Plant pathogenic and endophytic Botryosphaeriales known from culture

180 Pages·44.782 MB·English

by  Philips A.J.L., Slippers B., Groenewald J.Z., Crous P.W. (Ed.)

Studies in Mycology 76 (September 2013)
Plant pathogenic and endophytic
Botryosphaeriales known from culture
Alan J.L. Phillips, Bernard Slippers, Johannes Z. Groenewald and Pedro W. Crous, editors
CBS-KNAW Fungal Biodiversity Centre,
Utrecht, The Netherlands
An institute of the Royal Netherlands Academy of Arts and Sciences

Plant pathogenic and endophytic Botryosphaeriales known from culture
StudieS in Mycology 76, 2013
Studies in Mycology
The Studies in Mycology is an international journal which publishes systematic monographs of filamentous fungi and yeasts, and in rare occasions the
proceedings of special meetings related to all fields of mycology, biotechnology, ecology, molecular biology, pathology and systematics. For instructions for
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Dr Paul Cannon, CABI and Royal Botanic Gardens, Kew, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, U.K.
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Prof. dr Lori Carris, Associate Professor, Department of Plant Pathology, Washington State University, Pullman, WA 99164-6340, U.S.A.
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Prof. dr David M. Geiser, Department of Plant Pathology, 121 Buckhout Laboratory, Pennsylvania State University, University Park, PA, U.S.A. 16802.
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Prof. dr David S. Hibbett, Department of Biology, Clark University, 950 Main Street, Worcester, Massachusetts, 01610-1477, U.S.A.
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Dr Lorelei L. Norvell, Pacific Northwest Mycology Service, 6720 NW Skyline Blvd, Portland, OR, U.S.A. 97229-1309.
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Dr Amy Y. Rossman, Rm 304, Bldg 011A, Systematic Botany & Mycology Laboratory, Beltsville, MD, U.S.A. 20705.
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Prof. dr Hyeon-Dong Shin, Division of Environmental Science & Ecological Engineering, Korea University, Seoul 136-701, Korea.
E-mail: [email protected]
Dr Roger Shivas, Manager, Plant Biosecurity Science, Biosecurity Queensland, Department of Employment, Economic Development and Innovation, DEEDI, GPO Box 267,
Brisbane, Qld 4001, Dutton Park 4102, Queensland, Australia.
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Dr Marc Stadler, InterMed Discovery GmbH, Otto-Hahn-Straße 15, D-44227 Dortmund, Germany.
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Prof. dr Jeffrey K. Stone, Department of Botany & Plant Pathology, Cordley 2082, Oregon State University, Corvallis, OR, U.S.A. 97331-2902.
E-mail: [email protected]
Dr Richard C. Summerbell, 27 Hillcrest Park, Toronto, Ont. M4X 1E8, Canada.
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Prof. dr Brett Summerell, Royal Botanic Gardens and Domain Trust, Mrs. Macquaries Road, Sydney, NSW 2000, Australia.
E-mail: [email protected]
Prof. dr Ulf Thrane, DTU Systems Biology, Fungal Physiology and Biotechnology, Technical University of Denmark, Søltofts Plads 223, 2nd floor, DK-2800 Kgs. Lyngby,
Denmark.
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Copyright 2013 CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.
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Publication date: 30 September 2013
Published and distributed by CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands. Internet: www.cbs.knaw.nl.
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ISBN/EAN : 978-90-70351-97-7
Online ISSN : 1872-9797
Print ISSN : 0166-0616
Cover: Left column, Eucalyptus canker caused by Neofusicoccum sp. Right column, leaf spots caused by Phyllosticta cussonia. Central top row, asci of Botryosphaeria corticis, and conidia of Phyllosticta cussonia. Middle row, conidia
of Neofusicoccum arbuti, and Barriopsis iraniana. Bottom row, vertical section through ascostromata of Diplodia corticola, and conidia of Sphaeropsis sapinea.
