The Top 10 oomycete pathogens in molecular plant pathology

Summary

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant‐pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

Introduction

Oomycetes are eukaryotic organisms that superficially resemble filamentous fungi, but are phylogenetically related to diatoms and brown algae in the stramenopiles (Gunderson et al., 1987; Jiang and Tyler, 2012; Lamour and Kamoun, 2009; Thines, 2014; Thines and Kamoun, 2010). Fossil evidence indicates that a number of oomycetes emerged as endophytes of land plants at least by the Carboniferous period, approximately 300–350 million years ago (Krings et al., 2011). One species, Combresomyces williamsonii, described from ∼320‐million‐year‐old petrified stem cortex and rootlets of a seed fern, may have even been parasitic (Strullu‐Derrien et al., 2011). Phylogenetic analyses of modern taxa have revealed that plant parasitism has evolved independently in three lineages of oomycetes (Thines and Kamoun, 2010). Well‐known plant pathogens, namely downy mildews, Phytophthora and Pythium, appear to have radiated from a common plant‐parasitic ancestor (Thines and Kamoun, 2010). The impact of oomycetes on humankind is well documented as both a persistent threat to subsistence and commercial farming and as destructive pathogens of native plants (Agrios, 2005; Erwin and Ribeiro, 1996; Lamour and Kamoun, 2009). As a result, news related to plant diseases caused by oomycetes tends to capture the interest of the general public and is frequently featured in the media.

In the last two decades, increased awareness of the distinctive phylogeny and biology of oomycetes has driven the emergence of a specialist research community that is currently organized under the umbrella of the ‘Oomycete Molecular Genetics Network’. This community has moved the field beyond the gloomy view of the 1980s that oomycetes are a ‘fungal geneticist's nightmare’ (Shaw, 1983; discussed in Schornack et al., 2009). It has produced novel paradigms in understanding host–microbe interactions, effector biology and genome evolution (Bozkurt et al., 2012; Govers and Gijzen, 2006; Jiang and Tyler, 2012; Schornack et al., 2009; Vleeshouwers et al., 2011). The oomycete community was one of the first in plant pathology to initiate coordinated transcriptome and genome sequencing projects, and subsequently to exploit the resulting resources to drive conceptual advances (Govers and Gijzen, 2006; Pais et al., 2013; Schornack et al., 2009). These days, with the genomes serving as unique resources for basic and applied research, oomycetes are best portrayed as a ‘genomicist's dream’ (Govers and Gijzen, 2006; Jiang and Tyler, 2012; Pais et al., 2013; Schornack et al., 2009).

It is therefore particularly fitting that the oomycetes are at last covered by the Top 10 review series of Molecular Plant Pathology. The process to generate the list and the aim of this article are similar to those of previous contributions on plant‐pathogenic viruses (Scholthof et al., 2011), fungi (Dean et al., 2012), bacteria (Mansfield et al., 2012) and nematodes (Jones et al., 2013). We undertook a survey to query the community for their ranking of plant‐pathogenic oomycete taxa based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries that yielded the Top 10 species (Table 1). To some degree, the results reflect the sizes of the subcommunities. Six of the ten species belong to the genus Phytophthora, which is more commonly studied than any other oomycete genus. Obligate parasites are also well represented with three species (Hyaloperonospora arabidopsidis, Plasmopara viticola and Albugo candida, Table 1). Another 23 species received votes but ranked outside the Top 10 (Table 2). The fish parasite Saprolegnia parasitica received enough votes to place it in the Top 10, but was removed, given that the list focuses on plant pathogens (Table 2).

Table 1.

Top 10 oomycetes in molecular plant pathology

Rank	Species	Common disease name(s)	Number of papers (2005–2014)	Number of votes
1	Phytophthora infestans	Late blight	1230	51
= 2	Hyaloperonospora arabidopsidis	Downy mildew	137	25
= 2	Phytophthora ramorum	Sudden oak death; Ramorum disease	378	25
4	Phytophthora sojae	Stem and root rot	276	22
5	Phytophthora capsici	Blight; stem and fruit rot; various others	541	17
6	Plasmopara viticola	Downy mildew	326	15
7	Phytophthora cinnamomi	Root rot; dieback	315	13
= 8	Phytophthora parasitica	Root and stem rot; various others	142	10
= 8	Pythium ultimum	Damping off; root rot	319	10
10	Albugo candida	White rust	65	9

The ‘=’ sign before the ranking indicates that the species tied for that position. The number of papers published in 2005–2014 is based on searches of the Scopus database (http://www.scopus.com) using the species names as a query. For H. arabidopsidis, a search for the alternative name ‘Peronospora parasitica’ was also performed and the combined number is shown. Searches with the terms ‘oomycete*’ and ‘Phytophthora’ yielded 2068 and 4059 articles, respectively.

Table 2.

Other oomycete species that received votes

Rank	Species
11	Aphanomyces euteiches
12	Albugo laibachii
13	Bremia lactucae
14	Phytophthora palmivora
15	Pseudoperonospora cubensis
16	Plasmopara halstedii
17	Peronophythora litchi
18	Peronosclerospora sorghi
19	Peronospora belbahrii
20	Phytophthora alni
21	Phytophthora brassicae
22	Phytophthora cactorum
23	Phytophthora meadii
24	Phytophthora phaseoli
25	Phytophthora plurivora (formerly P. citricola)
26	Plasmopara obducens
27	Pythium aphanidermatum
28	Pythium oligandrum
29	Sclerophthora rayssiae
30	Hyaloperonospora brassicae
NR	Saprolegnia parasitica (fish parasite)
NR	Lagenidium giganteum (mosquito parasite)
NR	Pythium insidiosum (mammalian parasite)

NR, not ranked because the species is not associated with plants.

This article is based on contributions from the voters to provide an introduction to the 10 taxa and a snapshot of current research. Each section starts with a brief overview of the selected species, e.g. its importance, pathology, host range and life cycle. This is followed by a review of current research themes, particularly the unique findings that have emerged from the study of particular species, and an outlook on future research. We hope that this article will serve as a reference and resource for novice and experienced readers alike, as well as provide a benchmark for future trends in oomycete research.

1. Phytophthora infestans

Phytophthora infestans causes potato late blight (Fig. 1), a disease with major historical impact. Providing twice the calories of rye and wheat per hectare, potato was central to European agriculture between 1750 and 1850. In 1844, the arrival of P. infestans changed this situation. In addition to the well‐documented Irish famine (Fig. 2), crop failures in 1845 and 1846 contributed to an estimated 750 000 hunger‐associated deaths in continental Europe (Zadoks, 2008). The discovery that late blight was caused by a microbial pathogen, 15 years before Pasteur's formal confirmation of Germ Theory, places the 19th century migration of P. infestans as a significant milestone in the foundation of plant pathology as a scientific discipline. Today, late blight remains a major constraint to the production of potato, the world's third largest staple crop, and is thus a constant threat to food security (Fisher et al., 2012; Haverkort et al., 2008).

Figure 1.

Potato plants with typical late blight lesions. Infection starts when a spore lands on the leaf and germinates. The germ tube forms an appressorium and an emerging penetration peg pushes into an epidermal cell. Then the inner cell layers are colonized. During the biotrophic phase, hyphae grow in the intercellular space, whereas haustoria enter plant cell cavities and invaginate host cell plasma membrane. Later, Phytophthora infestans switches to necrotrophic growth, resulting in the death of plant cells and the appearance of necrotic lesions on the infected tissues. In this phase, hyphae escape through the stomata and produce numerous asexual spores, named sporangia, that easily detach and disperse by wind or water. A sporangium that finds a new host can either germinate directly and initiate a new cycle or, at lower temperatures, undergo cleavage resulting in a zoosporangium from which six to eight flagellated spores are released. These zoospores can swim for several hours but, once they touch a solid surface, they encyst and germinate to initiate new infections. Under favourable conditions, the pathogen can complete the cycle from infection to sporulation in 4 days. In the field, this cycle is repeated multiple times during one growing season, resulting in billions of spores and a continuous increase in disease pressure. In addition to leaves, stems and tubers are also infected and P. infestans can continue to flourish on the decaying plant material. If not managed properly, infected seed potatoes or waste on refuse piles are often the sources of inoculum for new infections in the spring. An alternative route for surviving the winter is via oospores, sexual spores that can survive in the soil for many years. Phytophthora infestans is heterothallic; isolates are either A1 or A2 mating type, and sex organs only develop when isolates of opposite mating type sense the sex hormone produced by the mate.

