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Plant–mycorrhizal interaction is an important association in the ecosystem with significant impacts on the physical, biological and chemical properties of the soil. In the present study, potential relationships that exist between organic acid production by ectomycorrhizal pine seedlings and plant parameters in the absence of any significant environmental stress were investigated. The aim of the study was to investigate the contribution of organic acid production to plant growth. Four different ectomycorrhizal fungi were used in a mycorrhizal synthesis experiment to colonise roots of Pinus patula. Ectomycorrhizal and non-ectomycorrhizal plants were used in a pot trial experiment that lasted for 24 weeks. After harvesting, plant materials as well as soil samples underwent different analyses, which included the determination of pH, organic acids, plant biomass, and foliar and root phosphorus and potassium. The results indicated a significant interaction (P < 0.0001) between fungal type and organic acid production. This reflects the influence of fungal type on organic acid production. However, it was observed that organic acids secreted into the soil are not directly linked with the quantity of nutrients detected in either the root or shoot, but seemed to positively influence plant growth as reflected in the result from root and shoot biomass.Keywords: ectomycorrhizal fungi, nutrients, organic acid, phosphorus, pine, potassium

Crop fungal infections such as those caused by Fusarium species often result in yield loss pre- and post-harvest and during storage, contaminate food and exacerbate food insecurity. Synthetic fungicides are becoming less attractive as they pose health risks to consumers and are not environmentally friendly. As an alternative to synthetic fungicides, medicinal plant species may present sustainable and affordable sources of environmentally friendly fungicides for controlling plant diseases. This study was aimed at evaluating the in vitro antifungal activity of different medicinal plant extracts individually or in combination against Fusarium proliferatum, F. solani, F. verticillioides and F. graminearum. Different solvent (water, acetone and ethyl acetate) extracts obtained from the leaves of thirteen medicinal plant species were evaluated for antifungal activity using the micro-plate dilution assay. Their combined effect was evaluated by determining their fractional inhibitory concentration index (FICI). When evaluated individually, acetone extracts obtained from Combretum erythrophyllum, Harpephyllum caffrum and Quercus acutissima were the most active extracts inhibiting the growth of all the four pathogens with minimum inhibitory concentration (MIC) values less than 0.1 mg/ml. Out of 204 extract combinations evaluated, 150 extract combinations demonstrated either synergistic or additive antifungal activity. among the best combinations, combined acetone extracts of Harpephyllum caffrum and Combretum erythrophyllum showed strong synergistic antifungal activity against F. graminearum, F. proliferatum and F. verticillioides (MIC values of 0.02 mg/ml, 0.002 mg/ml and 0.001 mg/ml, respectively), and strong additive antifungal activity against F. solani (MIC = 0.02 mg/ml). The approach of using medicinal plant extracts from renewable plant parts either individually or in combination is sustainable, affordable, environmentally friendly and may be more beneficial in the fight against crop pathogenic diseases, particularly in organic farming.

BACKGROUND: The uncontrolled overproduction of fruit and vegetable waste causes serious environmental challenges such as emission of greenhouse gases. Anaerobic digestion (AD) is becoming a widely adopted technology for treatment of food waste with the concomitant production of biogas. This study investigated the link between microbial community structure and biogas production when using cow dung and mixed fruit and vegetable waste (MFVW) as substrates. RESULTS: Semi‐continuous stir tank reactors were used for AD of cow dung and MFVW over a period of 40 days. The highest accumulative methane yield (112.9 L) was obtained from co‐ digestion, intermediate yield (59.5 L) was obtained from cow dung and lowest yield (6.1 L) from MFVW at the end of the digestion experiment. Polymerase chain reaction‐denaturing gradient gel electrophoresis (PCR‐DGGE) revealed higher bacterial and archaeal diversity indices in co‐digestion in comparison to mono‐digestion of cow dung and MFVW. High‐throughput sequence analyses showed that operational taxonomic units (OTUs) belonging to the phyla Bacteroidetes, followed by Firmicutes, Actinobacteria and Proteobacteria were dominant in all treatments. CONCLUSION: The results of the study demonstrated that the enhanced methane production in co‐digestion could be attributed to the neutral pH and partial shift of archaea from Methanosaeta to Methanosarcina rich communities. © 2019 Society of Chemical Industry

