Phylogeography, origin and population structure of the self-fertile emerging plant pathogen Phytophthora pseudosyringae.

Phytophthora pseudosyringae is a self-fertile pathogen of woody plants, particularly associated with tree species from the genera Fagus, Notholithocarpus, Nothofagus and Quercus, which is found across Europe and in parts of North America and Chile. It can behave as a soil pathogen infecting roots and the stem collar region, as well as an aerial pathogen infecting leaves, twigs and stem barks, causing particular damage in the United Kingdom and western North America. The population structure, migration and potential outcrossing of a worldwide collection of isolates were investigated using genotyping-by-sequencing. Coalescent-based migration analysis revealed that the North American population originated from Europe. Historical gene flow has occurred between the continents in both directions to some extent, yet contemporary migration is overwhelmingly from Europe to North America. Two broad population clusters dominate the global population of the pathogen, with a subgroup derived from one of the main clusters found only in western North America. Index of association and network analyses indicate an influential level of outcrossing has occurred in this preferentially inbreeding, homothallic oomycete. Outcrossing between the two main population clusters has created distinct subgroups of admixed individuals that are, however, less common than the main population clusters. Differences in life history traits between the two main population clusters should be further investigated together with virulence and host range tests to evaluate the risk each population poses to natural environments worldwide.

Cataloging Phytophthora Species of Agriculture, Forests, Horticulture, and Restoration Outplantings in California, U.S.A.: A Sequence-Based Meta-Analysis.

California contains a diverse flora, and knowledge of the pathogens that threaten those plants is essential to managing their long-term health. To better understand threats to California plant health, a meta-analysis of Phytophthora detections within the state was conducted using publicly available sequences as a primary source of data rather than published records. Accessions of internal transcribed spacer (ITS) ribosomal DNA were cataloged from 800 Californian Phytophthora isolates, analyzed, and determined to correspond to 80 taxa, including several phylogenetically distinct provisional species. A number of Phytophthora taxa not previously reported from California were identified, including 20 described species. Pathways of introduction and spread were analyzed by categorizing isolates' origins, grouped by land-use: (i) agriculture, (ii) forests and other natural ecosystems, (iii) horticulture and nurseries, or (iv) restoration outplantings. The pooled Phytophthora metacommunities of the restoration outplantings and horticulture land-use categories were the most similar, whereas the communities pooled from forests and agriculture were least similar. Phytophthora cactorum, P. pini, P. pseudocryptogea, and P. syringae were identified in all four land-use categories, while 13 species were found in three. P. gonapodyides was the most common species by number of ITS accessions and exhibited the greatest diversity of ITS haplotypes. P. cactorum, P. ramorum, and P. nicotianae were associated with the greatest number of host genera. In this analysis, the Phytophthora spp. most prevalent in California differ from those compiled from the scientific literature.

First Record of Colletotrichum anthrisci Causing Anthracnose on Avocado Fruits in Chile.

Anthracnose caused by Colletotrichum species is one of the most frequent and damaging fungal diseases affecting avocado fruits (Persea americana Mill.) worldwide. In Chile, the disease incidence has increased over the last decades due to the establishment of commercial groves in more humid areas. Since 2018, unusual symptoms of anthracnose have been observed on Hass avocado fruits, with lesions developing a white to gray sporulation. Morphological features and multi-locus phylogenetic analyses using six DNA barcodes (act, chs-1, gapdh, his3, ITS, and tub2) allowed the identification of the causal agent as Colletotrichum anthrisci, a member of the dematium species complex. Pathogenicity was confirmed by inoculating healthy Hass avocado fruits with representative isolates, reproducing the same symptoms initially observed, and successfully reisolating the same isolates from the margin of the necrotic pulp. Previously, several Colletotrichum species belonging to other species complexes have been associated with avocado anthracnose in other countries. To our knowledge, this is the first record of C. anthrisci and of a species of the dematium species complex causing anthracnose on avocado fruits in Chile and worldwide.

A Barcode-Based Phylogenetic Characterization of Phytophthora cactorum Identifies Two Cosmopolitan Lineages with Distinct Host Affinities and the First Report of Phytophthora pseudotsugae in California.