Figure 2.

One of the many Great Famine memorials around the world. These sculptures on Customs House Quays in Dublin, by artist Rowan Gillespie, stand as if walking towards the emigration ships on the Dublin Quayside (courtesy of Michael Seidl).

In the 1840s, trade in potatoes probably facilitated the long‐distance migration of the pathogen. Whole‐genome sequencing of European herbarium samples has revealed that populations belonging to the HERB‐1 genotype were different from US‐1, the genotype dominating the population globally in the mid‐ to late 20th century (Goodwin et al., 1994; Martin et al., 2013, 2014; Yoshida et al., 2013, 2014). Waves of migration and genotype displacements in the 20th century have been well documented. The introduction of the A2 mating type to Europe in the 1970s (Drenth et al., 1994) and, more recently, the emergence of new, more aggressive lineages, such as 13_A2 (Blue 13) in Europe (Cooke et al., 2012), US‐22 in the eastern USA (Fry et al., 2013; Hu et al., 2012) and US‐23/US‐24 in Canada (Peters et al., 2014), impose constant challenges to disease resistance breeding.

In the 1990s, P. infestans research led to the development of molecular approaches to study oomycete pathology and biology. The first DNA transformation system (Judelson et al., 1991) and the first transcriptional profiling during infection (Pieterse et al., 1991) paved the way to detailed molecular investigations of sexual and asexual development and pathogenicity (reviewed in Judelson, 1997). DNA fingerprinting revolutionized population studies (Goodwin et al., 1992) and was a prelude to the first genome‐wide genetic map of a Phytophthora species (van der Lee et al., 1997). Observations that gene silencing occurred in P. infestans transformants (e.g. Judelson and Whittaker, 1995) sparked important studies of the mechanisms underlying transcriptional silencing (van West et al., 1999). The first large‐scale transcript sequencing studies (Kamoun et al., 1999) ushered in the genomics era of Phytophthora research.

In the last 15 years, advanced genomic and functional approaches have placed P. infestans at the forefront of research to understand oomycete development (Judelson and Blanco, 2005) and pathogenicity (Kamoun, 2006). An elegant combination of bioinformatics, proteomics and functional genomics has revealed secreted proteins as potential factors influencing host–P. infestans interactions (Torto et al., 2003). Apoplastic effectors that inhibit host secreted proteases were first described in P. infestans (Tian et al., 2004), and the apoplastic phytotoxin‐like SCR74 (Liu et al., 2005) provided support for the use of diversifying selection as a criterion for the identification of candidate effectors. The apoplastic effectors EPIC1 and EPIC2B were found to converge on the host protease RCR3, which is also targeted by an independently evolved effector from a fungal plant pathogen (Song et al., 2009). Recently, diversifying selection of the EPIC1 protease inhibitor was implicated in functional adaptation to the equivalent protease target after ‘jumps’ to a new host (Dong et al., 2014).

The first reported P. infestans avirulence effector was AVR3a, the counterpart of resistance protein R3a (Armstrong et al., 2005). Comparison with avirulence effectors from Phytophthora sojae and H. arabidopsidis identified conserved amino acid motifs RXLR and EER (Rehmany et al., 2005), which act as signals for translocation into host cells (Whisson et al., 2007). The genome sequence of P. infestans revealed hundreds of genes predicted to encode RXLR effectors, plus a second class of candidate effectors called Crinklers (CRNs) (Haas et al., 2009), which may also be delivered inside plant cells (Schornack et al., 2010). These effector genes are rapidly evolving and are typically variable between different P. infestans isolates (Cooke et al., 2012). RXLR and CRN reside in gene‐sparse, repeat‐rich regions, potentially subject to rearrangement and rapid mutation, raising the concept of a ‘two‐speed’ genome in evolutionary terms (Haas et al., 2009; Raffaele et al., 2010). Recent years have witnessed intense efforts to determine the biochemical function of RXLR effectors, notably by determining their protein targets in the host. The first target identified was ubiquitin E3 ligase CMPG1, which AVR3a stabilizes to prevent programmed cell death in response to elicitors such as INF1 (Bos et al., 2010).

Breeding for late blight resistance was initiated by James Torbitt of Belfast in the 1870s, inspired by the theories of Charles Darwin, with whom he shared considerable correspondence (DeArce, 2008). More than 130 years later, breeding efforts have yet to provide a durable solution. Occasionally, local successes are reported; for example, variety C88, widely cultivated in China for over a decade, retains its resistance (Li et al., 2011). Many resistance (R) genes effective against races of P. infestans have been identified (Rodewald and Trognitz, 2013). Only with the recent identification of avirulence genes, all of which encode RXLR effectors, can breeders incorporate knowledge on how P. infestans evades detection into their breeding strategies (Vleeshouwers et al., 2011). Such information is critical for the prediction of the durability of R genes. The use of effectors as tools to rapidly identify R genes is a powerful step towards rational selection and combination of lasting resistance (Vleeshouwers et al., 2008).

We still know relatively little about how P. infestans effectors manipulate host plants to establish disease. How do they translocate into host cells? Do they define host range? How do they work in concert to modulate complex networks of regulatory processes occurring in the host? Only recently have researchers started to adopt structural biology to fully investigate functional relationships between interacting pathogen and plant proteins (Wirthmueller et al., 2013). Could such research catalyse the modification of molecular interactions in favour of the plant immune system through synthetic biology approaches?

The basic knowledge gained on P. infestans in the last decade is starting to have an impact on the management of late blight disease. For the control of late blight, farmers largely rely on agrochemicals, many with unknown modes of action. The emergence of insensitive strains is possibly a result of high mutation rates in the pathogen (Randall et al., 2014). The phenylamide metalaxyl was one of the first chemicals to exhibit specificity to oomycetes. Soon after its introduction and widespread use, fully insensitive strains emerged, but only 35 years later was the molecular basis of this insensitivity uncovered (Randall et al., 2014). Mining of the P. infestans genome has revealed many novel proteins with domain combinations that are unique to oomycetes (Seidl et al., 2011). Several probably function in signalling and may be promising fungicide targets. Mode‐of‐action studies are more accessible thanks to the available genomics resources, transformation tools and marker strains with tags to visualize the cytoskeleton and various subcellular compartments (Ah Fong and Judelson, 2003; Meijer et al., 2014). In resistance breeding, the efficacy of stacking R genes into favoured cultivars, by either introgression or trans‐ or cis‐genesis, is being investigated (Tan et al., 2010). However, for success, the R genes to be combined should be selected carefully on the basis of our knowledge on the variation in the pathogen population, and the attendant vulnerability to resistance being overcome (Vleeshouwers et al., 2011). Future efforts should consider the introduction of multiple barriers, perhaps combining R proteins with, for instance, membrane‐localized pattern recognition receptors or components governing non‐host resistance to P. infestans. Even then, it is unlikely that plant resistance can fully control late blight. Agrochemicals should not be abandoned. On the contrary, for more rational fungicide design, novel targets should be identified, an endeavour that will be enhanced by an even more profound insight into the biology of P. infestans.

