The rapid worldwide emergence of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) is having a profound negative impact on biodiversity. However, global research efforts are fragmented and an overarching synthesis of global infection data is lacking. Here, we provide results from a community tool for the compilation of worldwide Bd presence and report on the analyses of data collated over a four-year period. Using this online database, we analysed: 1) spatial and taxonomic patterns of infection, including amphibian families that appear over- and under-infected; 2) relationships between Bd occurrence and declining amphibian species, including associations among Bd occurrence, species richness, and enigmatic population declines; and 3) patterns of environmental correlates with Bd, including climate metrics for all species combined and three families (Hylidae, Bufonidae, Ranidae) separately, at both a global scale and regional (U.S.A.) scale. These associations provide new insights for downscaled hypothesis testing. The pathogen has been detected in 52 of 82 countries in which sampling was reported, and it has been detected in 516 of 1240 (42%) amphibian species. We show that detected Bd infections are related to amphibian biodiversity and locations experiencing rapid enigmatic declines, supporting the hypothesis that greater complexity of amphibian communities increases the likelihood of emergence of infection and transmission of Bd. Using a global model including all sampled species, the odds of Bd detection decreased with increasing temperature range at a site. Further consideration of temperature range, rather than maximum or minimum temperatures, may provide new insights into Bd-host ecology. Whereas caution is necessary when interpreting such a broad global dataset, the use of our pathogen database is helping to inform studies of the epidemiology of Bd, as well as enabling regional, national, and international prioritization of conservation efforts. We provide recommendations for adaptive management to enhance the database utility and relevance.

/pdf/mapping-the-global-emergence-of-batrachochytrium-3oru1bdp6d.pdf

Mapping the Global Emergence of Batrachochytrium dendrobatidis, the Amphibian Chytrid Fungus

Efficient targeting of conserved cryptic epitopes of infectious agents by single domain antibodies. African trypanosomes as paradigm

The variable domain of the trypanosome variant surface glycoprotein (VSG) ILTat 1.24 has been shown by X-ray crystallography to resemble closely the structures of VSG MITat 1.2, despite their low sequence similarity. Specific structural features of these VSGs, including substitution of carbohydrate for an alpha-helix, can be found in other VSG sequences. Thus antigenic variation in trypanosomes is accomplished by sequence variation, not gross structural alteration; the extensive sequence differences among VSGs may be required for another reason, such as the avoidance of recognition by helper T cells. Additionally, VSG sequences are found to define families, within a VSG superfamily, which have evolved in the trypanosome genome.

A structural motif in the variant surface glycoproteins of Trypanosoma brucei

Summary
The past decade has seen an explosion in the development and application of models aimed at estimating species occurrence and occupancy dynamics while accounting for possible non-detection or species misidentification.
We discuss some recent occupancy estimation methods and the biological systems that motivated their development. Collectively, these models offer tremendous flexibility, but simultaneously place added demands on the investigator.
Unlike many mark–recapture scenarios, investigators utilizing occupancy models have the ability, and responsibility, to define their sample units (i.e. sites), replicate sampling occasions, time period over which species occurrence is assumed to be static and even the criteria that constitute ‘detection’ of a target species. Subsequent biological inference and interpretation of model parameters depend on these definitions and the ability to meet model assumptions.
We demonstrate the relevance of these definitions by highlighting applications from a single biological system (an amphibian–pathogen system) and discuss situations where the use of occupancy models has been criticized. Finally, we use these applications to suggest future research and model development.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12100

Advances and applications of occupancy models

Habitat loss and disease are main drivers of global amphibian declines, yet the interaction between them remains largely unexplored. Here we show that paradoxically, habitat loss is negatively associated with occurrence, prevalence, and infection intensity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in amphibian populations in the tropics. At a large spatial scale, increased habitat loss predicted lower disease risk in amphibian populations across Costa Rica and eastern Australia, even after jointly considering the effect of potential biotic and abiotic correlates. Lower host-species richness and suboptimal microclimates for Bd in disturbed habitats are potential mechanisms underlying this pattern. Furthermore, we found that anthropogenic deforestation practices biased to lowlands and natural vegetation remaining in inaccessible highlands explain increased Bd occurrence at higher elevations. At a smaller spatial scale, holding constant elevation, latitude, and macroclimate, we also found a negative relationship between habitat loss, and both Bd prevalence and infection intensity in frog populations in two landscapes of the Brazilian Atlantic Forest. Our results indicate that amphibians will be disproportionately affected by emerging diseases in pristine environments, and that, paradoxically, disturbed habitats may act as shelters from disease, but only for the very few species that can tolerate deforestation. Thus, tropical amphibian faunas are threatened both by destruction of natural habitats as well as increased disease in pristine forests. To curb further extinctions and develop effective mitigation and restoration programs we must look to interactions between habitat loss and disease, the two main factors at the root of global amphibian declines.

https://www.pnas.org/content/pnas/108/24/9893.full.pdf

Tropical amphibian populations experience higher disease risk in natural habitats

