Not only climate: The importance of biotic interactions in shaping species distributions at macro scales.

Abiotic factors are usually considered key drivers of species distribution at macro scales, while biotic interactions are mostly used at local scales. A few studies have explored the role of biotic interactions at macro scales, but all considered a limited number of species and obligate interactions. We examine the role of biotic interactions in large-scale SDMs by testing two main hypotheses: (1) biotic factors in SDMs can have an important role at continental scale; (2) the inclusion of biotic factors in large-scale SDMs is important also for generalist species. We used a maximum entropy algorithm to model the distribution of 177 bat species in Africa calibrating two SDMs for each species: one considering only abiotic variables (noBIO-SDMs) and the other (BIO-SDMs) including also biotic variables (trophic resource richness). We focused the interpretation of our results on variable importance and response curves. For each species, we also compared the potential distribution measuring the percentage of change between the two models in each pixel of the study area. All models gave AUC >0.7, with values on average higher in BIO-SDMs compared to noBIO-SDMs. Trophic resources showed an importance overall higher level than all abiotic predictors in most of the species (~68%), including generalist species. Response curves were highly interpretable in all models, confirming the ecological reliability of our models. Model comparison between the two models showed a change in potential distribution for more than 80% of the species, particularly in tropical forests and shrublands. Our results highlight the importance of considering biotic interactions in SDMs at macro scales. We demonstrated that a generic biotic proxy can be important for modeling species distribution when species-specific data are not available, but we envision that a multi-scale analysis combined with a better knowledge of the species might provide a better understanding of the role of biotic interactions.

Bat selfies: photographic surveys of flying bats.

The recent pandemic and other environmental concerns have resulted in restrictions on research and surveys involving capture and handling bats. While acoustic surveys have been widely used as an alternative survey method, in this study, we show how photographic surveys can offer an important contribution to study and survey bats. We outline approaches, using high speed flash and automated trip beams to obtain photos of flying bats of sufficient quality for reliable identification of species. We show, through a series of examples of setups and photographs, that photography is effective for surveying bats at a variety of sites, where bats roost, drink, and forage. We note, however, that photographic surveys cannot replace capture in all situations. In addition, although photographing bats is less invasive than capturing them, it can involve disturbance, so we stress the importance of minimizing the impact of such operations on bats. Supplementary Information: The online version contains supplementary material available at 10.1007/s42991-022-00233-7.

Host conservation through their parasites: molecular surveillance of vector-borne microorganisms in bats using ectoparasitic bat flies.

Most vertebrates host a wide variety of haematophagous parasites, which may play an important role in the transmission of vector-borne microorganisms to hosts. Surveillance is usually performed by collecting blood and/or tissue samples from vertebrate hosts. There are multiple methods to obtain samples, which can be stored for decades if properly kept. However, blood sampling is considered an invasive method and may possibly be harmful to the sampled individual. In this study, we investigated the use of ectoparasites as a tool to acquire molecular information about the presence and diversity of infectious microorganism in host populations. We tested the presence of three distinct vector-borne microorganisms in both bat blood and bat flies: Bartonella bacteria, malaria-like Polychromophilus sp. (Apicomplexa), and Trypanosoma sp. (Kinetoplastea). We detected the presence of these microorganisms both in bats and in their bat flies, with the exception of Trypanosoma sp. in South African bat flies. Additionally, we found Bartonella sp. in bat flies from one population in Spain, suggesting its presence in the host population even if not detected in bats. Bartonella and Polychromophilus infection showed the highest prevalence in both bat and bat fly populations. Single, co- and triple infections were also frequently present in both. We highlight the use of haematophagous ectoparasites to study the presence of infectious microorganism in host blood and its use as an alternative, less invasive sampling method.

TITLE: Conservation des hôtes grâce à leurs parasites : surveillance moléculaire des microorganismes à transmission vectorielle chez les chauves-souris à l'aide de mouches ectoparasites. ABSTRACT: La plupart des vertébrés hébergent une grande variété de parasites hématophages, qui peuvent jouer un rôle important dans la transmission de microorganismes à transmission vectorielle à leurs hôtes. La surveillance est généralement effectuée en prélevant des échantillons de sang et/ou de tissus sur des hôtes vertébrés. Il existe plusieurs méthodes pour obtenir des échantillons, qui peuvent être conservés pendant des décennies dans des bonnes conditions. Cependant, le prélèvement sanguin est considéré comme une méthode invasive et peut éventuellement être nocif pour l'individu prélevé. Dans cette étude, nous avons étudié l'utilisation d'ectoparasites comme outil pour acquérir des informations moléculaires sur la présence et la diversité des microorganismes infectieux dans les populations hôtes. Nous avons testé la présence de trois microorganismes distincts, transmis par des vecteurs, dans le sang et les mouches des chauves-souris : les bactéries Bartonella, Polychromophilus sp. (Apicomplexa) et Trypanosoma sp. (Kinetoplastea). Nous avons détecté la présence de ces microorganismes à la fois chez les chauves-souris et chez leurs mouches des chauves-souris, à l'exception de Trypanosoma sp. chez les chauves-souris sud-africaines. De plus, nous avons trouvé Bartonella sp. chez les mouches des chauves-souris d'une population en Espagne, ce qui suggère sa présence dans la population hôte même si elle n'est pas détectée chez les chauves-souris elles-mêmes. Les infections à Bartonella et Polychromophilus ont montré la prévalence la plus élevée dans les populations de chauves-souris et de mouches des chauves-souris. Des infections simples, doubles et triples étaient également fréquemment présentes dans les deux cas. Nous mettons en évidence l'utilisation d'ectoparasites hématophages pour étudier la présence de microorganismes infectieux dans le sang de l'hôte et son utilisation comme méthode alternative et moins invasive d'échantillonnage.