Plant pathogenic and endophytic
Botryosphaeriales known from culture
edited by
Alan J.L. Phillips
Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516,
Caparica, Portugal
Bernard Slippers
Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
Johannes Z. Groenewald
CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
Pedro W. Crous
CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
CBS-KNAW Fungal Biodiversity Centre,
Utrecht, The Netherlands
An institute of the Royal Netherlands Academy of Arts and Sciences
INTRODUCTION
The present issue of Studies in Mycology revises the Botryosphaeriales, which represents a well-known order containing numerous plant
pathogenic fungi associated with fruit rot, leaf spots, die-back, gummosis and cankers of Angiosperms (e.g. Botryosphaeria, Diplodia,
Phyllosticta, Sphaeropsis, etc.), though some members are also associated with root rot (e.g. Macrophomina). Although the order has only
recently been introduced (Schoch et al. 2006), and presently contains two families, Botryosphaeriaceae and Planistromellaceae (Minnis et al.
2012), it is clear that several taxa could not be well accommodated in this familial structure (Liu et al. 2012). The present issue focuses firstly
on resolving the families that occur in the order, and secondly focuses on the species that are known from culture and DNA data, providing
morphological keys to their identification, and associated DNA barcodes.
REFERENCES
Liu J-K, Phookamsak R, Doilom M, Wikee S, Li YM, Ariyawansha H, et al. (2012). Towards a natural classification of Botryosphaeriales. Fungal Diversity 57: 149–210.
Minnis AM, Kennedy AH, Grenier DB, Palm ME, Rossman AY (2012). Phylogeny and taxonomic revision of the Planistromellaceae including its coelomycetous anamorphs:
contributions towards a monograph of the genus Kellermania. Persoonia 29: 11–28.
Schoch CL, Shoemaker RA, Seifert KA, Hambleton S, Spatafora JW, Crous PW (2006). A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98:
1041–1052.
DEDICATION: Robert (Bob) A. Shoemaker
Dr Shoemaker is well known to plant pathologists around the world for his taxonomic
studies on Dothideomycetes, having monographed several genera within the class. His
very thorough descriptions of ascomycete species in the class have set a high standard
for the field of ascomycete taxonomy, and many systematists have adopted his format
of description. He has published over 100 papers in his career (frequently being more
than 100 pages in length), which provide a valuable resource to mycologists and plant
pathologists alike. Several of these papers dealt with the Botryosphaeria complex, and
therefore it is also fitting that the present issue of Studies in Mycology is dedicated to him.
He has excelled in working out the life cycles of species in many genera, and has been
a constant source of information for the community. He has also served in an editorial
capacity on the Canadian Plant Disease Survey and Fungi Canadensis. Last but not least,
Bob has helped build a world-class mycological fungarium at Biodiversity (Mycology and
Microbiology), Agriculture and Agri-Food Canada, which is one of the most important
fungaria in North America. Dr Robert Shoemaker has been recognised for having made an
outstanding contribution to global mycology, and also has been honoured as Distinguished
Mycologist of the Mycological Society of America. Throughout his 46-year-long career, Bob
has collaborated with many plant pathologists on taxonomic issues pertaining to fungal plant diseases, and continues to provide valued
advice to his colleagues, and to the clients of the Canadian National Identification Service.
The Editors September 2013
CONTENTS
S. Wikee, L. Lombard, C. Nakashima, K. Motohashi, E. Chukeatirote, R. Cheewangkoon, E.H.C. McKenzie, K.D. Hyde, and P.W. Crous.
A phylogenetic re-evaluation of Phyllosticta (Botryosphaeriales) ..................................................................................................................... 1
B. Slippers, E. Boissin, A.J.L. Phillips, J.Z. Groenewald, L. Lombard, M.J. Wingfield, A. Postma, T. Burgess, and P.W. Crous. Phylogenetic
lineages in the Botryosphaeriales: a systematic and evolutionary framework .............................................................................................. 31
A.J.L. Phillips, A. Alves, J. Abdollahzadeh, B. Slippers, M.J. Wingfield, J.Z. Groenewald, and P.W. Crous. The Botryosphaeriaceae: genera
and species known from culture .................................................................................................................................................................... 51
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available online at www.studiesinmycology.org StudieS in Mycology 76: 1–29.
A phylogenetic re-evaluation of Phyllosticta (Botryosphaeriales)
S. Wikee1,2, L. Lombard3, C. Nakashima4, K. Motohashi5, E. Chukeatirote1,2, R. Cheewangkoon6, E.H.C. McKenzie7, K.D. Hyde1,2*, and P.W.
