Assessment of functional and structural changes of soil fungal and oomycete communities in holm oak declined dehesas through metabarcoding analysis

Proteomic and Metabolomic Analysis of the Quercus ilex-Phytophthora cinnamomi Pathosystem Reveals a Population-Specific Response, Independent of Co-Occurrence of Drought

Holm oak (Quercus ilex) is considered to be one of the major structural elements of Mediterranean forests and the agrosilvopastoral Spanish "dehesa", making it an outstanding example of ecological and socioeconomic sustainability in forest ecosystems. The exotic Phytophthora cinnamomi is one of the most aggressive pathogens of woody species and, together with drought, is considered to be one of the main drivers of holm oak decline. The effect of and response to P. cinnamomi inoculation were studied in the offspring of mother trees from two Andalusian populations, Cordoba and Huelva. At the two locations, acorns collected from both symptomatic (damaged) and asymptomatic (apparently healthy) trees were sampled. Damage symptoms, mortality, and chlorophyll fluorescence were evaluated in seedlings inoculated under humid and drought conditions. The effect and response depended on the population and were more apparent in Huelva than in Cordoba. An integrated proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, including amino acid metabolism pathways in Huelva, and terpenoid and flavonoid biosynthesis in Cordoba. However, no differential response was observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus was activated in response to defective photosynthetic activity in inoculated plants, which seemed to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may have conferred higher resistance in the Cordoba population. Some enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates.

Nanopore-Sequencing Metabarcoding for Identification of Phytopathogenic and Endophytic Fungi in Olive (Olea europaea) Twigs

Metabarcoding approaches for the identification of plant disease pathogens and characterization of plant microbial populations constitute a rapidly evolving research field. Fungal plant diseases are of major phytopathological concern; thus, the development of metabarcoding approaches for the detection of phytopathogenic fungi is becoming increasingly imperative in the context of plant disease prognosis. We developed a multiplex metabarcoding method for the identification of fungal phytopathogens and endophytes in olive young shoots, using the MinION sequencing platform (Oxford Nanopore Technologies). Selected fungal-specific primers were used to amplify three different genomic DNA loci (ITS, beta-tubulin, and 28S LSU) originating from olive twigs. A multiplex metabarcoding approach was initially evaluated using healthy olive twigs, and further assessed with naturally infected olive twig samples. Bioinformatic analysis of basecalled reads was carried out using MinKNOW, BLAST+ and R programming, and results were also evaluated using the BugSeq cloud platform. Data analysis highlighted the approaches based on ITS and their combination with beta-tubulin as the most informative ones according to diversity estimations. Subsequent implementation of the method on symptomatic samples identified major olive pathogens and endophytes including genera such as Cladosporium, Didymosphaeria, Paraconiothyrium, Penicillium, Phoma, Verticillium, and others.

Responses of a soil fungal community to severe windstorm damages in an old silver fir stand

Forests are increasingly threatened by climate change and the Anthropocene seems to have favored the emergence and adaptation of pathogens. Robust monitoring methods are required to prevent biodiversity and ecosystems losses, and this imposes the choice of bioindicators of habitat health. Fungal communities are increasingly recognized as fundamental components in nearly all natural and artificial environments, and their ecosystem services have a huge impact in maintaining and restoring the functionality of ecosystems. We coupled metabarcoding and soil analyses to infer the dynamics of a fungal community inhabiting the old silver fir stand in Vallombrosa (Italy), which is known to be afflicted by both Armillaria and Annosum root rot. The forest was affected in 2015, by a windstorm which caused a partial falling and uprooting of trees. The remaining stand, not affected by the windstorm, was used as a comparison to infer the consequences of the ecosystem disturbance. We demonstrated that the abundance of pathogens alone is not able to explain the soil fungal differences shown by the two areas. The fungal community as a whole was equally rich in the two areas, even if a reduction of the core ectomycorrhizal mycobiome was observed in the wind-damaged area, accompanied by the increase of wood saprotrophs and arbuscular mycorrhizas. We hypothesize a reshaping of the fungal community and a potentially ongoing re-generation of its functionalities. Our hypothesis is driven by the evidence that key symbiotic, endophytic, and saprotrophic guilds are still present and diversified in the wind-damaged area, and that dominance of single taxa or biodiversity loss was not observed from a mycological point of view. With the present study, we aim at providing evidence that fungal communities are fundamental for the monitoring and the conservation of threatened forest ecosystems.

Genetic diversity of Actinidia spp. shapes the oomycete pattern associated with Kiwifruit Vine Decline Syndrome (KVDS)

Kiwifruit Vine Decline Syndrome (KVDS) is an important soil-borne disease for the Italian kiwifruit industry, causing €300,000 in economic losses in 2020 alone. So far, the organisms recognized as involved in the aetiology of KVDS mainly belong to the Oomycota. As no effective management strategies exist, a promising approach to overcoming KVDS is the use of resistant species as rootstocks or for inclusion in breeding programs. Several Actinidia genotypes showing different level of resistance to KVDS were grown in disease-promoting soils. A metabarcoding approach was set up to identify KVDS-associated oomycetes and investigate whether the main species involved may vary according to plant genotype. Our results clearly showed significant differences between the genotypes in terms of oomycetes present in both plant rhizosphere and endosphere, which were strongly correlated with the symptoms displayed. We found out that the resistance of Actinidia macrosperma to KVDS is related to its ability to shape the pathobiome, particularly as far as the endosphere is concerned. In our conditions, Phytophthora sp. was predominantly found in sensitive genotypes, whilst Globisporangium intermedium was mainly detected in asymptomatic plants, suggesting that the latter species could compete with the recruitment of Phytophthora sp. in plants with different levels of resistance, consequently, explaining the onset of symptoms and the resistance condition.