2. Hyaloperonospora arabidopsidis

Hyaloperonospora arabidopsidis (formerly H. parasitica and Peronospora parasitica) is one of 700 downy mildew species within the Peronosporaceae (Thines, 2014). Downy mildew pathogens cause harmful diseases on many important crops, notably Peronospora and Hyaloperonospora spp. on brassica crops, Plasmopara viticola on grape, Peronosclerospora spp. on maize and sorghum, Pseudoperonospora cubensis on cucurbits and Bremia lactucae on lettuce (Lucas et al., 1995).

Most downy mildews have narrow host ranges and are completely dependent on their host for growth and reproduction. They can survive in the soil as quiescent oospores that initiate infection through roots. Spread of the pathogen mostly occurs through airborne sporangiospores that are formed on the lower leaf surface, giving downy patches (Fig. 3). These spores germinate on the plant surface and penetrate by forming appressoria (Koch and Slusarenko, 1990). Once past the epidermis, hyphae grow intercellularly and, similar to Phytophthora spp. and other downy mildews, develop haustoria, specialized structures that may function in feeding and the suppression of host defence by targeted secretion of effectors (Fig. 4, Whisson et al., 2007).

Figure 3.

Hyaloperonospora arabidopsidis disease symptoms on a 2‐week‐old Arabidopsis seedling. Mature sporangiophores are visible as white structures on the right side of the leaf.

Figure 4.

Diagram depicting a compatible interaction between Hyaloperonospora arabidopsidis and Arabidopsis initiated by a sporangiospore landing on the leaf surface. A, appressorium; C, cuticle; Ha, haustorium; Hy, hyphae; LE, lower epidermis; N, nucleus; PM, palisade mesophyll cells; S, sporangiospore; SM, spongy mesophyll cells; Sp, mature sporangiophore; UE, upper epidermis. Note: sporangiophores are not drawn to scale.

Hyaloperonospora arabidopsidis is a prominent pathogen in natural populations of Arabidopsis thaliana (Coates and Beynon, 2010; Holub, 2008). As such, it was adopted in the 1980s as one of two pathogens of Arabidopsis, together with the bacterium Pseudomonas syringae (Koch and Slusarenko, 1990). The Top 10 ranking of H. arabidopsidis reflects the subsequent success of the Arabidopsis–H. arabidopsidis pathosystem. H. arabidopsidis was initially utilized as a ‘physiological probe’ of the Arabidopsis immune system (Holub et al., 1994). This research led to the cloning of the first plant disease R genes against an oomycete, better understanding of the evolutionary dynamics of R genes, the definition of broadly important immune system regulators, the identification of downy mildew‐resistant mutants and genetic definition of the complexity of the plant immune signalling network (reviewed in Coates and Beynon, 2010; Lapin and Van den Ackerveken, 2013; Slusarenko and Schlaich, 2003). On the pathogen side, research is hampered by the lack of protocols for culture and genetic transformation, established techniques with other oomycetes such as P. infestans. However, work in the early 2000s led to the development of genetic maps and DNA libraries that enabled the discovery of the first avirulence effector (Allen et al., 2004), and later to the RXLR effector family (Rehmany et al., 2005).

Genome sequencing of H. arabidopsidis isolate Emoy2, completed in 2010, unveiled 134 predicted RXLR effectors and other components of the H. arabidopsidis secretome (Baxter et al., 2010). Notably, this report also revealed important genomic signatures of obligate biotrophy that have evolved convergently in other obligate oomycete and fungal lineages (reviewed in McDowell, 2011). Protein interaction assays have shown that H. arabidopsidis effectors target a highly interconnected host machinery, helping to define a representative plant–pathogen interaction network (Mukhtar et al., 2011). In addition, several high‐throughput functional studies have investigated effector subcellular localizations, suppression of immune responses, molecular targets and cognate immune receptors (Cabral et al., 2011, 2012; Caillaud et al., 2011; Fabro et al., 2011).

Future studies with the H. arabidopsidis experimental system will include: (i) direct or Agrobacterium‐mediated transformation for genetic manipulation required for the molecular analysis of downy mildew pathogenicity; (ii) the establishment of the temporal hierarchy of effectors during penetration, colonization and sporulation, which may serve as a blueprint for a better understanding of the molecular basis of biotrophy; (iii) the role of genetic recombination and epigenetics on the emergence of new effectors; (iv) the development of tools to understand how plant‐originated molecules regulate pathogen response; and (v) the relevance of interspecies transfer of small RNAs. These investigations on H. arabidopsidis will continue to provide new insights into the molecular mechanisms of downy mildew pathogenicity, and contribute to comparative and functional analysis of (obligate) biotrophic oomycete and fungal pathogens.

3. Phytophthora ramorum

Phytophthora ramorum is the most destructive disease of oaks worldwide and the cause of sudden oak death, sudden larch death and ramorum blight (Brasier and Webber, 2010; Grünwald et al., 2008; Rizzo et al., 2005; Werres et al., 2001) (Fig. 5). The host range of P. ramorum is one of the widest of any Phytophthora spp., and includes many species of hardwood trees and ornamentals. To date, four distinct clonal lineages have been recognized by various molecular markers and two mating types have been found (Grünwald et al., 2009; Van Poucke et al., 2012). These lineages appear to be anciently diverged, yet have emerged repeatedly in both North America and Europe (Goss et al., 2009a; Grünwald et al., 2012) (Fig. 6). Lineages NA1, NA2 and EU1 are currently found in Canada and the USA, whereas EU1 and EU2 exist in Europe (Goss et al., 2009b, 2011; Grünwald et al., 2012; Van Poucke et al., 2012). These lineages differ in aggressiveness in controlled assays, but field experiments have not been conducted given quarantine restrictions (Elliott et al., 2011; Grünwald et al., 2008; Hüberli et al., 2012; Kasuga et al., 2012; Van Poucke et al., 2012). Unique ecological attributes, such as a wide host range and survival in dry, hot Mediterranean summers, combined with the ability to reproduce from chlamydospores, are thought to provide the basis for sudden oak death in California (Garbelotto and Hayden, 2012).

Figure 5.

Impact of sudden oak death in California. Tanoak mortality evidenced by defoliated or wilted canopies on the Bolinas Ridge at Mt. Tamalpais, Marin County, CA, USA. Photograph courtesy of Janet Klein (Marin Municipal Open Space District).

Figure 6.

Inferred pattern of migration of the four clonal lineages of Phytophthora ramorum. Modified from Grünwald et al. (2012).

The availability of the genome sequence just a few years after the identification of the pathogen provided rapid and novel insights into the biology of this pathogen (Tyler et al., 2006). Like other Phytophthora spp., P. ramorum has a large number of candidate effectors interacting with the plant hosts, including RXLR, CRNs and the necrosis and ethylene‐inducing peptide 1 (Nep1)‐like protein (NLP) gene families (Goss et al., 2013; Tyler et al., 2006). RXLR effectors diversify rapidly, despite the clonality of this organism, using mechanisms such as loss or gain of repeated domains, recombination or gene conversion among paralogues and selection on point mutations (Goss et al., 2013). Recent work has focused on the discovery of endogenous small RNAs and description of the silencing machinery (Fahlgren et al., 2013). Phytophthora ramorum and two other Phytophthora spp. examined produce two primary, distinct 21‐ and 25‐nucleotide small RNA classes, including a novel microRNA family. Two argonaute classes and two dicer‐like proteins appear to be involved in each pathway (Fig. 7), but this remains to be formally tested. Epigenetic mechanisms have been implicated recently in phenotypic diversification, namely colony morphology, colony senescence and virulence on coast live oak and California bay laurel (Kasuga et al., 2012).

Figure 7.

Silencing machinery in Phytophthora. Phylogenetic placement of dicer‐like (DCL) (A) and argonaute (Ago) (B) proteins in the genus Phytophthora. For more details, see Fahlgren et al. (2013). Species correspond to: Arabidopsis thaliana, Paramecium tetraurelia, Phytophthora infestans, Phytophthora ramorum, Phytophthora sojae, Tetrahymena thermophila and Toxoplasma gondii.

