Novel disturbance interactions between fire and an emerging disease impact survival and growth of resprouting trees

Biotechnology and Genomic Approaches to Mitigating Disease Impacts on Forest Health

Outbreaks of insects and diseases are part of the natural disturbance regime of all forests. However, introduced pathogens have had outsized impacts on many dominant forest tree species over the past century. Mitigating these impacts and restoring these species are dilemmas of the modern era. Here, we review the ecological and economic impact of introduced pathogens, focusing on examples in North America. We then synthesize the successes and challenges of past biotechnological approaches and discuss the integration of genomics and biotechnology to help mitigate the effects of past and future pathogen invasions. These questions are considered in the context of the transgenic American chestnut, which is the most comprehensive example to date of how biotechnological tools have been used to address the impacts of introduced pathogens on naïve forest ecosystems.

Assessment of Fatty Acid and Oxylipin Profile of Resprouting Olive Trees Positive to Xylella fastidiosa subsp. pauca in Salento (Apulia, Italy)

Xylella fastidiosa subsp. pauca ST53 (XFP), the causal agent of olive quick decline syndrome (OQDS), was thoroughly investigated after a 2013 outbreak in the Salento region of Southern Italy. Some trees from Ogliarola Salentina and Cellina di Nardò, susceptible cultivars in the Gallipoli area, the first XFP infection hotspot in Italy, have resprouted crowns and are starting to flower and yield fruits. Satellite imagery and Normalized Difference Vegetation Index analyses revealed a significant improvement in vegetation health and productivity from 2018 to 2022 of these trees. Lipid molecules have long been recognized as plant defense modulators, and recently, we investigated their role in XFP-positive hosts and in XFP-resistant as well as in XFP-susceptible cultivars of olive trees. Here, we present a case study regarding 36 olive trees (12 XFP-positive resprouting, 12 XFP-positive OQDS-symptomatic, and 12 XFP-negative trees) harvested in 2022 within the area where XFP struck first, killing millions of trees in a decade. These trees were analyzed for some free fatty acid, oxylipin, and plant hormones, in particular jasmonic and salicylic acid, by targeted LC-MS/MS. Multivariate analysis revealed that lipid markers of resistance (e.g., 13-HpOTrE), along with jasmonic and salicylic acid, were accumulated differently in the XFP-positive resprouting trees from both cultivars with respect to XFP-positive OQDS symptomatic and XFP-negative trees, suggesting a correlation of lipid metabolism with the resprouting, which can be an indication of the resiliency of these trees to OQDS. This is the first report concerning the resprouting of OQDS-infected olive trees in the Salento area.

Predicting resprouting of Platanus × hispanica following branch pruning by means of machine learning

Introduction

Resprouting is a crucial survival strategy following the loss of branches, being it by natural events or artificially by pruning. The resprouting prediction on a physiological basis is a highly complex approach. However, trained gardeners try to predict a tree's resprouting after pruning purely based on their empirical knowledge. In this study, we explore how far such predictions can also be made by machine learning.

Methods

Table-topped annually pruned Platanus × hispanica trees at a nursery were LiDAR-scanned for two consecutive years. Topological structures for these trees were abstracted by cylinder fitting. Then, new shoots and trimmed branches were labelled on corresponding cylinders. Binary and multiclass classification models were tested for predicting the location and number of new sprouts.

Results

The accuracy for predicting whether having or not new shoots on each cylinder reaches 90.8% with the LGBMClassifier, the balanced accuracy is 80.3%. The accuracy for predicting the exact numbers of new shoots with the GaussianNB model is 82.1%, but its balanced accuracy is reduced to 42.9%.

Discussion

The results were validated with a separate dataset, proving the feasibility of resprouting prediction after pruning using this approach. Different tree species, tree forms, and other variables should be addressed in further research.

Repeated Emergence of Sudden Oak Death in Oregon: Chronology, Impact, and Management

It has been two decades since the first detection of the sudden oak death pathogen Phytophthora ramorum in Oregon forests. Although the epidemic was managed since its first discovery in 2001, at least three invasions of three separate variants (clonal lineages), NA1, EU1, and NA2, are documented to have occurred to date. Control of this epidemic has cost over US$32 million from 2001 to 2020. This is dwarfed by the predicted cost of the closure to the Coos Bay export terminal, estimated at $58 million per year, if the epidemic was allowed to spread unchecked. Management efforts in Oregon have reduced inoculum and limited the spread of the pathogen. An outreach and citizen scientist program has been piloted to help in early detection efforts and search for disease-resistant tanoak. This feature article documents the repeated emergence, impact, costs, and lessons learned from managing this devastating invasive pathogen.