Oomycete Soil Diversity Associated with Betula and Alnus in Forests and Urban Settings in the Nordic-Baltic Region

This study aimed to determine the differences and drivers of oomycete diversity and community composition in alder- and birch-dominated park and natural forest soils of the Fennoscandian and Baltic countries of Estonia, Finland, Lithuania, Norway, and Sweden. For this, we sequenced libraries of PCR products generated from the DNA of 111 soil samples collected across a climate gradient using oomycete-specific primers on a PacBio high-throughput sequencing platform. We found that oomycete communities are most affected by temperature seasonality, annual mean temperature, and mean temperature of the warmest quarter. Differences in composition were partly explained by the higher diversity of Saprolegniales in Sweden and Norway, as both total oomycete and Saprolegniales richness decreased significantly at higher longitudes, potentially indicating the preference of this group of oomycetes for a more temperate maritime climate. None of the evaluated climatic variables significantly affected the richness of Pythiales or Peronosporales. Interestingly, the relative abundance and richness of Pythiales was higher at urban sites compared to forest sites, whereas the opposite was true for Saprolegniales. Additionally, this is the first report of Phytophthora gallica and P. plurivora in Estonia. Our results indicate that the composition of oomycetes in soils is strongly influenced by climatic factors, and, therefore, changes in climate conditions associated with global warming may have the potential to significantly alter the distribution range of these microbes, which comprise many important pathogens of plants.

Tolerant Epitypes of Elicited Holm Oak Somatic Embryos Could Be Revealed by Challenges in Dual Culture with Phytophthora cinnamomi Rands

Holm oaks (Quercus ilex L.) can suffer severe infection by the oomycete Phytophthora cinnamomi Rands; the production of more tolerant plants is, therefore, required. Embryo formation is a key period in the establishment of epigenetic memory. Somatic embryos from three holm oak genotypes were elicited, either over 3 days or 60 days, with methyl-jasmonate, salicylic acid (SA), β-aminobutyric acid (BABA), or benzothiadiazole (all at 50 μM and 100 μM), or 10% and 30% of a filtered oomycete extract (FILT10 and FILT30) to activate plant immune responses. The number of embryos produced and conversion rate under all conditions were recorded. Some elicited embryos were then exposed to P. cinnamomi in dual culture, and differential mycelial growth and the progression of necrosis were measured. The same was performed with the roots of germinated embryos. Within genotypes, significant differences were seen among the elicitation treatments in terms of both variables. Embryos and roots of 60-day BABA, SA, or FILT10 treatments inhibited mycelium growth. The 3-day BABA (either concentration) and 60-day FILT10 induced the greatest inhibition of necrosis. Mycelium and necrosis inhibition were compared with those of tolerant trees. Both inhibitions might be a defense response maintained after primed embryo germination, thus increasing the likelihood of tolerance to infection.

Into the void: ECM fungal communities involved in the succession from rockroses to oak stands

Oak forests accompanied by Cistus species are a common landscape in the Mediterranean basin. It is argued that Cistus dominated fields serve as recruitment areas for Quercus seedlings, as they help in the transmission of the fungal community through vegetative succession in these ecosystems. To test these assumptions, we analyzed the fungal community in terms of its richness and composition, taking into account the effects of host (Oaks vs. Cistus) and forest structure, mainly based on age. Edaphic variables related to the different structures were also analyzed to examine how they evolve through succession and relate to shifts in the fungal community. No differences in fungal richness were observed between old Cistus stands and younger Quercus, while a brief increase in ECM richness was observed. Community composition also showed a greater overlap between old Cistus and young Quercus stands. We suggest that the most important step in fungal transfer from one host to another is the shift from the oldest Cistus fields to the youngest Quercus stands, with the genera Amanita, Cortinarius, Lactarius, Inocybe, Russula, and Tomentella probably playing a major role. In summary, our work has also revealed the network of fungal community structure in the succession of Cistus to Oak stands, it would suggest that the fungi share niches and significantly enhance the ecological setting of the transition from Cistus to Oak stands.

