Matteo Garbelotto

Phytophthora ramorum as the cause of extensive mortality of Quercus spp. and Lithocarpus densiflorus in California.

A new canker disease, commonly known as sudden oak death, of Lithocarpus densiflorus, Quercus agrifolia, Q. kelloggii, and Q. parvula var. shrevei in California is shown to be caused by Phytophthora ramorum. The pathogen is a recently described species that previously was known only from Germany and the Netherlands on Rhododendron spp. and a Viburnum sp. This disease has reached epidemic proportions in forests along approximately 300 km of the central coast of California. The most consistent and diagnostic symptoms on trees are cankers that develop before foliage symptoms become evident. Cankers have brown or black discolored outer bark and seep dark red sap. Cankers occur on the trunk at the root crown up to 20 m above the ground, but do not enlarge below the soil line into the roots. Individual cankers are delimited by thin black lines in the inner bark and can be over 2 m in length. In L. densiflorus saplings, P. ramorum was isolated from branches as small as 5 mm in diameter. L. densiflorus and Q. agrifolia were inoculated with P. ramorum in the field and greenhouse, and symptoms similar to those of naturally infected trees developed. The pathogen was reisolated from the inoculated plants, which confirmed pathogenicity.

Sudden oak death: endangering California and Oregon forest ecosystems

Sudden oak death is a new disease affecting tanoak (Lithocarpus densiflora) and oaks (Quercus spp) in California and Oregon, caused by the recently described pathogen Phytophthora ramorum. It has reached epidemic proportions in several counties in central California, leading to the death of tens of thousands of trees. In addition to oaks and tanoak, P ramorum has been found in nearly all woody plant species in mixed evergreen and redwood forests from central California to southern Oregon. Plant species that are not killed appear to serve as a reservoir for the pathogen. The high susceptibility of tanoak to infection and death suggests that P ramorum is an exotic pathogen, but its origins, and most details of its biology and ecology, remain unknown. Our limited knowledge only compounds our concern over the long-term implications of this epidemic for the ecology of coastal forests.

A sequence database for the identification of ectomycorrhizal basidiomycetes by phylogenetic analysis

We have assembled a sequence database for 80 genera of Basidiomycota from the Hymenomycete lineage (sensu Swann & Taylor 1993) for a small region of the mitochondrial large subunit rRNA gene. Our taxonomic sample is highly biased toward known ectomycorrhizal (EM) taxa, but also includes some related saprobic species. This gene fragment can be amplified directly from mycorrhizae, sequenced, and used to determine the family or subfamily of many unknown mycorrhizal basidiomycetes. The method is robust to minor sequencing errors, minor misalignments, and method of phylogenetic analysis. Evolutionary inferences are limited by the small size and conservative nature of the gene fragment. Nevertheless two interesting patterns emerge: (i) the switch between ectomycorrhizae and saprobic lifestyles appears to have happened convergently several and perhaps many times; and (ii) at least five independent lineages of ectomycorrhizal fungi are characterized by very short branch lengths. We estimate that two of these groups radiated in the mid-Tertiary, and we speculate that these radiations may have been caused by the expanding geographical range of their host trees during this period. The aligned database, which will continue to be updated, can be obtained from the following site on the WorldWide Web: http://mendel.berkeley.edu/boletus.html.

Microsatellite markers identify three lineages of Phytophthora ramorum in US nurseries, yet single lineages in US forest and European nursery populations

Analysis of 12 polymorphic simple sequence repeats identified in the genome sequence of Phytophthora ramorum, causal agent of ‘sudden oak death’, revealed genotypic diversity to be significantly higher in nurseries (91% of total) than in forests (18% of total). Our analysis identified only two closely related genotypes in US forests, while the genetic structure of populations from European nurseries was of intermediate complexity, including multiple, closely related genotypes. Multilocus analysis determined populations in US forests reproduce clonally and are likely descendants of a single introduced individual. The 151 isolates analysed clustered in three clades. US forest and European nursery isolates clustered into two distinct clades, while one isolate from a US nursery belonged to a third novel clade. The combined microsatellite, sequencing and morphological analyses suggest the three clades represent distinct evolutionary lineages. All three clades were identified in some US nurseries, emphasizing the role of commercial plant trade in the movement of this pathogen.

AFLP and phylogenetic analyses of North American and European populations of Phytophthora ramorum

The genetic structure within and between USA and European populations of the emerging phytopathogen Phytophthora ramorum was examined. Four primer combinations were used for amplified fragment length polymorphism (AFLP) fingerprinting of 67 USA isolates from California and Oregon, and 18 European isolates from Belgium, Germany, The Netherlands, Spain and the UK. In addition, three DNA regions (ITS, cox II, and nad 5) of additional Phytophthora species were amplified by polymerase chain reaction, sequenced, and analysed to provide better phylogenetic understanding of P. ramorum within the genus Phytophthora. AFLP banding patterns indicate that the 85 isolates form two distinct lineages within a monophyletic group, distinct from the closely related outgroup species P. lateralis. With the exception of two isolates from an Oregon nursery, European and USA isolates clustered separately within individual clades. The AFLP profiles also indicate that a single clonal lineage dominates the North American population, while the European population consists of an array of mainly unique, closely related AFLP types. Sequences from the three DNA regions were identical among all P. ramorum isolates, and phylogenetic analysis indicates that P. ramorum is closely related to P. lateralis and P. hibernalis.