Crous3,8,9
1School of Science, Mae Fah Luang University, Chiangrai 57100, Thailand; 2Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiangrai 57100, Thailand;
3CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; 4Graduate School of Bioresources, Mie University, Kurima-machiya 1577, Tsu,
Mie 514-8507, Japan; 5Electron Microscope Center, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo 156-8502, Japan; 6Department of Plant Pathology,
Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; 7Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland 1142, New Zealand;
8Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; 9Wageningen University and Research Centre (WUR), Laboratory of
Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
*Correspondence: K.D. Hyde, [email protected]
Abstract: Phyllosticta is a geographically widespread genus of plant pathogenic fungi with a diverse host range. This study redefines Phyllosticta, and shows that it clusters
sister to the Botryosphaeriaceae (Botryosphaeriales, Dothideomycetes), for which the older family name Phyllostictaceae is resurrected. In moving to a unit nomenclature for
fungi, the generic name Phyllosticta was chosen over Guignardia in previous studies, an approach that we support here. We use a multigene DNA dataset of the ITS, LSU, ACT,
TEF and GPDH gene regions to investigate 129 isolates of Phyllosticta, representing about 170 species names, many of which are shown to be synonyms of the ubiquitous
endophyte P. capitalensis. Based on the data generated here, 12 new species are introduced, while epitype and neotype specimens are designated for a further seven species.
One species of interest is P. citrimaxima associated with tan spot of Citrus maxima fruit in Thailand, which adds a fifth species to the citrus black spot complex. Previous
morphological studies lumped many taxa under single names that represent complexes. In spite of this Phyllosticta is a species-rich genus, and many of these taxa need to be
recollected in order to resolve their phylogeny and taxonomy.
Key words: Botryosphaeriales, foliar pathogens, Guignardia, Phyllosticta, Phyllostictaceae, Multi-Locus Sequence Typing (MLST), systematics.
Taxonomic novelties: New species – Phyllosticta abieticola Wikee & Crous, P. aloeicola Wikee & Crous, P. citrimaxima Wikee, Crous, K.D. Hyde & McKenzie, P. leucothoicola
Wikee, Motohashi & Crous, P. mangifera-indica Wikee, Crous, K.D. Hyde & McKenzie, P. neopyrolae Wikee, Motohashi, Crous, K.D. Hyde & McKenzie, P. pachysandricola
Wikee, Motohashi & Crous, P. paxistimae Wikee & Crous, P. podocarpicola Wikee, Crous, K.D. Hyde & McKenzie, P. rhaphiolepidis Wikee, C. Nakash. & Crous, P. rubra Wikee
& Crous, P. vacciniicola Wikee, Crous, K.D. Hyde & McKenzie; New combinations – P. foliorum (Sacc.) Wikee & Crous, P. philoprina (Berk. & M.A. Curtis) Wikee & Crous;
Epitypifications (basionyms) – P. concentrica Sacc., P. cussoniae Cejp, P. owaniana G. Winter; Neotypifications (basionyms) – Phyllosticta cordylinophila P.A. Young,
Physalospora gregaria var. foliorum Sacc., Sphaeropsis hypoglossi Mont., Sphaeropsis minima Berk. & M.A. Curtis.
Published online: 30 September 2013; doi:10.3114/sim0019. Hard copy: September 2013.
INTRODUCTION MycoBank.org; accessed August 2013), but many of these reflect
y old concepts of the genus, and have since been accommodated
The genus Phyllosticta was introduced by Persoon (1818) with P. elsewhere (van der Aa & Vanev 2002). Many species also produce
g
convallariae (nom. inval., lacking description) designated as the spermatial or sexual states, which in some cases have been named
o type species (Donk 1968), which is a synonym of P. cruenta (van in Leptodothiorella and Guignardia, respectively (van der Aa 1973).
der Aa 1973), which van der Aa & Vanev (2002) cited as type of For many years researchers have confused the generic
l
the genus. Species of Phyllosticta are mostly plant pathogens of circumscription of Phoma and Phyllosticta. Both genera were
o
a broad range of hosts, and responsible for numerous diseases, recognised as pycnidial fungi forming unicellular, hyaline conidia.