Diversity of Pythium Species Recovered from Float-Bed Tobacco Transplant Production Greenhouses

Pythium diseases are common in hydroponic crop production and often threaten the greenhouse production of cucumber, tomato, lettuce, and other crops. In tobacco transplant production, where float-bed hydroponic greenhouses are commonly used, Pythium diseases can cause up to 70% seedling loss. However, there have been few comprehensive studies on the composition and diversity of Pythium communities in tobacco greenhouses. In a 2017 survey, 360 Pythium isolates were collected from 41 tobacco greenhouses across four states (VA, MD, GA, and PA). Samples were collected from one to seven sites within each greenhouse. Twelve described Pythium species were identified (P. adhaerens, P. aristosporum, P. attrantheridium, P. catenulatum, P. coloratum, P. dissotocum, P. inflatum, P. irregulare, P. myriotylum, P. pectinolyticum, P. porphyrae, and P. torulosum) among the isolates obtained. Approximately 80% of the surveyed greenhouses harbored Pythium in at least one of four sites (bay water, tobacco seedlings, weeds, and center walkways) within the greenhouse. The structure of Pythium communities was diverse among the surveyed greenhouses: multiple Pythium species coexisted in the same sample, and multiple species were present within the same greenhouse at different sites. This diversity appeared to be influenced by the sampling sites within the surveyed tobacco greenhouses, sample type, and sampling time. Intraspecific variation may also exist among the P. dissotocum populations found in this study. These results uncovered the complexity and diversity of the Pythium communities within float tobacco transplant greenhouses, which could play a role in the variation in Pythium diseases observed in these production systems.

Soil Chemistry and Soil History Significantly Structure Oomycete Communities in Brassicaceae Crop Rotations

Oomycetes are critically important in soil microbial communities, especially for agriculture, where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure vary through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but this has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year, these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested internal transcribed spacer amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. IMPORTANCE Oomycetes cause global plant diseases that result in substantial losses, yet they are highly understudied compared to other microbes, like fungi and bacteria. We wanted to investigate how past soil events, like changing crops in rotation, would impact subsequent oomycete communities. We planted different oilseed crops in three different soil histories and found that each soil history structured a distinct oomycete community regardless of which new oilseed crop was planted, e.g., oomycete communities from last year's lentil plots were still detected the following year regardless of which new oilseed crops we planted. This study demonstrated how different agricultural practices can impact future microbial communities differently. Our results also highlight the need for continued monitoring of oomycete biodiversity and quantification.

Effects of Trichoderma harzianum biofertilizer on growth, yield, and quality of Bupleurum chinense

The use of chemical fertilizers and pesticides led to a decline in the quality and yield of Bupleurum chinense. The aim of this study was to determine the effects of Trichoderma harzianum biofertilizer on the growth, yield, and quality of radix bupleuri and microbial responses. The results showed that T. harzianum biofertilizer promoted the growth of B. chinense and increased the yield and quality of radix bupleuri. In addition, it increased the contents of NH₄ ⁺-N, NO₃ ^--N, available K, and available P and increased the activities of sucrase and catalase in the rhizosphere soil. High-throughput analysis showed that the dominant bacteria in the rhizosphere were Proteobacteria (28%), Acidobacteria (23%), and Actinobacteria (17%), whereas the dominant fungi were Ascomycota (49%), Zygomycota (30%), and Basidiomycota (6%). After the application of T. harzianum biofertilizer, the abundance of Proteobacteria and Actinobacteria (relative to total bacteria) and Ascomycota and Basidiomycota (relative to total fungi) increased, but the relative abundance of Acidobacteria decreased. Canonical correlation analysis (CCA) showed that the relative abundance of Pseudarthrobacter, Streptomyces, Rhizobium, Nocardioides, Minimedusa, and Chaetomium were positively correlated with NO₃ ^--N, NH₄ ⁺-N, available K, available P, sucrase, and catalase in microbial communities, whereas Aeromicrobium and Mortierella were positively correlated with soil organic matter and urease. These results suggest that T. harzianum biofertilizer could significantly improve the yield and quality of radix bupleuri by changing the structure of soil microbial flora and soil enzyme activity. Therefore, it could be recommended for commercial scale production of Bupleurum.

Methods used for the study of endophytic fungi: a review on methodologies and challenges, and associated tips

Endophytic fungi are microorganisms that colonize the interior of plant tissues (e.g. leaves, seeds, stem, trunk, roots, fruits, flowers) in intracellular and/or extracellular spaces without causing symptoms of disease in host plants. These microorganisms have been isolated from plant species in a wide variety of habitats worldwide, and it is estimated that all terrestrial plants are colonized by one or more species of endophytic fungus. In addition, these microorganisms have been drawing the attention of researchers because of their ability to synthesize a wide range of bioactive molecules with potential for applications in agriculture, medicine and biotechnology. However, several obstacles come up when studying the diversity and chemical potential of endophytic fungi. For example, the usage of an inappropriate surface disinfection method for plant tissue may not eliminate the epiphytic microbiota or may end up interfering with the endophytic mycobiota, which consequently generates erroneous results. Moreover, the composition of the culture medium and the culture conditions can favor the growth of certain species and inhibit others, which generates underestimated results. Other inconsistencies can arise from the fungus misidentification and consequent exploration of its chemical potential. Based on the methodological biases that may occur at all stages of studies dealing with endophytic fungi, the objective of this review is to discuss the main methods employed in these studies as well as highlight the challenges derived from the different approaches. We also report associated tips to help future studies on endophytic fungi as a contribution.