Batrachochytrium dendrobatidis is a fungal pathogen that is receiving attention around the world for its role in amphibian declines. Study of its occurrence patterns is hampered by false negatives: the failure to detect the pathogen when it is present. Occupancy models are a useful but currently underutilized tool for analyzing detection data when the probability of detecting a species is <1. We use occupancy models to evaluate hypotheses concerning the occurrence and prevalence of B. dendrobatidis and discuss how this application differs from a conventional occupancy approach. We found that the probability of detecting the pathogen, conditional on presence of the pathogen in the anuran population, was related to amphibian development stage, day of the year, elevation, and human activities. Batrachochytrium dendrobatidis was found throughout our study area but was only estimated to occur in 53.4% of 78 populations of native amphibians and 66.4% of 40 populations of nonnative Rana catesbeiana tested. We found little evidence to support any spatial hypotheses concerning the probability that the pathogen occurs in a population, but did find evidence of some taxonomic variation. We discuss the interpretation of occupancy model parameters, when, unlike a conventional occupancy application, the number of potential samples or observations is finite.

Using occupancy models to understand the distribution of an amphibian pathogen, Batrachochytrium dendrobatidis

Variable and conserved structural elements of trypanosome variant surface glycoproteins.

We found amphibian chytrid fungus (Bd = Batrachochytrium dendrobatidis) to be widespread within a coastal watershed at Point Reyes National Seashore, California and within two high elevation watersheds at Yosemite National Park, California Bd was associated with all six species that we sampled (Bufo boreas, B canorus, Pseudacris regilla, Rana draytonii, R sierrae, and Lithobates catesbeianus) For those species sampled at 10 or more sites within a watershed, the percentage of Bd-positive sites varied from a low of 207% for P regilla at one Yosemite watershed to a high of 796% for P regilla at the Olema watershed at Point Reyes At Olema, the percent of Bd-positive water bodies declined each year of our study (2005-2007) Because P regilla was the only species found in all watersheds, we used that species to evaluate habitat variables related to the sites where P regilla was Bd-positive At Olema, significant variables were year, length of shoreline (perimeter), percentage cover of rooted vegetation, and water depth At the two Yosemite watersheds, water depth, water temperature, and silt/mud were the most important covariates, though the importance of these three factors differed between the two watersheds The presence of Bd in species that are not declining suggests that some of the amphibians in our study were innately resistant to Bd, or had developed resistance after Bd became established

/pdf/amphibian-chytrid-fungus-batrachochytrium-dendrobatidis-in-3ae5nabd7g.pdf

Amphibian chytrid fungus (batrachochytrium dendrobatidis) in coastal and montane california, usa anurans

Incidence of the fungus Batrachochytrium dendrobatidis in amphibian populations along the northwest coast of North America

Increased reporting of amphibian malformations in North America has been noted with concern in light of reports that amphibian numbers and species are declining worldwide. Ribeiroia ondatrae has been shown to cause a variety of types of malformations in amphibians. However, little is known about the prevalence of R. ondatrae in North America. To aid in conducting field studies of Ribeiroia spp., we have developed a polymerase chain reaction (PCR)-based diagnostic. Herein, we describe the development of an accurate, rapid, simple, and cost-effective diagnostic for detection of Ribeiroia spp. infection in snails (Planorbella trivolvis). Candidate oligonucleotide primers for PCR were designed via DNA sequence analyses of multiple ribosomal internal transcribed spacer-2 regions from Ribeiroia spp. and Echinostoma spp. Comparison of consensus sequences determined from both genera identified areas of sequence potentially unique to Ribeiroia spp. The PCR reliably produced a diagnostic 290-base pair (bp) product in the presence of a wide concentration range of snail or frog DNA. Sensitivity was examined with DNA extracted from single R. ondatrae cercaria. The single-tube PCR could routinely detect less than 1 cercariae equivalent, because DNA isolated from a single cercaria could be diluted at least 1:50 and still yield a positive result via gel electrophoresis. An even more sensitive nested PCR also was developed that routinely detected 100 fg of the 290-bp fragment. The assay did not detect furcocercous cercariae of certain Schistosomatidae, Echinostoma sp., or Sphaeridiotrema globulus nor adults of Clinostomum sp. or Cyathocotyle bushiensis. Field testing of 137 P. trivolvis identified 3 positives with no overt environmental cross-reactivity, and results concurred with microscopic examinations in all cases.

David M. Reinitz

Papers

Using occupancy models to understand the distribution of an amphibian pathogen, Batrachochytrium dendrobatidis

Variable and conserved structural elements of trypanosome variant surface glycoproteins.

Amphibian chytrid fungus (batrachochytrium dendrobatidis) in coastal and montane california, usa anurans

Incidence of the fungus Batrachochytrium dendrobatidis in amphibian populations along the northwest coast of North America

A Ribeiroia spp. (class: Trematoda)--specific PCR-based diagnostic.