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Profiling the host-mycobiota interactions in healthy vs. diseased forest ecosystems helps understand the dynamics of understudied yet increasingly important threats to forest health that are emerging due to climate change. We analyzed the structural and functional changes of the mycobiota and the responses of Pinus contorta in the Lophodermella needle cast pathosystem through metabarcoding and metatranscriptomics. When needles transitioned from asymptomatic to symptomatic, dysbiosis of the mycobiota occurred, but with an enrichment of Lophodermella pathogens. Many pathogenicity-related genes were highly expressed by the mycobiota at the necrotrophic phase, showing an active pathogen response that are absent in asymptomatic needles. This study also revealed that Lophodermella spp. are members of a healthy needle mycobiota that have latent lifestyles suggesting that other pine needle pathogens may have similar biology. Interestingly, Pinus contorta upregulated defense genes in healthy needles, indicating response to fungal recognition, while a variety of biotic and abiotic stresses genes were activated in diseased needles. Further investigation to elucidate the possible antagonistic interplay of other biotic members leading to disease progression and/or suppression is warranted. This study provides insights into microbial interactions in non-model pathosystems and contributes to the development of new forest management strategies against emerging latent pathogens.

Recent studies have shown numerous Fusarium spp. are associated with symptomatic conifer seedlings in both bareroot and container nursery systems. Some of these species have been found pathogenic to conifer seedlings (e.g., F. avenaceum, F. commune, F. oxysporum, F. solani, and F. verticillioides), but the mechanisms and shared evolutionary history of these conifer pathogenic species have not been well studied in these pathosystems. We compared whole genomes of 17 Fusarium spp. associated with conifer seedlings to elucidate putative shared pathogenicity/virulence gene profiles presumably expressed for roles in causing damping‐off and/or root disease of conifer seedlings. In addition, this work provides draft genomes of conifer‐associated Fusarium spp. and genomes not previously referenced in public databases (e.g., F. lactis, F. fredkrugeri, F. ipomoeae, and F. flocciferum). We identified pathogenicity/virulence genes associated with Fusarium spp. pathogens of conifers including effectors, the secreted in xylem (SIX) genes 2, 4, 9 and 14 and secondary metabolites, and the mycotoxins fumonisin and deoxynivalenol. We conclude that gene profiles are shared within Fusarium species complexes and among closely related Fusarium species complexes; however, these shared profiles are widely distributed across all Fusarium pathogens. These findings highlight potential targets for detecting and/or identifying Fusarium pathogens of conifers, but multiple methods and/or targets will be required depending on the species complexes and clades. More research is needed to determine the roles of expressed pathogenicity/virulence genes and the downstream metabolic products that result in pathogenesis to conifers. [ABSTRACT FROM AUTHOR]

Calonectria vigiensis sp. nov. (Hypocreales, Nectriaceae) is a newly described species associated with cacao (Theobroma cacao L.) in Mérida state, Venezuela. This new species was identified using morphological methods as well as DNA sequencing and multigene phylogenetic analyses. Based on phylogenetic analyses of a combined dataset including translation elongation factor 1-[alpha] (tef1), calmodulin (cmdA), and [beta]-tubulin (btub) genes across closely related species within Calonectria, a new species was identified as Ca. vigiensis within the Calonectria naviculata species complex, but it was determined to be well-separated from genetically close species such as Calonectria multilateralis L. Lombard & Crous, Calonectria multinaviculata R.F. Alfenas, L. Lombard & Crous, and Calonectria naviculata Crous & M.J. Wingf. This work reports 1 previously undescribed fungal species (Ca. vigiensis) that is associated with dieback and sudden-death symptoms in T. cacao plantations in Mérida state, Venezuela. Key words: cacao, Calonectria, Cylindrocladium, Theobroma cacao L., Venezuela. Calonectria vigiensis sp. nov. (Hypocreales, Nectriaceae) est une espèce associée au cacao (Theobroma cacao L.) nouvellement décrite dans l'état de Mérida, au Venezuela. Cette nouvelle espèce a été identifiée à l'aide de méthodes morphologiques ainsi que du séquençage de l'ADN et d'analyses phylogénétiques multi-gènes. Sur la base d'analyses phylogénétiques d'un ensemble de données combinées comprenant les gènes du facteur d'élongation de la traduction 1-[alpha] (tef1), de la calmoduline (cmdA)etde la [beta]-tubuline (btub)sur des espèces proches au sein de Calonectria, une nouvelle espèce a été identifiée comme Ca. vigiensis au sein du complexe d'espèces Calonectria naviculata, mais bien séparée des espèces génétiquement proches qui comprennent Calonectria multilateralis L. Lombard & Crous, Calonectria multinaviculata R.F. Alfenas, L. Lombard & Crous et Calonectria naviculata Crous & M.J. Wingf. Ce travail rapporte l'existence d'une espèce fongique non décrite (Ca. vigiensis) auparavant qui est associée à des symptômes de dépérissement et de mort subite dans les plantations de T. cacao dans l'état de Mérida, au Venezuela. [Traduit par la Rédaction] Mots-clés : cacao, Calonectria, Cylindrocladium, Theobroma cacao L., Venezuela., Introduction The genus Calonectria (Ca.) (Hypocreales, Nectriaceae) was first described in 1867 (Rossman 1979), whereas its asexual morph genus, Cylindrocladium (Cy.), was described 25 years thereafter by Morgan (1892). The [...]

