A molecular toolbox to estimate the number and diversity of Variovorax in the environment: application in soils treated with the phenylurea herbicide linuron

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A molecular toolbox to estimate the number and diversity of Variovorax in the environment: application in soils treated with the phenylurea herbicide linuron. / Bers, Karolien; Sniegowski, Kristel; Albers, Pieter; Breugelmans, Philip; Hendrickx, Larissa; De Mot, René; Springael, Dirk.

In: FEMS Microbiology Ecology, Vol. 76, No. 1, 01.04.2011, p. 14-25.

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Bers, Karolien ; Sniegowski, Kristel ; Albers, Pieter ; Breugelmans, Philip ; Hendrickx, Larissa ; De Mot, René ; Springael, Dirk. / A molecular toolbox to estimate the number and diversity of Variovorax in the environment: application in soils treated with the phenylurea herbicide linuron. In: FEMS Microbiology Ecology. 2011 ; Vol. 76, No. 1. pp. 14-25.

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@article{c50c44e87573401aac58f1e3c12fb6ac,
title = "A molecular toolbox to estimate the number and diversity of Variovorax in the environment: application in soils treated with the phenylurea herbicide linuron",
abstract = "Real‐time PCR and PCR‐denaturing gradient gel electrophoresis (DGGE) approaches that specifically target the Variovorax 16S rRNA gene were developed to estimate the number and diversity of Variovorax in environmental ecosystems. PCR primers suitable for both methods were selected as such that the enclosed sequence showed maximum polymorphism. PCR specificity was maximized by combining PCR with a targeted endonuclease treatment of template DNA to eliminate 16S rRNA genes of the closely related Acidovorax . DGGE allowed the grouping of PCR amplicons according to the phylogenetic grouping within the genus Variovorax . The toolbox was used to assess the Variovorax community dynamics in agricultural soil microcosms (SMs) exposed to the phenylurea herbicide linuron. Exposure to linuron resulted in an increased abundance within the Variovorax community of a subgroup previously linked to linuron degradation through cultivation‐dependent isolation. SMs that were treated only once with linuron reverted to the initial community composition 70 days after linuron exposure. In contrast, SMs irrigated with linuron on a long‐term base showed a significant increase in Variovorax number after 70 days. Our data support the hypothesis that the genus Variovorax is involved in linuron degradation in linuron‐treated agricultural soils.",
keywords = "Variovorax, DGGE, Real-time PCR, Linuron, Agricultural soil",
author = "Karolien Bers and Kristel Sniegowski and Pieter Albers and Philip Breugelmans and Larissa Hendrickx and {De Mot}, Ren{\'e} and Dirk Springael",
note = "Score=10",
year = "2011",
month = "4",
day = "1",
doi = "10.1111/j.1574-6941.2010.01028.x",
language = "English",
volume = "76",
pages = "14--25",
journal = "FEMS Microbiology Ecology",
issn = "0168-6496",
publisher = "Oxford University Press",
number = "1",

}

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TY - JOUR

T1 - A molecular toolbox to estimate the number and diversity of Variovorax in the environment: application in soils treated with the phenylurea herbicide linuron

AU - Bers, Karolien

AU - Sniegowski, Kristel

AU - Albers, Pieter

AU - Breugelmans, Philip

AU - Hendrickx, Larissa

AU - De Mot, René

AU - Springael, Dirk

N1 - Score=10

PY - 2011/4/1

Y1 - 2011/4/1

N2 - Real‐time PCR and PCR‐denaturing gradient gel electrophoresis (DGGE) approaches that specifically target the Variovorax 16S rRNA gene were developed to estimate the number and diversity of Variovorax in environmental ecosystems. PCR primers suitable for both methods were selected as such that the enclosed sequence showed maximum polymorphism. PCR specificity was maximized by combining PCR with a targeted endonuclease treatment of template DNA to eliminate 16S rRNA genes of the closely related Acidovorax . DGGE allowed the grouping of PCR amplicons according to the phylogenetic grouping within the genus Variovorax . The toolbox was used to assess the Variovorax community dynamics in agricultural soil microcosms (SMs) exposed to the phenylurea herbicide linuron. Exposure to linuron resulted in an increased abundance within the Variovorax community of a subgroup previously linked to linuron degradation through cultivation‐dependent isolation. SMs that were treated only once with linuron reverted to the initial community composition 70 days after linuron exposure. In contrast, SMs irrigated with linuron on a long‐term base showed a significant increase in Variovorax number after 70 days. Our data support the hypothesis that the genus Variovorax is involved in linuron degradation in linuron‐treated agricultural soils.

AB - Real‐time PCR and PCR‐denaturing gradient gel electrophoresis (DGGE) approaches that specifically target the Variovorax 16S rRNA gene were developed to estimate the number and diversity of Variovorax in environmental ecosystems. PCR primers suitable for both methods were selected as such that the enclosed sequence showed maximum polymorphism. PCR specificity was maximized by combining PCR with a targeted endonuclease treatment of template DNA to eliminate 16S rRNA genes of the closely related Acidovorax . DGGE allowed the grouping of PCR amplicons according to the phylogenetic grouping within the genus Variovorax . The toolbox was used to assess the Variovorax community dynamics in agricultural soil microcosms (SMs) exposed to the phenylurea herbicide linuron. Exposure to linuron resulted in an increased abundance within the Variovorax community of a subgroup previously linked to linuron degradation through cultivation‐dependent isolation. SMs that were treated only once with linuron reverted to the initial community composition 70 days after linuron exposure. In contrast, SMs irrigated with linuron on a long‐term base showed a significant increase in Variovorax number after 70 days. Our data support the hypothesis that the genus Variovorax is involved in linuron degradation in linuron‐treated agricultural soils.

KW - Variovorax

KW - DGGE

KW - Real-time PCR

KW - Linuron

KW - Agricultural soil

UR - https://ecm.sckcen.be/OTCS/llisapi.dll/overview/39155846

U2 - 10.1111/j.1574-6941.2010.01028.x

DO - 10.1111/j.1574-6941.2010.01028.x

M3 - Article

VL - 76

SP - 14

EP - 25

JO - FEMS Microbiology Ecology

JF - FEMS Microbiology Ecology

SN - 0168-6496

IS - 1

ER -

ID: 6856198