Local Eradication of Phytophthora ramorum Is Effective on Both NA1 and EU1 Lineages in Oregon Tanoak Forests

Sudden oak death (SOD), caused by the oomycete Phytophthora ramorum, has been actively managed in Oregon since its discovery there in 2001. SOD is a devastating disease affecting an ecologically and culturally important tree species in southwestern Oregon. Initially infested with the NA1 lineage, the more virulent EU1 lineage was discovered in 2015. Management has adapted over time in response to experimental findings and administrative limitations. Current management practices present an opportunity to compare the efficacy of treatment on these lineages by analyzing P. ramorum inoculum at untreated and treated sites. Current treatment includes herbicide treatment on host stems followed by felling, piling, and burning on site. Infested sites were visited between 2018 and 2020 (n = 88), where understory vegetation and soil was collected. Generalized linear modeling demonstrated that treatment had a significant impact on P. ramorum prevalence from vegetation samples, with an average of 33% (± 10%) fewer positive samples at treated sites. Linear mixed-effects modeling of a subpopulation of EU1 sites visited before and after treatment showed a similar effect of treatment, with a 43% (± 15%) reduction in P. ramorum prevalence. Prevalence of P. ramorum in soil was not affected by treatment in either analysis. A third analysis taking into consideration recent wildfire incursion into infested areas revealed that wildfire alone is insufficient to reduce prevalence of P. ramorum. These results strongly suggest that management is successfully reducing P. ramorum inoculum found on understory vegetation, and that treatment remains necessary to reduce the spread of this major forest pathogen.

Community-level prevalence of a forest pathogen, not individual-level disease risk, declines with tree diversity

Understanding why diversity sometimes limits disease is essential for managing outbreaks; however, mechanisms underlying this 'dilution effect' remain poorly understood. Negative diversity-disease relationships have previously been detected in plant communities impacted by an emerging forest disease, sudden oak death. We used this focal system to empirically evaluate whether these relationships were driven by dilution mechanisms that reduce transmission risk for individuals or from the fact that disease was averaged across the host community. We integrated laboratory competence measurements with plant community and symptom data from a large forest monitoring network. Richness increased disease risk for bay laurel trees, dismissing possible dilution mechanisms. Nonetheless, richness was negatively associated with community-level disease prevalence because the disease was aggregated among hosts that vary in disease susceptibility. Aggregating observations (which is surprisingly common in other dilution effect studies) can lead to misinterpretations of dilution mechanisms and bias towards a negative diversity-disease relationship.

Sporulation Potential of Phytophthora ramorum Differs Among Common California Plant Species in the Big Sur Region

Sudden oak death (SOD), caused by the generalist pathogen Phytophthora ramorum, has profoundly impacted California coastal ecosystems. SOD has largely been treated as a two-host system, with Umbellularia californica as the most transmissive host, Notholithocarpus densiflorus less so, and remaining species as epidemiologically unimportant. However, this understanding of transmission potential primarily stems from observational field studies rather than direct measurements on the diverse assemblage of plant species. Here, we formally quantify the sporulation potential of common plant species inhabiting SOD-endemic ecosystems on the California coast in the Big Sur region. This study allows us to better understand the pathogen's basic biology, trajectory of SOD in a changing environment, and how the entire host community contributes to disease risk. Leaves were inoculated in a controlled laboratory environment and assessed for production of sporangia and chlamydospores, the infectious and resistant propagules, respectively. P. ramorum was capable of infecting every species in our study and almost all species produced spores to some extent. Sporangia production was greatest in N. densiflorus and U. californica and the difference was insignificant. Even though other species produced much less, quantities were nonzero. Thus, additional species may play a previously unrecognized role in local transmission. Chlamydospore production was highest in Acer macrophyllum and Ceanothus oliganthus, raising questions about the role they play in pathogen persistence. Lesion size did not consistently correlate with the production of either sporangia or chlamydospores. Overall, we achieved an empirical foundation to better understand how community composition affects transmission of P. ramorum.