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Microbial communities in organic substrates used for oil sands reclamation and their link to boreal seedling growthBeasse, Mark L Unknown Date
No description available.
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Associations between plasma fatty acids, dietary fatty acids and cardiovascular risk factors : the PURE study / Marilize RichterRichter, Marilize January 2014 (has links)
Background: Cardiovascular disease (CVD) is the leading global cause of death. CVD risk
factors are considered intermediaries for the association between dietary fatty acids and CVD.
Raised plasma total cholesterol, low density lipoprotein (LDL) cholesterol, raised triglycerides
and decreased levels of high density lipoprotein (HDL) cholesterol, as well as reduced
fibrinolytic potential (measured as increased clot lysis time) are known risk factors for CVD.
Plasminogen activator inhibitor-1 (PAI-1) is a major inhibitor of the fibrinolytic process and an
elevated PAI-1 level is therefore considered to be a potential risk factor for CVD. The growing
number of controversies around the role that fat intake (more specifically the type of dietary fat)
plays in CVD risk, is making it increasingly difficult for consumers and practitioners alike to form
conclusions, and make recommendations and decisions regarding fat intake. Knowledge of the
intake of individual fatty acids, fatty acid status (as opposed to subgroups of fat such as
polyunsaturated fatty acids) and their associations with blood lipids, PAI-1act and fibrinolytic
potential is lacking in black South Africans and other populations. Therefore we aimed to
investigate dietary fatty acid intake, as well as plasma phospholipid fatty acid status and their
associations with blood lipids, PAI-1act and clot lysis time, as a marker for fibrinolytic potential.
Methods: Cross-sectional data analysis within the Prospective Rural Urban Epidemiology
(PURE) baseline study of apparently healthy black South African men and women (n=1950, 35–
70 years) from rural and urban areas in the North West Province, from whom dietary data were
collected. Blood lipid analyses, as well as laboratory analyses of fibrinolysis markers such as
PAI-1act and clot lysis time were also performed. Plasma phospholipid fatty acid extraction and
isolation were performed on a random subsample (n = 716).
Results: The intake of individual fatty acids was significantly higher in urban than rural dwellers.
However, the intake of omega-3 polyunsaturated fatty acids was below recommendations in all
groups (rural and urban males, and rural and urban females). Total cholesterol and LDL
cholesterol were higher in females than in males, with no rural‒urban differences. Intake of
alpha-linolenic acid was positively associated with total cholesterol (β=0.143) and triglycerides
(β=0.256) in males. The risk of having elevated LDL cholesterol also increased with increased
intake of alpha-linolenic acid (OR 1.49, 95% CI 1.04, 2.14). In females, dietary arachidonic acid
and eicosapentaenoic acid (EPA) were positively associated with total cholesterol and LDL
cholesterol, whereas docosahexaenoic acid (DHA) was negatively associated with total
cholesterol and LDL cholesterol. Dietary alpha-linolenic acid was positively correlated with
plasma EPA (males r = 0.19, p = 0.002, females r = 0.25, p < 0.001) and DHA (males r = 0.33, p
< 0.001, females r = 0.30, p < 0.001). Plasma DHA was positively associated with triglycerides
in males (β = 0.410, p< 0.001) and in females (β = 0.379, p< 0.001). PAI-1act was positively
associated with clot lysis time, and plasma myristic acid and DHA were positively associated
with PAI-1act in females. However, these fatty acids were not associated with clot lysis time.
Different types of plasma fatty acids were associated with PAI-1act than with clot lysis time.
Plasma alpha-linolenic acid (β = 0.123, P = 0.037), mead acid (β = 0.176, P = 0.019),
arachidonic acid (β = 0.253, 0.025) and omega-3 docosapentaenoic acid (omega-3 DPA) (β =
0.224, P = 0.002) were positively associated with clot lysis time, while both myristic acid (β = -
0.130, P = 0.016) and EPA (β = -0.131, P = 0.021) were negatively associated with clot lysis
time in male subjects. Plasma oleic acid (C18:1n9) (β = -0.411, P = 0.001) and omega-6 DPA
(C22:5n6) (β = -0.285, P = 0.001) were negatively associated with clot lysis time, while dihomogamma-
liolenic acid (DGLA) (C20:3n6) were positively associated (β = 0.178, P = 0.001) with
clot lysis time in females.
