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Alan J. L. Phillips

Principal Researcher, Centro de Recursos Microbiológicos

 

PhD, University of Wolverhampton, England, 1980

 

 

 

 

 

 


Scientific Interests

In broad terms, my research interests focus on fungal plant pathogens. Until 1995, when I moved to Portugal, my work was concentrated on epidemiology of diseases, and development of control measures.  The principle disease I have studied are Sclerotinia head rot of sunflowers, white mould of beans and bean scab.

 More recently I have focussed my attention on the taxonomy of fungal plant pathogens with the aim of ensuring correct identification and distinguishing pathogenic from non-pathogenic species.  At present I am particularly interested in the genus Botryosphaeria.  Fungi in this genus are pathogens of a wide variety of plants and cause considerable economic damage.  This genus, created in 1863, has been surrounded by a great deal of confusion.  About 220 species have been described and of these less than 20 are currently recognised.  Of the 900 Diplodia anamorphs and 160 or so Fusicoccum anamorphs, only a few have been definitively linked to the teleomorph.  This has added further confusion and has made identifications difficult.  To unravel some of these species complexes I am using a combination of morphological and and molecular techniques to develop clear, unambiguous species definitions.  I am currently undertaking a revision of the genus Diplodia, which is one of the anamorph genera linked to Botryosphaeria. To help keep track of how things are changing in the genus, I have developed and maintain a web site devoted to Botryosphaeria.

In additon to Botryosphaeria, I keep an interest in the genus Diaporthe.  This genus has fascinated me for a number of years and I keep a low level project running with the hope that one day I will be able to secure funding to develop the work. 


Recent publications:

Phillips, A.J.L., Crous, P.W & Alves, A. (2007). Diplodia seriata, the anamorph of “Botryosphaeriaobtusa. Fungal Diversity 25: 141–155.

Alves, A., Phillips, A,J.L., Henriques, I. & Correia, A. (2007).  Rapid identification of Botryosphaeria species by PCR fingerprinting.  Research in Microbiology 158: 112–121.

Alves, A., Correia, A. & Phillips, A.J.L. (2006).  Multiple gene genealogies and morphological data support Diplodia cupressi sp. nov., previously recognized as D. pinea f. sp. cupressi, as a distinct species.  Fungal Diversity 23: 1–15.

Crous, P.W., Slippers, B., Wingfield, M.J., Rheeder, J., Marasas, W.F.O., Phillips, A.J.L., Alves, A., Burgess, T., Barber, P. & Groenewald, J.Z. (2006).  Resolving phylogenetic lineages in the BotryosphaeriaceaeStudies in Mycology 55: 235–253.

Phillips, A.J.L., Oudemans, P., Correia, A. & Alves, A. (2006).  Characterisation and epitypification of Botryosphaeria corticis, the cause of blueberry stem canker.  Fungal Diversity 21: 141–155.

Santos, C., Fragoeiro, S., Valentim H. & Phillips, A.J.L. (2006).  Phenotypic characterisation of Phaeoacremonium and Phaeomoniella strains isolated from grapevines: enzyme production and virulence of extra-cellular filtrate on grapevine calluses Scientia Horticulturae 107: 123–130.

Santos, C., Fragoeiro, S., Oliveira, H & Phillips, A.J.L. 2006.  Response of Vitis vinifera L. plants inoculated with Phaeoacremonium angustius and Phaeomoniella chlamydospora to thiabendazole, resveratrol and sodium arsenite. Scientia Horticulturae 107: 131–136.

 Luque, J., Martos, S. & Phillips, A.J.L. (2005).  Botryosphaeria viticola sp. nov on grapevines: a new species with a Dothiorella anamorph.  Mycologia 97: 111–1121.

Alves, A., Phillips, A. J. L., Henriques, I. & Correia A. (2005).  Evaluation of amplified ribosomal DNA restriction analysis (ARDRA) as a method for the identification of Botryosphaeria species.  FEMS Microbiology Letters 245: 221–229.

 Phillips, A. J. L., Rumbos, J., Alves, A. & Correia, A. (2005).  Morphology and phylogeny of Botryosphaeria dothidea causing fruit rot of olives.  Mycopathologia 159: 433–439.