Lyssaviruses in Insectivorous Bats, South Africa, 2003-2018.

We detected 3 lyssaviruses in insectivorous bats sampled in South Africa during 2003-2018. We used phylogenetic analysis to identify Duvenhage lyssavirus and a potentially new lyssavirus, provisionally named Matlo bat lyssavirus, that is related to West Caucasian bat virus. These new detections highlight that much about lyssaviruses remains unknown.

Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction.

Seasonal reproduction is a period of extreme physiological and behavioural changes, yet we know little about how it may affect host microbial communities (i.e. microbiota) and pathogen transmission. Here, we investigated shifts of the bacterial microbiota in saliva, urine and faeces during the seasonal reproduction of bats in South Africa, and test for an interaction in shedding patterns of both bacterial (Leptospira) and viral (adeno- and herpesviruses) agents. Based on a comparative approach in two cave-dwelling bat species and high-throughput sequencing of the 16S rRNA gene, we demonstrated a clear signature in microbiota changes over the reproduction season, consistent across the multiple body habitats investigated, and associated with the sex, age and reproductive condition of bats. We observed in parallel highly dynamic shedding patterns for both bacteria and viruses, but did not find a significant association between viral shedding and bacterial microbiota composition. Indeed, only Leptospira shedding was associated with alterations in both the diversity and composition of the urinary microbiota. These results illustrate how seasonal reproduction in bats substantially affects microbiota composition and infection dynamics, and have broad implications for the understanding of disease ecology in important reservoir hosts, such as bats.

A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa.

Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.

The excreted microbiota of bats: evidence of niche specialisation based on multiple body habitats.

Animal-associated microbiotas form complex communities, which play crucial functions for their host, including susceptibility to infections. Despite increasing attention to bats as reservoirs of zoonotic pathogens, their microbiota is poorly documented, especially for samples potentially implicated in pathogen transmission such as urine and saliva. Here, using low-biomass individual samples, we examined the composition and structure of bacterial communities excreted by insectivorous bats, focusing on three body habitats (saliva, urine and faeces). We show that niche specialisation occurs as bacterial community composition was distinct across body habitats with the majority of phylotypes being body habitat specific. Our results suggest that urine harbours more diverse bacterial communities than saliva and faeces and reveal potentially zoonotic bacteria such as Leptospira, Rickettsia, Bartonella and Coxiella in all body habitats. Our study emphasised that, in addition to the traditional use of gut-associated samples such as faeces, both urine and saliva are also of interest because of their diverse microbiota and the potential transmission of pathogenic bacteria. Our results represent a critical baseline for future studies investigating the interactions between microbiota and infection dynamics in bats.

Diversity of Bartonella and Rickettsia spp. in Bats and Their Blood-Feeding Ectoparasites from South Africa and Swaziland.

In addition to several emerging viruses, bats have been reported to host multiple bacteria but their zoonotic threats remain poorly understood, especially in Africa where the diversity of bats is important. Here, we investigated the presence and diversity of Bartonella and Rickettsia spp. in bats and their ectoparasites (Diptera and Siphonaptera) collected across South Africa and Swaziland. We collected 384 blood samples and 14 ectoparasites across 29 different bat species and found positive samples in four insectivorous and two frugivorous bat species, as well as their Nycteribiidae flies. Phylogenetic analyses revealed diverse Bartonella genotypes and one main group of Rickettsia, distinct from those previously reported in bats and their ectoparasites, and for some closely related to human pathogens. Our results suggest a differential pattern of host specificity depending on bat species. Bartonella spp. identified in bat flies and blood were identical supporting that bat flies may serve as vectors. Our results represent the first report of bat-borne Bartonella and Rickettsia spp. in these countries and highlight the potential role of bats as reservoirs of human bacterial pathogens.