Using “omics” and integrated multi-omits approaches to guide probiotic selection to mitigate chytridiomycosis and other emerging infectious diseases

Emerging infectious diseases in wildlife are responsible for massive population declines. In amphibians, chytridiomycosis caused by Batrachochytrium dendrobatidis, Bd, has severely affected many amphibian populations and species around the world. One promising management strategy is probiotic bioaugmentation of antifungal bacteria on amphibian skin. In vivo experimental trials using bioaugmentation strategies have had mixed results, and therefore a more informed strategy is needed to select successful probiotic candidates. Metagenomic, transcriptomic, and metabolomic methods, colloquially called “omics,” are approaches that can better inform probiotic selection and optimize selection protocols. The integration of multiple omic data using bioinformatic and statistical tools and in silico models that link bacterial community structure with bacterial defensive function can allow the identification of species involved in pathogen inhibition. We recommend using 16S rRNA gene amplicon sequencing and methods such as indicator species analysis, the Kolmogorov–Smirnov Measure, and co-occurrence networks to identify bacteria that are associated with pathogen resistance in field surveys and experimental trials. In addition to 16S amplicon sequencing, we recommend approaches that give insight into symbiont function such as shotgun metagenomics, metatranscriptomics, or metabolomics to maximize the probability of finding effective probiotic candidates, which can then be isolated in culture and tested in persistence and clinical trials. An effective mitigation strategy to ameliorate chytridiomycosis and other emerging infectious diseases is necessary; the advancement of omic methods and the integration of multiple omic data provide a promising avenue toward conservation of imperiled species

Preparing for a Bsal invasion into North America has improved multi-sector readiness

Western palearctic salamander susceptibility to the skin disease caused by the amphibian chytrid fungus Batrachochytrium salamandrivorans (Bsal) was recognized in 2014, eliciting concerns for a potential novel wave of amphibian declines following the B. dendrobatidis (Bd) chytridiomycosis global pandemic. Although Bsal had not been detected in North America, initial experimental trials supported the heightened susceptibility of caudate amphibians to Bsal chytridiomycosis, recognizing the critical threat this pathogen poses to the North American salamander biodiversity hotspot. Here, we take stock of 10 years of research, collaboration, engagement, and outreach by the North American Bsal Task Force. We summarize main knowledge and conservation actions to both forestall and respond to Bsal invasion into North America. We address the questions: what have we learned; what are current challenges; and are we ready for a more effective reaction to Bsal’s eventual detection? We expect that the many contributions to preemptive planning accrued over the past decade will pay dividends in amphibian conservation effectiveness and can inform future responses to other novel wildlife diseases and extreme threats

Potential risk of Batrachochytrium salamandrivorans in Mexico.

The recent decline in populations of European salamanders caused by the chytrid fungus Batrachochytrium salamandrivorans (Bsal) has generated worldwide concern, as it is a major threat to amphibians. Evaluation of the areas most suitable for the establishment of Bsal combined with analysis of the distribution of salamander species could be used to generate and implement biosecurity measures and protect biodiversity at sites with high salamander diversity. In this study, we identified the areas most suitable for the establishment of Bsal in Mexico. Mexico has the second-highest salamander species diversity in the world; thus, we identified areas moderately to highly suitable for the establishment of Bsal with high salamander diversity as potential hotspots for surveillance. Central and Southern Mexico were identified as high-risk zones, with 13 hotspots where 30% of Mexican salamander species occur, including range-restricted species and endangered species. We propose that these hotspots should be thoroughly monitored for the presence of Bsal to prevent the spread of the pathogen if it is introduced to the country

Temporal Variation of the Skin Bacterial Community and Batrachochytrium dendrobatidis Infection in the Terrestrial Cryptic Frog Philoria loveridgei