Conclusions: These results suggest that specific individual dietary fatty acids might be
associated with blood lipids in males differently than in females, irrespective of rural or urban
dwelling. It is not known however, if associations would still be present under conditions of
greater intake of alpha-linolenic acid. Our results further suggest that a higher percentage of
alpha-linolenic acid might be converted to DHA in this population with low intake of essential
and long-chain polyunsaturated fatty acids compared to populations with a high intake of these
fatty acids. These results suggest that plasma phospholipid fatty acids should not be used in
isolation as biomarkers for intake of fat, without taking dietary intake data into consideration
also. Associations between fatty acids and clot lysis time might be independent from PAI-1act.
The association between mead acid and clot lysis time indicates that clot lysis time might
increase with an essential fatty acid deficiency. This may be of particular concern in this
population with a documented lower fat intake. Because the study design of this study is crosssectional,
it is not able to determine cause-and-effect, and results should therefore be verified
with a randomised controlled trial. / PhD (Nutrition), North-West University, Potchefstroom Campus, 2015
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Associations between plasma fatty acids, dietary fatty acids and cardiovascular risk factors : the PURE study / Marilize RichterRichter, Marilize January 2014 (has links)
Background: Cardiovascular disease (CVD) is the leading global cause of death. CVD risk
factors are considered intermediaries for the association between dietary fatty acids and CVD.
Raised plasma total cholesterol, low density lipoprotein (LDL) cholesterol, raised triglycerides
and decreased levels of high density lipoprotein (HDL) cholesterol, as well as reduced
fibrinolytic potential (measured as increased clot lysis time) are known risk factors for CVD.
Plasminogen activator inhibitor-1 (PAI-1) is a major inhibitor of the fibrinolytic process and an
elevated PAI-1 level is therefore considered to be a potential risk factor for CVD. The growing
number of controversies around the role that fat intake (more specifically the type of dietary fat)
plays in CVD risk, is making it increasingly difficult for consumers and practitioners alike to form
conclusions, and make recommendations and decisions regarding fat intake. Knowledge of the
intake of individual fatty acids, fatty acid status (as opposed to subgroups of fat such as
polyunsaturated fatty acids) and their associations with blood lipids, PAI-1act and fibrinolytic
potential is lacking in black South Africans and other populations. Therefore we aimed to
investigate dietary fatty acid intake, as well as plasma phospholipid fatty acid status and their
associations with blood lipids, PAI-1act and clot lysis time, as a marker for fibrinolytic potential.
Methods: Cross-sectional data analysis within the Prospective Rural Urban Epidemiology
(PURE) baseline study of apparently healthy black South African men and women (n=1950, 35–
70 years) from rural and urban areas in the North West Province, from whom dietary data were
collected. Blood lipid analyses, as well as laboratory analyses of fibrinolysis markers such as
PAI-1act and clot lysis time were also performed. Plasma phospholipid fatty acid extraction and
isolation were performed on a random subsample (n = 716).
Results: The intake of individual fatty acids was significantly higher in urban than rural dwellers.
However, the intake of omega-3 polyunsaturated fatty acids was below recommendations in all
groups (rural and urban males, and rural and urban females). Total cholesterol and LDL
cholesterol were higher in females than in males, with no rural‒urban differences. Intake of
alpha-linolenic acid was positively associated with total cholesterol (β=0.143) and triglycerides
(β=0.256) in males. The risk of having elevated LDL cholesterol also increased with increased
intake of alpha-linolenic acid (OR 1.49, 95% CI 1.04, 2.14). In females, dietary arachidonic acid
and eicosapentaenoic acid (EPA) were positively associated with total cholesterol and LDL
cholesterol, whereas docosahexaenoic acid (DHA) was negatively associated with total
cholesterol and LDL cholesterol. Dietary alpha-linolenic acid was positively correlated with
plasma EPA (males r = 0.19, p = 0.002, females r = 0.25, p < 0.001) and DHA (males r = 0.33, p
< 0.001, females r = 0.30, p < 0.001). Plasma DHA was positively associated with triglycerides
in males (β = 0.410, p< 0.001) and in females (β = 0.379, p< 0.001). PAI-1act was positively
associated with clot lysis time, and plasma myristic acid and DHA were positively associated
with PAI-1act in females. However, these fatty acids were not associated with clot lysis time.
