Identification
and Specific Detection of a Novel Pseudomonadaceae
Cluster Associated with Soils from Winter Wheat Plots of a
Long-Term Agricultural Field Experiment
Manuel Pesaro† and Franco Widmer*
Molecular Ecology, Agroscope FAL Reckenholz, Swiss Federal
Research Station for Agroecology and Agriculture, Reckenholzstrasse
191, CH-8046 Zurich, Switzerland.
Abstract
The genus Pseudomonas (sensu stricto)
represents a group of microorganisms directly involved in
functions conferring plant health. We performed a study in
the DOK long-term agricultural field experiment on the basis
of previously published Pseudomonas-selective PCR
primers in order to investigate the community structure of
the microbial groups defined by the target range of these
primers. Three different agricultural management systems,
i.e., conventional, biodynamic, and bio-organic, along with
mineral and unfertilized controls were investigated, with
each system planted with either winter wheat or a grass-clover
ley. Amplified small-subunit rRNA gene fragments were analyzed
using the genetic profiling techniques restriction fragment
length polymorphism (RFLP) and denaturing gradient gel electrophoresis
(DGGE), revealing distinct differences between soils planted
with winter wheat and grass clover but only minor differences
between the management systems. Phylogenetic analyses of 59
clone sequences retrieved from bio-organic and unfertilized
systems identified sequences related to Pseudomonas fluorescens
and a novel cluster termed Cellvibrio-related Pseudomonadaceae
(CRP). The CRP clones were exclusively isolated from winter
wheat soil samples and were responsible for the crop-specific
differences observed in RFLP and DGGE profiles. New primers
were designed for the amplification of CRP targets directly
from soil DNA, yielding strong signals exclusively for winter
wheat soils. We concluded that crop-associated CRP exist in
agricultural soils and that genetic profiling followed by
specific probe design represents a valuable approach for identification
as well as sensitive and rapid monitoring of novel microbial
groups in the environment.
Keywords: Pseudomonas; denaturing
gradient gel electrophoresis; Pseudomonas fluorescens;
Cellvibrio;Pseudomonadaceae;rRNA
gene;restriction fragment length polymorphism;taxonomy.
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