In animals and plants, symbiotic bacteria can play an important role in disease resistance of host and are the focus of much current research. Globally, amphibian population declines and extinctions have occurred due to chytridiomycosis, a skin disease caused by the pathogen Batrachochytrium dendrobatidis (Bd). Currently amphibian skin bacteria are increasingly recognized as important symbiont communities with a relevant role in the defense against pathogens, as some bacteria can inhibit the growth of B. dendrobatidis. This study aims to document the B. dendrobatidis infection status of wild populations of a terrestrial cryptic frog (Philoria loveridgei), and to determine whether infection status is correlated with changes in the skin microbial communities. Skin samples of P. loveridgei were collected along an altitudinal range within the species distribution in subtropical rainforests in southeast Australia. Sampling was conducted in two years during two breeding seasons with the first classified as a "La Niña" year. We used Taqman real-time PCR to determine B. dendrobatidis infection status and 16S amplicon sequencing techniques to describe the skin community structure. We found B. dendrobatidis-positive frogs only in the second sampling year with low infection intensities, and no correlation between B. dendrobatidis infection status and altitude, frog sex or size. Skin bacterial diversity was significantly higher in P. loveridgei frogs sampled in the 1st year than in the 2nd year. In addition, 7.4% of the total OTUs were significantly more abundant in the 1st year compared to the 2nd year. We identified 67 bacterial OTUs with a significant positive correlation between infection intensity and an OTU's relative abundance. Forty-five percent of these OTUs belonged to the family Enterobacteriaceae. Overall, temporal variation was strongly associated with changes in B. dendrobatidis infection status and bacterial community structure of wild populations of P. loveridgei. © 2017 Familiar López, Rebollar, Harris, Vredenburg and Hero

Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence

Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes

Temporal Variation of the Skin Bacterial Community and Batrachochytrium dendrobatidis Infection in the Terrestrial Cryptic Frog Philoria loveridgei

In animals and plants, symbiotic bacteria can play an important role in disease resistance of host and are the focus of much current research. Globally, amphibian population declines and extinctions have occurred due to chytridiomycosis, a skin disease caused by the pathogen Batrachochytrium dendrobatidis (Bd). Currently amphibian skin bacteria are increasingly recognized as important symbiont communities with a relevant role in the defense against pathogens, as some bacteria can inhibit the growth of B. dendrobatidis. This study aims to document the B. dendrobatidis infection status of wild populations of a terrestrial cryptic frog (Philoria loveridgei), and to determine whether infection status is correlated with changes in the skin microbial communities. Skin samples of P. loveridgei were collected along an altitudinal range within the species distribution in subtropical rainforests in southeast Australia. Sampling was conducted in two years during two breeding seasons with the first classified as a “La Niña” year. We used Taqman real-time PCR to determine B. dendrobatidis infection status and 16S amplicon sequencing techniques to describe the skin community structure. We found B. dendrobatidis-positive frogs only in the second sampling year with low infection intensities, and no correlation between B. dendrobatidis infection status and altitude, frog sex or size. Skin bacterial diversity was significantly higher in P. loveridgei frogs sampled in the 1st year than in the 2nd year. In addition, 7.4% of the total OTUs were significantly more abundant in the 1st year compared to the 2nd year. We identified 67 bacterial OTUs with a significant positive correlation between infection intensity and an OTU’s relative abundance. Forty-five percent of these OTUs belonged to the family Enterobacteriaceae. Overall, temporal variation was strongly associated with changes in B. dendrobatidis infection status and bacterial community structure of wild populations of P. loveridgei

Seasonal Changes in a Maize-Based Polyculture of Central Mexico Reshape the Co-occurrence Networks of Soil Bacterial Communities

The milpa is a traditional maize-based polyculture in Mexico that is typically practiced as rainfed agriculture. Because milpa cultivation has been practiced over a vast range of environmental and cultural conditions, this agroecosystem is recognized as an important repository of biological and cultural diversity. As for any agroecosystem, the relationship between plant development and the biogeochemical processes of the soil is critical. Although the milpa has been studied from different perspectives, the diversity and structure of microbial communities within milpa soils remain largely unexplored. In this study, we surveyed a milpa system in Central Mexico across cropping season: before planting (dry season; t1), during the early growth of plants (onset of the rainy season; t2), and before harvest (end of the rainy season; t3). In order to examine changes in community structure through time, we characterized bacterial diversity through high-throughput sequencing of 16S rRNA gene amplicons and recorded the nutrient status of multiple (5–10) soil samples from our milpa plots. We estimated microbial diversity from a total of 90 samples and constructed co-occurrence networks. Although we did not find significant changes in diversity or composition of bacterial communities across time, we identified significant rearrangements in their co-occurrence network structure. We found particularly drastic changes between the first and second time points. Co-occurrence analyses showed that the bacterial community changed from a less structured network at (t1) into modules with a non-random composition of taxonomic groups at (t2). We conclude that changes in bacterial communities undetected by standard diversity analyses can become evident when performing co-occurrence network analyses. We also postulate possible functional associations among keystone groups suggested by biogeochemical processes. This study represents the first contribution on soil microbial diversity of a maize-based polyculture and shows its dynamic nature in short-term scales