Oligotrophic bacteria and root disease suppression in organically managed soils

I.V. Senechkin

Research output: Thesisinternal PhD, WU

Abstract

 

The objective of this thesis was to obtain a better understanding of soil health in terms of microbial and chemical characteristics as well as suppression of soil borne plant pathogens. Organic soils were chosen as an appropriate model for studying soil health. Four different organic amendments were applied on two experimental fields with different crop history, providing a diverse range of soil quality levels. Many soil microbial variables were measured, including copiotrophic and oligotrophic bacterial populations, the abundance and diversity of Eubacteria, Alphaproteobacteria, Pseudomonas and fungal communities, as well as several microbial genes involved in nitrogen cycling. Plant disease suppressiveness was used as a quantitative integrative parameter reflecting the health status of soils. Rhizoctonia solani on beet and Fusarium oxysporum on flax were selected as pathosystems; areas under disease progress curves were measured in bioassays with differentially amended field soils and were related to soil parameters. Combined rather than single amendments enhanced Fusarium suppression, but Rhizoctonia suppression was more related to crop history than organic amendments. No universal correlations were found between disease suppression and microbial and chemical parameters, although pH and organic matter affected microbial communities and Fusarium wilt. A significant relation between ammonia oxidizing bacteria and disease suppression was observed for both pathogens; this relation was likely indirect via nitrogen availability and pH. No direct relationship was found between quantities of N cycling genes and disease suppression. A specific emphasis was put on the potential role of oligotrophic bacteria in soil health and disease suppression. Bacteria isolated on low carbon medium (10 mg C/L) were repeatedly transferred onto this medium to select true oligotrophic bacteria. Most isolates could grow on both low carbon and higher carbon (1000 mg C/L) media and belonged to Streptomyces, Rhizobium, Bradyrhizobium and Mesorhizobium. A new oligotrophic isolate was identified as Collimonas sp. IS343 and its interaction with R. solani was studied. This strain was better adapted to oligotrophic conditions than a copiotrophic Collimonas reference strain and was more effective in controlling R. solani. This thesis provided a better understanding of some aspects of soil health and emphasized the role of oligotrophic bacteria, a poorly understood but very important group of soil inhabitants.

Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
Supervisors/Advisors
  • van Bruggen, Ariena, Promotor
  • van Overbeek, Leo, Co-promotor
Award date19 Dec 2013
Place of PublicationWageningen
Publisher
Print ISBNs9789461738035
Publication statusPublished - 2013

Fingerprint

root diseases
soil quality
disease control
Thanatephorus cucumeris
bacteria
Eubacteria
cropping sequence
soil
carbon
Mesorhizobium
suppressive soils
Bradyrhizobium
Rhizoctonia
Fusarium wilt
alpha-Proteobacteria
fungal communities
Streptomyces
flax
nitrogen
beets

Keywords

  • soilborne pathogens
  • plant pathogens
  • thanatephorus cucumeris
  • fusarium oxysporum
  • soil bacteria
  • soil management
  • organic farming
  • linum usitatissimum
  • flax
  • models
  • soil suppressiveness

Cite this

Senechkin, I. V. (2013). Oligotrophic bacteria and root disease suppression in organically managed soils. Wageningen: Wageningen University.
Senechkin, I.V.. / Oligotrophic bacteria and root disease suppression in organically managed soils. Wageningen : Wageningen University, 2013. 141 p.
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Senechkin, IV 2013, 'Oligotrophic bacteria and root disease suppression in organically managed soils', Doctor of Philosophy, Wageningen University, Wageningen.

Oligotrophic bacteria and root disease suppression in organically managed soils. / Senechkin, I.V.

Wageningen : Wageningen University, 2013. 141 p.

Research output: Thesisinternal PhD, WU

TY - THES

T1 - Oligotrophic bacteria and root disease suppression in organically managed soils

AU - Senechkin, I.V.

