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The estimated global population growth of 81 million people per year, combined with increased rates of urbanization and associated industrial processes, result in volumes of high strength ammonia wastewater that cannot be treated in a cost-effective or sustainable manner using the floc-based conventional activated sludge approach of nitrification and denitrification. Biofilm and aerobic granular sludge technologies have shown promise to significantly improve the performance of biological nitrogen removal systems treating high strength wastewater. This is partly due to enhanced biomass retention and their ability to sustain diverse microbial populations with juxtaposing growth requirements. Recent research has also demonstrated the value of hybrid systems with heterogeneous bioaggregates to mitigate biofilm and granule instability during long-term operation. In the context of high strength ammonia wastewater treatment, conventional nitrification–denitrification is hampered by high energy costs and greenhouse gas emissions. Anammox-based processes such as partial nitritation–anammox and partial denitrification–anammox represent more cost-effective and sustainable methods of removing reactive nitrogen from wastewater. There is also growing interest in the use of photosynthetic bacteria for ammonia recovery from high strength waste streams, such that nitrogen can be captured and concentrated in its reactive form and recycled into high value products. The purpose of this review is to explore recent advancements and emerging approaches related to high strength ammonia wastewater treatment.

Globally, water resources are under constant threat of being polluted by a diverse range of man-made chemicals, and South Africa is no exception. These contaminants can have detrimental effects on both human and wildlife health. It is increasingly evident that several chemicals may modulate endocrine system pathways in vertebrate species, and these are collectively referred to as endocrine disrupting contaminants (EDCs). Although the endocrine-disrupting effect of water pollutants has been mainly linked to agricultural pesticides and industrial effluents, other pollutants such as pharmaceuticals and personal care products (PPCPs) are largely unnoticed, but also pose a potentially significant threat. Here we present for the first time in a South African context, a summarised list of PPCPs and other EDCs detected to date within South African water systems, as well as their possible endocrine-disrupting effect in-vitro and in-vivo. This review addresses other factors which should be investigated in future studies, including endocrine disruption, PPCP metabolites, environmental toxicology, and antibiotic resistance. The challenges of removing EDCs and other pollutants at South African wastewater treatment works (WWTWs) are also highlighted. The need for focused research involving both in-vitro and in-vivo studies to detect PPCPs in water systems, and to delineate adverse outcome pathways (AOPs) of priority PPCPs to aid in environmental impact assessment (EIA), are discussed.

Fundamental ecological principles of ecosystem-level respiration are extensively applied in greenhouse gas and elemental cycle studies. A laboratory system termed CEMS (Carbon Dioxide Evolution Measurement System), developed to explore microbial biofilm growth and metabolic responses, was evaluated as an early-warning system for microbial disturbances in industrial settings: in (a) potable water system contamination, and (b) bioreactor inhibition. Respiration was detected as CO 2 production, rather than O 2 consumption, including aerobic and anaerobic metabolism. Design, thresholds, and benefits of the remote CO 2 monitoring technology were described. Headspace CO 2 correlated with contamination levels, as well as chemical (R 2 > 0.83–0.96) and microbiological water quality indicators (R 2 > 0.78–0.88). Detection thresholds were limiting factors in monitoring drinking water to national and international standards (0 CFU/100 mL fecal coliforms) in both open- (>1500 CFU/mL) and closed-loop CO 2 measuring regimes (>100 CFU/100 mL). However, closed-loop detection thresholds allow for the detection of significant contamination events, and monitoring less stringent systems such as irrigation water (<100 CFU/mL). Whole-system respiration was effectively harnessed as an early-warning system in bioreactor performance monitoring. Models were used to deconvolute biological CO 2 fluctuations from chemical CO 2 dynamics, to optimize this real-time, sustainable, low-waste technology, facilitating timeous responses to biological disturbances in bioreactors.

South Africa's rivers are frequently used by communities lacking proper sanitation infrastructure for domestic purposes; however, these surface waters may pose a health risk to immunocompromised individuals due to the presence of opportunistic pathogenic fungi in the polluted water. Although only a few studies have focused on the presence of clinically relevant fungal species in South African rivers, many known opportunistic pathogenic species were found to be predominant in these waters. Furthermore, strong evidence exists that increased numbers of clinically relevant species may be observed in future due to fungi acquiring thermotolerance in response to the global increase in temperature. Thermotolerance is a major factor contributing to pathogenesis in fungi, due to the generally low tolerance of most fungi toward mammalian body temperatures. It is therefore contended that combinatorial efects of water pollution and rising environmental temperatures could lead to an increase in the incidence of mycoses in South Africa. This is especially concerning since a relatively large population of immunocompromised individuals, represented mostly by HIV-infected people, resides in the country.

