Profiling of microbial communities in environmental samples often utilizes phospholipid fatty acid (PLFA) analysis. This method has been used for more than 35 years and is still popular as a means to ...characterize microbial communities in a diverse range of environmental matrices. This review examines the various recent applications of PLFA analysis in environmental studies with specific reference to the interpretation of the PLFA results. It is evident that interpretations of PLFA results do not always correlate between different investigations. These discrepancies in interpretation and their subsequent applications to environmental studies are discussed. However, in spite of limitations to the manner in which PLFA data are applied, the approach remains one with great potential for improving our understanding of the relationship between microbial populations and the environment. This review highlights the caveats and provides suggestions towards the practicable application of PLFA data interpretation.
Root‐knot nematodes are destructive phytopathogens that damage agricultural crops globally, and there is growing interest in the use of biocontrol based on rhizobacteria such as Bacillus to combat ...Meloidogyne species. It is hypothesized that nematicidal activity of Bacillus can be attributed to the production of secondary metabolites and hydrolytic enzymes. Yet, few studies have characterized these metabolites and their identities remain unknown. Others are speculative or fail to elaborate on how secondary metabolites were detected or distinguished from primary metabolites. Metabolites can be classified based on their origin as either intracellular or extracellular and based on their function, as either primary or secondary. Although this classification is in general use, the boundaries are not always well defined. An understanding of the secondary metabolite and hydrolytic enzyme classification of Bacillus species will facilitate investigations aimed at bionematicide development. This review summarizes the significance of Bacillus hydrolytic enzymes and secondary metabolites in bionematicide research and provides an overview of known classifications. The importance of appropriate cultivation conditions for optimum metabolite and enzyme production is also discussed. Finally, the use of metabolomics for the detection and identification of nematicidal compounds is considered.
The lipid composition of microbial communities can indicate their response to changes in the surrounding environment induced by anthropogenic practices, chemical contamination or climatic conditions. ...A considerable number of analytical techniques exist for the examination of microbial lipids. This article reviews a selection of methods available for environmental samples as applied for lipid extraction, fractionation, derivatization and quantification. The discussion focuses on the origin of the standard methods, the different modified versions developed for investigation of microbial lipids, as well as the advantages and limitations of each. Current modifications to standard methods show a number of improvements for each of the different steps associated with analysis. The advantages and disadvantages of lipid analysis compared to other popular techniques are clarified. Accordingly, the preferential utilization of signature lipid biomarker analysis in current research is considered. It is clear from recent literature that this technique stays relevant – mainly for the variety of microbial properties that can be determined in a single analysis.
Temporal changes in microbial community function (enzymatic activities) and structure (phospholipid fatty acids) were studied in a post-mining chronosequence of coal discard sites of different ...rehabilitation ages. The objective was to determine whether temporal changes in microbial community function and structure were related to rehabilitation age or management practices. No trends consistent with the rehabilitation ages (1 to 11 years) of the respective sites were observed. A canonical correspondence analysis showed that sites clustered according to the time of sampling irrespective of their individual rehabilitation ages. Sites sampled in 2002 clustered together, while sites sampled in 2004 and 2005 clustered separately from the 2002 sites. This corresponded with a change in management practices applied after 2002. Dehydrogenase, β-glucosidase, acid phosphatase, and alkaline phosphatase activities for all sites were higher after 2002. Urease activities were lower after 2002, with the exception of Site 3 (4 years old in 2002). Phospholipid fatty acid data showed significant (p < 0.05) differences between sites of different rehabilitation ages over the study period. There was a decrease in microbial biomass in all sites from 2002 to 2004 but an increase in 2005. Fungal to bacterial abundance ratios for all sites decreased over the study period. The proportion of the total microbial community comprised of Gram positive bacteria increased from 2002 to 2005. These data show the value of microbial community function and structure to elucidate management effects that may not be apparent through traditional assessments of rehabilitation status such as aboveground indicators.
The objective of this study was to characterize concentrations of atrazine, terbuthylazine, and other pesticides in amphibian habitats in surface waters of a corn-production area of the western ...Highveld region (North-West Province) of South Africa. The study was conducted from November 2001 to June 2002, coinciding with the corn-production season. Pesticide residues were measured at regular intervals in surface water from eight ponds, three in a non-corn-growing area (NCGA) and five within the corn-growing area (CGA). Measured atrazine concentrations differed significantly among sites and between samples. In the five CGA sites, the maximum atrazine concentrations measured during the study ranged from 1.2 to 9.3
μg/L. Although no atrazine was recorded as being applied in the catchment of the three NCGA sites, maximum concentrations from 0.39 to 0.84
μg/L were measured during the study, possibly as a result of atmospheric transport. Maximum measured concentrations of terbuthylazine ranged from 1.22 to 2.1
μg/L in the NCGA sites and from 1.04 to 4.1
μg/L in the CGA sites. The source of terbuthylazine in the NCGA sites may have been in use other than in corn. The triazine degradation products, deisopropylatrazine (DIA) and deethylatrazine (DEA) and diaminochlorotriazine (DACT) were also found in water from both the CGA and NCGA sites. Concentrations of DIA were ≥1
μg/L throughout the season, while DEA concentrations were mostly <0.5
μg/L before planting but increased after planting and application of herbicides to concentrations >2
μg/L in some locations. Concentrations of DACT were highly variable (LOD to 8
μg/L) both before and after planting and application, suggesting that they resulted from historical use of triazines in the area. Other herbicides such as simazine and acetochlor were only detected infrequently and pesticides such as S-metolachlor, cypermethrin, monocrotophos, and terbuphos, known to be used in the CGA, were not detected in any of the samples. Because of dilution by higher than normal rainfall in the study period, these concentrations may not be predictive of those in years of normal rainfall.