Different types of plasma fatty acids were associated with PAI-1act than with clot lysis time.
Plasma alpha-linolenic acid (β = 0.123, P = 0.037), mead acid (β = 0.176, P = 0.019),
arachidonic acid (β = 0.253, 0.025) and omega-3 docosapentaenoic acid (omega-3 DPA) (β =
0.224, P = 0.002) were positively associated with clot lysis time, while both myristic acid (β = -
0.130, P = 0.016) and EPA (β = -0.131, P = 0.021) were negatively associated with clot lysis
time in male subjects. Plasma oleic acid (C18:1n9) (β = -0.411, P = 0.001) and omega-6 DPA
(C22:5n6) (β = -0.285, P = 0.001) were negatively associated with clot lysis time, while dihomogamma-
liolenic acid (DGLA) (C20:3n6) were positively associated (β = 0.178, P = 0.001) with
clot lysis time in females.
Conclusions: These results suggest that specific individual dietary fatty acids might be
associated with blood lipids in males differently than in females, irrespective of rural or urban
dwelling. It is not known however, if associations would still be present under conditions of
greater intake of alpha-linolenic acid. Our results further suggest that a higher percentage of
alpha-linolenic acid might be converted to DHA in this population with low intake of essential
and long-chain polyunsaturated fatty acids compared to populations with a high intake of these
fatty acids. These results suggest that plasma phospholipid fatty acids should not be used in
isolation as biomarkers for intake of fat, without taking dietary intake data into consideration
also. Associations between fatty acids and clot lysis time might be independent from PAI-1act.
The association between mead acid and clot lysis time indicates that clot lysis time might
increase with an essential fatty acid deficiency. This may be of particular concern in this
population with a documented lower fat intake. Because the study design of this study is crosssectional,
it is not able to determine cause-and-effect, and results should therefore be verified
with a randomised controlled trial. / PhD (Nutrition), North-West University, Potchefstroom Campus, 2015
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Soil microbial community function and structure as assessment criteria for the rehabilitation of coal discard sites in South Africa / Sarina ClaassensClaassens, Sarina January 2003 (has links)
Mining activities cause severe disturbance to the soil environment in terms of soil quality
and productivity and are of serious concern worldwide. Under South African legislation,
developers are required to ecologically rehabilitate damaged environments. The application
of agronomic approaches for the rehabilitation of coal discard sites has failed dismally in
the arid areas of southern Africa. It is obvious that compliance with mitigation and
rehabilitation requirements cannot be enforced without a thorough understanding of the
ecological principles that ensure ecological stability and subsequent sustainability of soil
ecosystems. Soil micro organisms are crucial role-players in the processes that make energy
and nutrients available for recycling in the soil ecosystem. Poor management practices and
other negative impacts on soil ecosystems affect both the physical and chemical properties
of soil, as well as the functional and structural properties of soil microbial communities.