Phytophthora ramorum provides a unique opportunity for the study of the evolution of a genome that has two mating types, yet appears to lack sexual reproduction in the known field populations. The epigenome, transcriptome and proteome of P. ramorum remain a mystery. The apparent documented phenotypic variation driven by host association might be epigenetic in nature and invites further study. Several basic questions remain unanswered. Why does P. ramorum have such a large number of RXLR effectors, given that the genome is adapted to a wide host range? What are the genes conferring a wide host range compared with P. infestans and P. sojae? Is there a centre of origin? This centre might be located in Asia where the closest relative, P. lateralis, has been found in an old growth Chamaecyparis forest (Brasier et al., 2010). The discovery of a centre of origin might also reveal a host with which P. ramorum might have co‐evolved, providing a mechanism of R gene discovery, a critical tool needed for the management of sudden oak death. Comparative genomics of related species, such as P. lateralis, P. syringae and P. hibernalis, amongst others, will provide novel insights into core effectors and genes under purifying selection in the clade, but diverged among clades.

4. Phytophthora sojae

Root rot disease of soybean caused by P. sojae was first recognized in North America in the 1950s (Hildebrand, 1959; Kaufmann and Gerdemann, 1958). The alternative names P. megasperma var. sojae and P. megasperma f.sp. glycinea were commonly used for this species in the past (Erwin and Ribeiro, 1996). Infection of soybean by P. sojae, which is a hemibiotroph, typically initiates below ground and eventually produces spreading cankers that destroy root tissues and travel up the stem (Fig. 8). The pathogen thrives in wet conditions and in compacted or heavy clay soils. Motile, water‐borne zoospores are released from sporangia and are attracted to soybean root exudates (Morris and Ward, 1992). Phytophthora sojae is homothallic and creates abundant, thick‐walled sexual oospores that are long lived and provide a soil‐borne inoculum. Phytophthora sojae has a narrow host range and its economic damage is limited to soybean. It has been suggested that P. sojae originated in North America as a pathogen of lupins, as some 26 species of the genus Lupinus are susceptible to infection (Erwin and Ribeiro, 1996). In laboratory tests, P. sojae can also be made to infect lima bean (Phaseolus lunatus), string bean (Phaseolus vulgaris) and cranesbill (Geranium carolinianum) (Erwin and Ribeiro, 1996; Hildebrand, 1959). Phytophthora sojae is one of the most damaging disease problems confronting soybean growers (Wrather and Koenning, 2006). The management of P. sojae in soybean has primarily relied on breeding for resistance.

Figure 8.

Phytophthora sojae. (A) Diseased soybean plants in the field, infected with P. sojae. Plant height is 20–30 cm. (B) Susceptible (left) and resistant (right) soybean plants inoculated in the stem with P. sojae, 7 days after infection, illustrating R‐gene‐mediated resistance. Pots are 10 cm in diameter. (C) Germinating oospore of P. sojae growing on water agar. Oospore is 35 μm in diameter. (D) Germinating P. sojae cysts growing on water agar. Cysts are 15 μm in diameter. (E) Etiolated soybean hypocotyls inoculated with a 10‐μL water droplet containing 10³ zoospores from a virulent (top) and avirulent (bottom) strain of P. sojae, 48 h after infection, illustrating strain‐specific variation in avirulence effectors and the hypersensitive response. Soybean hypocotyls are 5 mm in diameter.

Research on P. sojae has focused on the mechanisms of pathogen virulence, host resistance and the molecular basis of recognition between P. sojae and soybean (Dorrance and Grünwald, 2009; Gijzen and Qutob, 2009; Tyler, 2007). Phytophthora sojae, together with P. ramorum, was the first oomycete to have its genome sequenced (Tyler et al., 2006). Genomic information, including gene expression data and multiple genome sequences, have driven rapid progress (Qutob et al., 2000; Torto‐Alalibo et al., 2007; Wang et al., 2011). The genome of P. sojae, and later other oomycetes (Haas et al., 2009), was found to be partitioned into stable regions rich in housekeeping genes displaying extensive synteny with other oomycete genomes, interspersed with dynamic, transposon‐rich regions that contained rapidly evolving genes implicated in virulence (Jiang & Tyler, 2012; Tyler et al., 2006) (Fig. 9). Multiple large, rapidly diversifying families of genes with functions in virulence were discovered (Jiang and Tyler, 2012; Tyler et al., 2006), including hydrolases, hydrolase inhibitor proteins, toxin‐like proteins, such as the NLP family (Qutob et al., 2006), and two huge, diverse classes of effector proteins (RXLR and CRN effectors) (Haas et al., 2009; Jiang et al., 2008; Tyler et al., 2006) that can cross into the cytoplasm of host plant cells (Dou et al., 2008; Kale et al., 2010) (Fig. 9). All 11 avirulence genes cloned from P. sojae proved to encode RXLR effectors detected by host R proteins (Jiang and Tyler, 2012) (Fig. 9). Genetic inheritance studies in P. sojae using molecular markers led to discoveries of high‐frequency gene conversion (also referred to as loss of heterozygosity) (Chamnanpunt et al., 2001) and epigenetic silencing (Qutob et al., 2013) as important mechanisms underlying pathogen variation.

Figure 9.

Large diverse families of virulence proteins encoded by the Phytophthora sojae genome. (A) The Phytophthora sojae genome contains clusters of conserved housekeeping genes (brown) that have conserved orders among Phytophthora species, separated by dynamic transposon‐rich regions that contain genes (red) encoding virulence proteins, many of which are secreted. (B) Secreted virulence proteins (effectors) may act in the apoplast, or be transported inside the cell. Cell‐entering effectors may have targets in the nucleus or cytoplasm, and may be detected by resistance proteins (Rps; resistance against P. sojae).

Many areas of future research into P. sojae will be shared with those of other oomycete and fungal pathogens. One area will be to define in detail how apoplastic and host cell‐entering effectors of P. sojae manipulate soybean physiology to enable infection, including the soybean molecules targeted by the effectors (Fig. 9) and the mechanisms by which RXLR and CRN effectors gain entry (Fig. 9). The identification of the P. sojae effectors most important for infection (e.g. using new tools for genetic manipulation, such as tailored nucleases) should lead to new targets for disease control. The cell biology of P. sojae infection (Enkerli et al., 1997) must be defined in much more detail, incorporating the spatial distributions of pathogen and host transcripts, proteins and metabolites. Understanding fully the role of epigenetic mechanisms in the generation of variation in pathogen populations will also be important for the design of effective strategies for disease control. Sequencing the genomes and transcriptomes of numerous isolates of P. sojae and its nearest sister species will shed light on the genetic adaptability of the pathogen. In practical terms, a large translational research effort will be required to convert the rapidly accumulating knowledge about the basic biology and pathology of P. sojae and other oomycetes into effective disease control solutions.

5. Phytophthora capsici

Phytophthora capsici is a highly destructive invasive pathogen that attacks solanaceous (pepper, tomato), legume (lima and snap beans) and most cucurbit hosts (Hausbeck and Lamour, 2004; Leonian, 1922). Disease is favoured by warm (25–28 °C) and wet conditions, and the asexual epidemiology is often explosive (Granke et al., 2009). Initial infection is biotrophic, followed by transitions within 24–48 h to necrotrophy and the production of deciduous sporangia on the surface of infected tissues (Fig. 10). The importance of the sexual stage differs by region. In Peru and Argentina and across much of China, long‐lived and widely dispersed clonal lineages dominate (Gobena et al., 2012; Hu et al., 2013; Hurtado‐Gonzales et al., 2008; Sun et al., 2008). This is in contrast with the USA, South Africa and the northern provinces of China, where populations have high levels of genotypic diversity and outcrossing is frequent (Dunn et al., 2010; Gobena et al., 2012; Meitz et al., 2010). Once introduced to a field site, P. capsici is difficult to control and often impossible to eradicate. Phytophthora capsici grows rapidly and sporulates heavily on simple media, and isolates from sexual field populations are often fecund (Gobena et al., 2012; Lamour and Hausbeck, 2000). Phytophthora capsici is one of the most genetically diverse eukaryotic organisms yet described, and there is significant genetic variation in the form of single nucleotide polymorphisms within individual genomes and across world populations (Lamour et al., 2012).