Introduction: Soil-borne pathogens cause considerable crop losses and food insecurity in smallholder systems of sub-Saharan Africa. Soil and crop testing is critical for estimating pathogen inoculum levels and potential for disease development, understanding pathogen interactions with soil nutrient and water limitations, as well as for developing informed soil health and disease management decisions. However, formal laboratory analyses and diagnostic services for pathogens are often out of reach for smallholder farmers due to the high cost of testing and a lack of local laboratories. Methods: To address this challenge, we assessed the performance of a suite of simplified soil bioassays to screen for plant parasitic nematodes (e.g., Meloidogyne, Pratylenchus) and other key soil-borne pathogens (Pythium and Fusarium). We sampled soils from on-farm trials in western Kenya examining the impact of distinct nutrient inputs (organic vs. synthetic) on bean production. Key soil health parameters and common soil-borne pathogens were evaluated using both simple bioassays and formal laboratory methods across eleven farms, each with three nutrient input treatments (66 samples in total). Results and Discussion: The soil bioassays, which involved counting galls on lettuce roots and lesions on soybean were well correlated with the abundance of gall forming (Meloidogyne) and root lesion nematodes (e.g., Pratylenchus) recovered in standard laboratory-based extractions. Effectiveness of a Fusarium bioassay, involving the counting of lesions on buried bean stems, was verified via sequencing and a pathogenicity test of cultured Fusariumstrains. Finally, a Pythium soil bioassay using selective media clearly distinguished pathogen infestation of soils and infected seeds. When examining management impact on nematode communities, soils amended with manure had fewer plant parasites and considerably more bacterivore and fungivore nematodes compared to soils amended with synthetic N and P. Similarly, Pythium presence was 35% lower in soils amended with manure, while the Fusarium assays indicated 23% higher Fusarium infection in plots with amended manure. Our findings suggest that relatively simple bioassays can be used to help farmers assess soil-borne pathogens in a timely manner, with minimal costs, thus enabling them to make informed decisions on soil health and pathogen management. [ABSTRACT FROM AUTHOR]

Areca ipot, a Philippine endemic species, is categorized as endangered primarily due to habitat loss. A severe outbreak of a new leaf spot disease was observed on A. ipot seedlings in a nursery. Morphological and molecular features of isolates from diseased samples were identified as Neopestalotiopsis sp. and Calonectria sp. The pathogenicity of the isolates was confirmed by fulfilling Koch's postulates. This is the first report of Neopestalotiopsis sp. and Calonectria sp. causing leaf spot on A. ipot in the Philippines. [ABSTRACT FROM AUTHOR]