Disturbances of soil ecosystems that impact on the normal functioning of microbial
communities are potentially detrimental to soil formation, energy transfers, nutrient
cycling, plant reestablishment and long-term stability. In this regard, an extensive overview
of soil properties and processes indicated that the use of microbiological and biochemical
soil properties, such as microbial biomass, enzymatic activity and the analysis of microbial
community structure by the quantification of specific 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 the physical and chemical characteristics and different biological
indicators of soil quality in the topsoil covers of seven coal discard sites under
rehabilitation in South Africa, as well as three reference sites was investigated. Through the
assimilation of basic quantitative data and the assessment of certain physical, chemical and
biological properties of the topsoil covers obtained from the various coal discard sites as
well as the reference sites, the relative success or progress of rehabilitation and the possible
correlation between the biological indicators of soil quality and the establishment of self sustaining
vegetation covers was determined. Results from soil physical and chemical
analyses and percentage vegetation cover were correlated with the results obtained for the
functional and structural diversity of microbial communities at the various sites. All results
were investigated through statistical and multivariate analysis and the most prominent
physical and chemical parameters that influence the biological and biochemical properties
of the soil and possibly the establishment of self-sustainable vegetation cover on these
mine-tailing sites were identified. Results obtained from this study indicated no significant
difference (p>0.05) between the various discard sites based on conventional
microbiological enumeration techniques. However, significant differences (p<0.05) could
be observed between the three reference sites. All enzymatic activities assayed for the
rehabilitation sites, with the exception of urease and alkaline phosphatase displayed a
strong, positive association with the organic carbon content (%C). Ammonium
concentration had a weak association with all the enzymes studied and pH only showed a
negative association with acid phosphatase activity. A positive association was observed
between the viable microbial biomass, vegetation cover and the organic carbon content,
ammonium, nitrate and phosphorus concentrations of the soil. The various rehabilitation
and reference sites could be differentiated based on the microbial community structure as
determined by phospholipid fatty acid (PLFA) analysis. It is hypothesised that the
microbial community structure of the Hendrina site is not sustainable when classified along
an r-K gradient and that the high percentage of vegetation cover and high levels of
estimated viable microbial biomass are an artificial reflection of the current management
practices being employed at this site. Results obtained during this study, suggest that an
absence or low percentage of vegetation cover and associated lower organic matter content
of the soil have a significant negative impact on soil biochemical properties (enzymatic
activity) as well as microbial population size. Furthermore, prevailing environmental
physico-chemical and management characteristics significantly influences the vegetation
cover and subsequently the microbial community structure. The results indicate that the
microbial ecosystems in the coal discard sites could become more stable and ecologically
self-regulating, provided effective management to enhance the organic carbon content of
the soil. This could enhance nutrient cycling, resulting in changes of soil structure and
eventually an improved soil quality which could facilitate the establishment of self sustaining
vegetation cover. Results obtained during this study suggest that a polyphasic
assessment of physical and chemical properties; microbial activities by enzymatic analysis;
the characterisation of microbial community structure by analysis of phospholipid fatty
acids; and the multifactorial analysis of the data obtained can be used as complementary
assessment criteria for the evaluation of the trend of rehabilitation of mine tailings and
discard sites. Strategic management criteria are recommended based on the soil
quality environmental sustainability indices to facilitate the establishment of self sustainable
vegetation covers. The contribution of this research to soil ecology is
significant with regards to the intensive investigation and explanation of characteristics and
processes that drive ecological rehabilitation and determine the quality of the soil
environment. The multidisciplinary approach that is proposed could, furthermore, assist in
the successful rehabilitation and establishment of self-sustaining vegetation covers at
industrially disturbed areas, as well as assist in improving degraded soil quality associated
with both intensive and informal agriculture. Additionally, this approach could negate the
negative social and environmental impacts frequently associated with these activities. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2004.
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5 |
Soil microbial community function and structure as assessment criteria for the rehabilitation of coal discard sites in South Africa / Sarina ClaassensClaassens, Sarina January 2003 (has links)
Mining activities cause severe disturbance to the soil environment in terms of soil quality
and productivity and are of serious concern worldwide. Under South African legislation,
developers are required to ecologically rehabilitate damaged environments. The application
of agronomic approaches for the rehabilitation of coal discard sites has failed dismally in
the arid areas of southern Africa. It is obvious that compliance with mitigation and
rehabilitation requirements cannot be enforced without a thorough understanding of the
ecological principles that ensure ecological stability and subsequent sustainability of soil
ecosystems. Soil micro organisms are crucial role-players in the processes that make energy
and nutrients available for recycling in the soil ecosystem. Poor management practices and
other negative impacts on soil ecosystems affect both the physical and chemical properties
of soil, as well as the functional and structural properties of soil microbial communities.