c including leaf and fruit spots. Some of these pathogens cause Allescher (1898) separated the two genera based on the infected
diseases of significant economic importance, e.g., P. citricarpa, the part of the plant part, with Phyllosticta as foliar pathogens, and
y
cause of citrus black spot, which is regarded as a quarantine pest Phoma on other plant parts. This concept was further refined by
M in Europe and the USA (Baayen et al. 2002, Glienke et al. 2011). Grove (1935) who regarded Phyllosticta as a parasite and Phoma
Other economically important plant pathogenic species include as saprobe or wound parasite. Seaver (1922) and Grove (1935)
the P. ampelicida species complex that causes black rot disease separated “Phyllosticta” species based on host preference, as was
n on grapevines (Wicht et al. 2012), and the P. musarum species common taxonomic practice in the 20th century. Seaver (1922)
complex that causes banana freckle disease (Pu et al. 2008, Wong described 300 species, and Grove (1935) approximately 150. In
i
et al. 2012). Some species of Phyllosticta have also been isolated both cases the host plant was the main criterion on which species
s as endophytes from a wide range of hosts, e.g., P. capitalensis. were separated. Indeed, Seaver’s classification was largely
Other species are regarded as saprobes, e.g., P. carpogena and P. characterised on spore size on host plants, while Grove arranged
e
ericae (van der Aa 1973, Baayen et al. 2002, van der Aa & Vanev species under the alphabetically arranged host genera. Many
i 2002, Glienke et al. 2011, Wikee et al. 2011). Presently there Phyllosticta species were given specific epithets based on the host
d
are approximately 3 340 epithets known for Phyllosticta (www. family, genus or species. For example, P. iridis on Iris versicolor
u
Copyright CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.
t You are free to share - to copy, distribute and transmit the work, under the following conditions:
S Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work).
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No derivative works: You may not alter, transform, or build upon this work.
For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get
permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights.
1
Wikee et al.
(Iridaceae), P. eugeniae on Eugenia buxifolia (Myrtaceae), P. Phyllosticta s. str. was first monographed by van der Aa (1973),
minor on Vinca minor (Apocynaceae), etc. (Seaver 1922). For the who described and illustrated 46 species, and listed the sexual
plant pathogenic Phyllosticta species, separation based on host morphs for 12 species, and the spermatial morphs for 17 based
species (or sometimes genus) has proven to be a good method to mostly on material collected in Europe and North America. More
distinguish species, but this does not hold true for the endophytic recently van der Aa & Vanev (2002) revised all species names
or saprobic species. described in Phyllosticta, and provided a list of 190 accepted
Viala & Ravaz (1892) introduced Guignardia as a replacement epithets, as well as a second list of excluded names that indicated
name for Laestadia Auersw. (1869), which was a later homonym their current disposition if known.
of Laestadia Kunth ex Lessing (1832). Viala & Ravaz applied the In recent years DNA sequencing of conserved loci has vastly
name only to Sphaeria bidwellii (≡ G. bidwellii), a species that improved our knowledge of fungal phylogeny. Several studies have
is different from L. alnea, the type species of Laestadia Auersw. shown that phylogenetic analysis can resolve the taxonomy and
(Bissett 1986). Petrak (1957) concluded that G. bidwellii and identification of Phyllosticta spp. (Baayen et al. 2002, Wulandari
related species could be accommodated in Botryosphaeria, and et al. 2009, Glienke et al. 2011, Wikee et al. 2011). Indeed, new
Barr (1970, 1972) agreed with Petrak and placed Guignardia species of Phyllosticta are increasingly described based on
and Phyllosticta in Botryosphaeria, and other related species in molecular results (Crous et al. 2012, Wang et al. 2012, Su & Cai
Discosphaerina. 2012, Wong et al. 2012, Zhang et al. 2012).
Punithalingam (1974) suggested that the genus Guignardia Phyllosticta was placed in the order Botryosphaeriales by
must be confined to only those taxa with Phyllosticta morphs as Schoch et al. (2006), who proposed that the Botryosphaeriaceae
typified by G. bidwellii (= P. ampelicida, see Zhang et al. 2013). contained both Botryosphaeria and Phyllosticta, although no
He stated that Botryosphaeria usually has larger ascomata and support was obtained for this relationship. Crous et al. (2006) and Liu
ascospores, and also a multilocular stroma, features that distinguish et al. (2012) also classified Phyllosticta in the Botryosphaeriaceae.
