Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities

Armillaria species show considerable variation in ecological roles and virulence, from mycorrhizae and saprophytes to important root pathogens of trees and horticultural crops. We studied two Armillaria species that can be found in coniferous forests of northwestern USA and southwestern Canada. Armillaria altimontana is considered as a weak, opportunistic pathogen of coniferous trees, but it also appears to exhibit in situ biological control against A. solidipes, formerly North American A. ostoyae, which is considered a virulent pathogen of coniferous trees. Here, we describe their genome assemblies and present a functional annotation of the predicted genes and proteins for the two Armillaria species that exhibit contrasting ecological roles. In addition, the soil microbial communities were examined in association with the two Armillaria species within a 45-year-old plantation of western white pine (Pinus monticola) in northern Idaho, USA, where A. altimontana was associated with improved tree growth and survival, while A. solidipes was associated with reduced growth and survival.

Development of a real-time loop mediated isothermal amplification assay for Stromatinia cepivora in response to an outbreak in Northern Idaho

Stromatinia cepivora is the causal agent of white rot disease of Allium species. In 2018, white rot was observed in Boundary county in Northern Idaho in garlic and onion plants in a variety of home and market garden operations. As the university diagnostic lab for Idaho is situated in Parma within a regulated area for Stromatinia cepivora, a point of care (POC) assay using real-time loop mediated isothermal amplification (LAMP) was developed to minimize the amount of material potentially sent to the diagnostic lab. The LAMP assay was used with a BioRanger platform and although the limit of detection was one hundred times less than TaqMan, it was capable of detecting a single sclerotia. This study demonstrates the rapid development and deployment of a POC suitable LAMP assay. Despite limitations in sensitivity and dynamic range compared to real-time PCR, POC LAMP assays are advantageous where biosecurity concerns prohibit the movement of material suitable for diagnosis as well as facilitating engagement with growers.

Introduction

The Introduction describes the revitalization of one of the most controversial religious and political movements in recent American history. During a period of significant demographic and cultural change, a large number of religious and political conservatives have migrated into the Pacific Northwest. Many of these migrants are influenced by the claims of Christian Reconstruction, or “theonomy.” From their base in northern Idaho, these latter-day theonomists are developing the work of R. J. Rushdoony, Gary North, and others of the first generation of the writers of Christian Reconstruction, reiterating their optimistic view of the future, an eschatological position known as postmillennialism, as well as their expectation that the expansion of Christian influence around the world will be marked by changes in government and by a widespread return to the demands of Old Testament law.

Annually resolved sediments in the classic Clarkia lacustrine deposits (Idaho, USA) during the middle Miocene Climate Optimum

The world-renowned Miocene Clarkia paleolake in northern Idaho (USA) is closely associated with Columbia River Basalt Group volcanism. The flood basalt dammed a local drainage system to form the paleolake, which preserved a plant fossil Lagerstätte in its deposits. However, the precise age and temporal duration of the lake remain unsettled. We present the first unequivocal U-Pb zircon ages from interbedded volcanic ashes at the P-33 type location, constraining the deposition to 15.78 ± 0.039 Ma. Using micro–X-ray fluorescence and petrographic and spectral analyses, we establish the annual characteristics of laminations throughout the stratigraphic profile using the distribution of elemental ratios, mineral assemblages, and grain-size structures, as well as organic and fossil contents. Consequently, the ~7.5-m-thick varved deposit at the type location P-33 represents ~840 yr of deposition, coincident with the end of the main phase of Columbia River Basalt Group eruptions during the Miocene Climate Optimum. The timing and temporal resolution of the deposit offer a unique opportunity to study climate change in unprecedented detail during global warming associated with carbon-cycle perturbations.