Take-all is the name given to the disease caused by a soilborne fungus
Gaeumannomyces graminis (Sacc.) von Arx and Olivier var. tritici Walker (Ggt), an
ascomycete of the family Magnaportheaceae (Cook, 2003). This fungus is an
aggressive soil-borne pathogen causing root rot of wheat (primary host), barley and rye
crops (secondary host). The flowering, seedling, and vegetative growth stages can be
affected by the infection of the whole plant, leaves, roots, and stems. Infections of roots
result in losses in crop yield and quality primarily due to a lowering in nutrient uptake.
Take-all is most common in regions where wheat is cultivated without adequate crop
rotation. Crop rotation allows time between the planting dates of susceptible crops,
which causes a decrease in the inoculum potential of soilborne plant pathogens to
levels below an economic threshold by resident antagonistic soil microbial communities.
Soilborne disease suppressiveness is an inherent characteristic of the physical,
chemical, and/or biological structure of a particular soil which might be induced by
agricultural practices and activities such as the cultivation of crops, or the addition of
organisms or nutritional amendments, causing a change in the microfloral environment.
Disturbances of soil ecosystems that impact on the normal functioning of microbial
communities are potentially detrimental to soil formation, energy transfers, nutrient
cycling, and long-term stability. In this regard, an overview of soil properties and
processes indicated that the use of microbiological and biochemical soil properties,
such as microbial biomass, the analysis of microbial functional diversity and microbial
structural diversity by the quantification of community level physiological profiles and
signature lipid biomarkers are useful as indicators of soil ecological stress or restoration
properties because they are more responsive to small changes than physical and
chemical characteristics. In this study, the relationship between physico-chemical
characteristics, and different biological indicators of soil quality of agricultural soils
conducive, suppressive, and neutral with respect to take-all disease of wheat as caused
by the soilborne fungus Gaeumannomyces graminis var. tritici (Ggt), were investigated
using various techniques. The effect of crop rotation on the functional and structural
diversity of soils conducive to take-all disease was also investigated. Through the
integration of quantitative and qualitative biological data as well as the physico-chemical
characteristics of the various soils, the functional and structural diversity of microbial
IV
communities in the soils during different stadia of take-all disease of wheat were
characterised. All results were evaluated statistically and the predominant physical and
chemical characteristics that influenced the microbiological and biochemical properties
of the agricultural soils during different stadia of take-all disease of wheat were identified
using multivariate analyses. Although no significant difference @ > 0.05) could be
observed between the various soils using conventional microbiological enumeration
techniques, the incidence of Gliocladium spp. in suppressive soils was increased.
Significant differences @ < 0.05) were observed between agricultural soils during
different stadia of take-all disease of wheat. Although no clear distinction could be made
between soils suppressive and neutral to take-all disease of wheat, soils suppressive
and conducive to take-all disease of wheat differed substantially in their community level
physiological profiles (CLPPs). Soils suppressive / neutral to take-all disease were
characterised by enhanced utilisation of carboxylic acids, amino acids, and
carbohydrates, while conducive soils were characterised by enhanced utilisation of
carbohydrates. Shifts in the functional diversity of the associated microbial communities
were possibly caused by the presence of Ggt and associated antagonistic fungal and
bacterial populations in the various soils. It was evident that the relationships amongst
the functionality of the microbial communities within the various soils had undergone
changes through the different stages of development of take-all disease of wheat, thus
implying different substrate utilisation capabilities of present soil microbial communities.
Diversity indices were calculated as Shannon's diversity index (H') and substrate
equitability (J) and were overall within the higher diversity range of 3.6 and 0.8,
respectively, indicating the achievement of very high substrate diversity values in the
various soils. A substantial percentage of the carbon sources were utilised, which
contributed to the very high Shannon-Weaver substrate utilisation indices. Obtained
substrate evenness (equitability) (J) indices indicated an existing high functional
diversity. The functional diversity as observed during crop rotation, differed significantly
(p < 0.05) from each other, implying different substrate utilisation capabilities of present
soil microbial communities, which could possibly be ascribed to the excretion of root
exudates by sunflowers and soybeans. Using the Sorenson's index, a clear distinction
could be made between the degrees of substrate utilisation between microbial
populations in soils conducive, suppressive, and neutral to take-all disease of wheat, as
well as during crop rotation. Furthermore, the various soils could also be differentiated
on the basis of the microbial community structure as determined by phospholipid fatty
acid (PLFA) analysis. Soil suppressive to take-all disease of wheat differed significantly
(p < 0.05) from soils conducive, and neutral to take-all disease of wheat, implying a shift
in relationships amongst the structural diversity of microbial communities within the
various soils. A positive association was observed between the microbial phospholipid
fatty acid profiles, and dominant environmental variables of soils conducive,
suppressive, and neutral to take-all disease of wheat. Soils conducive and neutral to
take-all disease of wheat were characterised by high concentrations of manganese, as
well as elevated concentrations of monounsaturated fatty acids, terminally branched
saturated fatty acids, and polyunsaturated fatty acids which were indicative of Gram-negative
bacteria, Gram-positive bacteria and micro eukaryotes (primarily fungi),
respectively. These soils were also characterised by low concentrations of
phosphorous, potassium, percentage organic carbon, and percentage organic nitrogen,
as well as low soil pH. Soil suppressive to take-all disease of wheat was characterised
by the elevated levels of estimated of biomass and elevated concentrations of normal
saturated fatty acids, which is ubiquitous to micro-organisms. The concentration of
normal saturated fatty acids in suppressive soils is indicative of a low structural
diversity. This soil was also characterised by high concentrations of phosphorous,
potassium, percentage organic carbon, and percentage organic nitrogen, as well as
elevated soil pH. The relationship between PLFAs and agricultural soils was
investigated using principal component analysis (PCA), redundancy analysis (RDA) and
discriminant analysis (DA). Soil suppressive to take-all disease of wheat differed
significantly (p < 0.05) from soils conducive, and neutral to take-all disease of wheat,
implying a shift in relationships amongst the structural diversity of microbial communities
within the various soils. A positive association was observed between the microbial
phospholipid fatty acid profiles, and dominant environmental variables of soils
conducive, suppressive, and neutral to take-all disease of wheat. Hierarchical cluster
analysis of the major phospholipid fatty acid groups indicated that the structural diversity
differed significantly between soils conducive, suppressive, and neutral to take-all
disease of wheat caused by Gaeumannomyces graminis var. tritici. The results indicate
that the microbial community functionality as well as the microbial community structure
was significantly influenced by the presence of take-all disease of wheat caused by
Gaeumannomyces graminis var. tritici, and that the characterisation of microbial
functional and structural diversity by analysis of community level physiological profiles
and phospholipid fatty acid analysis, respectively, could be successfully used as an
assessment criteria for the evaluation of agricultural soils conducive, suppressive, and
neutral to take-all disease of wheat, as well as in crop rotation systems. This
methodology might be of significant value in assisting in the management and
evaluation of agricultural soils subject to the prevalence of other soilborne diseases. / Thesis (M.Sc. (Microbiology))--North-West University, Potchefstroom Campus, 2004.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:nwu/oai:dspace.nwu.ac.za:10394/415 |
| Date | January 2003 |
| Creators | Habig, Johannes Hendrikus |
| Publisher | North-West University |
| Source Sets | South African National ETD Portal |
| Detected Language | English |
| Type | Thesis |
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