it from Guignardia. Van der Aa (1973) also pointed out that these In both studies it was noted that Phyllosticta was distinct from
two genera had different growth characteristics in culture. Following other genera in the Botryosphaeriaceae, and that these authors
molecular studies, Schoch et al. (2006) placed Phyllosticta in the eventually expected it to be placed elsewhere. Seaver (1922) used
Botryosphaeriales. Since Botryosphaeria has been shown to be the order Phyllostictales and family Phyllostictaceae for the genus
poly- and paraphyletic, numerous genera have been distinguished
Phyllosticta. The family name Phyllostictaceae (as Phyllostictei)
in the Botryosphaeriaceae (Crous et al. 2006, Phillips et al. 2008,
was first proposed by Fries (1849) and accepted by Hawksworth
Liu et al. 2012). With the increasing use of molecular data to link
& David (1989). This family name is still available for use, and we
asexual and sexual morphs, and the end of dual nomenclature for
suggest that Phyllosticta again be placed in this family, which is
fungi (Hawksworth et al. 2011, Wingfield et al. 2012), the oldest,
sister to the Botryosphaeriaceae (Botryosphaeriales).
more important and commonly used name, Phyllosticta, was
Although phylogenetic analysis has become a standard approach
chosen over that of Guignardia (Glienke et al. 2011, Sultan et al.
in fungal identification, phylogenetic studies should combine both
2011, Wikee et al. 2011, 2013, Wong et al. 2012).
molecular and morphological data to help discriminate taxa (Crous
The principal character by which a fungus is recognised as a
& Groenewald 2005, Hyde et al. 2010). Suitable type material that
species of Phyllosticta is by the production of pycnidia containing
can be sequenced is not available for many species of fungi, and
aseptate, hyaline conidia that are usually covered by a mucoid
thus neo- or epitypification is required in order to create a stable
layer and bearing a single apical appendage (van der Aa 1973).
and workable taxonomy. The objectives of this study are: (1) to
However, the mucoid layer and appendage is not necessarily a
clarify relationships among species of Phyllosticta using multi-gene
universal feature, and some species such as P. colocasiicola, P.
sequence data [internal transcribed spacer region (ITS), translation
minima, and P. sphaeropsoidea lack these features. Furthermore,
elongation factor 1-α gene (TEF1), actin gene (ACT), 28S rRNA
mucoid appendages formed on agar media may disappear with
gene (LSU) and glyceraldehyde-3-phosphate dehydrogenase
age, or vary in size and shape when the same isolate is compared
gene (GPDH)] combined with morphological characteristics; (2) to
on different media, e.g., pine needle agar, oatmeal agar, or potato
provide a phylogenetic backbone for the genus Phyllosticta, and
dextrose agar. Presently Phyllosticta is circumscribed by pycnidia
(3) to designate neo- or epitype specimens for fungal isolates that
that are usually globose to subglobose, flattened above, and
correlate well with original type material, thereby fixing the genetic
closely connected with the subepidermal pseudostroma. They
application of these names.
are mostly unilocular but may be multilocular. The conidia are
commonly hyaline, aseptate, ovoid, obovoid to ellipsoid, or short
cylindrical, seldomly pyriform, globose or subglobose, and usually
MATERIAL AND METHODS
covered by a mucoid layer and bearing a single apical appendage
(van der Aa 1973). The sexual morph is characterised by erumpent
ascomata that are globose to pyriform in section, often irregularly Isolates
shaped, unilocular, and with a central ostiole. The peridium is
thin, comprising a few layers of angular cells. Asci are 8-spored, A global collection of 160 strains of Phyllosticta associated with
bitunicate, clavate to broadly ellipsoid, with a wide, obtusely rounded both leaf spot diseases and healthy leaves of various host plants
or slightly square apex, tapering gradually to a small pedicel, and were studied (Table 1). All isolates were sequenced and analysed
with a well-developed ocular chamber. Ascospores are ellipsoid together with sequences downloaded from GenBank. If fruit bodies
to limoniform, sometimes slightly elongated, aseptate, hyaline, were present on diseased tissue then a single spore isolation
often multiguttulate or with a large central guttule, and may have procedure as described by Chomnunti et al. (2011) was used to
mucilaginous polar appendages or a sheath. A spermatial state obtain cultures. To obtain isolates of Phyllosticta from diseased
may form in culture. Spermatia are hyaline, aseptate, cylindrical leaves of host plants when fruit bodies were not present, the leaf
to dumbbell-shaped with guttules at each end (van der Aa 1973). surface was cleaned by wiping with 70 % ethanol. Small pieces of
2