Highlights • Serratia marcescens 39_H1 could enhance the hydrolysis of lignocellulosic biomass. • Serratia marcescens 39_H1 is a plant growth promoting organism. • Genome analysis showed diverse potential biotechnological application of organism. • This is an original report on the hydrolytic and acidogenic attributes ofSerratia marcescens 39_H1 for biogas production., Here, we report a high quality annotated draft genome of Serratia marcescens 39_H1, a Gram-negative facultative anaerobe that was isolated from an anaerobic digester. The strain exhibited hydrolytic/acidogenic properties by significantly improving methane production when used as a single isolate inoculum during anaerobic digestion of water hyacinth and cow dung. The total genome size of the isolate was 5,106,712 bp which corresponds to an N50 of 267,528 and G + C content of 59.7 %. Genome annotation with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) predicted a total of 4,908 genes of which 4,755 were protein coding genes; there were no plasmids detected. A number of genes associated with hydrolytic/acidogenic activities as well as other metabolic activities were identified and discussed.

Until recently, research has focused on Clostridium perfringens in clinical settings without considering environmental isolates. In this study, environmental genomes were used to investigate possible antibiotic resistance and the presence of virulence traits in C. perfringens strains from raw surface water. In silico assembly of three C. perfringens strains, DNA generated almost complete genomes setting their length ranging from 3.4 to 3.6 Mbp with GC content of 28.18%. An average of 3,175 open reading frames was identified, with the majority associated with carbohydrate and protein metabolisms. The genomes harboured several antibiotic resistance genes for glycopeptides, macrolide–lincosamide–streptogramin B, β-lactam, trimethoprim, tetracycline and aminoglycosides and also the presence of several genes encoding for polypeptides and multidrug resistance efflux pumps and 35 virulence genes. Some of these encode for haemolysins, sialidase, hyaluronidase, collagenase, perfringolysin O and phospholipase C. All three genomes contained sequences indicating phage, antibiotic resistance and pathogenic islands integration sites. A genomic comparison of these three strains confirmed high similarity and shared core genes with clinical C. perfringens strains, highlighting their health security risks. This study provides a genomic insight into the potential pathogenicity of C. perfringens present in the environment and emphasises the importance of monitoring this niche in the future.

Soil microbial communities are suitable soil ecosystem health indicators due to their sensitivity to management practices and role in soil ecosystem processes. Presently, information on structural and functional differentiation of bacterial communities in post-coal mining reclamation soils of South Africa is sparse. Here, bacterial communities in three post-coal mining reclamation soils were investigated using community-level physiological profiling (CLPP), enzyme activities, and next-generation sequencing of 16S rRNA gene. Inferences were drawn in reference to adjacent unmined soils. CLPP-based species diversity and proportionality did not differ significantly (P > 0.05) whereas activities of β-glucosidase, urease and phosphatases were significantly (P P P > 0.05), suggesting redundancy in bacterial community functions between reclamation and unmined soils. Silt content, bulk density, pH, electrical conductivity, Na and Ca significantly influenced soil bacterial communities. Overall, results indicate that bacterial community structure reflects underlying differences between soil ecosystems, and suggest the restoration of bacterial diversity and functions over chronological age in reclamation soils.

The rising fossil fuel prices as well as negative climatic conditions caused by fossil fuel emissions have prompted technologists and scientists to develop alternative value-added fuels. These fuels can be produced from renewable bio-based materials and have less negative impacts on the environment. Much attention has been drawn to advanced fuels such as bio-based butanol, which is considered a promising fuel compared to ethanol. Its properties such as low volatility, less ignition problems and high inter-solubility make it an ideal drop-in fuel for conventional vehicles. This type of fuel can be utilised either in pure or blended form with petrol or diesel. Conventionally, butanol is produced through the acetone–butanol–ethanol (ABE) process using mainly Clostridium species to ferment sugars obtained from biomass. This method makes use of sustainable/cost-effective bacteria that are easily accessible. Alternatively, butanol can be directly produced from bio-based ethanol through aldol condensation using metal oxides/hydroxyapatite catalysts. Catalyst synthesis involves short reaction times, but high reaction temperatures. This chapter highlights the use of butanol as a fuel, reviews different methods employed and discusses current status and potential for future prospects.