Microbiota Modulation in Blueberry Rhizosphere by Biocontrol Bacteria

Microbial interactions in agricultural soils can play important roles in the control of soil-borne phytopathogenic diseases. Yields from blueberry plantations from southern Spain have been impacted by the pathogenic fungus, Macrophomina phaseolina. The use of chemical fungicides has been the common method for preventing fungal infections, but due to their high environmental impact, legislation is increasingly restricting its use. Biocontrol alternatives based on the use of microorganisms is becoming increasingly important. Using the metabarcoding technique, fungi and bacteria were characterized (via 16S and ITS regions, respectively) from rhizosphere soils of healthy and dead blueberry plants infected by M. phaseolina, and which had undergone three different treatments: two biocontrol strategies—one of them a mix of Pseudomonas aeruginosa and Bacillus velezensis and the other one with Bacillus amyloliquefaciens—and a third treatment consisting of the application of a nutrient solution. The treatments produced changes in the bacterial microbiota and, to a lesser extent, in the fungi. The abundance of Fusarium was correlated with dead plants, likely favoring the infection by M. phaseolina. The presence of other microorganisms in the soil, such as the fungi Archaeorhizomyces or the bacteria Actinospica, were correlated with healthy plants and could promote their survival. The different genera detected between dead and healthy plants opens the possibility of studying new targets that can act against infection and identify potential microorganisms that can be used in biocontrol strategies.

Comparison of Primers for the Detection of Phytophthora (and Other Oomycetes) from Environmental Samples

Many oomycetes are important plant pathogens that cause devastating diseases in agricultural fields, orchards, urban areas, and natural ecosystems. Limitations and difficulties associated with isolating these pathogens have led to a strong uptake of DNA metabarcoding and mass parallel sequencing. At least 21 primer combinations have been designed to amplify oomycetes, or more specifically, Phytophthora species, from environmental samples. We used the Illumina sequencing platform to compare 13 primer combinations on mock communities and environmental samples. The primer combinations tested varied significantly in their ability to amplify Phytophthora species in a mock community and from environmental samples; this was due to either low sensitivity (unable to detect species present in low concentrations) or a lack of specificity (an inability to amplify some species even if they were present in high concentrations). Primers designed for oomycetes underestimated the Phytophthora community compared to Phytophthora-specific primers. We recommend using technical replicates, primer combinations, internal controls, and a phylogenetic approach for assigning a species identity to OTUs or ASVs. Particular care must be taken if sampling substrates where hybrid species could be expected. Overall, the choice of primers should depend upon the hypothesis being tested.

New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?

The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as "What's in my soil?", to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.

Phytophthora spp. Associated with Appalachian Oak Forests and Waterways in Pennsylvania, with P. abietivora as a Pathogen of Five Native Woody Plant Species

To document the distribution of potentially harmful Phytophthora spp. within Pennsylvania, the Pennsylvania Department of Agriculture collected 89 plant, 137 soil, and 48 water samples from 64 forested sites during 2018 to 2020. In total, 231 Phytophthora strains were isolated using baiting assays and identified based on morphological characteristics and sequences of nuclear and mitochondrial loci. Twenty-one Phytophthora spp. in nine clades and one unidentified species were present. Phytophthora abietivora, a recently described clade 7a species, was recovered from diseased tissue of 10 native broadleaved plants and twice from soil from 12 locations. P. abietivora is most likely endemic to Pennsylvania based on pathogenicity tests on six native plant species, intraspecific genetic diversity, wide distribution, and recoveries from Abies Mill. and Tsuga Carrière plantations dating back to 1989. Cardinal temperatures and morphological traits are provided for this species. Other taxa, in decreasing order of frequency, include P. chlamydospora, P. plurivora, P. pini, P. cinnamomi, P. xcambivora, P. irrigata, P. gonapodyides, P. cactorum, P. pseudosyringae, P. hydropathica, P. stricta, P. xstagnum, P. caryae, P. intercalaris, P. 'bitahaiensis', P. heveae, P. citrophthora, P. macilentosa, P. cryptogea, and P. riparia. Twelve species were associated with diseased plant tissues. This survey documented 53 new plant-Phytophthora associations and expanded the known distribution of some species.

DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

Isolation techniques supplemented by sequencing of DNA from axenic cultures have provided a robust methodology for the study of Phytophthora communities in agricultural and natural ecosystems. Recently, metabarcoding approaches have emerged as new paradigms for the detection of Phytophthora species in environmental samples. In this study, Illumina DNA metabarcoding and a conventional leaf baiting isolation technique were compared to unravel the variability of Phytophthora communities in different environments. Overall, 39 rhizosphere soil samples from a natural, a semi-natural and a horticultural small-scale ecosystem, respectively, were processed by both baiting and metabarcoding. Using both detection techniques, 28 out of 39 samples tested positive for Phytophthora. Overall, 1,406,613 Phytophthora internal transcribed spacer 1 (ITS1) sequences and 155 Phytophthora isolates were obtained, which grouped into 21 taxa, five retrieved exclusively by baiting (P. bilorbang; P. cryptogea; P. gonapodyides; P. parvispora and P. pseudocryptogea), 12 exclusively by metabarcoding (P. asparagi; P. occultans; P. psycrophila; P. syringae; P. aleatoria/P. cactorum; P. castanetorum/P. quercina; P. iranica-like; P. unknown sp. 1; P. unknown sp. 2; P. unknown sp. 3; P. unknown sp. 4; P. unknown sp. 5) and four with both techniques (P. citrophthora, P. multivora, P. nicotianae and P. plurivora). Both techniques complemented each other in describing the variability of Phytophthora communities from natural and managed ecosystems and revealing the presence of rare or undescribed Phytophthora taxa.

