Underestimated ranges and overlooked refuges from amphibian chytridiomycosis

Aim

Accurately documenting and predicting declines and shifts in species’ distributions is fundamental for implementing effective conservation strategies and directing future research; species distribution models (SDM) have become a powerful tool for such work. Nevertheless, much of the data used to create these models are opportunistic and often violate some of their basic assumptions. We use amphibian declines and extinctions linked to the fungus Batrachochytrium dendrobatidis (Bd) to examine how sampling biases in data collection can affect what we know of this disease and its effect on amphibians in the wild.

Location

Queensland, Australia.

Methods

We developed a distribution model for Bd incorporating known locality records for Bd and a subset of climatic variables that should correctly characterize its distribution. We tested this (original) model with additional surveys, recorded new Bd observations in novel environments and reran the distribution model. We then investigated the difference between the original and new models, and used frog abundance and infection status data from two of these new localities to look at the susceptibility of the torrent frog Litoria nannotis to chytridiomycosis.

Results

While largely correct, the original SDM underestimated the distribution of Bd; sampling in ‘unsuitable’ drier environments discovered abundant populations of susceptible frogs with pathogen prevalences of up to 100%. The validation surveys further uncovered a new population of the frog Litoria lorica coexisting with the pathogen; this species was previously believed to be an extinct rain forest endemic.

Main conclusion

Our results indicate that SDMs constructed using opportunistically collected data can be biased if species are not at equilibrium with their environment or because environmental gradients have not been adequately sampled. For disease ecology, the better estimations of pathogen distribution may lead to the discovery of new populations persisting at the edge of their range, which has important implications for the conservation of species threatened by chytridiomycosis.

     

Vaccine-related mumps infections in Thailand and the identification of a novel mutation in the mumps fusion protein

An outbreak of nine cases of mumps was reported from a total of 97 vaccinated nursing students at two medical colleges in Thailand in 2010, 16–26 days after administration of MMR vaccine containing the L-Zagreb mumps strain. Symptoms ranged in severity from fever and parotid swelling to orchitis. Clinical samples were obtained from seven patients and three were suitable for further study.Sequencing confirmed that the SH gene of the mumps virus in the unpassaged clinical specimens was identical to the L-Zagreb SH gene in the vaccine. Further analysis of the viral genome identified nucleotide position 5170 as a novel mutation which corresponds to an amino acid change in the fusion protein.This study provides another virologically confirmed example of mumps resulting from the L-Zagreb vaccine strain.     

Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or “haplotypes.” However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics, and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here, we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.     

Role of emergent and submerged vegetation and algal communities on nutrient retention and management in a subtropical urban stormwater treatment wetland

A 4.6-ha urban stormwater treatment wetland complex in southwest Florida has been investigated for several years to understand its nutrient retention dynamics. This study investigates the role of aquatic vegetation, both submerged vegetation (such as benthic macrophytic and algal communities) and emergent plant communities, on changes in nutrient fluxes through the wetlands. Gross and net primary productivity of water column communities and net primary productivity of emergent macrophytes were used to estimate nutrient fluxes through vegetation in these wetlands using biannual biomass, nutrient concentrations of plant material, and areal coverage data. Emergent macrophyte net primary productivity was estimated as the difference between the increase of productivity during the wet season and the loss during the dry season which, in turn, suggested approximately 0.11g-N m^??2 y^??1 and 0.09g-P m^??2 yr^??2 being removed, primarily from the soil, by emergent vegetation. Water column primary productivity accounted for a much larger flux of nutrients with approximately 39.6g-N m^??2 yr^??1 and 2.4g-P m^??2 yr^??1 retained in algal communities. These fluxes, combined with measurements in parallel studies, allowed us to develop preliminary nutrient budgets for these wetlands and identify gaps, or missing fluxes, in our models for these wetlands. The results further validated previous findings that suggested that there are large inputs of nitrogen (up to 62.3g-N m^??2 yr^??1) that are not accounted for by the pumped inflow. Additionally, management suggestions are provided to improve water quality by identifying vegetative species that are most effective at retaining nutrients.

     

Estimating the capacity of Chamaecrista fasciculata for adaptation to change in precipitation

Adaptation through natural selection may be the only means by which small and fragmented plant populations will persist through present day environmental change. A population's additive genetic variance for fitness (V_A(W)) represents its immediate capacity to adapt to the environment in which it exists. We evaluated this property for a population of the annual legume Chamaecrista fasciculata through a quantitative genetic experiment in the tallgrass prairie region of the Midwestern United States, where changing climate is predicted to include more variability in rainfall. To reduce incident rainfall, relative to controls receiving ambient rain, we deployed rain exclusion shelters. We found significant V_A(W) in both treatments. We also detected a significant genotype‐by‐treatment interaction for fitness, which suggests that the genetic basis of the response to natural selection will differ depending on precipitation. For the trait‐specific leaf area, we detected maladaptive phenotypic plasticity and an interaction between genotype and environment. Selection for thicker leaves was detected with increased precipitation. These results indicate capacity of this population of C. fasciculata to adapt in situ to environmental change.     

Elements of disease in a changing world: modelling feedbacks between infectious disease and ecosystems

An overlooked effect of ecosystem eutrophication is the potential to alter disease dynamics in primary producers, inducing disease‐mediated feedbacks that alter net primary productivity and elemental recycling. Models in disease ecology rarely track organisms past death, yet death from infection can alter important ecosystem processes including elemental recycling rates and nutrient supply to living hosts. In contrast, models in ecosystem ecology rarely track disease dynamics, yet elemental nutrient pools (e.g. nitrogen, phosphorus) can regulate important disease processes including pathogen reproduction and transmission. Thus, both disease and ecosystem ecology stand to grow as fields by exploring questions that arise at their intersection. However, we currently lack a framework explicitly linking these disciplines. We developed a stoichiometric model using elemental currencies to track primary producer biomass (carbon) in vegetation and soil pools, and to track prevalence and the basic reproduction number (R₀) of a directly transmitted pathogen. This model, parameterised for a deciduous forest, demonstrates that anthropogenic nutrient supply can interact with disease to qualitatively alter both ecosystem and disease dynamics. Using this element‐focused approach, we identify knowledge gaps and generate predictions about the impact of anthropogenic nutrient supply rates on infectious disease and feedbacks to ecosystem carbon and nutrient cycling.