This study investigated 13-commercial biofertilisers for their microbial contents and potential functional capabilities using a culture-based approach. Isolates obtained were identified by sequencing the partial I6S rRNA gene and ITS 1 and 2 regions and screened for plant growth-promoting capabilities. A total of 58 bacterial and three fungal isolates were obtained from all biofertilisers, with major genera being Bacillus, Rhizobium, Pseudomonas, Candida and Aspergillus. Five of the biofertilisers had the microbes (all or some) listed in the label detected while eight products had none detected. All the products had more microbes than that declared in the labels, suggesting the presence of potential contaminants. Generally, all the identified microbes, including the potential contaminants, had different beneficial capabilities. Approximately 40% of the isolates showed potential for nitrogen-fixation, while 27% exhibited high phosphate-solubilisation ability. Additionally, 87% of the isolates produced indole acetic acid in the range of 0.1–114.4 μg/mL. High levels of siderophore production were mainly observed amongst Bacillus and Pseudomonas genera. The potential of the microbes, including those not listed in the label, to fix nitrogen and produce acid phosphatase, indole acetic acid and siderophore, was highest in four products. This suggests the products have multiple functional abilities in improving crop productivity. However, other qualities of biofertiliser, such as viable cell count and level of contamination, must always be within the acceptable standards. This will guarantee high product quality as well as efficiency when applied in the field. Overall, the results show that there is a high correlation between microbial compositions and potential capability of biofertilisers for plant-growth promotion., Agricultural sciences, Ecology, Microbiology, Environmental science, Biotechnology, Commercial biofertiliser, Efficiency; Crop productivity, Correlation, Nitrogen-fixation, Sequencing

North-West University, Potchefstroom Campus PhD (Microbiology), North-West University, Potchefstroom Campus At present, there is no comprehensive soil quality assessment practice for the coal mining industry in South Africa. Studies have shown that belowground soil biota are crucial to soil ecosystem functioning and are sensitive bioindicators for soil quality monitoring. Due to the limitations of some previously developed methods for analysing microbial community structure, a more robust approach involving high-throughput culture-independent molecular techniques was utilised to assess post-coal-mining reclamation soils for potential ecosystem recovery, support function and potential microbial bioindicators. Also, the potential impact of soil physicochemical properties in shaping soil biotic communities were assessed. The study was conducted in three stages. Firstly, the potential contribution of soil stockpiles to post-mining reclamation success was assessed by analysing arbuscular mycorrhizal fungal (AMF) spore density and viability as well as microbial community diversity and structure. Overall, results suggest that AMF spore density in stockpiles do not differ significantly (P 0.05) differences in microbial community richness and diversity amongst samples while enzyme activities were highly variable within-sites. The assemblages of the obligate plant symbiont, AMF, were less differentiated when compared to other microbial groups suggesting that AMF assemblages could be less suitable bioindicators of ecosystem recovery. Some genera with soil quality indicator potential such as Acidothermus, Bryobacter and Halingium, as well as plant-growth promotion potentials such as Mesorhizobium, Bradyrhizobium and Microvirga were relatively more abundant across soils, whereas a vast majority of other microbial species and their functions in reclamation soils are still largely unknown. Lastly, the capability of the soil to serve as a habitat to support soil biota association and functions was assessed using an ecotoxicological approach by utilising earthworms as bioindicators. Endpoints such as avoidance behaviour, growth, reproduction and mortality of earthworms were assessed. There was no evidence to suggest that the ecosystem habitat function of stockpile and reclamation soils is significantly limited compared to the Organisation of Economic Cooperation and Development’s artificial control soil. Nevertheless, support functions were highest in unmined soils as determined by the earthworm avoidance behaviour test. Data generated in this study strongly supports that microbial species richness and diversity levels are restored over the years since reclamation, though community composition and structure still differ from the pre-disturbance community. Furthermore, microbial communities of reclamation soil environments are predominantly shaped by pH, phosphorus and nitrogen sources. Overall, bacterial communities are the most responsive and indicative of ecological changes during soil ecosystem restoration. In conclusion, as molecular methods are not without limitations, and because the soil ecosystem environment is governed by an interplay of factors, a comprehensive soil monitoring programme for post-mining reclamation soils in South Africa must comprise a combination of physicochemical properties and microbial community diversity indices as part of a minimum dataset. Furthermore a responsible stockpiling procedure which entails proper excavation and storage of topsoil, as well as the inclusion of microbial inoculants during post-mining reclamation operations, is strongly recommended. Such an approach will help improve coal-mining disturbed soil quality as well as facilitate a quicker ecosystem recovery period. Doctoral

