Tracking, Synthesizing, and Sharing Global Batrachochytrium Data at AmphibianDisease.org.

Michelle S Koo,Kathryn L Ronnenberg,Deanna H Olson,Vance T Vredenburg,David B Wake,John B Deck

doi:10.3389/fvets.2021.728232

Abstract

Emerging infectious diseases have been especially devastating to amphibians, the most endangered class of vertebrates. For amphibians, the greatest disease threat is chytridiomycosis, caused by one of two chytridiomycete fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). Research over the last two decades has shown that susceptibility to this disease varies greatly with respect to a suite of host and pathogen factors such as phylogeny, geography (including abiotic factors), host community composition, and historical exposure to pathogens; yet, despite a growing body of research, a comprehensive understanding of global chytridiomycosis incidence remains elusive. In a large collaborative effort, Bd-Maps was launched in 2007 to increase multidisciplinary investigations and understanding using compiled global Bd occurrence data (Bsal was not discovered until 2013). As its database functions aged and became unsustainable, we sought to address critical needs utilizing new technologies to meet the challenges of aggregating data to facilitate research on both Bd and Bsal. Here, we introduce an advanced central online repository to archive, aggregate, and share Bd and Bsal data collected from around the world. The Amphibian Disease Portal (https://amphibiandisease.org) addresses several critical community needs while also helping to build basic biological knowledge of chytridiomycosis. This portal could be useful for other amphibian diseases and could also be replicated for uses with other wildlife diseases. We show how the Amphibian Disease Portal provides: (1) a new repository for the legacy Bd-Maps data; (2) a repository for sample-level data to archive datasets and host published data with permanent DOIs; (3) a flexible framework to adapt to advances in field, laboratory, and informatics technologies; and (4) a global aggregation of Bd and Bsal infection data to enable and accelerate research and conservation. The new framework for this project is built using biodiversity informatics best practices and metadata standards to ensure scientific reproducibility and linkages across other biological and biodiversity repositories.

Highlights

The amphibian vertebrate lineage evolved over 360 million years ago, and has survived multiple mass extinction events, yet today amphibians are the most endangered class of vertebrates and may be harbingers of a new sixth mass-extinction event [1]
We created a middleware application programming interface (API) that communicates with the GEOME “backend.” Together, they comprise of the frontend, API, and backend components forming the Amphibian Disease Portal (Figure 1); all code is open-source and available on Github in two code repositories licensed as GNU General Public License [33], one for its frontend website and one for the API
When amphibians were first reported to be mysteriously declining and disappearing in the late 1970s and early 1980s in Australia, Central America, and western North America [45], few imagined so much of the decline could be driven by epizootics caused by a single pathogen [(46, 47) but see [48]]

Summary

Introduction

The amphibian vertebrate lineage evolved over 360 million years ago, and has survived multiple mass extinction events, yet today amphibians are the most endangered class of vertebrates and may be harbingers of a new sixth mass-extinction event [1]. Chytridiomycosis is a potentially lethal amphibian skin disease caused by one of two chytridiomycete fungal pathogens, Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal). A comprehensive understanding of the lethal, sublethal, and benign effects of these fungal pathogens and their long-term effects on vertebrates in class Amphibia is still incomplete. Chytridiomycosis has raised alarms and the World Organization of Animal Health (OIE) has listed Bd and Bsal as reportable pathogens [10] on the global stage. The discovery of chytridiomycosis and the documentation of its impacts on amphibians have fundamentally altered the way scientists view emerging infectious diseases, their contributions to global biodiversity losses, and biodiversity conservation approaches to emerging disease threats [3, 8, 16]

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