Advances in understanding bat infection dynamics across biological scales.

Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.

A Faithful Gut: Core Features of Gastrointestinal Microbiota of Long-Distance Migratory Bats Remain Stable despite Dietary Shifts Driving Differences in Specific Bacterial Taxa.

Migratory animals live in a world of constant change. Animals undergo many physiological changes preparing themselves for the migration. Although this field has been studied extensively over the last decades, we know relatively little about the seasonal changes that occur in the microbial communities that these animals carry in their guts. Here, we assessed the V4 region of the 16S rRNA high-throughput sequencing data as a proxy to estimate microbiome diversity of tequila bats from fecal pellets and evaluate how the natural process of migration shapes the microbiome composition and diversity. We collected samples from individual bats at two localities in the dry forest biome (Chamela and Coquimatlán) and one site at the endpoint of the migration in the Sonoran Desert (Pinacate). We found that the gut microbiome of the tequila bats is dominated largely by Firmicutes and Proteobacteria. Our data also provide insights on how microbiome diversity shifts at the same site in consecutive years. Our study has demonstrated that both locality and year-to-year variation contribute to shaping the composition, overall diversity, and "uniqueness" of the gut microbiome of migratory nectar-feeding female bats, with localities from the dry forest biome looking more like each other compared to those from the desert biome. In terms of beta diversity, our data show a stratified effect in which the samples' locality was the strongest factor influencing the gut microbiome but with significant variation between consecutive years at the same locality. IMPORTANCE Migratory animals live in a world of constant change. The whole-body ecosystem needs a strong adapting capacity to thrive despite the changes. Our study used next-generation sequencing to determine how gut microbial change along the migratory path of the nectar-feeding tequila bats. The study of the gut microbiome is a great tool that can provide important insights that are relevant not just for management and conservation but also an initial investigation of the extent of the adaptation and preparedness of the individual animals, with respect not just to their current environment but also to all the environments involved in their yearly cycle.

Setting the Terms for Zoonotic Diseases: Effective Communication for Research, Conservation, and Public Policy.

Many of the world's most pressing issues, such as the emergence of zoonotic diseases, can only be addressed through interdisciplinary research. However, the findings of interdisciplinary research are susceptible to miscommunication among both professional and non-professional audiences due to differences in training, language, experience, and understanding. Such miscommunication contributes to the misunderstanding of key concepts or processes and hinders the development of effective research agendas and public policy. These misunderstandings can also provoke unnecessary fear in the public and have devastating effects for wildlife conservation. For example, inaccurate communication and subsequent misunderstanding of the potential associations between certain bats and zoonoses has led to persecution of diverse bats worldwide and even government calls to cull them. Here, we identify four types of miscommunication driven by the use of terminology regarding bats and the emergence of zoonotic diseases that we have categorized based on their root causes: (1) incorrect or overly broad use of terms; (2) terms that have unstable usage within a discipline, or different usages among disciplines; (3) terms that are used correctly but spark incorrect inferences about biological processes or significance in the audience; (4) incorrect inference drawn from the evidence presented. We illustrate each type of miscommunication with commonly misused or misinterpreted terms, providing a definition, caveats and common misconceptions, and suggest alternatives as appropriate. While we focus on terms specific to bats and disease ecology, we present a more general framework for addressing miscommunication that can be applied to other topics and disciplines to facilitate more effective research, problem-solving, and public policy.

Jumping the green wall: The use of PNA-DNA clamps to enhance microbiome sampling depth in wildlife microbiome research.

