Thembekile Ncube

The need to secure and safeguard protein for human and livestock dietary needs is an age-old conundrum. Available evidence shows that traditional protein sources such as animal and plant-based foods are insufficient in the short to long term, triggering the need to search for alternative protein sources. Single cell protein (SCP), a type of protein produced from microbial biomass, is a promising source of sustainable protein for human, fish, and livestock consumption. In this chapter, SCP, as a safe and sustainable alternative protein source for human and livestock consumption, is reviewed. This includes a discussion of microbial strains used, available substrates and their pretreatment, as well as the different fermentation strategies in SCP production. Finally, current challenges of SCP production and prospects for the future are explored.

Microplastic pollution in freshwater ecosystems is an emerging and pressing environmental concern with implications in aquatic, ecosystem and human health. While extensive research has focused on marine environments, freshwater ecosystems particularly in sub-Saharan Africa remain under-assessed. The Victoria Falls area is a key hydrological hub within the Zambezi basin, and faces increasing anthropogenic pressures, yet the sources and pathways remain poorly quantified. The study investigated the role of waste management systems as primary sources of microplastic pollution in the Masuwe River, a tributary of Zambezi River. The transport mechanism was determined through quantifying and characterizing the microplastics using stereomicroscopy and Fourier transform infrared spectroscopy. The results indicated an anthropogenic, with microplastic abundance increasing from 2 particles/L upstream to 8 particles/L downstream of waste management sites, with wastewater treatment plant effluent and dumpsite runoff contributing 4 particles/L and 6 particles/L, respectively. The direct link between terrestrial waste management practices and aquatic contamination is emphasized by the morphological and chemical similarities observed in the microplastics.

The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQ^R) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Pseudomonadota and Bacillota. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola, underscoring the importance of haloalkaliphiles in the Buhera soda pans. Functional profiling revealed the possession of diverse carbohydrate-metabolising pathways by the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs possessed pathways that implicated them in some key aspects of the nitrogen and sulphur cycle. Some MAGs harboured both sulphate reduction and respiratory pathways, suggesting a possible mechanism of ATP biosynthesis through sulphate respiration. This study demonstrates the feasibility of the recovery and taxonomic and functional annotation of high quality microbial genomes from extreme environments, making it possible to establish the ecological roles and biotechnological potential of uncultured microorganisms.

The Victoria Falls rainforest is a protected site whose forest floors harbor a host of cellulolytic microorganisms involved in biomass degradation. This study collected decaying logs and soil from the rainforest for bioprospecting cellulases from their metagenomes. Metagenomic DNA was isolated from the compound sample. Degenerate cellulase primers were used to amplify cellulase genes in the metagenome. The resulting amplicons cloned into Z-competent Escherichia coli DH5α were analyzed by functional screening for the production of cellulase extracellularly. Functional screening of the clones resulted in one clone (Clone-i) testing positive for extracellular cellulase production. Submerged fermentation of Clone-i was carried out for cellulase production. The cellulases were characterized to determine their activity’s optimum pH and temperature. The diversity of the cellulases produced by Clone-i was determined. Clone-i’s optimum enzyme activity was observed after 72 hours of incubation at 50°C and pH 5. Clone-i produced 80% more exoglucanases as compared to endoglucanases. The cellulolytic Clone-i’ isolate shows Victoria Falls rainforest’s potential as an enzyme bioprospecting site, reflecting that metagenomics is a valuable tool in microbial ecology.

Mutagenesis can generate genetic diversity and novel phenotypes in yeast strains. This study evaluated physical and chemical mutagenesis for improvement of an industrial Saccharomyces cerevisiae opaque beer strain. The yeast strain was exposed to mutagens, long enough to cause 50-95 % lethality with subsequent assessment of surviving cells for favourable characteristics. Yeast batches were mutagenized using ethyl methanesulfonate (EMS), and by exposure to ultraviolet light and visible light. EMS caused a dose-dependent decrease in survival from 100 % viable cells without EMS addition, to 10 % at 100 μg/mL, and 0 % at 200-300 μg/mL. There was approximately 10 % survival under ultraviolet light exposure observed at 25 minutes. Ultraviolet light resulted in approximately 10 % survival at 25 minutes of exposure. Visible light showed negligible mutagenic effects, with white light had the least impact on survival. EMS mutagenized cells achieved 4% alcohol content in 48 hours, versus 72 hours for controls, indicating accelerated fermentation. EMS mutants utilized 37 % more sugar on average than controls but produced lower total acidity in the final product. Thus, EMS mutagenesis produced favourable phenotypes including faster fermentation, higher alcohol yield, increased sugar consumption, and low off-flavours. With appropriate screening, EMS mutagenesis could generate improved opaque beer strains with desirable industrial characteristics. This study demonstrates the potential of random mutagenesis to sustainably enhance yeast strains for modern beer production.

Why was the work done: To investigate the impact of pasteurisation and storage in bottle on aroma compounds in pale lager beer. How was the work done: Pale lager beer was produced at an industrial scale with 100% pilsner malt and a bottom fermenting yeast. Samples were taken of unpasteurised beer from bright beer tank, after flash pasteurisation and six months after packaging in amber glass bottles. What are the main findings: Post pasteurisation, a marked increase was found in the concentration of 2,3-pentanedione (50%) and diacetyl (33%), presumably reflecting the decomposition by heat of precurser acetohydroxy acids. There was also a marginal increase in dimethyl sulphide (6%) with little or no change in other aroma compounds. Storage for six months in bottle, also resulted in an increase in the level of 2,3-pentanedione, diacetyl and dimethyl sulphide. The linear (Pearson) correlation was > 0.8 for both dimethyl sulphide and diacetyl, and 2,3-pentanedione and diacetyl. Accordingly, it was concluded that the levels in beer of dimethyl sulphide and 2,3-pentanedione are proportionally related to diacetyl. Why is the work important: This work provides an insight into the effects on flavour and aroma of lager of flash pasteurisation and subsequent storage in bottle. The inter-relationship between aroma compounds in beer suggests that such synergies may undermine the sensory perception of threshold levels and identification of specific aromas.

Yeast–insect interactions are one of the most interesting long‐standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect‐derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern‐day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.