Concentrations of atrazine in an agricultural region vary greatly and are influenced by rainfall amounts.
Assessment of soil microbial diversity, in terms of the actively growing population, may be a sensitive indicator of ecological stress and restoration processes. During this study, the relationship ...between microbial community structure; vegetation cover; and physical and chemical characteristics of topsoil covers at seven coal discard rehabilitation sites in South Africa were evaluated. A positive association was observed between the microbial biomass, vegetation cover and the organic carbon, ammonium, nitrate and phosphorus contents. Although the seven coal discard sites had different rehabilitation ages (1-8 years), there was no statistically significant difference between these sites based on physical and chemical characteristics. The various rehabilitation sites could be differentiated based on the microbial community structure. The Hendrina site was characterised by the highest viable biomass, monounsaturated fatty acids, and high ground cover. Bethal and Ermelo sites were the youngest sites (1 and 3 years) in terms rehabilitation age. Both these sites were associated with higher abundances of fungi and Actinomycetes than the other sites. Ratios of trans- to cis-monoenoic fatty acids and cyclopropyl fatty acids to their monoenoic precursors indicated stress in all sites sampled.
Environmental pressure from mining activities such as those from the platinum sector occurs through the fine-grounded slurry from the processing plants, with its associated extracting chemicals that ...reach the tailings disposal facility (TDF). It is important that the effects of these activities on the environment are examined, especially in South Africa where there is a general paucity on data pertaining to pollution from platinum mining. The aim of this study was to do a preliminary assessment of the possible effects of platinum TDFs on the surrounding soil environment from a microbial perspective that might be used as a possible indicator in future environmental assessment studies. This was achieved by using enzymatic analyses (β-glucosidase, urease, phosphatase and dehydrogenase activity) and signature lipid biomarkers. From a soil physical perspective there was a significant difference between the soil at the TDF site in comparison to the sites situated further along (increasing distances away from TDF) the area investigated. Chemically the soil on the TDF had higher C, N, NH^sub 4^ and K levels in comparison to the other sampling sites as well as higher Cu and Ni levels. Results from the enzymatic activities indicated a decrease in activity further away from the TDF although the sampling site the furthest away from the TDF had the highest viable biomass as indicated by the phospholipid fatty acids (PLFA's).PUBLICATION ABSTRACT
The much publicised problem with major asbestos pollution and related health issues in South Africa, has called for action to be taken to negate the situation. The aim of this project was to ...establish a prioritisation index that would provide a scientifically based sequence in which polluted asbestos mines in Southern Africa ought to be rehabilitated. It was reasoned that a computerised database capable of calculating such a Rehabilitation Prioritisation Index (RPI) would be a fruitful departure from the previously used subjective selection prone to human bias. The database was developed in Microsoft Access and both quantitative and qualitative data were used for the calculation of the RPI value. The logical database structure consists of a number of mines, each consisting of a number of dumps, for which a number of samples have been analysed to determine asbestos fibre contents. For this system to be accurate as well as relevant, the data in the database should be revalidated and updated on a regular basis.
Haemophilus paragallinarum, the causative agent of infectious coryza in poultry, is an extremely fastidious organism requiring specific growth conditions for isolation. For complete control of the ...disease in regions where more that one of the serovars of the different serogroups occurs, it is essential that the bacterium causing the problem be isolated and serotyped. This work describes the modification and testing of transport media, which will ensure the survival of the causative agents in suspected infectious coryza cases for transport to a laboratory where the bacterium can be isolated and serotyped. The various transport media used are based on commercially available Amies Transport Medium supplemented with the different supplements used for the growth of H. paragallinarum. It was established that the bacterium remains viable for up to 18 days in Amies Transport Medium containing all the supplements when stored at 4 oC or 37 oC. At room temperature or 25 oC, there was no difference in the survival of H. paragallinarum in commercial Amies Transport Medium (without charcoal) and Amies Transport Medium with supplements.
Microbial properties have been reported to be useful indicators of soil quality and could possibly serve as assessment criteria of successful rehabilitation of ecologically disturbed areas. During ...this study, the application value of microbial enumeration techniques and enzymatic assays as a measure of the progress of rehabilitation of coal discard sites was evaluated. Each site was analysed for physical and chemical characteristics of the topsoil; vegetation cover; potential enzymatic activities (dehydrogenase, beta -glucosidase, urease, acid and alkaline phosphatase) and quantification of aerobic oligotrophic and copiotrophic bacteria and fungi (selective enumeration). The relationship between soil properties, vegetation cover and microbial properties was analysed using multivariate ordination techniques. Although the discard sites had different rehabilitation ages (1-8 years), no statistically significant difference existed between these sites based on physical and chemical characteristics or selective enumeration (p>0.05). Differentiation was possible based on enzymatic activities, where sites with relatively higher vegetation cover and organic carbon content had a positive association with enzymatic activities. Organic carbon content correlated significantly with beta -glucosidase (r = 0.80, p<0.05), urease (r = 0.96, p<0.05), acid phosphatase (r = 0.76, p<0.05), dehydrogenase (r = 0.69, p<0.10) and microbial biomass (r = 0.73, p<0.10). The characterisation of microbial activity holds potential as complementary criteria for evaluating rehabilitation progress on mine discard sites.
PDF
