Neotropical Bats from Costa Rica harbour Diverse Coronaviruses

Bats are hosts of diverse coronaviruses (CoVs) known to potentially cross the host–species barrier. For analysing coronavirus diversity in a bat species‐rich country, a total of 421 anal swabs/faecal samples from Costa Rican bats were screened for CoV RNA‐dependent RNA polymerase (RdRp) gene sequences by a pancoronavirus PCR. Six families, 24 genera and 41 species of bats were analysed. The detection rate for CoV was 1%. Individuals (n = 4) from four different species of frugivorous (Artibeus jamaicensis, Carollia perspicillata and Carollia castanea) and nectivorous (Glossophaga soricina) bats were positive for coronavirus‐derived nucleic acids. Analysis of 440 nt. RdRp sequences allocated all Costa Rican bat CoVs to the α‐CoV group. Several CoVs sequences clustered near previously described CoVs from the same species of bat, but were phylogenetically distant from the human CoV sequences identified to date, suggesting no recent spillover events. The Glossophaga soricina CoV sequence is sufficiently dissimilar (26% homology to the closest known bat CoVs) to represent a unique coronavirus not clustering near other CoVs found in the same bat species so far, implying an even higher CoV diversity than previously suspected.     

Dramatic decline in bat species richness in Singapore, with implications for Southeast Asia

Literature searches and recent surveys of the bat fauna of Singapore indicate that of the 24 species of Microchiroptera and six species of Megachiroptera documented for this small equatorial island just 15 and 5, respectively, are still present. These recorded declines in chiropteran species richness almost certainly understate the true losses as extensive land transformation/habitat loss (>95%) and biota loss occurred early in Singapore’s colonial history before comprehensive surveys of bats were made. In an effort to reconstruct the pre-settlement bat fauna, we inferred an upper bound of pre-settlement species richness using a checklist from a well-known bat assemblage in neighbouring Peninsular Malaysia, and a lower bound based on species common to Peninsular Malaysia, Borneo and Sumatra. The Singapore records were compared with these two species list predictions. Based on this analysis, we infer that between 60 and 72 species would have inhabited Singapore before 1819. We also estimate that between 33% (based on the confirmed inventory) and 72% of the species (based on the upper-bound estimate of species richness) are now locally extinct. For Microchiroptera the data suggest that the documented local extinction rate of 38% may project to between 69% and 75%. Forest-dependant bats are particularly affected and comprise a much lower proportion of the bat fauna than is seen in intact forest in Peninsular Malaysia. All hipposiderids and 40% of the documented rhinolophid taxa have been lost and almost half (6) of the surviving microchiropteran species are locally endangered. Projected local extinction rates for Megachiroptera raise the documented value (17%) to about 60%, with most of the survivors being widespread species known to forage in cultivated or secondary forest habitats or to commute long distances between fragmented resources. The dramatic decline in Singapore bat species richness and a concomitant change in chiropteran guild and trophic structure (Microchiroptera vs. Megachiroptera) reflect patterns of diversity change seen elsewhere in the region in response to loss of forest habitat. In Singapore, the decline in diversity (species richness and abundances) for both mega- and microbats may also relate to urbanisation and deliberate or accidental destruction of bats and their roost sites in a land that has one of the highest human population densities on the planet. Although these losses (actual and inferred) represent a microcosm of mainly local extinctions, a wider geographical extrapolation over the 21st century indicates that heavy deforestation in progress in Southeast Asia might be expected to lead to extinction of many bat taxa, with upper-bound estimates of regional species losses exceeding 40% and global extirpation anticipated for at least 23% of Southeast Asia’s bat fauna by 2100.     

Bat activity on riparian zones and upper slopes in Australian timber production forests and the effectiveness of riparian buffers