As microbiome research moves away from model organisms to wildlife, new challenges for microbiome high-throughput sequencing arise caused by the variety of wildlife diets. High levels of contamination are commonly observed emanating from the host (mitochondria) or diet (chloroplast). Such high contamination levels affect the overall sequencing depth of wildlife samples thus decreasing statistical power and leading to poor performance in downstream analysis. We developed an amplification protocol utilizing PNA-DNA clamps to maximize the use of resources and to increase the sampling depth of true microbiome sequences in samples with high levels of plastid contamination. We chose two study organisms, a bat (Leptonyteris yerbabuenae) and a bird (Mimus parvulus), both relying on heavy plant-based diets that sometimes lead to traces of plant-based fecal material producing high contamination signals from chloroplasts and mitochondria. On average, our protocol yielded a 13-fold increase in bacterial sequence amplification compared with the standard protocol (Earth Microbiome Protocol) used in wildlife research. For both focal species, we were able to increase significantly the percentage of sequences available for downstream analyses after the filtering of plastids and mitochondria. Our study presents the first results obtained by using PNA-DNA clamps to block the PCR amplification of chloroplast and mitochondrial DNA from the diet in the gut microbiome of wildlife. The method involves a cost-effective molecular technique instead of the filtering out of unwanted sequencing reads. As 33% and 26% of birds and bats, respectively, have a plant-based diet, the tool that we present here will optimize the sequencing and analysis of wild microbiomes.

Effectiveness of protected areas for representing species and populations of terrestrial mammals in Costa Rica.

Costa Rica has one of the greatest percentages (26%) of protected land in the world. The National Protected Areas System (NPAS) of Costa Rica was established in 1976 and currently includes >190 protected areas within seven different protection categories. The effectiveness of the NPAS to represent species, populations, and areas with high species richness has not been properly evaluated. Such evaluations are fundamental to understand what is necessary to strengthen the NPAS and better protect biodiversity. We present a novel assessment of NPAS effectiveness in protecting mammal species. We compiled the geographical ranges of all terrestrial Costa Rican mammals then determined species lists for all protected areas and the estimated proportion of each species' geographic range protected. We also classified mammal species according to their conservation status using the IUCN Red List of Threatened Species. We found almost complete representation of mammal species (98.5%) in protected areas, but low relative coverage (28.3% on average) of their geographic ranges in Costa Rica and 25% of the species were classified as underprotected according to a priori representation targets. Interestingly, many species-rich areas are not protected, and at least 43% of cells covering the entire country are not included in protected areas. Though protected areas in Costa Rica represent species richness well, strategic planning for future protected areas to improve species complementarity and range protection is necessary. Our results can help to define sites where new protected areas can have a greater impact on mammal conservation, both in terms of species richness and range protection.

Dinámica espacio-temporal de organismos precursores de marea roja en la costa Pacífica de América del Norte y Centroamérica / Spatial-temporal dynamics of red tide precursor organisms at the Pacific coast of North and Central America

La región costera del Pacífico de Centro y Norte America ha sido afectada de manera frecuente por fenómenos que se denominan proliferaciones algales nocivas o en inglés, "Harmful Algal Blooms" (HAB). A pesar de la gran cantidad de efectos en la salud pública, las actividades económicas y el medio ambiente, aún existe una abrumadora carencia de información en el tema. Esto no permite establecer si las causas principales de este evidente aumento en el número e intensidad de los eventos son naturales o antropogénicas. La incrementada utilización de las zonas costeras para actividades humanas encuentra paralelo en el denominado cambio climático, lo que dificulta discriminar entre la posible influencia de estos dos fenómenos. Series de datos de larga duración en regiones reducidas, así como las observaciones esporádicas realizadas cuando se presenta algún evento, nos permite comparar regímenes climáticos, condiciones geográficas, disponibilidad de nutrientes (incluyendo la eutroficación) y parámetros oceanográficos que promueven o permiten el desarrollo y mantenimiento de las proliferaciones, haciendo evidentes cambios drásticos en la biodiversidad y la biogeografía de los organismos productores de HAB

The Pacific coast of Central and North America has long been and still is impacted by the flourishing of microalgal populations known as Harmful Algal Blooms (HABs). The organisms that have caused recent HABs episodes in the region are among others, Gymnodinium catenatum, Pyrodinium bahamense var. compressum, and recently Cochlodinium cf. catenatum. In spite of the accumulated effects on the human health, the economic activities and the environment, scarce information is available on the subject. The augmented use of coastal zones for human activities is also paralleled by increased awareness of global climate changes. Thus, it is not an easy task to discriminate anthropogenic or natural phenomena, or both, as the major driving forces. The long-term data sets available for limited regions, as well as some sporadic observations during notorious blooms, allowed us to discriminate major changes in the biodiversity and biogeography of HAB organisms. Main changes refer to number of events, covered area, duration and frequency, number of blooming species and appearance of not previously reported harmful taxa. The variables more clearly related to these dynamic phenomena, seems to be sea surface temperature and wind force, but it is not yet possible to weight their contributions. The participation of rain is not fully evaluated to date. The collaborative communication among small-budget monitoring operations in the region allowed to "pass the voice" about peaking concentrations of HAB organisms, diminishing the risk of poisoning

[Spatial-temporal dynamics of red tide precursor organisms at the Pacific coast of North and Central America]. / Dinámica espacio-temporal de organismos precursores de marea roja en la costa Pacífica de América del Norte y Centroamérica.

