S. Claassens

Phospholipid fatty acid profiling of microbial communities: a review of interpretations and recent applications

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.

Microbial signature lipid biomarker analysis – an approach that is still preferred, even amid various method modifications

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.

Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae)

Busseola fusca (Fuller) (Lepidoptera: Noctuidae) is a stemborer pest that attacks maize (Zea mays) throughout sub-Saharan Africa. Genetically modified maize has been shown to be effective against B. fusca. However, resistance of B. fusca against Bt-maize has developed and spread throughout South Africa. Previous studies suggested that gut microbiota contribute to mortality across a range of Lepidoptera. To fully assess the role of microbiota within the gut, it is essential to understand the microbiota harboured by natural B. fusca populations. This study aimed to identify the gut-associated bacteria by 16S rRNA gene sequencing. A total of 78 bacterial strains were characterised from the midgut of B. fusca larvae that were collected from 30 sites across the maize producing region of South Africa. Molecular phylogenetic analyses revealed bacteria affiliated to Proteobacteria, Actinobacteria, and Firmicutes. Taxonomic distribution placed these isolates into 15 different genera representing 20 species. The majority of bacteria identified belong to the genera Bacillus, Enterococcus, and Klebsiella. The B. fusca gut represents an intriguing and unexplored niche for analysing microbial ecology. The study could provide opportunities for developing new targets for pest management and contribute to understanding the phenomenon of resistance evolution of this species.Graphical Abstract

Microbial community function and structure on coal mine discard under rehabilitation

The rehabilitation of coal mine discard is problematic, especially since the lack of measures to evaluate the success of rehabilitation in terms of the self-sustainability of soil ecosystems established on these sites. In this study, the potential for using microbial community function and structure as such a measure was investigated using enzymatic assays (dehydrogenase, ß-glucosidase, urease and acid and alkaline phosphatase) and signature lipid biomarkers (PLFAs). Samples from seven coal discard sites in South Africa currently under rehabilitation, were investigated and the relationship between soil properties, vegetation cover and microbial properties analysed using PCA and RDA ordination techniques. Although the discard sites had different rehabilitation ages (one to eight years), no statistically significant differences existed between these sites based on physical and chemical characteristics. Differentiation was possible based on enzymatic activities and PLFA profiles. Sites with relatively higher vegetation cover and organic carbon content had a positive association with enzymatic activities and microbial biomass. Organic carbon content correlated significantly with ß-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 community function and structure holds potential for evaluating rehabilitation progress on mine discard sites.

Foraging at wastewater treatment works affects brown adipose tissue fatty acid profiles in banana bats

ABSTRACT In this study we tested the hypothesis that the decrease in habitat quality at wastewater treatment works (WWTW), such as limited prey diversity and exposure to the toxic cocktail of pollutants, affect fatty acid profiles of interscapular brown adipose tissue (iBrAT) in bats. Further, the antioxidant capacity of oxidative tissues such as pectoral and cardiac muscle may not be adequate to protect those tissues against reactive molecules resulting from polyunsaturated fatty acid auto-oxidation in the WWTW bats. Bats were sampled at two urban WWTW, and two unpolluted reference sites in KwaZulu-Natal, South Africa. Brown adipose tissue (BrAT) mass was lower in WWTW bats than in reference site bats. We found lower levels of saturated phospholipid fatty acids and higher levels of mono- and polyunsaturated fatty acids in WWTW bats than in reference site bats, while C18 desaturation and n-6 to n-3 ratios were higher in the WWTW bats. This was not associated with high lipid peroxidation levels in pectoral and cardiac muscle. Combined, these results indicate that WWTW bats rely on iBrAT as an energy source, and opportunistic foraging on abundant, pollutant-tolerant prey may change fatty acid profiles in their tissue, with possible effects on mitochondrial functioning, torpor and energy usage. Summary: Brown adipose tissue of banana bats foraging at wastewater treatment works contained lower saturated and higher mono- and polyunsaturated phospholipid fatty acids than that of bats foraging at reference sites.

The effect of canola (Brassica napus) as a biofumigant on soil microbial communities and plant vitality: a pot study

Canola (Brassica napus) may be incorporated into soil as a biofumigant for control of pathogens such as Sclerotinia sclerotiorum. Yet, the effect of biofumigants on natural microbial communities required to maintain soil functions is still unclear. A pot experiment with sunflowers as the crop plant was conducted to assess the biofumigation effect of canola on the soil microbial community. The study consisted of 32 pots containing four treatments of eight replicates each. Each pot contained one sunflower plant. The treatments included (1) soil only, (2) soil incorporated with canola, (3) soil incorporated with canola and inoculated with S. sclerotiorum, and (4) soil inoculated with S. sclerotiorum. Microbial community function and structure were assessed through assays of dehydrogenase activity, substrate utilisation profiles and signature biomarker analysis. Chlorophyll a fluorescence measurements were performed as a measure of sunflower vitality. Canola incorporation brought about transient changes in the soil microbial community, none of which were detrimental. Plant vitality showed no negative effects due to the biofumigant or the inoculated pathogen. Canola can be suitable as a biofumigant, without having harmful effects on the indigenous soil microbial community.

Bacillus-based bionematicides: development, modes of action and commercialisation

ABSTRACT Agricultural crops are severely damaged by root-knot nematodes causing extensive financial losses globally. Historically, agrochemicals have been the preferred method to combat these pests; however, threats to humans and the environment posed by these agrochemicals led to the need for developing new biocontrol agents. Importantly, the latter should adhere to biosafety regulations while being highly effective. Root-knot nematodes live in soil and thus the use of rhizobacteria such as Bacillus for biocontrol development have shown potential. Although various Bacillus species have been tested in this capacity, little is known about their secondary metabolites and the mechanisms of action responsible for their nematicidal activity. If these secondary metabolites can be qualitatively and quantitatively characterised, metabolic features could be synthetically engineered and used to combat root-knot nematodes. Although there is great potential for bionematicides, the commercialisation and development of such products can be difficult. This review summarises the importance of Bacillus species as natural antagonists of root-knot nematodes through the production of secondary metabolites. It provides an overview of the significance of root-knot nematodes in agriculture and the advances of chemical nematicides in recent years. The potential of Bacillus species as biocontrol agents, the known mechanisms of action responsible for the nematicidal activity demonstrated by Bacillus species, non-target effects of biocontrol agents and the commercialisation of Bacillus-based bionematicides are discussed.