A collection of 30 Phytophthora cactorum and 12 P. pseudotsugae (subclade 1a) strains isolated from several recent surveys across California was phylogenetically compared to a worldwide collection of 112 conspecific strains using sequences from three barcoding loci. The surveys baited P. cactorum from soil and water across a wide variety of forested ecosystems with a geographic range of more than 1000 km. Two cosmopolitan lineages were identified within the widespread P. cactorum, one being mainly associated with strawberry production and the other more closely associated with apple orchards, oaks and ornamental trees. Two other well-sampled P. cactorum lineages, including one that dominated Californian restoration outplantings, were only found in the western United States, while a third was only found in Japan. Coastal California forest isolates of both Phytophthora species exhibited considerable diversity, suggesting both may be indigenous to the state. Many isolates with sequence accessions deposited as P. cactorum were determined to be P. hedraiandra and P. ×serendipita, with one hybrid lineage appearing relatively common across Europe and Asia. This study contains the first report of P. pseudotsugae from the state of California and one of the only reports of that species since its original description.

Identification and Characterization of Phytophthora Species Associated with Crown and Root Rot of Pistachio Trees in California.

Pistachio is one of the most widely cultivated nut crops in California, with approximately 115,000 ha of bearing pistachio trees. In recent years, several orchards were identified, with declining trees leading to substantial tree losses. Symptoms included trees with poor vigor, yellowing and wilting of leaves, crown rot, and profuse gumming on the lower portion of trunks. Thirty-seven Phytophthora-like isolates were obtained from crown rot tissues in the rootstock of grafted pistachio trees and characterized by means of multilocus phylogeny comprising internal transcribed spacer rDNA, beta-tubulin, and mt cox1 sequence data. The analysis provided strong support for the delineation and identification of three Phytophthora species associated with declining pistachio trees, including P. niederhauserii, P. mediterranea, and Phytophthora taxon walnut. Pathogenicity studies in potted University of California Berkeley I (UCBI) rootstocks (clonal and seeded) confirmed that all three Phytophthora species can cause crown and root rot of pistachio, thus fulfilling Koch's postulates. The widespread occurrence of Phytophthora crown rot in recently planted pistachio orchards and the susceptibility of UCBI rootstocks suggest this disease constitute an emerging new threat to the pistachio industry of California. To the best of our knowledge, this study is the first to report P. niederhauserii, P. mediterranea, and Phytophthora taxon walnut as causal agents of crown and root rots of pistachio.

The population of oomycetes in a recycled irrigation water system at a horticultural nursery in southern California.

Recapture and recycling of irrigation water is often required to meet enormous water demands at horticultural nurseries. We tested four water types associated with a recycled irrigation system at a commercial container nursery in southern California for presence of oomycete plant pathogens from July 2015 to December 2017. These water types included: the main source of water originating from a reservoir, retention water from an on-site collection pond, irrigation water received by different growing areas within the nursery, and irrigation runoff captured in polyethylene sheet-lined runoff channels. The genera Phytophthora, Pythium, and Phytopythium together contributed more than 85% of the total oomycete population detected in the recycled irrigation system. The Phytophthora and Pythium genera were represented by member species from nine (1-4, 6-10) and eight (A, B, D-F, H-J) different sub-generic clades, respectively. Incoming water sourced from the reservoir was found to harbor known plant pathogens such as Phytophthora citricola-complex, P. capsici-cluster, P. tropicalis,P citrophthora-cluster, P. nemorosa-cluster, P. riparia, P. cryptogea-complex, P. parsiana-cluster, P. sp. nov. aff. kernoviae, Pythium dissotocum-complex, Py. oligandrum-cluster, Py. irregulare, and Phytopythium litorale. Runoff water showed the highest oomycete species richness and frequency of detection with both filtration and leaf baiting methods. In addition to plant pathogens, oomycete fish pathogens such as Aphanomyces laevis, Pythium chondricola-complex, Pythium flevoense-complex, and Saprolegnia diclina-complex were also detected in greater abundance in the recycled irrigation water. The oomycete species richness in the runoff water was correlated with several environmental parameters such as soil temperature. Greater oomycete richness in incoming water was associated with higher soil temperatures, whereas richness in runoff declines with increasing soil temperature, likely suggesting connections to weather-dependent nursery operations.

Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora.

Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the "subgeneric" clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.