Localized reshaping of the fungal community in response to a forest fungal pathogen reveals resilience of Mediterranean mycobiota

Mediterranean forests are facing the impact of pests such as the soilborne Phytophthora cambivora, the causal agent of Ink disease, and this impact is made more severe by global changes. The status and resilience of the soil microbial ecosystem in areas with such a disturbance are little known; however, the assessment of the microbial community is fundamental to preserve the ecosystem functioning under emerging challenges. We profile soil fungal communities in a chestnut stand affected by ink disease in Italy using metabarcoding, and couple high-throughput sequencing with physico-chemical parameters and dendrometric measurements. Since the site also includes an area where the disease symptoms seem to be suppressed, we performed several analyses to search for determinants that may contribute to such difference. We demonstrate that neither pathogen presence nor trees decline associate with the reduction of the residing community diversity and functions, but rather with microbial network reshaping through substitutions and new interactions, despite a conservation of core taxa. We predict interactions between taxa and parameters such as soil pH and C/N ratio, and suggest that disease incidence may also relate with disappearance of pathogen antagonists, including ericoid- and ectomycorrhizal (ECM) fungi. By combining metabarcoding and field studies, we infer the resilient status of the fungal community towards a biotic stressor, and provide a benchmark for the study of other threatened ecosystems.

MALDI-TOF MS as a method for rapid identification of Phytophthora de Bary, 1876

The number of described species of the oomycete genus Phytophthora is growing rapidly, highlighting the need for low-cost, rapid tools for species identification. Here, a collection of 24 Phytophthora species (42 samples) from natural as well as anthropogenic habitats were genetically identified using the internal transcribed spacer (ITS) and cytochrome c oxidase subunit I (COI) regions. Because genetic identification is time consuming, we have created a complementary method based on by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Both methods were compared and hypothesis that the MALDI-TOF MS method can be a fast and reliable method for the identification of oomycetes was confirmed. Over 3500 mass spectra were acquired, manually reviewed for quality control, and consolidated into a single reference library using the Bruker MALDI Biotyper platform. Finally, a database containing 144 main spectra (MSPs) was created and published in repository. The method presented in this study will facilitate the use of MALDI-TOF MS as a complement to existing approaches for fast, reliable identification of Phytophthora isolates.

Antagonistic Potential of Native Trichoderma spp. against Phytophthora cinnamomi in the Control of Holm Oak Decline in Dehesas Ecosystems

Phytophthora root rot caused by the pathogen Phytophthora cinnamomi is one of the main causes of oak mortality in Mediterranean open woodlands, the so-called dehesas. Disease control is challenging; therefore, new alternative measures are needed. This study focused on searching for natural biocontrol agents with the aim of developing integrated pest management (IPM) strategies in dehesas as a part of adaptive forest management (AFM) strategies. Native Trichoderma spp. were selectively isolated from healthy trees growing in damaged areas by P. cinnamomi root rot, using Rose Bengal selective medium. All Trichoderma (n = 95) isolates were evaluated against P. cinnamomi by mycelial growth inhibition (MGI). Forty-three isolates presented an MGI higher than 60%. Twenty-one isolates belonging to the highest categories of MGI were molecularly identified as T. gamsii, T. viridarium, T. hamatum, T. olivascens, T. virens, T. paraviridescens, T. linzhiense, T. hirsutum, T. samuelsii, and T. harzianum. Amongst the identified strains, 10 outstanding Trichoderma isolates were tested for mycoparasitism, showing values on a scale ranging from 3 to 4. As far as we know, this is the first report referring to the antagonistic activity of native Trichoderma spp. over P. cinnamomi strains cohabiting in the same infected dehesas. The analysis of the tree health status and MGI suggest that the presence of Trichoderma spp. might diminish or even avoid the development of P. cinnamomi, protecting trees from the worst effects of P. cinnamomi root rot.

Holm oak death is accelerated but not sudden and expresses drought legacies

The increase in abiotic and biotic stress driven by global change threatens forest ecosystems and challenges understanding of mechanisms producing mortality. Phytophthora spp. like P. cinnamomi (PHYCI) are among the most lethal pathogens for many woody species including Quercus spp. Dynamics of biotic agents and their hosts are complex and influenced by climatic conditions. We analysed radial growth trends of dead and live adult Quercus ilex trees from agrosilvopastoral open woodlands under intense land-use. A pronounced warming trend since the 1980s has coincided in these woodlands with high oak mortality rates generally attributed to PHYCI. Yet, tree mortality and latency of the pathogen could be expressed at variable time spans, whereas, like in many other forests worldwide, tree death could also be explained by other factors like drought. PHYCI was isolated from roots of all dead oaks from one region. Trees were younger than generally believed and ages of dead trees ranged between 38 and 230 years. Growth of dead trees reached a tipping point in 1980 and 1990 coincident with two-year extraordinary droughts. These dates set the start of growth declines up to 30 years before tree death. Live trees did not exhibit any recent growth decline. Tree growth was highly sensitive to climatic variability associated with water stress and climate-growth relationships suggested phenological changes since the 1980s. Live and dead trees showed differences in their sensitivity to moisture availability and temperature. The sensitivity of growth to climate was partially related to site environmental conditions. Simulated gross and net primary productivity were higher in live sites with less atmospheric demand for water. Tree death was not sudden but a slow multiannual process as expressed by radial growth declines likely triggered by drought. Regardless of the causal agent or mechanism, the observed mortality affected trees exhibiting negative drought and land-use legacies.

