Abstract. Anthrax, caused by the bacterium Bacillus anthracis, is a seasonally occurring infectious disease affecting primarily herbivorous wildlife and livestock. The seasonality of anthrax outbreaks varies among locations, making it difficult to develop a single consistent ecological description of this disease. Over 44 years of mortality surveillance, most anthrax cases in Etosha National Park, Namibia are observed in the wet season, although elephants have an anthrax mortality peak in the dry season. Focusing on three host species (plains zebra, Equus quagga; African elephant, Loxodonta africana; and springbok, Antidorcas marsupialis) occupying the endemic anthrax area of Etosha National Park, Namibia, we tested two commonly posited causes of anthrax seasonality in herbivores: increased pathogen exposure due to greater soil contact, and increased host susceptibility due to seasonal nutritional stress. These hypotheses were assessed using fecal sampling and measurement of the percentage of fecal silicates as an index of soil ingestion and fecal nitrogen, phosphorus and crude fiber as nutritional indices. Nutritional quality for all three species was higher in wet than dry seasons. Comparing among wet seasons, nutritional indices showed either a decline in nutrition with increasing rainfall or no significant pattern. All three species had greater soil ingestion in the wet season than the dry season. Higher soil contact during the anthrax peak suggests that anthrax seasonality may in part be due to heightened exposure to B. anthracis in wet seasons, for zebra and springbok. Elephant anthrax deaths do not correspond with the season of increased soil ingestion or grazing, suggesting that other behavioral mechanisms may overshadow foraging-based risk factors for this species. Nutritional stress is unlikely the primary causative factor in wet season anthrax systems, although nutritional stress sufficient to reduce resistance is difficult to assess non-invasively in wild herbivores. In contrast, increased soil ingestion may be an important predisposing factor for wet season anthrax outbreaks. Ultimately, the amount of soil ingested and its importance in the transmission of soil-borne pathogens will vary based on foraging behaviors, intake rates, grassland structure and on the likelihood that foraging areas intersect with pathogen aggregations in the environment.

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Recent gut microbiome studies in model organisms emphasize the effects of intrinsic and extrinsic factors on the variation of the bacterial composition and its impact on the overall health status of the host. Species occurring in the same habitat might share a similar microbiome, especially if they overlap in ecological and behavioral traits. So far, the natural variation in microbiomes of free-ranging wildlife species has not been thoroughly investigated. The few existing studies exploring microbiomes through 16S rRNA gene reads clustered sequencing reads into operational taxonomic units (OTUs) based on a similarity threshold (e.g., 97%). This approach, in combination with the low resolution of target databases, generally limits the level of taxonomic assignments to the genus level. However, distinguishing natural variation of microbiomes in healthy individuals from “abnormal” microbial compositions that affect host health requires knowledge of the “normal” microbial flora at a high taxonomic resolution. This gap can now be addressed using the recently published oligotyping approach, which can resolve closely related organisms into distinct oligotypes by utilizing subtle nucleotide variation. Here, we used Illumina MiSeq to sequence amplicons generated from the V4 region of the 16S rRNA gene to investigate the gut microbiome of two free-ranging sympatric Namibian carnivore species, the cheetah (Acinonyx jubatus) and the black-backed jackal (Canis mesomelas). Bacterial phyla with proportions >0.2% were identical for both species and included Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria. At a finer taxonomic resolution, black-backed jackals exhibited 69 bacterial taxa with proportions ≥0.1%, whereas cheetahs had only 42. Finally, oligotyping revealed that shared bacterial taxa consisted of distinct oligotype profiles. Thus, in contrast to 3% OTUs, oligotyping can detect fine-scale taxonomic differences between microbiomes.

The aim of the paper is to present a story about the 2015 to early 2017 Windhoek drought in the context of climate change while using the narrative approach. The story that is presented here is derived from the engagement of participants in a transdisciplinary, co-productive workshop, the Windhoek Learning Lab 1 (March 2017), as part of the FRACTAL Research Programme. The results show that the story starts with the ‘complication’ where the drought had reached crisis levels where the water demand increasingly exceeded the supply in the face of the drought. The City of Windhoek (CoW) was unable to address the problem, particularly the recharging of the Windhoek aquifer due to lack of funding. Phase 2 then shows four reactions to the drought: water conservation by water demand management; a Water Saving campaign; the Windhoek Managed Aquifer Recharge Scheme; and, the setting up of the Cabinet Technical Committee of Supply Security. The resolution of the story, Phase 4, is when the national government instructs NamWater to provide the funds for CoW to complete the recharging of the aquifer, which supplied water to the city at the last minute at the end of 2016. The final situation of the story is that ongoing collaborative work by CoW with FRACTAL on the city’s burning issues is planned to integrate climate change into future decision making for the longer term. The main actors in the story are the Ministry of Agriculture and NamWater as hero and villain, and CoW a hero, with the victims of the story, the residents of informal settlements. The main learnings from this story are that the lack of decentralization of power and resources serve to exacerbate water crises at the local level and hamper climate adaptation, despite a proactive and innovative local municipality. The paper also shows that the narrative approach provides the thread of the story to simplify a very complex set of arrangements and contradictions.