Emergence of the sudden oak death pathogen Phytophthora ramorum

The recently emerged plant pathogen Phytophthora ramorum is responsible for causing the sudden oak death epidemic. This review documents the emergence of P. ramorum based on evolutionary and population genetic analyses. Currently infection by P. ramorum occurs only in Europe and North America and three clonal lineages are distinguished: EU1, NA1 and NA2. Ancient divergence of these lineages supports a scenario in which P. ramorum originated from reproductively isolated populations and underwent at least four global migration events. This recent work sheds new light on mechanisms of emergence of exotic pathogens and provides crucial insights into migration pathways.

Insight into trade???off between wood decay and parasitism from the genome of a fungal forest pathogen

Parasitism and saprotrophic wood decay are two fungal strategies fundamental for succession and nutrient cycling in forest ecosystems. An opportunity to assess the trade-off between these strategies is provided by the forest pathogen and wood decayer Heterobasidion annosum sensu lato. We report the annotated genome sequence and transcript profiling, as well as the quantitative trait loci mapping, of one member of the species complex: H. irregulare. Quantitative trait loci critical for pathogenicity, and rich in transposable elements, orphan and secreted genes, were identified. A wide range of cellulose-degrading enzymes are expressed during wood decay. By contrast, pathogenic interaction between H. irregulare and pine engages fewer carbohydrate-active enzymes, but involves an increase in pectinolytic enzymes, transcription modules for oxidative stress and secondary metabolite production. Our results show a trade-off in terms of constrained carbohydrate decomposition and membrane transport capacity during interaction with living hosts. Our findings establish that saprotrophic wood decay and necrotrophic parasitism involve two distinct, yet overlapping, processes.

Impacts of climate change on plant diseases—opinions and trends

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases. This overview addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies on the impacts of climate change on plant health. Sudden Oak Death is used as an introductory case study: Californian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronicity between host cambium activity and pathogen colonization rate. A summary of observed and predicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Prediction and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertainty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to interdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in mountain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (including our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycorrhiza, using long-term and large-scale datasets and considering various plant disease control methods.

Detection and Quantification of Phytophthora ramorum from California Forests Using a Real-Time Polymerase Chain Reaction Assay

ABSTRACT The timely and accurate detection of pathogens is a critical aid in the study of the epidemiology and biology of plant diseases. In the case of regulated organisms, the availability of a sensitive and reliable assay is essential when trying to achieve early detection of the pathogen. We developed and tested a real-time, nested polymerase chain reaction (PCR) assay for the detection of Phytophthora ramorum, causal agent of sudden oak death. This technique then was implemented as part of a widespread environmental screen throughout California. The method here described is sensitive, detecting less than 12 fg of pathogen DNA, and is specific for P. ramorum when tested across 21 Phytophthora spp. Hundreds of symptomatic samples from 33 sites in 14 California counties were assayed, resulting in the discovery of 10 new host species and 23 infested areas, including 4 new counties. With the exception of a single host, PCR-based discovery of new hosts and infested areas always was confirmed by traditional pathogen isolations and inoculation studies. Nonetheless, molecular diagnostics were key in early pathogen detection, and steered the direction of further research on this newly discovered and generalist Phytophthora species.

Reconstruction of the Sudden Oak Death epidemic in California through microsatellite analysis of the pathogen Phytophthora ramorum

The genetic structure of the clonally reproducing Sudden Oak Death (SOD) pathogen in California was investigated using seven variable microsatellites. A total of 35 multilocus genotypes were identified among 292 samples representative of populations from 14 forest sites and of the nursery trade. amova indicated significant genetic variability both within (44.34%) and among populations (55.66%). Spatial autocorrelation analyses indicated that Morans index of similarity reached a minimum of 0.1 at 350 m, increased to 0.4 at 1500 m and then decreased to zero at 10 km. These results suggest a bimodal pattern of spread, with medium range dispersal (1500–10 000 m) putatively attributed to the presence of strong winds. Lack of genetic structure was identified for three groups of populations. One group notably included the nurseries’ population and two forest populations, both linked to early reports of the pathogen. A neighbour‐joining analysis based on pairwise ΦST values indicated that the clade inclusive of the nurseries’ populations is basal to all California populations. A network analysis identified three common genotypes as the likely founders of the California infestation and proposes a stepwise model for local evolution of novel genotypes. This was supported by the identification in the same locations of novel genotypes and of their 1‐ or 2‐step parents. We hypothesize that the few undifferentiated population groups indicate historical human spread of the pathogen, while the general presence of genetically structured populations indicates that new infestations are currently generated by rare medium or long‐range natural movement of the pathogen, followed by local generation of new genotypes.