Unlogged buffers are used to ameliorate impacts to riparian areas in timber production forests. One function of these buffers is to protect the biodiversity of riparian areas. We measured bat activity in buffered streams with ultrasonic detectors across four different stream orders in logged, regrowth and mature forests (60 sites). Bat activity, foraging rates and species richness were similar in buffered streams surrounded by logged, regrowth and mature forests, suggesting that riparian areas effectively provide habitat for foraging and commuting bats in selectively logged forests. Vespadelus pumilus was the only species that responded to logging history, with decreased activity in mature forests. We found higher activity on larger rather than smaller order streams, a pattern also not affected by logging history. Bat activity along paired forest trail flyways on upper slopes (60 sites) was measured simultaneously with riparian flyway activity (for a total of 120 sites) to determine the importance of riparian areas relative to other available flyways. Activity was higher on upper slopes than on small streams, but similar to levels on larger streams. Total foraging activity was similar between riparian zones and upper slopes. Upper slopes contained higher species diversity, with Chalinolobus gouldii, Miniopterus schreibersii, Mormopterus norfolkensis, Scotorepens sp., Vespadelus pumilus and, to a lesser extent, Vespadelus darlingtoni detected more often than along streams. Other species (Rhinolophus megaphyllus, Nyctophilus spp. and Miniopterus australis) were not affected by topography. Estimates of total vegetation cover and, in particular, rainforest cover, were negatively associated with bat activity, highlighting the need for management of forest ‘clutter’ in regrowth forests for a suite of bat species. Streams and forest trails provide areas of lower clutter, which assist in maintaining high species diversity in regrowth forests. Our results support the use of riparian buffers, and point to the need for greater recognition of tracks on upper slopes as important habitat.     

Bat diversity in montane rainforest and shaded coffee under different management regimes in southeastern Chiapas, Mexico

Differences in alpha and beta bat diversity among montane rainforest and five shaded coffee plantations under different management regimes, as well as some environmental factors and vegetation parameters influencing bat richness, were evaluated for the first time in southeastern Chiapas, Mexico. In each site, bats were captured every 2 months from March 2004 to July 2005, with six mist-nets, during two nights, using the capture-recapture method. We captured 2970 individuals of 43 bat species. Montane rainforest had the greatest alpha diversity (H′ = 2.681; n = 37), whereas alpha diversity was similar among coffee plantations (H′ = 2.229-2.364; n = 23-26). The number of frugivorous and nectarivorous species was similar among the sites; the greatest exchange in species composition (beta diversity) occurred for insectivorous bats, which reduce their number in coffee plantations as pesticides are incorporated. Bat richness species was significantly related to the number of vegetation strata, height, and cover of trees. We suggest that coffee plantations could act as corridors, facilitating connection among different elements of the landscape in the Sierra Madre de Chiapas for some frugivorous and nectarivorous bats.     

Location of roosts of the lesser long-eared bat Nyctophilus geoffroyi and Gould's wattled bat Chalinolobus gouldii in a fragmented landscape in south-eastern Australia

The location of roosts of two species of vespertilionid bats, the lesser long-eared bat (Nyctophilus geoffroyi) and Gould’s wattled bat (Chalinolobus gouldii), was investigated in a remnant vegetation-farmland mosaic and adjacent floodplain forest in south-eastern Australia. A total of 45 individuals of N. geoffroyi and 27 C. gouldii were fitted with radio transmitters, which resulted in the location of 139 and 89 roosts respectively. Selection of roosting habitat showed both inter- and intra-specific differences. At the landscape level, locations of roosts used by male and female N. geoffroyi differed markedly. Most males roosted in the farmland mosaic within 3 km (mean 1.9±2.9 km) of where they were captured while foraging in remnant vegetation. In contrast, roost sites of females were predominantly in the floodplain forest, 6-12 km from their capture site in farmland (mean for all females, 6.7±2.9 km). All maternity roosts were in the extensive floodplain forest, 4-10 km from foraging areas. Distances moved by this species were greater than previously recorded and further than predicted by flight morphology. Most C. gouldii roosted in the floodplain forest, 4-10 km from their capture site (6.9±1.6 km). Within the floodplain forest, both species roosted in areas that had higher densities of hollow-bearing trees than generally available; dead hollow-bearing trees for N. geoffroyi and large, live trees for C. gouldii. The scale of movements undertaken by these species means that they can obtain resources from multiple landscape elements. Both species used different habitats for roosting and foraging despite the energetic costs of commuting relatively large distances. Conservation of bat populations in rural environments needs to be considered at the landscape scale, with particular attention to identifying landscape elements that provide key resources.     