Phillips, A.J.L., Alves, A., Correia, A. & Luque, J. (2005).  Two new species of Botryosphaeria with brown, one-septate ascospores and Dothiorella anamorphs.  Mycologia 97: 513–529.

 Santos, C., Fragoeiro, S & Phillips, A.J.L. (2005).  Physiological response of grapevine cultivars and a rootstock to infection with Phaeoacremonium and Phaeomoniella isolates: an in vitro approach using plants and calluses.  Scientia Horticulturae 103: 187–198.

Alves, A., Henriques, I., Fragoeiro, S., Santos, C., Phillips, A. & Correia, A. (2004).  Applicability of rep-pcr genomic fingerprinting to molecular discrimination of members of the genera Phaeoacremonium and Phaeomoniella. Plant Pathology 53: 629–634.

Alves, A., Correia, A., Luque, J, & Phillips, A.J.L. (2004).  Botryosphaeria corticola sp. nov. on Quercus species, with notes and description of Botryosphaeria stevensii and its anamorph, Diplodia mutila.  Mycologia 96 (3), 598–613.

Phillips, A.J.L. (2003).  Morphological characterization of Diaporthe foeniculacea and related species on Foeniculum vulgaris.  Sydowia 54 (2), 274285.

Sánchez, M.E., Venegas, J., Phillips, A.J.L. & Trapero, A. (2003).  Botryosphaeria and related taxa causing oak canker in southwestern Spain.  Plant Disease 87, 1515–1521.

Phillips, A.J.L. (2002).  Botryosphaeria species associated with diseases of grapevines in Portugal.  Phytopathologia Mediterranea 41, 3–18.

Phillips, A.J.L., Fonseca, F., Povoa V. Castilho, R. & Nolasco, G. (2002).  A reassessement of the anamorphic fungus Fusicoccum luteum and description of its teleomorph Botryosphaeria lutea sp. nov.  Sydowia 54 (1), 59–77.

Mostert, L,. Crous, P. W., Kang, J-C. & Phillips A. J.L. (2001).  Species of Phomopsis and a Libertella sp. occurring on grapevines with specific reference to South Africa: morphological, cultural, molecular and pathological characterization.  Mycologia 93, 146–167.

Phillips, A.J.L. (2000).  Excoriose, cane blight and related diseases of grapevines: a taxonomic review of the pathogens.  Phytopathologia Mediterranea 39: 339–354.

Phillips, A.J.L. (2000).  Botryosphaeria populi sp. nov. and its anamorph Fusicoccum populi sp. nov. on poplar trees in Portugal.  Mycotaxon 76, 135–140.

Rego, C., Oliveira, H., Carvalho, A. & Phillips, A. (2000).  Involvement of Phaeoacremonium spp. and Cylindrocarpon destructans with grapevine decline in Portugal.  Phytopathologia Mediterranea 39: 76–79.

Phillips, A.J.L. (1999).  The relationship between Diaporthe perjuncta and Phomopsis viticola on grapevines.  Mycologia 91: 1001–1007.

Mchau, G.R.A., Crous, P.W., & Phillips, A.J.L. (1998).  Molecular characterisation.of some Elsinoë isolates from leguminous hosts.  Plant Pathology 47: 773–779.

Phillips, A.J.L. (1998).  Botryosphaeria dothidea and other fungi associated with excoriose and dieback of grapevines in Portugal.  Journal of Phytopathology 146, 327–332.

Phillips, A.J.L. & Lucas, M. T. (1997).  The taxonomic status of Macrophoma flaccida and Macrophoma reniformis and their relationship to Botryosphaeria dothidea.  Sydowia 49, 150–159.

 


Current Projects:

The plant pathogenic genus Phomopsis and its teleomorph (Diaporthe): Development and application of morphological, biological and phylogenetic species concepts.

 Funded by Fundação para a Ciência e a Tecnologia

POCTI/AGR/56140/2004

Summary

The genus Phomopsis and its teleomorph genus Diaporthe include several economically important plant pathogens. They are not all host specific; the same species can occur on several different hosts and more than one species can occur on a single host. In this way, common weed species can act as alternative hosts for pathogens of economically important crops. Furthermore, these fungi frequently live as endophytes that cause no visible harm to the host, but under the right conditions they can become pathogens.