Figure 10.

Heavy sporulation and spontaneous morphological variation in the vegetable pathogen Phytophthora capsici. (A) Naturally infected tomato fruit with sporangium production on the surface of the fruit. (B) A single zoospore‐derived field isolate of P. capsici sectoring on V8 agar medium following long‐term storage.

Current research includes the investigation of resistance (host and nonhost) in commercial vegetable and experimental plants, the discovery and characterization of genes and proteins driving pathogenicity and virulence, and studies to measure the evolution of natural and laboratory populations. Under controlled conditions, P. capsici infects at least 26 plant families (Granke et al., 2012). Natural resistance to P. capsici in pepper and cucurbits appears to be rare (Mallard et al., 2013) but, in tomato, it may be extensive (Quesada‐Ocampo and Hausbeck, 2010). Recent molecular studies of the CRN class of effectors have indicated that they are often localized to the host nucleus and play an important role in the infection process (Chen et al., 2013; Stam et al., 2013a, 2013b). Transcriptome studies using RNAseq and microarrays have indicated dramatic changes from pre‐infective spores through the early biotrophic and later necrotrophic stages of infection (Chen et al., 2013; Jupe et al., 2013). Studies of individual effectors have suggested that some manipulate the host to allow infection, whereas others trigger plant cell death (Chen et al., 2013; Feng and Li, 2013; Feng et al., 2010; Sun et al., 2009).

A high‐quality reference genome and a high‐density single nucleotide polymorphism‐based genetic linkage map have been completed recently (Lamour et al., 2012). These important resources illuminated an important source of asexual genetic variation, known as loss of heterozygosity (Lamour et al., 2012). Loss of heterozygosity occurs when variable length tracts (300 bp to >1 Mbp) of the diploid genome switch to one of the two possible haplotypes. Loss of heterozygosity has been described in laboratory‐produced sexual progeny, field isolates maintained on agar medium and field isolates genotyped directly from naturally infected tissue (Gobena et al., 2010; Hu et al., 2013; Hulvey et al., 2010). Loss of heterozygosity is associated with spontaneous switches from the A2 to the A1 mating type, loss of pathogenicity and reduced virulence (Hu et al., 2013; Lamour et al., 2012).

The diversity and plasticity of P. capsici present challenges and unique opportunities for research (Fig. 10). Future research questions include the following. What is the significance of a highly diverse effector arsenal? Are these effectors important for host‐specific interactions and the broad host range? How important is loss of heterozygosity in laboratory and field populations? The genomic plasticity of P. capsici and the ease of laboratory manipulation provide a unique opportunity to measure genome stability and adaptive evolution at a fine scale, and may provide useful insights into this and other oomycete pathogens (Lamour and Hu, 2013).

6. Plasmopara viticola

The obligate biotrophic oomycete Pl. viticola, the causal agent of grape downy mildew, is native to North America and was inadvertently introduced into Europe at the end of the 19th century (Millardet, 1881; Viennot‐Bourgin, 1949), causing severe damage to Vitis vinifera, which had evolved in the absence of this pathogen (Galet, 1977; Gessler et al., 2011). Plasmopara viticola belongs to the family Peronosporaceae; its life cycle includes an asexual multiplication phase occurring during the plant vegetative period and a sexual phase that ensures pathogen overwinter survival (Wong et al., 2001). The pathogen overwinters as oospores in dead leaf lesions or as mycelium in infected twigs. In spring, and in particular during rainy periods, oospores germinate to produce sporangia, which are transported by wind or water to the wet leaves near the ground, which they infect through stomata on the lower surface. The mycelium then spreads into the intercellular spaces of the leaf from which sporangiophores arise and emerge through the stoma, ready to start new infection cycles (Gobbin et al., 2005). Downy mildew affects leaves, fruits and shoots, with young tissues being particularly susceptible to infection (Fig. 11) (Kennelly et al., 2007). A disease cycle may take from 5 to 18 days, depending on the temperature, humidity and varietal susceptibility (Agrios, 2005; Gessler et al., 2011).

Figure 11.

Downy mildew symptoms with well‐evident sporangiophores on the lower side of a grape leaf (A) and a young cluster (B).

Downy mildew is still most destructive in Europe and in the eastern half of the USA, where it may cause severe epidemics year after year (Agrios, 2005; Madden et al., 1995). When the weather is favourable and no protection against the disease is provided, downy mildew can easily destroy up to 75% of production in a single season (Madden et al., 2000; Rossi and Caffi, 2012). Occasionally, Pl. viticola can be destructive in other humid parts of the world in which V. vinifera is cultivated.

In the last 50 years, research on grapevine downy mildew has focused on the pathogen life cycle and epidemiology (reviewed in Gessler et al., 2011), and on the genetic identification of host resistance loci for the establishment of molecular markers (revised in Töpfer et al., 2011). In the last decade, studies on Pl. viticola have highlighted its enormous potential in the development of fungicide resistance (Blum et al., 2010; Chen et al., 2007) and in breaking down plant resistance of interspecific hybrids, such as ‘Bianca’ (Casagrande et al., 2011; Peressotti et al., 2010) and ‘Regent’ (Delmotte et al., 2013). Population genetic studies have been carried out (Fontaine et al., 2013 and references therein) to assess pathogen dynamics and diversity in Europe. Moreover, it has been proposed that grapevine downy mildew is not caused by a single species, but instead by a complex of cryptic species that have diverged on Vitaceae (Rouxel et al., 2013). Trade‐offs between the size and number of sporangia produced have been reported, leading to ecological advantages for this pathogen (Delmotte et al., 2013). For these reasons, the Vitis–Pl. viticola pathosystem was elected as a prime candidate for the study of host specialization of biotrophic plant pathogens (Rouxel et al., 2013) and pathogen adaptation to partial host resistance (Delmotte et al., 2013).

Control methods against Pl. viticola are essentially based on the use of chemical fungicides and the application of disease models that serve as decision support systems (Lalancette et al., 1987; Rossi et al., 2009, 2013; Vercesi et al., 2010). As a result of the growing public concern on the use of chemical pesticides, and the need to adhere to the European Directive 2009/128/EC encompassing a framework ‘to achieve a sustainable use of pesticides’ by promoting Integrated Pest Management (IPM), the search for alternative methods for the control of Pl. viticola on grapevine appears to be urgent. Several alternative approaches have been proposed in the last 20 years, but none has been transferred to practical use (Gessler et al., 2011). Moreover, the lack of precise characterization of Pl. viticola isolates is dramatically limiting the reliable control of the pathogen. Although molecular studies have previously confirmed a high diversity in the pathogen population, there is a surprising lack of phenotypic characterization of pathotype strains or races which could be used to study the mechanisms of interaction with host genotypes with different levels of resistance (Gómez‐Zeledón et al., 2013). In conclusion, interdisciplinary studies and consistent resources should be invested for the study of the Pl. viticola–V. vinifera pathosystem in order to find new, effective alternatives for the IPM of this highly adaptive and destructive pathogen.