Transgenerational Induction of Resistance to Phytophthora cinnamomi in Holm Oak

The maternal environment of a tree species can influence the development and resistance of its offspring. Transgenerational induction of resistance is well known in plants but its occurrence in forest tree species has been less reported. Quercus ilex L. (holm oak) is a widespread Mediterranean tree species threatened by the invasive Phytophthora cinnamomi Rands pathogen. The influence of P. cinnamomi on the offspring of infected Q. ilex mother trees has not been studied. This study compared the performance and tolerance to P. cinnamomi of seedlings from non-infected and P. cinnamomi-infected trees. Acorns from Q. ilex trees were collected from five forests. After isolations were conducted in the rhizosphere of several trees, in each forest, three trees were selected as non-infected and three were selected as P. cinnamomi-infected. Forty acorns per tree were weighed and sown under greenhouse conditions, and when plants were aged ~9 months they were challenged with P. cinnamomi. Plant mortality was higher in the offspring of non-infected trees than in the offspring of P. cinnamomi-infected trees (26.2% vs. 21.1%, respectively). Consistently, survival probabilities of seedlings from P. cinnamomi-infected trees were higher than those of seedlings from non-infected trees, particularly in seedlings with reduced growth. Although acorns from healthy Q. ilex trees were heavier than acorns from P. cinnamomi-infected trees, the time to death of inoculated seedlings was not influenced by seed weight. The time to death of seedlings was positively related to belowground mass, particularly to an increased proportion of fine secondary roots. We report transgenerational-induced resistance to P. cinnamomi in Q. ilex triggered by an unknown mechanism independent of acorn mass. Information about the persistence of transgenerational effects in Q. ilex offspring and the influence of these effects on plant fitness is crucial to improve the management and regeneration of this declining species.

The fungal community associated with the ambrosia beetle Xylosandrus compactus invading the mediterranean maquis in central Italy reveals high biodiversity and suggests environmental acquisitions

In summer 2016 a severe infestation of the alien ambrosia beetle Xylosandrus compactus was recorded from the Mediterranean maquis in the Circeo National Park in Central Italy. Trees and shrubs were infested and displayed wilting and necrosis of terminal branches caused by the combined impact of the insect and associated pathogenic fungi. A preliminary screening carried out on captured adults resulted in the isolation of a discrete number of fungal taxa with different life strategies, ranging from true mutualist (e.g. Ambrosiella xylebori) to plant pathogens (Fusarium spp.). In the present study, high-throughput sequencing was applied to determine the total diversity and functionality of the fungal community associated with X. compactus adults collected in the galleries of three Mediterranean woody hosts, Quercus ilex, Laurus nobilis, and Ceratonia siliqua. The effect of season and host in determining the composition of the associated fungal community was investigated. A total of 206 OTUs composed the fungal community associated with X. compactus. Eighteen OTUs were shared among the three hosts, including A. xylebori and members of the Fusarium solani complex. All but two were previously associated with beetles. Sixty-nine out of 206 OTUs were resolved to species level, identifying 60 different fungal species, 22 of which already reported in the literature as associated with beetles or other insects. Functional guild assigned most of the fungal species to saprotrophs and plant pathogens. Effects of seasonality and host on fungal community assemblage were highlighted suggesting the acquisition by the insect of new fungal taxa during the invasion process. The consequences of enriched fungal community on the risk of the insurgence of novel threatful insect-fungus association are discussed considering direct and indirect effects on the invaded habitat.

An Overview of Phytophthora Species Inhabiting Declining Quercus suber Stands in Sardinia (Italy)

Cork oak forests are of immense importance in terms of economic, cultural, and ecological value in the Mediterranean regions. Since the beginning of the 20th century, these forests ecosystems have been threatened by several factors, including human intervention, climate change, wildfires, pathogens, and pests. Several studies have demonstrated the primary role of the oomycete Phytophthora cinnamomi Ronds in the widespread decline of cork oaks in Portugal, Spain, southern France, and Italy, although other congeneric species have also been occasionally associated. Between 2015 and 2019, independent surveys were undertaken to determine the diversity of Phytophthora species in declining cork oak stands in Sardinia (Italy). Rhizosphere soil samples were collected from 39 declining cork oak stands and baited in the laboratory with oak leaflets. In addition, the occurrence of Phytophthora was assayed using an in-situ baiting technique in rivers and streams located throughout ten of the surveyed oak stands. Isolates were identified by means of both morphological characters and sequence analysis of internal transcribed spacer (ITS) regions of ribosomal DNA. In total, 14 different Phytophthora species were detected. Phytophthora cinnamomi was the most frequently isolated species from rhizosphere soil, followed by P. quercina, P. pseudocryptogea, and P. tyrrhenica. In contrast, P. gonapodyides turned out to be the most dominant species in stream water, followed by P. bilorbang, P. pseudocryptogea, P. lacustris, and P. plurivora. Pathogenicity of the most common Phytophthora species detected was tested using both soil infestation and log inoculation methods. This study showed the high diversity of Phytophthora species inhabiting soil and watercourses, including several previously unrecorded species potentially involved in the decline of cork oak forests.

