Host-Associated Distribution of Two Novel Mammarenaviruses in Rodents from Southern Africa

Mammarenaviruses are hosted by several rodent species, a small number of which have been known to be zoonotic. Host surveillance among small mammals has identified a large diversity of previously undescribed mammarenaviruses. Intensified biosurveillance is warranted to better understand the diversity of these agents. Longitudinal host surveillance involving non-volant small mammals at a site in the Limpopo province, South Africa, was conducted. The study reports on the screening results of 563 samples for the presence of mammarenavirus RNA. PCR-positive samples were subjected to sequencing using Miseq amplicon sequencing. Sequences with close similarity to Mariental and Lunk viruses were identified from two rodent species, Micaelamys namaquensis and Mus minutoides. This represents the first description of these viruses from South Africa. The genomic sequences reported here partially satisfied the requirements put forward by the International Committee on the Taxonomy of Viruses' criteria for species delineation, suggesting that these may be new strains of existing species. The known distribution of these mammarenaviruses is thus expanded further south in Africa.

Towards evidence-based conservation of subterranean ecosystems

Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems have traditionally been overlooked in global conservation agendas and multilateral agreements, a quantitative assessment of solution-based approaches to safeguard subterranean biota and associated habitats is timely. This assessment allows researchers and practitioners to understand the progress made and research needs in subterranean ecology and management. We conducted a systematic review of peer-reviewed and grey literature focused on subterranean ecosystems globally (terrestrial, freshwater, and saltwater systems), to quantify the available evidence-base for the effectiveness of conservation interventions. We selected 708 publications from the years 1964 to 2021 that discussed, recommended, or implemented 1,954 conservation interventions in subterranean ecosystems. We noted a steep increase in the number of studies from the 2000s while, surprisingly, the proportion of studies quantifying the impact of conservation interventions has steadily and significantly decreased in recent years. The effectiveness of 31% of conservation interventions has been tested statistically. We further highlight that 64% of the reported research occurred in the Palearctic and Nearctic biogeographic regions. Assessments of the effectiveness of conservation interventions were heavily biased towards indirect measures (monitoring and risk assessment), a limited sample of organisms (mostly arthropods and bats), and more accessible systems (terrestrial caves). Our results indicate that most conservation science in the field of subterranean biology does not apply a rigorous quantitative approach, resulting in sparse evidence for the effectiveness of interventions. This raises the important question of how to make conservation efforts more feasible to implement, cost-effective, and long-lasting. Although there is no single remedy, we propose a suite of potential solutions to focus our efforts better towards increasing statistical testing and stress the importance of standardising study reporting to facilitate meta-analytical exercises. We also provide a database summarising the available literature, which will help to build quantitative knowledge about interventions likely to yield the greatest impacts depending upon the subterranean species and habitats of interest. We view this as a starting point to shift away from the widespread tendency of recommending conservation interventions based on anecdotal and expert-based information rather than scientific evidence, without quantitatively testing their effectiveness.

Assessing the extent of land-use change around important bat-inhabited caves

Background

Modification and destruction of natural habitats are bringing previously unencountered animal populations into contact with humans, with bats considered important zoonotic transmission vectors. Caves and cave-dwelling bats are under-represented in conservation plans. In South Africa, at least two cavernicolous species are of interest as potential zoonotic hosts: the Natal long-fingered bat Miniopterus natalensis and the Egyptian fruit bat Rousettus aegyptiacus. Little information is available about the anthropogenic pressures these species face around important roost sites. Both bats are numerous and widespread throughout the country; land-use changes and urban expansions are a rising concern for both conservation and increased bat-human contact.

Results

Our study addressed this shortfall by determining the extent of land-cover change around 47 roosts between 2014 and 2018 using existing land cover datasets. We determined the land-cover composition around important roost sites (including maternity, hibernacula and co-roosts), distances to urban settlements and assessed the current protection levels of roost localities. We detected an overall 4% decrease in natural woody vegetation (trees) within 5 km buffer zones of all roost sites, with a 10% decrease detected at co-roost sites alone. Agricultural land cover increased the most near roost sites, followed by plantations and urban land-cover. Overall, roosts were located 4.15 ± 0.91 km from urban settlements in 2018, the distances decreasing as urban areas expand. According to the South African National Biodiversity Institute Ecosystem Threat Status assessment, 72% of roosts fall outside of well-protected ecosystems.

Conclusions

The current lack of regulatory protection of cavernicolous bats and their roosts, increasing anthropogenic expansions and proximity to human settlements raises concerns about increased human-bat contact. Furthermore, uncontrolled roost visitation and vandalism are increasing, contributing to bat health risks and population declines, though the extent of roosts affected is yet to be quantified. In an era where pandemics are predicted to become more frequent and severe due to land-use change, our research is an urgent call for the formal protection of bat-inhabited caves to safeguard both bats and humans.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40850-021-00095-5.