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ABSTRACT: Aim: The aim of this study was to develop molecular assays for investigating the presence and diversity of pathogenicity genes from the pea footrot pathogen Nectria haematococca (anamorph Fusarium solani f.sp. pisi) in soils.Methods and Results: Polymerase chain reaction (PCR) assays were developed to amplify four N. haematococca pathogenicity genes (PDA, PEP1, PEP3 and PEP5) from isolates and soil-DNA from five agricultural fields with a prior footrot history. A collection of 15 fungi isolated on medium selective for Fusarium spp. exhibited variation in their virulence to peas as assessed via a disease index (DI: 0–5; no virulence to the highest virulence). PCR analyses showed that three isolates in which all four pathogenicity genes were detected resulted in the highest DI (>3·88). All four pathogenicity genes were detected in soil-DNA obtained from all five fields with a footrot disease history, but were not amplified from soils, which had no footrot history. Denaturing gradient gel electrophoresis and/or sequence analysis revealed diversity amongst the pathogenicity genes.Conclusion: The PCR assays developed herein enable the specific detection of pathogenic N. haematococca in soils without recourse to culture.Significance and Impact of the Study: Molecular assays that specifically target pathogenicity genes have the capacity to assess the presence of the footrot-causing pathogen in agricultural soils.
Journal of Applied Microbiology 04/2009; 106(5):1629 - 1639. · 2.34 Impact Factor
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ABSTRACT: The aim of this study was to develop molecular assays for investigating the presence and diversity of pathogenicity genes from the pea footrot pathogen Nectria haematococca (anamorph Fusarium solani f.sp. pisi) in soils.
Polymerase chain reaction (PCR) assays were developed to amplify four N. haematococca pathogenicity genes (PDA, PEP1, PEP3 and PEP5) from isolates and soil-DNA from five agricultural fields with a prior footrot history. A collection of 15 fungi isolated on medium selective for Fusarium spp. exhibited variation in their virulence to peas as assessed via a disease index (DI: 0-5; no virulence to the highest virulence). PCR analyses showed that three isolates in which all four pathogenicity genes were detected resulted in the highest DI (>3.88). All four pathogenicity genes were detected in soil-DNA obtained from all five fields with a footrot disease history, but were not amplified from soils, which had no footrot history. Denaturing gradient gel electrophoresis and/or sequence analysis revealed diversity amongst the pathogenicity genes.
The PCR assays developed herein enable the specific detection of pathogenic N. haematococca in soils without recourse to culture.
Molecular assays that specifically target pathogenicity genes have the capacity to assess the presence of the footrot-causing pathogen in agricultural soils.
Journal of Applied Microbiology 03/2009; 106(5):1629-39. · 2.34 Impact Factor
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ABSTRACT: To provide an independent assessment of azoxystrobin effects on nontarget soil bacteria and fungi and generate some baseline information on azoxystrobin's persistence in soil.
Plate based assay showed that azoxystrobin exhibited differential toxicity upon cultured fungi at different application rates. While (14)C labelled isotopes experiments showed that less than 1% of azoxystrobin was mineralized, degradation studies revealed over 60% azoxystrobin breakdown over 21 days. PCR DGGE analysis of 16S and 18S rRNA genes from different soil microcosms showed that azoxystrobin had some effects on fungal community after 21 days (up to 84 days) of incubation in either light or dark soil microcosms. Light incubations increased fungal diversity while dark incubations reduced fungal diversity. Bacterial diversity was unaffected.
Significant biotic breakdown of parent azoxystrobin occurred within 21 days even in the absence of light. Azoxystrobin under certain conditions can reduce fungal soil diversity.
One of the few independent assessments of azoxystrobin (a widely used strobilurins fungicide) effects on soil fungi when used at the recommended rate. Azoxystrobin and metabolites may persist after 21 days and affect soil fungi.
Journal of Applied Microbiology 01/2009; 105(6):1777-90. · 2.34 Impact Factor
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ABSTRACT: Aims: To provide an independent assessment of azoxystrobin effects on nontarget soil bacteria and fungi and generate some baseline information on azoxystrobin’s persistence in soil.Methods and Results: Plate based assay showed that azoxystrobin exhibited differential toxicity upon cultured fungi at different application rates. While 14C labelled isotopes experiments showed that less than 1% of azoxystrobin was mineralized, degradation studies revealed over 60% azoxystrobin breakdown over 21 days. PCR DGGE analysis of 16S and 18S rRNA genes from different soil microcosms showed that azoxystrobin had some effects on fungal community after 21 days (up to 84 days) of incubation in either light or dark soil microcosms. Light incubations increased fungal diversity while dark incubations reduced fungal diversity. Bacterial diversity was unaffected.Conclusions: Significant biotic breakdown of parent azoxystrobin occurred within 21 days even in the absence of light. Azoxystrobin under certain conditions can reduce fungal soil diversity.Significance and Impact of the Study: One of the few independent assessments of azoxystrobin (a widely used strobilurins fungicide) effects on soil fungi when used at the recommended rate. Azoxystrobin and metabolites may persist after 21 days and affect soil fungi.
Journal of Applied Microbiology 11/2008; 105(6):1777 - 1790. · 2.34 Impact Factor
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ABSTRACT: Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.
Microbial Ecology 02/2005; 49(1):50-62. · 2.91 Impact Factor
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ABSTRACT: Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.
Microbial Ecology 12/2004; 49(1):50-62. · 2.91 Impact Factor