Surprising low diversity of the plant pathogen Phytophthora in Amazonian forests

The genus Phytophthora represents a group of plant pathogens with broad global distribution. The majority of them cause the collar and root-rot of diverse plant species. Little is known about Phytophthora communities in forest ecosystems, especially in the Neotropical forests where natural enemies could maintain the huge plant diversity via negative density dependence. We characterized the diversity of soil-borne Phytophthora communities in the North French Guiana rainforest and investigated how they are structured by host identity and environmental factors. In this little-explored habitat, 250 soil cores were sampled from 10 plots hosting 10 different plant families across three forest environments (Terra Firme, Seasonally Flooded and White Sand). Phytophthora diversity was studied using a baiting approach and metabarcoding (High-Throughput Sequencing) on environmental DNA extracted from both soil samples and baiting-leaves. These three approaches revealed very similar communities, characterized by an unexpected low diversity of Phytophthora species, with the dominance of two cryptic species close to Phytophthora heveae. As expected, the Phytophthora community composition of the French Guiana rainforest was significantly impacted by the host plant family and environment. However, these plant pathogen communities are very small and are dominated by generalist species, questioning their potential roles as drivers of plant diversity in these Amazonian forests.

Soil-borne pathogens as determinants of regeneration patterns at community level in Mediterranean forests

Emergent diseases are an increasing problem in forests worldwide. Exotic pathogens are now threatening forests where pathogens have not traditionally been considered to be major ecological drivers of tree demography, such as water-limited Mediterranean forests. However, how pathogens might limit regeneration in invaded forests is largely unknown. Here we used fungicide to analyse the impact of soil-borne oomycete pathogens on seedling establishment at community level in Mediterranean forests invaded by the exotic oomycete Phytophthora cinnamomi. Fungicide effects were modelled as a function of the tree neighbourhood composition, the seed mass of the target species, and the abiotic environment. Fungicide application had positive effects on seedling performance that varied in magnitude and spatial structure among coexisting species. Seed mass predicted fungicide effects on seedling emergence, but not on survival or growth. Positive fungicide effects were modulated by levels of abiotic resources, mainly water, increasing with soil moisture. Our results support a novel role for soil-borne oomycete pathogens as one more axis of the regeneration niche of woody species in water-limited forests. Given the increasing numbers of exotic oomycete pathogens worldwide, more research is needed to understand the role of this relevant microbial group as a factor shaping seedling establishment.

Microhabitat and ectomycorrhizal effects on the establishment, growth and survival of Quercus ilex L. seedlings under drought

The success of tree recruitment in Mediterranean holm oak (Quercus ilex) forests is threatened by the increasing intensity, duration and frequency of drought periods. Seedling germination and growth are modulated by complex interactions between abiotic (microhabitat conditions) and biotic factors (mycorrhiza association) that may mitigate the impacts of climate change on tree recruitment. To better understand and anticipate these effects, we conducted a germination experiment in a long-term precipitation reduction (PR) field experiment where we monitored seedling establishment and survival, micro-habitat conditions and ectomycorrhizal (ECM) colonization by different mycelia exploration types during the first year of seedling growth. We hypothesized that (i) the PR treatment decreases seedling survival relative to the control with ambient conditions, (ii) microhabitat conditions of water and light availability are better predictors of seedling survival than the PR treatment, (iii) the PR treatment will favour the development of ECM exploration types with drought-resistance traits such as differentiated rhizomorphs. Contrary to our first hypothesis, seedling survival was lower in control plots with overall higher soil moisture. Micro-habitat light and soil moisture conditions were better predictors of seedling survival and growth than the plot-level PR treatment, confirming our second hypothesis. Furthermore, in line with our third hypothesis, we found that ECM with longer extramatrical mycelia were more abundant in the PR treatment plots and were positively correlated to survival, which suggests a potential role of this ECM exploration type in seedling survival and recruitment. Although summer drought was the main cause of seedling mortality, our study indicates that drier conditions in spring can increase seedling survival, presumably through a synergistic effect of drought adapted ECM species and less favourable conditions for root pathogens.

Small-Scale Abiotic Factors Influencing the Spatial Distribution of Phytophthora cinnamomi under Declining Quercus ilex Trees

Phytophthora root rot is considered one of the main factors associated with holm oak (Quercus ilex L.) mortality. The effectiveness and accuracy of soilborne pathogen and management could be influenced by soil spatial heterogeneity. This factor is of special relevance in many afforestation of southwestern Spain, which were carried out without phytosanitary control of the nursery seedlings. We selected a study area located in a 15 year-old afforestation of Q. ilex, known to be infested by Phytophthora cinnamomi Rands. Soil samples (ntotal = 132) were taken systematically from a grid under 4 trees, and analysed to quantify 12 variables, the colony forming units (cfu) of P. cinnamomi plus 11 physical and chemical soil properties. The combined analysis of all variables was performed with linear mixed models (GLMM), and the spatial patterns of cfu were characterised using an aggregation index (Ia) and a clustering index (ν) by SADIE. Cfu values ranged from 0 to 211 cfu g−1, and the GLMM built with the variables silt, P, K and soil moisture explained the cfu distribution to the greatest extent. The spatial analysis showed that 9 of the 12 variables presented spatial aggregation (Ia > 1), and the clustering of local patches (νi ≥ 1.5) for organic matter, silt, and Ca. The spatial patterns of the P. cinnamomi cfu under planted holm oak trees are related to edaphic variables and canopy cover. Small-scale spatial analysis of microsite variability can predict which areas surrounding trees can influence lower oomycetes cfu availability.

