Mining new sources of natural history observations for disease interactions

Quantitative disease resistance in wild Silene vulgaris to its endemic pathogen Microbotryum silenes-inflatae

The evolution of disease resistances is an expected feature of plant-pathogen systems, but whether the genetics of this trait most often produces qualitative or quantitative phenotypic variation is a significant gap in our understanding of natural populations. These two forms of resistance variation are often associated with differences in number of underlying loci, the specificities of host-pathogen coevolution, as well as contrasting mechanisms of preventing or slowing the infection process. Anther-smut disease is a commonly studied model for disease of wild species, where infection has severe fitness impacts, and prior studies have suggested resistance variation in several host species. However, because the outcome of exposing the individual host to this pathogen is binary (healthy or diseased), resistance has been previously measured at the family level, as the proportion of siblings that become diseased. This leaves uncertain whether among-family variation reflects contrasting ratios of segregating discrete phenotypes or continuous trait variation among individuals. In the host Silene vulgaris, plants were replicated by vegetative propagation in order to quantify the infection rates of the individual genotype with the endemic anther-smut pathogen, Microbotryum silenes-inflatae. The variance among field-collected families for disease resistance was significant, while there was unimodal continuous variation in resistance among genotypes. Using crosses between genotypes within ranked resistance quartiles, the offspring infection rate was predicted by the parental resistance values. While the potential remains in this system for resistance genes having major effects, as there were suggestions of such qualitative resistance in a prior study, here the quantitative disease resistance to the endemic anther-smut pathogen is indicated for S. vulgaris. The variation in natural populations and strong heritability of the trait, combined with severe fitness consequences of anther-smut disease, suggests that resistance in these host populations is highly capable of responding to disease-induced selection.

Herbaria preserve plant microbiota responses to environmental changes

Interaction between plants and their microbiota is a central theme to understand adaptation of plants to their environment. Considering herbaria as repositories of holobionts that preserved traces of ancient plant-associated microbial communities, we propose to explore these historical collections to evaluate the impact of long-lasting global changes on plant-microbiota interactions.

Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes

Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.

Resistance Correlations Influence Infection by Foreign Pathogens

AbstractReciprocal selection promotes the specificity of host-pathogen associations and resistance polymorphisms in response to disease. However, plants and animals also vary in response to pathogen species not previously encountered in nature, with potential effects on new disease emergence. Using anther smut disease, we show that resistance (measured as infection rates) to foreign pathogens can be correlated with standing variation in resistance to an endemic pathogen. In Silene vulgaris, genetic variation in resistance to its endemic anther smut pathogen correlated positively with resistance variation to an anther smut pathogen from another host, but the relationship was negative between anther smut and a necrotrophic pathogen. We present models describing the genetic basis for assessing resistance relationships between endemic and foreign pathogens and for quantifying infection probabilities on foreign pathogen introduction. We show that even when the foreign pathogen has a lower average infection ability than the endemic pathogen, infection outcomes are determined by the sign and strength of the regression of the host's genetic variation in infection rates by a foreign pathogen on variation in infection rates by an endemic pathogen as well as by resistance allele frequencies. Given that preinvasion equilibria of resistance are determined by factors including resistance costs, we show that protection against foreign pathogens afforded by positively correlated resistances can be lessened or even result in elevated infection risk at the population level, depending on local dynamics. Therefore, a pathogen's emergence potential could be influenced not only by its average infection rate but also by resistance variation resulting from prior selection imposed by endemic diseases.

From generalist to specialists: Variation in the host range and performance of anther-smut pathogens on Dianthus

Determining the processes that drive the evolution of pathogen host range can inform our understanding of disease dynamics and the potential for host shifts. In natural populations, patterns of host range could be driven by genetically based differences in pathogen infectivity or ecological differences in host availability. In northwestern Italy, four reproductively isolated lineages of the fungal plant-pathogen Microbotryum have been shown to co-occur on several species in the genus Dianthus. We carried out cross-inoculation experiments to determine whether patterns of realized host range in these four lineages were driven by differences in infectivity and to test whether there was evidence of a trade-off between host range and within-host reproduction. We found strong concordance between field patterns of host range and pathogen infectivity on different Dianthus species using experimental inoculation, indicating that infection ability is a major driving force of host range. However, we found no evidence of a trade-off between the ability to infect a wider range of host species and spore production on a shared host.

Transparency and secrecy in citizen science: Lessons from herping

In this paper I will outline a worry that citizen science can promote a kind of transparency that is harmful. I argue for the value of secrecy in citizen science. My argument will consist of analysis of a particular community (herpers), a particular citizen science platform (iNaturalist, drawing contrasts with other platforms), and my own travels in citizen science. I aim to avoid a simple distinction between science versus non-science, and instead analyze herping as a rich practice [MacIntyre, 2007]. Herping exemplifies citizen science as functioning simultaneously within and outside the sphere of science. I show that herpers have developed communal systems of transmitting and protecting knowledge. Ethical concerns about secrecy are inherently linked to these systems of knowledge. My over-arching aim is to urge caution in the drive to transparency, as the concepts of transparency and secrecy merit close scrutiny. The concerns I raise are complementary to those suggested by previous philosophical work, and (I argue) resist straightforward solutions.

The role of passive surveillance and citizen science in plant health

The early detection of plant pests and diseases is vital to the success of any eradication or control programme, but the resources for surveillance are often limited. Plant health authorities can however make use of observations from individuals and stakeholder groups who are monitoring for signs of ill health. Volunteered data is most often discussed in relation to citizen science groups, however these groups are only part of a wider network of professional agents, land-users and owners who can all contribute to significantly increase surveillance efforts through "passive surveillance". These ad-hoc reports represent chance observations by individuals who may not necessarily be looking for signs of pests and diseases when they are discovered. Passive surveillance contributes vital observations in support of national and international surveillance programs, detecting potentially unknown issues in the wider landscape, beyond points of entry and the plant trade. This review sets out to describe various forms of passive surveillance, identify analytical methods that can be applied to these "messy" unstructured data, and indicate how new programs can be established and maintained. Case studies discuss two tree health projects from Great Britain (TreeAlert and Observatree) to illustrate the challenges and successes of existing passive surveillance programmes. When analysing passive surveillance reports it is important to understand the observers' probability to detect and report each plant health issue, which will vary depending on how distinctive the symptoms are and the experience of the observer. It is also vital to assess how representative the reports are and whether they occur more frequently in certain locations. Methods are increasingly available to predict species distributions from large datasets, but more work is needed to understand how these apply to rare events such as new introductions. One solution for general surveillance is to develop and maintain a network of tree health volunteers, but this requires a large investment in training, feedback and engagement to maintain motivation. There are already many working examples of passive surveillance programmes and the suite of options to interpret the resulting datasets is growing rapidly.