Listeria monocytogenes biofilms are ubiquitous in the food-processing environment, where they frequently show resistance against treatment with disinfectants such as peracetic acid (PAA) due to sub-lethal damage resulting in biofilm persistence or the formation of secondary biofilms. L. monocytogenes serovar ½a EGD-e biofilms were cultivated under continuous flow conditions at 10 °C, 22 °C, and 37 °C and exposed to industrially relevant PAA concentrations. The effect of PAA on biofilm metabolic activity and biomass was monitored in real-time using the CEMS-BioSpec system, in addition to daily measurement of biofilm-derived planktonic cell production. Biofilm-derived planktonic cell yields proved to be consistent with high yields during biofilm establishment (≥106 CFU.mL−1). The exposure of biofilms to the minimum inhibitory PAA concentration (0.16%) resulted in only a brief disruption in whole-biofilm metabolic activity and biofilm biomass accumulation. The recovered biofilm accumulated more biomass and greater activity, but cell yields remained similar. Increasing concentrations of PAA (0.50%, 1.5%, and 4.0%) had a longer-lasting inhibitory effect. Only the maximum dose resulted in a lasting inhibition of biofilm activity and biomass–a factor that needs due consideration in view of dilution in industrial settings. Better disinfection monitoring tools and protocols are required to adequately address the problem of Listeria biofilms in the food-processing environment, and more emphasis should be placed on biofilms serving as a “factory” for cell proliferation rather than only a survival mechanism.

The detachment of single cells from biofilms is an intrinsic part of this surface-associated mode of bacterial existence. Pseudomonas sp. strain CT07gfp biofilms, cultivated in microfluidic channels under continuous flow conditions, were subjected to a range of liquid shear stresses (9.42 mPa to 320 mPa). The number of detached planktonic cells was quantified from the effluent at 24-h intervals, while average biofilm thickness and biofilm surface area were determined by confocal laser scanning microscopy and image analysis. Biofilm accumulation proceeded at the highest applied shear stress, while similar rates of planktonic cell detachment was maintained for biofilms of the same age subjected to the range of average shear rates. The conventional view of liquid-mediated shear leading to the passive erosion of single cells from the biofilm surface, disregards the active contribution of attached cell metabolism and growth to the observed detachment rates. As a complement to the conventional conceptual biofilm models, the existence of a biofilm surface-associated zone of planktonic cell proliferation is proposed to highlight the need to expand the traditional perception of biofilms as promoting microbial survival, to include the potential of biofilms to contribute to microbial proliferation.

As the effects of climate change become increasingly evident, the need for effective CO 2 management is clear. Microalgae are well-suited for CO 2 sequestration, given their ability to rapidly uptake and fix CO 2 . They also readily assimilate inorganic nutrients and produce a biomass with inherent commercial value, leading to a paradigm in which CO 2 -sequestration, enhanced wastewater treatment, and biomass generation could be effectively combined. Natural non-axenic phototrophic cultures comprising both autotrophic and heterotrophic fractions are particularly attractive in this endeavour, given their increased robustness and innate O 2 -CO 2 exchange. In this study, the interplay between CO 2 -consuming autotrophy and CO 2 -producing heterotrophy in a non-axenic phototrophic biofilm was examined. When the biofilm was cultivated under autotrophic conditions (i.e. no organic carbon), it grew autotrophically and exhibited CO 2 uptake. After amending its growth medium with organic carbon (0.25 g/L glucose and 0.28 g/L sodium acetate), the biofilm rapidly toggled from net-autotrophic to net-heterotrophic growth, reaching a CO 2 production rate of 60 μmol/h after 31 hours. When the organic carbon sources were provided at a lower concentration (0.125 g/L glucose and 0.14 g/L sodium acetate), the biofilm exhibited distinct, longitudinally discrete regions of heterotrophic and autotrophic metabolism in the proximal and distal halves of the biofilm respectively, within 4 hours of carbon amendment. Interestingly, this upstream and downstream partitioning of heterotrophic and autotrophic metabolism appeared to be reversible, as the position of these regions began to flip once the direction of medium flow (and hence nutrient availability) was reversed. The insight generated here can inform new and important research questions and contribute to efforts aimed at scaling and industrializing algal growth systems, where the ability to understand, predict, and optimize biofilm growth and activity is critical.