Diversity of Phytophthora Species Associated with Quercus ilex L. in Three Spanish Regions Evaluated by NGS

The diversity of Phytophthora species in declining Fagaceae forests in Europe is increasing in the last years. The genus Quercus is one of the most extended Fagaceae genera in Europe, and Q. ilex is the dominant tree in Spain. The introduction of soil-borne pathogens, such as Phytophthora in Fagaceae forests modifies the microbial community present in the rhizosphere, and has relevant environmental and economic consequences. A better understanding of the diversity of Phytophthora spp. associated with Q. ilex is proposed in this study by using Next Generation Sequencing (NGS) in six Q. ilex stands located in three regions in Spain. Thirty-seven Phytophthora phylotypes belonging to clades 1 to 12, except for clades 4, 5 and 11, are detected in this study, which represents a high diversity of Phytophthora species in holm oak Spanish forests. Phytophthora chlamydospora, P. citrophthora, P. gonapodyides, P. lacustris, P. meadii, P. plurivora, P. pseudocryptogea, P. psychrophila and P. quercina were present in the three regions. Seven phylotypes could not be associated with known Phytophthora species, so they were putatively named as Phytophthora sp. Most of the detected phylotypes corresponded to terrestrial Phytophthora species but aquatic species from clades 6 and 9 were also present in all regions.

Oomycete metabarcoding reveals the presence of Lagenidium spp. in phytotelmata

The oomycete genus Lagenidium, which includes the mosquito biocontrol agent L. giganteum, is composed of animal pathogens, yet is phylogenetically closely related to the well characterized plant pathogens Phytophthora and Pythium spp. These phylogenetic affinities were further supported by the identification of canonical oomycete effectors in the L. giganteum transcriptome. In this study, culture-independent, metabarcoding analyses aimed at detecting L. giganteum in bromeliad phytotelmata (a proven mosquito breeding ground) microbiomes were performed. Two independent and complementary microbial detection strategies based on the amplification of cox1 DNA barcodes were used and produced globally concordant outcomes revealing that two distinct Lagenidium phylotypes are present in phytotelmata. A total of 23,869 high quality reads were generated from four phytotelmata, with 52%, and 11.5% of these reads taxonomically associated to oomycetes, and Lagenidium spp., respectively. Newly designed Lagenidium-specific cox1 primers combined with cloning/Sanger sequencing produced only Lagenidium spp. sequences, with a majority of variants clustering with L. giganteum. High throughput sequencing based on a Single Molecule Real Time (SMRT) approach combined with broad range cox1 oomycete primers confirmed the presence of L. giganteum in phytotelmata, but indicated that a potentially novel Lagenidium phylotype (closely related to L. humanum) may represent one of the most prevalent oomycetes in these environments (along with Pythium spp.). Phylogenetic analyses demonstrated that all detected Lagenidium phylotype cox1 sequences clustered in a strongly supported, monophyletic clade that included both L. giganteum and L. humanum. Therefore, Lagenidium spp. are present in phytotelmata microbiomes. This observation provides a basis to investigate potential relationships between Lagenidium spp. and phytotelma-forming plants, and reveals phytotelmata as sources for the identification of novel Lagenidium isolates with potential as biocontrol agents against vector mosquitoes.

Fungal community associated with adults of the chestnut gall wasp Dryocosmus kuriphilus after emergence from galls: Taxonomy and functional ecology

The diversity of the fungal community associated with adults of Dryocosmus kuriphilus following emergence was examined using HTS analysis. Ascomycota dominated the fungal core-biome community. The functional guilds of the 90 taxa forming the core-biome were assessed, demonstrating three main groups: saprotrophs, plant pathogens and entomopathogens. Twenty-nine OTUs out of 90 were resolved to species level identifying 26 different fungal species. Among these species, many were cosmopolitan or previously recorded in Europe. Ten taxa were previously recorded on chestnut, including some recognized plant pathogens associated with foliage and green tissues such as Epicoccum nigrum, Gnomoniopsis castanea, Colletotrichum acutatum, Stromatoseptoria castaneicola, Ramularia endophylla. Beauveria bassiana; within the core microbiome, Fusarium larvarum represented the most abundant entomopathogenic species. Some of these species are known to impact directly or indirectly the vitality of the insects in the galls. The chestnut blight pathogen, Cryphonectria parasitica, was never found associated with D. kuriphilus. Based on the present study, an active role for D. kuriphilus as a vector of chestnut fungal endophyte/pathogens cannot be demonstrated but neither ruled out.