7. Phytophthora cinnamomi

Some call it the ‘biological bulldozer’ for its capacity to destroy natural plant communities across the globe, and disease caused by P. cinnamomi has broad and economically important impacts in forestry and horticulture, and in the nursery industry. Like other Phytophthora spp., P. cinnamomi has a number of strategies for survival, propagation and dissemination. The motile zoospore is recognized as the main infective propagule following encystment and attachment to roots and stems (Fig. 12). Recent work has suggested that, in addition to chlamydospores, P. cinnamomi is also associated with lignituber formation which enables survival under harsh conditions (Jung et al., 2013). Both A1 and A2 mating types are pathogenic, but wide differences in the distribution and frequency of occurrence suggest that the A2 mating type is more invasive and is generally recognized as being the more aggressive of the two mating types. Where introduced, this pathogen has had enormous impacts on natural systems, including those of Australia, southern Europe and the USA. In Australia, for example, it has been estimated that >3000 largely endemic plant species from numerous plant families are under threat, and a new National Threat Abatement Plan has been urgently implemented (Australian Government Department of Environment, 2014) (Fig. 13). The control of disease, especially across the large areas of native vegetation affected, is still a great problem, but some success has been achieved by the use of phosphite in both natural systems and in agriculture (Akinsanmi and Drenth, 2013; Crane and Shearer, 2014), by the use of calcium amendments to soil (Serrano et al., 2013) and by containment and eradication of spot infections (Dunstan et al., 2010). Climate change is predicted to have a significant influence on the intensity and distribution of disease (Thompson et al., 2014).

Figure 12.

Cryo‐scanning electron micrograph of a Phytophthora cinnamomi cyst between two epidermal cells on a root of tobacco. Note the adhesive material that surrounds the cyst that has been expelled by zoospore peripheral vesicles. Photograph courtesy of Adrienne Hardham, Australian National University.

Figure 13.

(A) Individual plants of Xanthorrheoa australis (austral grass tree), a highly suscpetible native Australian species, infected by Phytophthora cinnamomi within a dry sclerophyll eucalypt forest at Anglesea, Victoria, Australia. Note the dead and dying plants that have brown, collapsed leaves compared with the healthy green and erect leaves of plants which are yet to be killed. These individual plants range in age from approximately 20 years (the smallest in the centre) to around 70 years (green individual on the right of the image). (B) Advancing disease front caused by invasion by P. cinnamomi in Xanthorrhoea australis‐dominated understorey in eucalyptus open forest at Wilsons Promontory, Victoria, Australia. The disease has moved from the foregound of the picture, where all susceptible vegetation including X. australis has been killed, and its progress can be seen as a line of dead and dying X. australis (brown collapsed plants) at the disease margin. Healthy green plants behind them will soon be killed. Loss of the major understorey components, as in the forground, results in complete structural change and loss of all susceptible species.

Phytophthora cinnamomi is a challenging organism to work with. Sequencing of its genome has recently been completed (JGI; http://genome.jgi‐psf.org/) and has opened up a variety of opportunities to investigate the critical features that enable this pathogen to be so wide‐ranging in its hosts. A real change in emphasis in research on P. cinnamomi has occurred in recent times, with an increasing number of groups using genomic, transcriptomic and proteomic approaches to understand the pathogen and/or its interaction with the host (for example, Reeksting et al., 2014). Experimental plants, including Arabidopsis, Zea mays and Eucalyptus, for which comprehensive genomic information is available, are increasingly being used as host–pathogen platforms (for example, Allardyce et al., 2013; Dempsey et al., 2012; Rookes et al., 2008). Fundamental studies on P. cinnamomi plant cell wall‐degrading enzymes and the genes that encode them are being undertaken (Hee et al., 2013; Adrienne Hardham, Australian National University, Canberra, ACT, Australia, personal communication), as well as examination, at the molecular level, of defence pathways and their control (Eshraghi et al., 2014; Gunning et al., 2013).

High‐throughput, genome sequencing is emerging as an exciting way to examine the pathogen, its hosts and the soil environment, and is now being used to examine pathogen ecology and diversity within soils, and for the analysis of the response of host plants (Treena Burgess, Murdoch University, Perth, WA, Australia, personal communication). Much of our progress in understanding host–pathogen interactions will come from such approaches. We still lack knowledge on why plants are resistant to this pathogen and what is the basis for induced resistance, for example, following phosphite treatment. The search for host resistance to P. cinnamomi is an active area in which signalling pathways and their control are being elucidated. Mapping the disease over the large invaded areas is still not straightforward, although advances in remote sensing, high‐resolution digital photography, hyperspectral imaging (David Guest, Sydney University, Sydney, NSW, Australia, personal communication) and ‘drone’ technology will probably see our ability in this area being greatly enhanced in the near future. The era of nanotechnology offers new opportunities for the delivery of molecules that can influence disease outcome, yet this area has not been explored to date, although preliminary research with various nanoparticle systems (Hussain et al., 2013; Nadiminti et al., 2013) has indicated that these may be useful in delivering molecules, including pathogen effectors, DNA and miRNA, which may modify host processes and their response to pathogen infection.

Future research will focus on the following questions. (i) What are the virulence factors that enable P. cinnamomi to infect and colonize susceptible species and therefore should be targeted for control? (ii) What constitutes host resistance and how can it be manipulated? Can we look to nanotechnology for some answers? (iii) Is phosphite the only chemical that we can use to control P. cinnamomi, and how does phosphite alter the host response?

8. Phytophthora parasitica

Phytophthora parasitica (= P. nicotianae) is a worldwide distributed pathogen (Erwin and Ribeiro, 1996). Primarily known to cause tobacco black shank and citrus root rot and gummosis (Fig. 14), it is also responsible for severe foliar and fruit diseases, as well as root and crown rots on herbaceous and perennial plant species in more than 250 genera, including solanaceous crops (Fig. 15), and horticultural and fruit trees (Cline et al., 2008). Phytophthora parasitica produces both asexual zoospores and thick‐walled sexual oospores. Oospores constitute a potential source of genetic variation and, with resting chlamydospores, contribute to survival in unfavourable conditions in soil or within infected plant tissues.

Figure 14.

Impact of Phytophthora parasitica infection on citrus plants. (A, B) Five‐year‐old citrus plants not infected and infected, respectively, with Phytophthora parasitica. (C, D) Symptoms of P. parasitica on stems: (C) not infected; (D) infected plant displaying gummosis symptoms. (E, F) Leaves and fruits of infected (left) and healthy (right) plants. (G, H) Scanning electron microscope images of citrus fine roots infected with P. parasitica. Yellow arrows show encysted zoospores and germ tube of P. parasitica. Bar represents 20 μm. (A–F) Photographs courtesy of R. J. D. Dalio. (G, H) Photographs courtesy of M. E. Escanferla.

Figure 15.

Severe infection of brinjal fruit with Phytophthora parasitica. Typical symptoms are brown, soft, water‐soaked patches which rapidly cover the whole fruit. Brinjal is also known as aubergine or eggplant (Solanum melongena). Photograph courtesy of S. Guha Roy.

Contrasting with the broad host range observed at the species level, most individual P. parasitica isolates display host preference (Erwin and Ribeiro, 1996). Frequent cases of differential virulence on a range of hosts have been revealed (Colas et al., 1998; Matheron and Matejka, 1990), pointing out the need to decipher the genetic structure of P. parasitica on a global scale. In agreement with pathogenicity tests, recent single nucleotide polymorphism analyses conducted with mitochondrial and nuclear genes have revealed a specific association between the host of origin and genetic grouping which was particularly evident for tobacco and citrus isolates (Mammella et al., 2011, 2013). In contrast, no clear genetic structure was revealed for isolates from other hosts, especially potted ornamentals in nurseries. A significant geographical structuring was revealed for tobacco, but not for citrus, isolates (Bonnet et al., 1994; Colas et al., 2001; Mammella et al., 2013). Further studies relying on whole‐genome sequencing programmes (see below) are necessary to determine whether these molecular groups represent evidence of physiological races, pathotypes or even subspecies within P. parasitica.