Environmental factors are common forces driving infectious disease dynamics. We compared interannual and seasonal patterns of anthrax infections in two multihost systems in southern Africa: Etosha National Park, Namibia, and Kruger National Park, South Africa. Using several decades of mortality data from each system, we assessed possible transmission mechanisms behind anthrax dynamics, examining (1) within-and between-species temporal case correlations and (2) associations between anthrax mortalities and environmental factors, specifically rainfall and the Normalized Difference Vegetation Index (NDVI), with empirical dynamic modeling. Anthrax cases in Kruger had wide interannual variation in case numbers, and large outbreaks seemed to follow a roughly decadal cycle. In contrast, outbreaks in Etosha were smaller in magnitude and occurred annually. In Etosha, the host species commonly affected remained consistent over several decades, although plains zebra

When a transmission hotspot for an environmentally persistent pathogen establishes in otherwise high-quality habitat, the disease may exert a strong impact on a host population. However, fluctuating environmental conditions lead to heterogeneity in habitat quality and animal habitat preference, which may interrupt the overlap between selected and risky habitats. We evaluated spatio-temporal patterns in anthrax mortalities in a plains zebra ( Equus quagga ) population in Etosha National Park, Namibia, incorporating remote-sensing and host telemetry data. A higher proportion of anthrax mortalities of herbivores was detected in open habitats than in other habitat types. Resource selection functions showed that the zebra population shifted habitat selection in response to changes in rainfall and vegetation productivity. Average to high rainfall years supported larger anthrax outbreaks, with animals congregating in preferred open habitats, while a severe drought forced animals into otherwise less preferred habitats, leading to few anthrax mortalities. Thus, the timing of anthrax outbreaks was congruent with preference for open plains habitats and a corresponding increase in pathogen exposure. Given shifts in habitat preference, the overlap in high-quality habitat and high-risk habitat is intermittent, reducing the adverse consequences for the population.

Host traits and environmental factors drive the natural variation in gut microbiota, and disruption in homeostasis can cause infections and chronic diseases. African wildlife is increasingly facing human-induced agricultural habitats, which also amplifies the contact probability with livestock with unknown consequences for wildlife gut microbiotas and the risk of transmission of potentially pathogenic bacteria. We applied high-throughput sequencing of bacterial 16S rRNA genes and microsatellite genotyping to investigate the impact of host traits and habitat use on the gut microbiotas of black-backed jackals (Canis mesomelas). This abundant carnivore inhabits livestock and game farms in central Namibia and is often persecuted as pathogen reservoir and vector. We further compared the gut microbiotas of black-backed jackals to other wild and domestic carnivores, herbivores and an omnivore, to disentangle the effects of environment, host species and dietary preference. In black-backed jackals, intrinsic host traits had a stronger impact in shaping the host-bacteria relationship than environmental factors. Nevertheless, the abundance of bacterial operational taxonomic units (OTUs) differed in individuals from livestock and game farms for specific bacterial genera such as Lactobacillus and Clostridium. We found, however, no evidence that black-backed jackals harbour abnormal levels of OTUs related to potential bacterial pathogens or that livestock farming has a negative impact on their health. We present here the first study investigating simultaneously the impact of host traits and environmental factors on gut microbiotas of a wildlife carnivore that occurs in a human-modified habitat.

Southern African cities face several challenges including management of rapid urbanization, rising populations, expanding informal settlements; adequate water and other service provision, and a host of governance challenges. Climate change and variability add a compounding effect to this complex, multi stressor context. Addressing the complexity requires an understanding of urban ecosystems functioning and interactions amongst the built and natural environment (climate) and human systems. In this paper we argue that learning is essential for cities to be resilient to current and future challenges. We profile the Future Resilience for African CiTies And Lands (FRACTAL) project which contributed towards climate resilient development by providing relevant climate information for decision-making at the city regional scale in southern Africa. Following FRACTAL's city-to-city learning approach of sharing good practices, knowledge and experiences framed around transdisciplinary research, the study cities of Harare, Lusaka, Windhoek and Durban conducted city learning exchange visits between 2017 and 2018. We used a mixed methods approach to collect and analyze historical climate and hydrological data and current socioeconomic and development data among the cities. A qualitative, in-depth, case study comparative analysis was used to identify similarities and differences as well as lessons drawn from the learning process during the city exchanges and these were complimented by desktop studies. Results showed water scarcity, large informal settlements, reliance on external water and energy sources, inadequate protection of ecologically sensitive resources and service provision as some of the common complications in the cities. Several lessons and transferable practices learnt from the cities included effective water conservation and waste management and the use of public-private partnerships in Windhoek, community engagements in Durban and Lusaka while lessons on decisive leadership in dealing with informal settlements emanated from Harare's limited informal settlements. Lastly, Durban's Adaptation Charter and integrated climate planning provided lessons for biodiversity protection and mainstreaming