 There has been no critical reappraisal of the genera in recent years. Wehmeyer (1933) considered host association to be of minor importance when he revised the genus Diaporthe. In so doing he reduced the 650 species to only 70. However, his work was based solely on morphology of the teleomorph and no anamorph characters were taken into account. This treatment is considered too conservative and several of his synonymies are thought to include distinct species. Phomopsis species were also described largely on host association. This resulted in a proliferation of names and currently more than 1000 species are known. Although host is now considered to be of minor importance in defining species, there has been no revision of the genus. A Diaporthe state has been described for only about 20% of Phomopsis species.

 Correct identification of a pathogen is an essential step towards meaningful studies on epidemiology and control of a disease. It is also essential for the implementation of phytosanitary measures. However, identifications of species within these two genera are difficult because the species are not clearly defined and there is considerable overlap of morphological features between them. Indeed it is virtually impossible to identify many of the species with any degree of certainty. Therefore there is a need for robust concepts that can be used to define the species in Phomopsis.

 To stabilize species names, living cultures linked to the type specimen should be available. These can then be used for isolation of DNA and subsequent analyses of gene sequences. In the absence of an ex-type culture (which is the case for most Phomopsis species) it is necessary to select a suitable epitype specimen with an associated ex-epitype culture.  Ideally this should be done for all species that have been described in Phomopsis. However, considering the number of species described in the genus, this is clearly not possible within the timeframe of the proposed project. Therefore a selection of hosts and associated Phomopsis species will be studied as models. Hosts to be studied are the stone fruit crops almond and peach, which are important crops in Portugal and are known to be affected by Phomopsis. In addition we aim to study the species that ocurr on selected weeds and ornamentals including Foeniculum vulgare, Hydrangea spp. and Cytisus spp. These weeds are common, widespread and known to harbour Phomopsis spp.

 The hosts will be sampled and isolations made from single conidia, or single ascospores if the Diaporthe state is present. Isolates will be characterised in terms of morphology, growth habit, and MSP-PCR profiles. The ITS1-5.8S-ITS2 region will be sequenced and compared with sequences available in GenBank. The EF1-a and other genes will also be sequenced if necessary. Mating behaviour will also be studied and used as a means to determine biological species limits. By comparing the morphological data with type specimens and original descriptions, species names will be applied. Typical specimens will be selected, proposed as epitype and deposited in a herbarium. Ex-epitype cultures will be deposited in a publicly accessible, international culture collection. Species will be described in terms of morphological, biological and phylogenetic species concepts.

 The outcome of this project will include 1) knowledge of the complexes of species that ocurr on each of the hosts to be studied. 2) Full descriptions in terms of morphological, biological and phylogenetic species concepts. 3) Epitype specimens and ex-epitype cultures of each species. 4) robust concepts that can be applied to circumscribe species in Phomopsis and Diaporthe. 5) Connections between some Phomopsis species and their corresponding Diaporthe anamorphs.

 

The genus Boryosphaeria in Portugal: Species with anamorphs in Diplodia and Dothiorella and pathogens of woody hosts.

 Funded by Fundação para a Ciência e a Tecnologia

POCTI/AGR/56140/2004

Summary

The genus Botryosphaeria includes species that are pathogens, saprophytes or endophytes on a wide range of Angiosperm and Gymnosperm hosts. The pathogenic species are responsible for considerable economic losses, mainly on woody hosts. Significant diseases known from Portugal include canker and dieback of cork oak (B. corticola), dieback and berry rot of grapevines (B. parva, B. stevensii, B. obtusa), black rot of apples (B. obtusa) white rot of apple (B. stevensii), dieback and drupe rot of olives (B. obtusa, B. dothidea) and blight of pine trees (D. pinea).

 Teleomorphs of Botryosphaeria species are uncommon in nature and their morphology differs little between species. Thus, taxonomy of the genus and species differentiation is based mainly on the anamorphs, which show considerable variation in morphology.

 Botryosphaeria anamorphs belong in Fusicoccum (hyaline, aseptate conidia), or Diplodia (hyaline or coloured, aseptate or one-septate conidia). The PI recently proposed that Dothiorella should be reinstated for species with coloured, one-septate conidia. Lasiodiplodia has been applied to species with striate conidia. These four anamorph genera are well-supported by ITS sequence data.