Disturbances of soil ecosystems that impact on the normal functioning of microbial
communities are potentially detrimental to soil formation, energy transfers, nutrient
cycling, plant reestablishment and long-term stability. In this regard, an extensive overview
of soil properties and processes indicated that the use of microbiological and biochemical
soil properties, such as microbial biomass, enzymatic activity and the analysis of microbial
community structure by the quantification of specific 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 the physical and chemical characteristics and different biological
indicators of soil quality in the topsoil covers of seven coal discard sites under
rehabilitation in South Africa, as well as three reference sites was investigated. Through the
assimilation of basic quantitative data and the assessment of certain physical, chemical and
biological properties of the topsoil covers obtained from the various coal discard sites as
well as the reference sites, the relative success or progress of rehabilitation and the possible
correlation between the biological indicators of soil quality and the establishment of self sustaining
vegetation covers was determined. Results from soil physical and chemical
analyses and percentage vegetation cover were correlated with the results obtained for the
functional and structural diversity of microbial communities at the various sites. All results
were investigated through statistical and multivariate analysis and the most prominent
physical and chemical parameters that influence the biological and biochemical properties
of the soil and possibly the establishment of self-sustainable vegetation cover on these
mine-tailing sites were identified. Results obtained from this study indicated no significant
difference (p>0.05) between the various discard sites based on conventional
microbiological enumeration techniques. However, significant differences (p<0.05) could
be observed between the three reference sites. All enzymatic activities assayed for the
rehabilitation sites, with the exception of urease and alkaline phosphatase displayed a
strong, positive association with the organic carbon content (%C). Ammonium
concentration had a weak association with all the enzymes studied and pH only showed a
negative association with acid phosphatase activity. A positive association was observed
between the viable microbial biomass, vegetation cover and the organic carbon content,
ammonium, nitrate and phosphorus concentrations of the soil. The various rehabilitation
and reference sites could be differentiated based on the microbial community structure as
determined by phospholipid fatty acid (PLFA) analysis. It is hypothesised that the
microbial community structure of the Hendrina site is not sustainable when classified along
an r-K gradient and that the high percentage of vegetation cover and high levels of
estimated viable microbial biomass are an artificial reflection of the current management
practices being employed at this site. Results obtained during this study, suggest that an
absence or low percentage of vegetation cover and associated lower organic matter content
of the soil have a significant negative impact on soil biochemical properties (enzymatic
activity) as well as microbial population size. Furthermore, prevailing environmental
physico-chemical and management characteristics significantly influences the vegetation
cover and subsequently the microbial community structure. The results indicate that the
microbial ecosystems in the coal discard sites could become more stable and ecologically
self-regulating, provided effective management to enhance the organic carbon content of
the soil. This could enhance nutrient cycling, resulting in changes of soil structure and
eventually an improved soil quality which could facilitate the establishment of self sustaining
vegetation cover. Results obtained during this study suggest that a polyphasic
assessment of physical and chemical properties; microbial activities by enzymatic analysis;
the characterisation of microbial community structure by analysis of phospholipid fatty
acids; and the multifactorial analysis of the data obtained can be used as complementary
assessment criteria for the evaluation of the trend of rehabilitation of mine tailings and
discard sites. Strategic management criteria are recommended based on the soil
quality environmental sustainability indices to facilitate the establishment of self sustainable
vegetation covers. The contribution of this research to soil ecology is
significant with regards to the intensive investigation and explanation of characteristics and
processes that drive ecological rehabilitation and determine the quality of the soil
environment. The multidisciplinary approach that is proposed could, furthermore, assist in
the successful rehabilitation and establishment of self-sustaining vegetation covers at
industrially disturbed areas, as well as assist in improving degraded soil quality associated
with both intensive and informal agriculture. Additionally, this approach could negate the
negative social and environmental impacts frequently associated with these activities. / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2004.
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6 |
Soilborne disease suppressiveness / conduciveness : analysis of microbial community dynamics / by Johannes Hendrikus HabigHabig, Johannes Hendrikus January 2003 (has links)
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.
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7 |
Soilborne disease suppressiveness / conduciveness : analysis of microbial community dynamics / by Johannes Hendrikus HabigHabig, Johannes Hendrikus January 2003 (has links)
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.
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Tracking Carbon Flow during Methane Oxidation into Methanotrophs using 13C-PLFA Labeling in Pulsing Freshwater WetlandsRoy Chowdhury, Taniya 18 July 2012 (has links)
No description available.
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