As some isolates may also infect many hosts, including Arabidopsis thaliana (Attard et al., 2008, 2010), P. parasitica has emerged as an ideal pathogen to develop specific studies with the aim to advance our knowledge on the mechanisms underlying general pathogenicity and those governing host specificity. Furthermore, P. parasitica is phylogenetically related to P. infestans in Phytophthora clade 1, and overlaps its host range, which includes potato (Taylor et al., 2008). Comparative analyses on these two species varying in genome size (83 and 240 Mb for P. parasitica and P. infestans, respectively) will facilitate the understanding of the evolution behind pathogenicity and host range among Phytophthora spp. Through the sequencing of the genome of isolates of diverse host range and geographical origins, the international ‘Phytophthora parasitica genome initiative’ project will enable the characterization of genes that determine host range. In‐depth genomic and transcriptomic analyses of 14 sequenced genomes are currently being performed. Special efforts are being devoted to characterize the repertoire of effector proteins. As a broad host range pathogen, P. parasitica provides a unique opportunity for intra‐ and interspecific comparative analyses, looking for the presence of various effector families, their organization, their role in plant recognition and infection, and their evolution among strains and species that display broad or restricted host ranges. The identification of conserved effector groups, as well as of other pathogenicity genes, will allow the evaluation of the evolutionary pressures of exposure to different host defence responses to the diversification of effectors and their role in adaptation to host plants.

Phytophthora parasitica has not been as extensively studied as its economic importance should warrant. However, it is likely to gain importance in the foreseeable future for the following reasons. First, it is prominent in nurseries of potted ornamentals and fruit tree species, the trade of which seems to represent one of the most efficient dissemination pathways of Phytophthora (Moralejo et al., 2009; Olson and Benson, 2011). This makes P. parasitica an ideal species to study diffusion pathways of Phytophthora and other soil‐borne pathogens on a global scale. For aesthetic reasons, the ornamental industry requires the extensive use of anti‐oomycete chemicals (Olson et al., 2013). The global nursery trade thus increases the risk of the rapid spread of resistant P. parasitica strains to new areas following the inappropriate use of fungicides, and constitutes a growing threat to local agriculture and natural ecosystems (Brasier, 2008). In addition, P. parasitica will probably benefit from the warming climate. Its host range generally includes those of other species of prime economic importance (P. infestans, P. capsici, P. citrophthora), but generally requires warmer conditions than these potential competitors (Erwin and Ribeiro, 1996). Consequently, the foreseen global warming is likely to provide a catalyst for the geographical expansion of this species, as has already been proposed in Mediterranean climates (Andres et al., 2003; Saadoun and Allagui, 2008) and in eastern India (Guha Roy et al., 2009) .

9. Pythium ultimum

Pythium resides in the peronosporalean lineage of oomycetes, with Phytophthora and downy mildews (Dick, 2001). One of its most significant members is Py. ultimum, which causes damping off and root rot on >300 diverse hosts, including corn, soybean, wheat, Douglas fir and ornamentals (Farr and Rossman, 2014). Pythium ultimum is a common inhabitant of fields, ponds and streams, and of decomposing vegetation worldwide. Contributing to the ubiquity of the species is its ability to grow saprotrophically in soil and plant residue, a trait shared by most Pythium spp., but not other peronosporaleans, which must colonize living hosts. Pythium ultimum is also homothallic, producing oospores capable of long‐term survival (Martin and Loper, 1999). Mycelia and oospores in soil can thus initiate infections of seeds or roots, leading to wilting, reduced yield and mortality (Fig. 16A). Disease management is difficult, but focuses on sanitation, fungicides and biological control, particularly in glasshouses. Quantitative resistance has been reported in several hosts, but has a limited effect (Lucas and Griffiths, 2004; Wang and Davis, 1997).

Figure 16.

Pythium ultimum var. ultimum. (A) Pre‐emergence damping‐off in okra, resulting in the death of most plants at the front of the row. At the back, disease was controlled using metalaxyl. (B) Terminal hyphal swellings; bar, 10 μm. (C) Oospore within oogonium; bar, 10 μm. Images adapted from Kida et al. (2006) with permission.

The role of asexual spores depends on the strain. Pythium ultimum is a species complex that includes Py. ultimum var. ultimum and var. sporangiiferum, which have indistinguishable internal transcribed spacer (ITS) sequences (Schroeder et al., 2013). Sporangia and zoospores are produced rarely by the former, but abundantly by the latter. Pythium ultimum var. ultimum forms sporangia‐like hyphal swellings which germinate to yield infective hyphae (Fig. 16B; Stanghellini and Hancock, 1971). Similar to other oomycetes, it also produces sexual oospores (Fig. 16C).

Genome sequencing of several Pythium spp., including Py. ultimum var. ultimum and var. sporangiiferum, has provided insight into their biology (Adhikari et al., 2013; Levesque et al., 2010). Annotated in the c. 43‐Mb genomes of two subspecies are 15 290 and 14 086 genes, respectively, which is less than the smallest Phytophthora, but more than downy mildews. Whether this difference in gene number is significant requires more analysis, as the two assemblies vary in quality and only single isolates were sequenced. Large size variation between isolates was reported on the basis of electrophoretic karyotyping (Martin, 1995).

Nevertheless, it is evident from genome analysis that there are many differences between Pythium and Phytophthora, including a 25% reduction in Pythium of the fraction of proteins that are secreted. In part, this reflects the absence of RXLR effectors, which may not be needed for necrotrophic lifestyles. Pythium also lacks haustoria, which appear to be used by biotrophic and hemibiotrophic oomycetes to deliver RXLRs to host cells (Whisson et al., 2007). Another likely sign of the necrotrophy of Pythium is its greater abundance of lipases and proteases. However, Pythium lacks cutinases and pectin esterases, but this is probably because it infects primarily nonsuberized tissue, whereas Phytophthora (which encodes these enzymes) can penetrate plant cuticles. Pythium encodes sufficient enzymes for the maceration of host cell walls, but cannot degrade some ubiquitous wall components, such as xylans, which suggests that soluble sugars may be a more important carbon source (Zerillo et al., 2013).

Markers derived from Py. ultimum genomes should help reveal what distinguishes the subspecies and provide more resolution to population studies, which can help to identify the sources of outbreaks. Studies of Py. ultimum var. ultimum have indicated that populations are not clonal and some outcrossing may occur (Francis and St. Clair, 1997). A greater evolutionary question concerns the organization of the Pythium genus as a whole. Division of the >120 Pythium species over five new genera has been proposed on the basis of the sequence analysis of two loci (Uzuhashi et al., 2010). If accepted by the community, Py. ultimum would be renamed Globisporangium ultimum.

Of much interest is the interaction between Py. ultimum and biocontrol agents, such as Trichoderma, Streptomyces, Pythium oligandrum (a mycoparasitic member of the genus) and others (Gracia‐Garza et al., 2003; Martin and Loper, 1999). The extent to which these organisms function by altering rhizosphere microflora or attacking Py. ultimum directly is an open question (Naseby et al., 2000; Vallance et al., 2012); Pythium ultimum competes poorly with organisms having higher saprotrophic capabilities.

Pythium ultimum is just one of many destructive members of the genus, with Py. aphanidermatum and Py. irregulare also topping lists of important pathogens (Martin and Loper, 1999). Opportunities for understanding their biology, ecology and evolution have been enhanced by genome sequencing. DNA‐mediated transformation has been achieved for several species, but few studies of gene function have been reported (Grenville‐Briggs et al., 2013; Weiland, 2003). As core promoter structure appears to be conserved within the Peronosporales, vectors and technologies applied to species, such as Phytophthora, should be transferable to Pythium (Roy et al., 2013). Pythium spp. are easily grown and have the potential to develop into valuable experimental systems for necrotrophic and saprotrophic oomycete lifestyles. Their growth on byproducts of the agro‐food industry has also attracted interest as sources of polyunsaturated fatty acids for human consumption (Stredansky et al., 2000).