The Pacific coast of Central and North America has long been and still is impacted by the flourishing of microalgal populations known as Harmful Algal Blooms (HABs). The organisms that have caused recent HABs episodes in the region are among others, Gymnodinium catenatum, Pyrodinium bahamense var. compressum, and recently Cochlodinium cf. catenatum. In spite of the accumulated effects on the human health, the economic activities and the environment, scarce information is available on the subject. The augmented use of coastal zones for human activities is also paralleled by increased awareness of global climate changes. Thus, it is not an easy task to discriminate anthropogenic or natural phenomena, or both, as the major driving forces. The long-term data sets available for limited regions, as well as some sporadic observations during notorious blooms, allowed us to discriminate major changes in the biodiversity and biogeography of HAB organisms. Main changes refer to number of events, covered area, duration and frequency, number of blooming species and appearance of not previously reported harmful taxa. The variables more clearly related to these dynamic phenomena, seems to be sea surface temperature and wind force, but it is not yet possible to weight their contributions. The participation of rain is not fully evaluated to date. The collaborative communication among small-budget monitoring operations in the region allowed to "pass the voice" about peaking concentrations of HAB organisms, diminishing the risk of poisoning.

[Red tide bloom produced by Lingulodinium polyedrum (Peridiniales, Dinophyceae) in Bahía Culebra, Papagayo Gulf, Costa Rica]. / Marea roja producida por Lingulodinium polyedrum (Peridiniales, Dinophyceae) en Bahía Culebra, Golfo de Papagayo, Costa Rica.

This is the first record of the dinoflagellate Lingulodinium polyedrum in a red tide bloom in the North Pacific coast of Costa Rica. The sample was collected on April 2000 at Culebra Bay, Gulf of Papagayo, from a patch of aproximatly 2000 m2, which produced a red discoloration of the water and a peculiar strong odor. This species produces spherical hypnocysts that may remain for decades when dark or anoxic conditions are present; L. polyedrum had been associated with the production of paralyzing toxins such as saxitoxins and yessotoxins. A second smaller patch was observed close Panama beach, into the bay, where we found seven puffer fish (Diodontidae) and two lobsters dead in the sand. It is important to develop a monitoring program to identify seasonal behavior of this species and ameliorate its impact on coastal human communities.

[Paralytic shellfish poisoning by Spondylus calcifer contaminated with Pyrodinium bahamense, Costa Rica, 1989-1990]. / Intoxicación paralítica por mariscos (IPM) por Spondylus calcifer contaminado con Pyrodinium bahamense, Costa Rica, 1989-1990.

This paper describes an outbreak of paralytic shellfish poisoning (PSP), affecting human populations on the Pacific Coast of Costa Rica in October 1989. Numbness in arms, face and legs occurred 30 to 45 minutes after ingestion of the large clam Spondylus calcifer. Paralysis of legs and respiratory symptoms followed, often persisting for one week. Large amounts of the dinoflagellate Pyrodinium bahamense were found in the intestine of the mollusk. A toxin was detected in crude or filtered and heated macerates of intestine, muscle, mantle and hepatopancreas of S. calcifer, and to a lesser extent Tagelus sp., by injection of its crude or diluted extracts in white mice. The effects in mice consisted in paralysis and asphyxia generally leading to death in less than 5 minutes, compatible with saxitoxin. Mice were killed by the toxin in macerates diluted 1:100 to 1:1000. No toxin was detected in Anadara tuberculosa (Bivalvia) or in peneids. Prevention rests on intersectoral actions between state and private sectors in charge of fishing, distribution and marketing of shellfish, as well as on education of the population at large.