Clostridioides difficile in bat guano

Bats are associated with the emergence of several mammalian diseases. Their sessional migration, and tendency to form large colonies in close proximity to human habitats enables effective intra- and inter-species transmission of pathogens. Clostridioides difficile is an important enteric pathogen in humans and animals; however, the source of its dissemination in the population is unknown. The purpose of this study was to determine the prevalence of C. difficile in bats, and to characterize C. difficile isolates.Feces (n = 93) was sampled from bats during their migration across Europe. Eighteen samples (19.4%) were positive for C. difficile; ribotypes 078, 056, and a new ribotype CDB3 were identified.Clostridioides difficile ribotypes 078 and 056 are associated with human and animal diseases. The C. difficile prevalence and ribotypes in this study do not necessarily identify bats as a significant source, but more likely as an indicator of C. difficile perpetuation in the environment.     

Antimicrobial resistance in Escherichia coli isolates from frugivorous (Eidolon helvum) and insectivorous (Nycteris hispida) bats in Southeast Nigeria,with detection of CTX-M-15 producing isolates

Thirty-five Escherichia coli isolates obtained from the liver, spleen and intestines of 180 frugivorous and insectivorous bats were investigated for antimicrobial resistance phenotypes/genotypes, prevalence of Extended-Spectrum beta-lactamase (ESBL) production, virulence gene detection and molecular typing. Eight (22.9 %) of the isolates were multidrug resistant (MDR). Two isolates were cefotaxime-resistant, ESBL-producers and harbored the bla_CTX-M-15 gene; they belonged to ST10184-D and ST2178-B1 lineages. tet(A) gene was detected in all tetracycline-resistant isolates while int1 (n = 8) and bla_TEM (n = 7) genes were also found. Thirty-three of the E. coli isolates were assigned to seven phylogenetic groups, with B1 (45.7 %) being predominant. Three isolates were enteropathogenic E. coli (EPEC) pathovars, containing the eae gene (with the variants gamma and iota), and lacking stx1/stx2 genes. Bats in Nigeria are possible reservoirs of potentially pathogenic MDR E. coli isolates which may be important in the ecology of antimicrobial resistance at the human-livestock-wildlife-environment interfaces. The study reinforces the importance of including wildlife in national antimicrobial resistance monitoring programmes.     

Rabies virus and Histoplasma suramericanum coinfection in a bat from southeastern Brazil

Bats are essential to the global ecosystem, but their ability to harbour a range of pathogens has been widely discussed, as well as their role in the emergence and re‐emergence of infectious diseases. This paper describes the first report of coinfection by two zoonotic agents, rabies virus (RABV) and the fungus Histoplasma suramericanum in a bat. The bat was from the Molossus molossus species, and it was found during the daytime in the hallway of a public psychiatric hospital in a municipality in São Paulo State, southeastern Brazil. RABV infection was diagnosed by the direct fluorescent antibody test and mouse inoculation test. The fungus was isolated by in vitro culture. Both diagnoses were confirmed by molecular techniques. Phylogenetic analysis showed that the fungus isolate had proximity to H. suramericanum in the Lam B clade, while the RABV isolate was characterized in the Lasiurus cinereus lineage. Since the M. molossus bat was found in a peri‐urban transition area (urban/peri‐urban), the possibility of cross‐species transmission of this RABV lineage becomes more plausible, considering that this scenario may provide shelter for both M. molossus and L. cinereus. These are relevant findings since there has been an increase in bat populations in urban and peri‐urban areas, particularly due to environmental modifications and anthropogenic impacts on their habitat. Thus, the detection of two zoonotic agents in a bat found in a public hospital should raise awareness regarding the importance of systematic surveillance actions directed towards bats in urban areas.     

Habitat selection by the Mediterranean horseshoe bat, Rhinolophus euryale (Chiroptera: Rhinolophidae) in a rural area of southern Italy and implications for conservation

We studied habitat selection by Rhinolophus euryale in a rural area of southern Italy in 1998-2000 by radio-tracking. Two comparisons were carried out, one between habitat occurrence within individual home ranges and within the study area, the other between time spent in each foraging habitat and habitat occurrence within the home range. The first analysis showed that olive groves and conifer plantations were, respectively, the most and the least important habitats. The second analysis highlighted the importance of woodland for R. euryale, while urban sites, open areas and conifer plantations were avoided. We recommend that clearing of continuous, large areas of woodland for tree harvesting should be avoided. Conifers should not be used for reforestation. Urbanisation should be limited in the areas of greatest importance for the species, and linear landscape elements such as tree lines and hedgerows should be maintained.