 The taxonomy and pathology of Fusicoccum has been studied intensively. Diplodia, on the other hand, has received little attention and several taxonomic problems need to be resolved. Thus, B. obtusa and D. pinea form a large complex with some isolates restricted to pine trees, while others from diverse hosts differ in their pathogenicity. Preliminary studies by the PI have shown that isolates of B. stevensii from apples, grapevines and Fraxinus are morphologically and phylogenetically distinct from one another.

 Diagnosis of a disease relies on correct identification of the pathogen. At present it is not possible to accurately diagnose diseases caused by Botryosphaeria species with Diplodia anamorphs. Therefore, the aim of this project is to resolve the complexes into species that relate to their pathology. These studies will be based on a large collection of isolates with Diplodia and Dothiorella anamorphs from various hosts. The isolates will be characterized in terms of micromorphology, cultural characters and MSP-PCR fingerprints. Species names will be assigned according to the current concepts. Relationships amongst and between these morphological species will be determined through analysis of ITS sequences and supplemented with data from EF1-alpha and beta-tubulin gene sequences. It is envisaged that sequences of several other protein coding genes will be needed to resolve the B. obtusa-D. pinea complex. Finally, attempts will be made to develop a rapid, PCR-based identification system to discriminate the different species in these complexes.

 

Previous projects

Characterization and genetic diversity of Botryosphaeria stevensii and other species of Botryosphaeria associated with cork oak (Quercus suber).

 Funded by Fundação para a Ciência e a Tecnologia

POCTI/AGR/44348/2002

Summary

The cork oak (Quercus suber) is native to the western parts of the Mediterranean basin and is abundant in the southern parts of Portugal.  It is not only the source of considerable income from exports of the product, but it also plays an important role in protecting soils from desertification. Together with other species, cork oak forests form a unique ecosystem that is home to rare and threatened bird and animal species including the Iberian Lynx.

Since the 1980's, a decline type disease of oaks has been recognised throughout the mediterranean basin. Amongst other factors, dieback and cankers caused by Botryosphaeria species, especially B. stevensii, are thought to contribute to the decline. However, taxonomy of this fungus genus is confused, the species are not always clearly defined and identification is difficult. Indeed, two concepts have been applied to the species most often quoted as the cause of dieback and canker of cork oaks (B. stevensii). Since species of Botryosphaeria can be pathogens, endophytes or saprophytes, correct identification is critical for a complete understanding of their role in cork oak decline.

This project aims to determine the species of Botryosphaeria that occur as pathogens, saprophytes or endophytes on cork oak. Identification will initially be based on micromorphology of the anamorph and teleomorph and confirmed by phylogenetic analyses of the nuclear ribosomal DNA internal transcribed spacers, and protein encoding genes such as beta tubulin or chitin synthase. Data generated by these studies will be augmented by pathogenicity tests and cultural characters. This will provide knowledge of the species of Botryosphaeria that occur on cork oak and indicate which are able to cause disease.

In addition to the identifications and phylogenetic studies, genetic variation and variability within B. stevensii will be studied. This will be based on populations isolated from diseased and healthy trees so that endophytic and presumptive pathogenic isolates can be compared. Isolations will be made from material collected from a hierarchical sampling of cork groves in the main production areas of Alentejo and from non-commercial stands in other regions. These strains will be compared with others from Spain and Italy. Genetic variability will be gauged on the basis of MSP-PCR, ARDRA and ribotyping which allow differentiation at either species or strain level.  In addition to the PCR-based techniques, strains will be characterised by electrophoretic karyotyping.

The outcome of this study will be a fuller understanding of the species of Botryosphaeria that are associated with cork oaks and their association with oak decline. The species will be fully characterised thus enabling clear separation and application of solid species concepts. The relationship between endophytic and pathogenic species will established, which will indicate the possible role of endophytes in disease.