Ready-to-eat foods (RTEs) are foods consumed without any further processing. They are widely consumed as choice meals especially by school-aged children and the fast-paced working class in most low- and middle-income countries (LMICs), where they contribute substantially to the dietary intake. Depending on the type of processing and packaging material, RTEs could be industrially or traditionally processed. Typically, RTE vendors are of low literacy level, as such, they lack knowledge about good hygiene and food handling practices. In addition, RTEs are often vended in outdoor environments such that they are exposed to several contaminants of microbial origin. Depending on the quantity and type of food contaminant, consumption of contaminated RTEs may result in foodborne diseases and several other adverse health effects in humans. This could constitute major hurdles to growth and development in LMICs. Therefore, this review focuses on providing comprehensive and recent occurrence and impact data on the frequently encountered contaminants of microbial origin published in LMICs within the last decade (2009 to 2018). We have also suggested viable food safety solutions for preventing and controlling the food contamination and promoting consumer health.

MSc (Environmental Sciences), North-West University, Potchefstroom Campus Faecal pollution of water has long been an issue of great concern due to the potential health risks associated with faeces. A lack of understanding the implications of sewage contamination in water combined with inadequate municipal management practices contribute toward deterioration of water infrastructure. Poor management practices, particularly in developing countries, combined with limited financial resources restrict the extent of water quality monitoring which takes place, especially in rural areas. Recent large-scale sewage contamination of the Vaal River in South Africa is an example of where microbial source tracking (MST) by means of Bacteroides host-associated assays could be applied advantageously in mitigation efforts. Bacteroides species make up the majority of mammalian intestinal bacterial communities. The intestinal community composition of hosts may however still vary regionally and per individual due to factors such as diet. Unlike conventionally applied faecal indicator bacteria (FIB), Bacteroides has very limited survival capabilities in the environment due to their anaerobic nature. Subsequently by detection of the host source and quantification of marker levels the extent of contamination as well as possible points of entry into an area of interest may be determined. Unfortunately, as with any developing technique, increased popularity and frequency of application have brought several shortcomings of Bacteroides related assays to light. A systematic literature review was performed identifying recurring themes with regard to challenges and limitations faced by researchers applying Bacteroides related assays to environmental water samples. It is evident from the literature that a lack of marker specificity both by host species and geographically hinders the application of these techniques worldwide. Markers that were thought of as host-specific were frequently detected in other animal host groups in the reviewed literature. Another shortcoming of these techniques is sensitivity to inhibitory substances commonly found in faeces and environmental water. Data interpretation according to different parameters such as a set sample volume regardless of DNA concentration or DNQ (detected but not quantified) samples in quantitative PCR assays being seen as either positive or negative may complicate data comparability between datasets or across similar studies. Cost reduction of these techniques will increase the opportunities for application in developing countries. These methods are best applied in a toolbox approach along with several other assays or markers in order to estimate the full extent of contamination in a sampling area. Standardisation of Bacteroides host-associated assays is crucial for successful application of these techniques, especially with regards to comparability of data. Masters

BACKGROUND Water hyacinth (Eichhornia crassipes) is a fast growing water weed that threatens the aquatic ecosystem and human activities, hence control of the plant is essential. One such control approach is to harvest and utilize hyacinth as a substrate for anaerobic digestion (AD). Various factors influence AD performance, including substrate pre‐treatment and microbial community composition, amongst others. This study was aimed at establishing the link between method of substrate pre‐treatment, microbial diversity, inoculum addition and biogas yield during AD of hyacinth. RESULTS The addition of an inoculum resulted in microbial community stability and early biomethane production of up to 0.4 L irrespective of pre‐treatment method. However, cultures that lacked inoculum showed distinct microbial community structure variation in response to pre‐treatment method, and minimal early biomethane production (up to 0.1 L). Biogas produced by cultures lacking inoculum was initially mostly composed of carbon dioxide (up to 100% of total biogas), but as digestion proceeded, an increase in biomethane production was observed (up to 60% of total biogas), which correlated with the shift in microbial community structure and increased microbial diversity. This indicates the presence of biogas‐producing microorganisms associated with the collected hyacinth. Canonical correspondence analysis proved that dynamic changes in microbial community structure and biogas yield were strongly correlative. CONCLUSION This study proves that hyacinth pre‐treatment influences microbial community structure and concomitant biogas yield in the absence of an inoculum. The addition of an inoculum aids in stability of microbial community structure and biogas yield irrespective of method of hyacinth pre‐treatment