N1 - WU thesis 5658

PY - 2013

Y1 - 2013

N2 -   The objective of this thesis was to obtain a better understanding of soil health in terms of microbial and chemical characteristics as well as suppression of soil borne plant pathogens. Organic soils were chosen as an appropriate model for studying soil health. Four different organic amendments were applied on two experimental fields with different crop history, providing a diverse range of soil quality levels. Many soil microbial variables were measured, including copiotrophic and oligotrophic bacterial populations, the abundance and diversity of Eubacteria, Alphaproteobacteria, Pseudomonas and fungal communities, as well as several microbial genes involved in nitrogen cycling. Plant disease suppressiveness was used as a quantitative integrative parameter reflecting the health status of soils. Rhizoctonia solani on beet and Fusarium oxysporum on flax were selected as pathosystems; areas under disease progress curves were measured in bioassays with differentially amended field soils and were related to soil parameters. Combined rather than single amendments enhanced Fusarium suppression, but Rhizoctonia suppression was more related to crop history than organic amendments. No universal correlations were found between disease suppression and microbial and chemical parameters, although pH and organic matter affected microbial communities and Fusarium wilt. A significant relation between ammonia oxidizing bacteria and disease suppression was observed for both pathogens; this relation was likely indirect via nitrogen availability and pH. No direct relationship was found between quantities of N cycling genes and disease suppression. A specific emphasis was put on the potential role of oligotrophic bacteria in soil health and disease suppression. Bacteria isolated on low carbon medium (10 mg C/L) were repeatedly transferred onto this medium to select true oligotrophic bacteria. Most isolates could grow on both low carbon and higher carbon (1000 mg C/L) media and belonged to Streptomyces, Rhizobium, Bradyrhizobium and Mesorhizobium. A new oligotrophic isolate was identified as Collimonas sp. IS343 and its interaction with R. solani was studied. This strain was better adapted to oligotrophic conditions than a copiotrophic Collimonas reference strain and was more effective in controlling R. solani. This thesis provided a better understanding of some aspects of soil health and emphasized the role of oligotrophic bacteria, a poorly understood but very important group of soil inhabitants.

AB -   The objective of this thesis was to obtain a better understanding of soil health in terms of microbial and chemical characteristics as well as suppression of soil borne plant pathogens. Organic soils were chosen as an appropriate model for studying soil health. Four different organic amendments were applied on two experimental fields with different crop history, providing a diverse range of soil quality levels. Many soil microbial variables were measured, including copiotrophic and oligotrophic bacterial populations, the abundance and diversity of Eubacteria, Alphaproteobacteria, Pseudomonas and fungal communities, as well as several microbial genes involved in nitrogen cycling. Plant disease suppressiveness was used as a quantitative integrative parameter reflecting the health status of soils. Rhizoctonia solani on beet and Fusarium oxysporum on flax were selected as pathosystems; areas under disease progress curves were measured in bioassays with differentially amended field soils and were related to soil parameters. Combined rather than single amendments enhanced Fusarium suppression, but Rhizoctonia suppression was more related to crop history than organic amendments. No universal correlations were found between disease suppression and microbial and chemical parameters, although pH and organic matter affected microbial communities and Fusarium wilt. A significant relation between ammonia oxidizing bacteria and disease suppression was observed for both pathogens; this relation was likely indirect via nitrogen availability and pH. No direct relationship was found between quantities of N cycling genes and disease suppression. A specific emphasis was put on the potential role of oligotrophic bacteria in soil health and disease suppression. Bacteria isolated on low carbon medium (10 mg C/L) were repeatedly transferred onto this medium to select true oligotrophic bacteria. Most isolates could grow on both low carbon and higher carbon (1000 mg C/L) media and belonged to Streptomyces, Rhizobium, Bradyrhizobium and Mesorhizobium. A new oligotrophic isolate was identified as Collimonas sp. IS343 and its interaction with R. solani was studied. This strain was better adapted to oligotrophic conditions than a copiotrophic Collimonas reference strain and was more effective in controlling R. solani. This thesis provided a better understanding of some aspects of soil health and emphasized the role of oligotrophic bacteria, a poorly understood but very important group of soil inhabitants.

KW - bodempathogenen

KW - plantenziekteverwekkers

KW - thanatephorus cucumeris

KW - fusarium oxysporum

KW - bodembacteriën

KW - bodembeheer

KW - biologische landbouw

KW - linum usitatissimum

KW - vlas

KW - modellen

KW - bodemweerbaarheid

KW - soilborne pathogens

KW - plant pathogens

KW - thanatephorus cucumeris

KW - fusarium oxysporum

KW - soil bacteria

KW - soil management

KW - organic farming

KW - linum usitatissimum

KW - flax

KW - models

KW - soil suppressiveness

M3 - internal PhD, WU

SN - 9789461738035

PB - Wageningen University

CY - Wageningen

ER -

Senechkin IV. Oligotrophic bacteria and root disease suppression in organically managed soils. Wageningen: Wageningen University, 2013. 141 p.