Languages:  eng     Pagination:  23-34     Citation Subset:  -    
Copyright Information:
© 2007 The Authors.
Affiliation:
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.
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