10. Albugo candida

White blister rust is a disease caused in many dicotyledonous plant species by obligate biotrophic parasites. For example, A. candida infection of Brassica juncea (Indian mustard) has resulted in significant crop losses in India (Awasthi et al., 2012), Canada (Rimmer et al., 2000) and Australia (Kaur et al., 2008). The white rusts, order Albuginales, are phylogenetically distant from the Peronosporales, and probably represent an independent acquisition of biotrophy (Thines and Kamoun, 2010; Thines and Spring, 2005). All Albugo species infecting the Brassicaceae were thought to be races of A. candida, but molecular studies of isolates from various hosts and locations have led to the description of specialists, for example Albugo laibachii on Arabidopsis thaliana (Thines, 2014; Thines et al., 2009). Specific A. candida races can grow on diverse plant hosts, including Brassicaceae, Cleomaceae and Capparaceae (Thines, 2014). Albugo spp. provide an interesting experimental system for the study of plant immune suppression, disease resistance and host–pathogen co‐evolution.

Albugo spp. reproduce asexually via zoosporangia, which release flagellated motile zoospores on incubation in water. On the surface of a plant leaf, zoospores settle in stomata, and each extends a germ tube into the substomatal chamber (Holub et al., 1994). Coenocytic hyphae then grow intercellularly through the plant. Small globose haustoria penetrate into plant cells (Soylu et al., 2003). When an Albugo infection is mature, zoosporangia rupture the plant epidermis with force and enzymatic digestion (Heller and Thines, 2009). This results in characteristic ‘white blister’ pustules. Albugo also has a sexual cycle, producing tough oospores that can survive difficult environmental conditions (Petrie, 1975). During the systemic infection of Brassicaceae hosts, the inflorescences become misshapen, forming so‐called ‘stagheads’ (Fig. 17A).

Figure 17.

Disease symptoms of Albugo infections. (A) Disease resulting from the infection of Brassica juncea with an unknown Albugo species. The misshapen inflorescence phenotype is known as a ‘staghead’. (B) An example of immunity suppression by Albugo laibachii: A. thaliana Col‐0 is resistant to Hyaloperonospora arabidopsidis Emoy2 via RPP1 but, when pre‐infected with A. laibachii, can support the growth of both pathogens.

Albugo infection has long been associated with ‘green islands’, where infected tissue appears to be healthy and senescence is delayed. Infection by Albugo also greatly enhances susceptibility to co‐infections with downy mildews (Bains and Jhooty, 1985; Crute et al., 1994). Cooper et al. (2008) investigated the ability of A. laibachii and A. candida to suppress host immunity. They showed that A. laibachii can suppress the ‘runaway cell death’ of Arabidopsis lsd1 mutants after inoculation with avirulent H. arabidopsidis. Furthermore, when pre‐infected with virulent A. laibachii, resistant Arabidopsis accessions were no longer resistant to avirulent H. arabidopsidis isolates (Fig. 17B), lettuce downy mildew or powdery mildew. Suppression was also observed on B. juncea with A. candida and Brassica downy mildew (Cooper et al., 2008). These results suggest that Albugo is effective at broad suppression of plant immunity, including effector‐triggered immunity.

The first step in understanding how Albugo spp. impose such susceptibility is to examine their genomes. Links et al. (2011) and Kemen et al. (2011) sequenced A. candida and A. laibachii genomes, respectively. The genomes are around 40 Mb and compact; about 50% of the assemblies consist of coding sequences (see Fig. 18). Both genomes show adaptations to obligate biotrophy; they are missing sulfite oxidases, nitrate and nitrite reductases and, in the case of A. laibachii, the whole molybdopterin biosynthesis pathway. The A. candida secretome consists of 929 proteins (without transmembrane domains), compared with 672 in A. laibachii, perhaps reflecting its wider host range. Within the secretomes, there is no enrichment of putative RXLR effectors. Kemen et al. (2011) discovered the CHXC (cysteine, histidine, any amino acid, cysteine) motif at the N‐terminus of a class of candidate effectors. The CHXC‐containing N‐terminus is sufficient to translocate the C‐terminus of P. infestans AVR3a (an RXLR effector) into host cells (Kemen et al., 2011).

Figure 18.

Albugo spp. have compact genomes. Synteny between Albugo laibachii, Pythium ultimum, Hyaloperonospora arabidopsidis and Phytophthora infestans. The region shown is an example of the relatively dense clustering of genes in Albugo species. With increasing genome size, the distance between both genes increases and re‐organizations occur (red, synteny without inversion; blue, inverted regions). Reproduced from Kemen et al. (2011).

Several A. candida races can infect some, but not all, A. thaliana accessions and, from crosses between resistant and susceptible accessions, an R gene against four A. candida races, WRR4 [encoding a toll interleukin 1 receptor‐nucleotide‐binding‐leucine‐rich repeat (TIR‐NB‐LRR) R protein], was identified (Borhan et al., 2008). WRR4 can also provide resistance to A. candida when transformed into susceptible cultivars of B. napus and B. juncea (Borhan et al., 2010). In A. thaliana, RAC1 (also encoding a TIR‐NB‐LRR R protein) confers resistance to A. laibachii (Borhan et al., 2004). The inheritance of avirulence of a B. juncea isolate (Ac2V) was studied through a cross between two A. candida isolates; this work predicted a single avirulence gene for the incompatibility between Ac2V and B. rapa (Adhikari et al., 2003).

There are open questions about Albugo from both fundamental and translational perspectives. Thines (2014) speculated that the broad host range of the A. candida meta‐population is maintained through frequent genetic exchange where the host range of individual isolates overlap. Comparing the genomes of multiple isolates from different hosts would test this hypothesis and build up a clear picture of population variation. This would also aid the discovery of new effector candidates through the identification of secreted proteins under strong selective pressure. A more extensive analysis of Albugo effectors should be made. The presence of the CHXC effectors inside host cells needs to be confirmed and the translocation mechanism elucidated. It is unclear which Albugo effector proteins are recognized by the few known R proteins. Arabidopsis thaliana cannot be colonized by most A. candida isolates. The molecular basis for this resistance could be exploited to introduce durable resistance to Brassica crops.

Lastly, and perhaps most interestingly, is the question: how does the remarkable defence suppression by Albugo work? We need to define the extent of this suppression. What other pests or pathogens can grow on plants infected with Albugo? What changes occur in the microbiome of Albugo‐infected leaves in the field? Recent data have suggested that Albugo could be widespread as an asymptomatic endophyte (Ploch and Thines, 2011). The implications of these infections as a reservoir for (i) Albugo and (ii) further Albugo suppression‐enabled infections by other species remain to be discovered.

Conclusion

Although the study of oomycete plant pathogens has always been an important topic in plant pathology, it has recently taken an even more central role with the advent of genomics and the discovery of large effector repertoires in oomycete genomes. This article provides a benchmark for future trends. Many topics remain to be investigated in more depth. For example, the large number of pathogenic species and the wide diversity of host species and host ranges should provide a rich basis for the investigation of the genetic and physiological mechanisms of host adaptation and specialization. It will also be interesting to track how the Top 10 list will develop in the coming years. Many pathogenic oomycetes among the 33 listed (Table 2) have evolved unique adaptations in their parasitic lifestyle that will undoubtedly reveal fascinating processes and mechanisms. Thus, future research efforts should take into account a diverse spectrum of taxa beyond the widely studied species.

Author Contributions

All authors voted and contributed to the writing of the 10 sections. SK oversaw the voting and writing. Other authors are listed in reverse order based on the species ranking. The species coordinators are listed last in their section and are preceded by other contributors listed in alphabetical order. The species coordinators are: Albugo candida (OF and JDGJ), Pythium ultimum (HSJ), Phytophthora parasitica (FP), Phytophthora cinnamomi (DC), Plasmopara viticola (MR and AF), Phytophthora capsici (KL), Phytophthora sojae (MG and BMT), Phytophthora ramorum (NJG), Hyaloperonospora arabidopsidis (GvdA and JMcD) and Phytophthora infestans (PRJB and FG).