A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats

M.H.M. Holterman, K.D. Rybarczyk-Mydlowska, S.J.J. van den Elsen, H.H.B. van Megen, P.J.W. Mooijman, R.P. Santiago, A.M.T. Bongers, J. Bakker, J. Helder

Research output: Contribution to journalArticleAcademicpeer-review

80 Citations (Scopus)

Abstract

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
Original languageEnglish
Pages (from-to)23-34
JournalMolecular Ecology Resources
Volume8
DOIs
Publication statusPublished - 2008

Fingerprint

Ribosomal DNA
ribosomal DNA
Ecosystem
nematode
Soil
Nematoda
DNA
habitat
habitats
nucleotide sequences
soil quality
Longidoridae
Health
Biosensing Techniques
soil
Fresh Water
soil nematodes
biosensors
Sequence Analysis
Real-Time Polymerase Chain Reaction

Keywords

  • phylogenetic-relationships
  • maturity index
  • rna gene
  • sequences
  • classification
  • dorylaimida
  • evolution
  • reveals

Cite this

@article{e32f1ae7ded04b6e8df7f9219a5013ac,
title = "A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats",
abstract = "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",
keywords = "phylogenetic-relationships, maturity index, rna gene, sequences, classification, dorylaimida, evolution, reveals",
author = "M.H.M. Holterman and K.D. Rybarczyk-Mydlowska and {van den Elsen}, S.J.J. and {van Megen}, H.H.B. and P.J.W. Mooijman and R.P. Santiago and A.M.T. Bongers and J. Bakker and J. Helder",
year = "2008",
doi = "10.1111/j.1471-8286.2007.01963.x",
language = "English",
volume = "8",
pages = "23--34",
journal = "Molecular Ecology Resources",
issn = "1755-098X",
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}

A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats. / Holterman, M.H.M.; Rybarczyk-Mydlowska, K.D.; van den Elsen, S.J.J.; van Megen, H.H.B.; Mooijman, P.J.W.; Santiago, R.P.; Bongers, A.M.T.; Bakker, J.; Helder, J.

In: Molecular Ecology Resources, Vol. 8, 2008, p. 23-34.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - A ribosomal DNA-based framework for the detection and quantification of stress-sensitive nematode families in terrestrial habitats

AU - Holterman, M.H.M.

AU - Rybarczyk-Mydlowska, K.D.

AU - van den Elsen, S.J.J.

AU - van Megen, H.H.B.

AU - Mooijman, P.J.W.

AU - Santiago, R.P.

AU - Bongers, A.M.T.

AU - Bakker, J.

AU - Helder, J.

PY - 2008

Y1 - 2008

N2 - 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

AB - 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

KW - phylogenetic-relationships

KW - maturity index

KW - rna gene

KW - sequences

KW - classification

KW - dorylaimida

KW - evolution

KW - reveals

U2 - 10.1111/j.1471-8286.2007.01963.x

DO - 10.1111/j.1471-8286.2007.01963.x

M3 - Article

VL - 8

SP - 23

EP - 34

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

SN - 1755-098X

ER -