This study extends probiotic cleaning research to a built environment. Through an eight-month cleaning trial, we compared the effect of three cleaning products (disinfectant, plain soap, and a probiotic cleaner containing a patented Bacillus spore consortium), and tap water as the control, on the resident microbiome of three common hospital surfaces (linoleum, ceramic, and stainless steel). Pathogens, Escherichia coli and Staphylococcus aureus, were deposited and desiccated, and competitive exclusion was assessed for each microbiome. Cell survival was shown to be an incomplete tool for measuring microbial competitive exclusion. Biofilm competition offered a fuller understanding of competitive dynamics. A test for culturable cell survival showed that both plain soap and probiotic cleaner regimes established a surface microbiome that outcompeted the two pathogens. A different picture emerged when observing biofilms with a deposited and desiccated GFP-labeled pathogen, Pseudomonas aeruginosa. Competitive exclusion was again demonstrated. On surfaces cleaned with disinfectant the pathogen outcompeted the microbiomes. On surfaces cleaned with plain soap, the microbiomes outcompeted the pathogen. However, on surfaces cleaned with probiotic cleaner, despite the exponentially higher surface microbial loads, the microbiome did not completely outcompete the pathogen. Thus, the standard culturable cell test for survival on a surface confirmed the competitive advantage that is typically reported for probiotic cleaners. However, observation of competition in biofilms showed that the more diverse microbiome (according to alpha and beta indices) established on a surface cleaned with plain soap had a better competitive advantage than the monoculture established by the probiotic cleaner. Therefore, microbial diversity appears to be as critical to the competitive exclusion principle as cell numbers. The study showed that both plain soap and probiotic cleaner fostered competitive exclusion far more effectively than disinfectant. Probiotic cleaners with microbial diversity could be worth considering for hospital cleaning.

Riverine fungi have the capacity for both pathogenicity, pertinent for countries with elevated immunosuppressed individuals, and bioremediation potential. The purpose was (i) to screen for the presence of clinically relevant riverine fungi and associations with anthropogenic influence, and (ii) the acclimatisation of environmental communities toward potential bioremediation application. Communities were harvested from polluted rivers in Stellenbosch, South Africa, and mycobiomes characterised by high-throughput amplicon sequencing. The remainder of the biomass was inoculated into continuous bioreactors with filtered river water or sterile minimal medium. Seven weeks later, the mycobiomes were re-sequenced. At least nine clinically relevant species were detected, including agents of mycoses belonging to the genus Candida. The occurrence of genera that harbour opportunisticstrains was significantly higher (P = 0.04) at more polluted sites. Moreover, positive correlations occured between some genera and pollution indices, demonstrating the potential of fungi for addition to water quality indicators. Despite biomass increase, almost all pathogens were undetectable after seven weeks, demonstrating less resilience in conditions mimicking rivers. Thus, when screening riverine biomes for bioremediation potential, ambient reactors select against human pathogens. This indicates a transient introduction of allochthonous opportunistic species into rivers due to insufficient sanitation, and the potential of bioremediation strategies that selects for environmental rather than pathogenic traits.

Toxic phytoplankton in the aquatic ecosystems are dynamic, affecting water quality. It remains unclear as to how possible toxic phytoplankton assemblages vary vertically and temporally in Swakoppoort and Von Bach dams, located in a dry subtropical desert region in central Namibia. The following variables were analyzed: pH, Secchi depths, turbidity, water temperature, total phosphorus, orthophosphate, chlorophyll-a, phytoplankton cells, and water depths. Cyanobacteria dominated the phytoplankton community in the autumn, winter and spring (dry) and summer (wet) seasons, at all the depth ranges in both dams. Microcystis dominated the vertical and temporal dynamics, followed by Dolichospermum. In the dry seasons, higher cyanobacteria cell numbers were observed in comparison to the rainy season in both dams. Spring blooms of cyanobacteria were evident in the Von Bach Dam while autumn and spring cyanobacteria blooms were observed in the Swakoppoort Dam. In the Swakoppoort Dam, the preferable depth ranges for toxic cyanobacteria species were at 5 to 10 m while in the Von Bach Dam at 0 to 5 m range. The findings of the current study indicate that the traditional selective withdrawal of water in the two dams should be performed with vertical and temporal dynamics of possible toxic cyanobacteria accounted for to aid the abstraction of water with the lowest possible toxic phytoplankton numbers, which could lower the public health risk.