 

 

Black foot of grapevine: distribution, characterisation, genetic diversity and control of Cylindrocarpon species associated with the disease

Funded by Fundação para a Ciência e a Tecnologia

POCTI/AGR/46239/2002

Co-worker

Summary

Black-foot disease of grapevine, caused by Cylindrocarpon spp., is a serious problem in several grape-growing regions of the world, and one of the major threats to the stable production of grapes. Both C. destructans and C. obtusisporum have been reported to incite the disease, but criteria used to distinguish these two closely related species remains ambiguous and are based mainly on morphological characteristics. Cylindrocarpon destructans (teleomorph: Neonectria radicicola) is a fungus with wide morphological variation and it is possible that this variation could encompass those of C. obtusisporum.

In the present study a polyphasic approach is proposed to assess the inter- and intraspecific variability of Cylindrocarpon species infecting grapevines and other hosts to resolve their taxonomy and phylogeny. Different  morphological characters, mating studies and molecular data from ITS, mtSSU and beta-tubulin sequences will be used to characterise a wide Cylindrocarpon collection providing knowledge of the species associated with black-foot disease of grapevine, on the basis of a clear and unambiguous species concept. The genetic diversity of Cylindrocarpon spp. infecting grapevine will be assessed by using  wide-molecular markers (AP-PCR tools, such as RAPDs and ISSRs, and AFLPs). Data from these studies will allow a better understanding of  the structure of the Cylindrocarpon populations infecting grapevine and the development of species-specific primers to detect the pathogens associated with black-foot disease.

Cylindrocarpon destructans is a soil-borne fungus with a wide host-range but in some host-pathogen combinations  it has been considered an opportunistic pathogen. However, in addition to grapevine, economic impacts due to C. destructans have been reported worldwide on replanted apple orchards and forest nurseries. Cross-pathogenicity of Cylindrocarpon sp. isolates obtained  from different hosts (grapevine, apple, forest plants, vegetables) will be tested to establish the relationship between host-range and virulence, and aiming to determine other inoculum sources than grapevine. These findings  will provide a better understanding on disease epidemiology and the basis for the development of an efficient integrated control of grapevine in what concerns black-foot disease. Chemical and biological control measures will be developed  for commercial use.

The outcome of this research is expected to contribute towards greater productivity and stability of the grapevine industry, improving the international competitiveness of this industry.

 

 The genus Diaporthe and its Phomopsis anamorphs in Portugal; development of morphological, biological and molecular species concepts.

Not presently funded

 The genus Diaporthe and its anamorph genus Phomopsis include several economically important plant pathogens. They are not all host specific; the same species can occur on several different hosts and more than one species can occur on a single host. A Diaporthe state has been described for only about 20% of Phomopsis species. Identifications within these two genera are difficult because the species are not clearly defined and there is considerable overlap of morphological features between them. However, correct identification is an essential step towards meaningful studies on epidemiology and control of the diseases they cause.

There has been no critical reappraisal of the genera in recent years. Wehmeyer (1933) considered host association to be of minor importance when he revised the genus Diaporthe. In so doing he reduced the 600 or more species to about 60. However, his work was based solely on morphology of the teleomorph and no anamorph characters were taken into account. This treatment is considered too conservative and several of his synonymies are thought to include distinct species. Phomopsis species were also described largely based on host association. This resulted in a proliferation of names and currently more than 1000 species are known. Although host is now considered to be of minor importance in defining species, there has been no revision of the genus.

Over the last four years the PI has been studying several Diaporthe species. These studies have revealed the following: 1. several new connections between anamorph and teleomorph have been established; 2. some species included as synonyms of D. eres are in fact distinct; 3. a species transferred to Diaporthopsis should be retained in Diaporthe; 4. the mating behaviour of several species has been determined; 5. complexes of species are common on a single host, but normally only one is the primary pathogen. Although some of this work has been published, much of it has not because it is still incomplete and can be concluded only once proper funding is secured. Indeed, the entire program awaits proper funding before it can continue, develop and reach a proper conclusion.  These preliminary data do, however, provide a base on which to develop the proposed work.

The aims of the proposed project are to: 1. connect Phomopsis species with their Diaporthe teleomorphs; 2. redefine the species in terms of morphology of the holomorph; 3. support and expand on the morphological concept by the application of molecular data; 4. where possible, apply a biological concept to evaluate the morphological and molecular characters in species definitions. The expected outcome would be the establishment of clear concepts on which to base species names in Diaporthe. Connexions between anamorph and teleomorph will be established and it is hoped that some of the species complexes on individual hosts will be resolved.

 

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