Symbiotic fungi associated with tree-killing bark beetles can alter host-tree physiology with consequences for tree survival, and symbiont genetic variation and environmental variability may impact these interactions. Here, we test whether multiple genetically distinct isolates of a symbiotic fungus (Leptographium abietinum (Peck) M.J. Wingf.) associated with North American spruce beetle (Dendroctonus rufipennis (Kirby, 1837)) vary in their ability to manifest defensive responses consistent with disease symptoms in seedlings of Engelmann spruce (Picea engelmannii Parry ex Engelm.), a primary host-tree species for the beetle-fungus complex in North America. Our experiments incorporate variation in both host-tree water availability and host defenses (phloem monoterpene concentration). Three central findings emerged: (i) isolates varied considerably in their effects on host trees--inoculation with L. abietinum isolates from Colorado caused significantly larger phloem lesions than isolates from Wyoming, though all isolates caused phloem oxidation; (ii) neither water availability nor spruce phloem monoterpene concentrations impacted lesion formation; and (iii) both inoculation with L. abietinum and water deficit inhibited the formation of callus tissue at wound sites. We conclude that L. abietinum isolates vary in their virulence and that inoculation is not lethal but may benefit beetles by altering tree defensive responses. Key words: Dendroctonus, ophiostomatoid fungi, phytopathogen, symbiosis. Les champignons symbiotiques associes aux scolytes qui causent la mort des arbres peuvent modifier la physiologie de l'arbre hote, ce qui a des repercussions sur la survie des arbres, et la variation genetique des symbiotes ainsi que la variabilite environnementale peuvent avoir un impact sur ces interactions. Dans cette etude, nous avons teste si de multiples isolats genetiquement distincts du champignon symbiotique (Leptographium abietinum (Peck) M.J. Wingf.) associe au dendroctone nordamericain de l'epinette (Dendroctonus rupipennis (Kirby, 1837)) varient quant a leur capacite a susciter des reactions de defenses consistantes avec les symptomes de maladie chez des semis d'epinette d'Engelmann (Picea engelmannii Parry ex Engelm.), une des principales especes d'arbre hote du complexe scolyte-champignon en Amerique du Nord. Nos experiences incorporent a la fois la variation de la disponibilite de l'eau pour l'arbre hote et celle des defenses de l'arbre hote (concentration des monoterpenes dans le phloeme). Trois resultats principaux ressortent : (i) les isolats variaient considerablement quant a leurs effets sur les arbres hotes; l'inoculation avec des isolats de L. abietinum provenant du Colorado a cause des lesions significativement plus importantes dans le phloeme que les isolats provenant du Wyoming, quoique tous les isolats aient cause l'oxydation du phloeme, (ii) cependant, ni la disponibilite de l'eau, ni la concentration des monoterpenes dans le phloeme de l'epinette n'ont eu d'impact sur la formation des lesions, (iii) tant l'inoculation avec L. abietinum qu'un deficit hydrique ont inhibe la formation de tissus calleux a l'endroit de la blessure. Nous concluons que les isolats de L. abietinum varient quant a leur virulence et que l'inoculation n'est pas letale mais peut etre benefique pour les scolytes en alterant les reactions de defense de l'arbre. [Traduit par la Redaction] Mots-cles : Dendroctonus, champignons ophiostomatoides, phytopathogene, symbiose., Introduction Over the past decade, significant decline of spruce-fir forest has been documented across the western United States; much of this decline is attributed to North American spruce beetle (Dendroctonus [...]

Needle diseases caused by pathogens within Rhytismataceae are increasing in frequency globally where pines are either a predominate species or are grown commercially, and yet remain poorly understood. Here, we provide background information on the current knowledge and management strategies of needle pathogens in the Rhytismataceae and discuss research opportunities using molecular tools to fill knowledge gaps. Many of the aggressive needle pathogens within this group lack morphological features to delimit species and are difficult to grow in axenic cultures, which complicates scientific investigations. Molecular research has greatly advanced knowledge of this unique group of pathogens. Nucleotide sequences from multiple gene loci identified greater diversity within this group of pathogens than previously thought, as new and cryptic species are being discovered in broader geographic regions. High throughput sequencing and analyses revealed that an endophytic lifestyle is a common trait among fastidious if not obligate needle pathogens within Rhytismataceae. Further, molecular analyses showed the impact these pathogens have on the diversity of endophytic microbiota is underestimated. Early detection in healthy‐looking needles using PCR‐based markers greatly improves capabilities for disease diagnosis and monitoring. Despite growing number of molecular studies on Rhytismataceae needle pathogens, fundamental questions on the taxonomy, phylogeny, ecology and pathology of many Rhytismataceae needle pathogens remain unanswered. Nonetheless, with the projected changes in the occurrence and severity of Rhytismataceae pathogens, increased accessibility to molecular tools vastly expands the potential to gain more insights into understudied needle pathosystems to help define and address its impact under changing environments and consequently inform forest disease management more effectively. [ABSTRACT FROM AUTHOR]

Leptographium wageneri is a native fungal pathogen in western North America that causes black stain root disease (BSRD) of conifers. Three host-specialized varieties of this pathogen were previously described: L. wageneri var. wageneri on pinyon pines (Pinus monophylla and P. edulis); L. wageneri var. ponderosum, primarily on hard pines (e.g., P. ponderosa, P. jeffreyi); and L. wageneri var. pseudotsugae on Douglas-fir (Pseudotsuga menziesii). Morphological, physiological, and ecological differences among the three pathogen varieties have been previously determined; however, DNA-based characterization and analyses are needed to determine the genetic relationships among these varieties. The objective of this study was to use DNA sequences of 10 gene regions to assess phylogenetic relationships among L. wageneri isolates collected from different hosts. The multigene phylogenetic analyses, based on maximum likelihood and Bayesian inference, strongly supported species-level separation of the three L. wageneri varieties. These results, in conjunction with previously established phenotypic differences, support the elevation of L. wageneri var. ponderosum and L. wageneri var. pseudotsugae to the species level as L. ponderosum comb. nov. and L. pseudotsugae comb. nov., respectively, while maintaining L. wageneri var. wageneri as Leptographium wageneri. Characterization of the three Leptographium species, each with distinct host ranges, provides a baseline to further understand the ecological interactions and evolutionary relationships of these forest pathogens, which informs management of black stain root disease. [ABSTRACT FROM AUTHOR]