Jean Beagle Ristaino

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world’s population. Current annual worldwide potato crop losses due to late blight are conservatively estimated at

Organic and synthetic fertility amendments influence soil microbial, physical and chemical properties on organic and conventional farms

6.7 billion. Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars. Here we report the sequence of the P. infestans genome, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for ∼74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer

Field experiments were conducted to examine the effects of organic and synthetic soil fertility amendments on soil microbial communities and soil physical and chemical properties at three organic and three conventional vegetable farms in Virginia and Maryland in 1996 and 1997. Two treatments, including either an alternative organic soil amendment (composted cotton-gin trash, composted yard waste, or cattle manure) or synthetic soil amendment (fertilizer) were applied to three replicated plots at each grower field location. Production history and time affected propagule densities of Trichoderma species which remained higher in soils from organic farms. Propagule densities of Trichoderma species, thermophilic microorganisms, and enteric bacteria were also detected in greater numbers in soils amended with alternative than synthetic amendments, whereas propagule densities of Phytophthora and Pythium species were lower in soils amended with alternative than synthetic fertility amendments. Concentrations of Ca, K, Mg, and Mn were higher in soils amended with alternative than synthetic fertility amendments. Canonical correlations and principle component analyses indicated significant correlation between these soil chemical factors and the biological communities. First-order canonical correlations were more negative in fields with a conventional history, and use of synthetic fertilizers, whereas canonical correlations were more positive in fields with a history of organic production and alternative soil amendments. In the first year, yields of corn or melon were not different in soil amended with either synthetic or organic amendments at four of six farms. In the second year, when all growers planted tomatoes, yields were higher on farms with a history of organic production, regardless of soil amendment type. Alternative fertility amendments, enhanced beneficial soil microorganisms reduced pathogen populations, increased soil organic matter, total carbon, and cation exchange capacity (CEC), and lowered bulk density thus improving soil quality.

Ecologically Based Approaches to Management of Phytophthora Blight on Bell Pepper

Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes.

PCR amplification of the Irish potato famine pathogen from historic specimens

Phytophthora blight, caused by the oomycete pathogen, Phytophthora capsici, is a devastating disease on bell pepper and cucurbit crops in the United States and worldwide (29,40). P. capsici causes a root and crown rot, as well as an aerial blight of leaves, fruit, and stems, on bell pepper (Capsicum annuum), tomatoes, cucumber, watermelon, squash, and pumpkin (29,35, 40,57,73). The disease was first described on bell pepper in New Mexico in 1922 (40). In recent years, epidemics have been severe in areas of North Carolina, Florida, Georgia, Michigan, and New Jersey. Oospores are believed to provide the initial source of inoculum in the field, and the disease is polycyclic within seasons (1,7,59,60,67). In this article, we discuss the biology and epidemiology of Phytophthora blight on bell pepper and also describe management strategies that can be implemented based on existing knowledge of the ecology of this devastating pathogen. The objectives of ecologically based pest management (EBPM) are the safe, profitable, and durable management of pests that includes a total systems approach (25). EBPM relies primarily on biological input of knowledge concerning a pathogen life cycle, and secondarily, when necessary, on physical, chemical, and biological supplements for disease management. An understanding of the ecological processes that are suppressive to plant diseases is emphasized rather than secondary inputs (25). Fortunately, we have a considerable amount of information available on the biology and ecology of P. capsici, which can now be integrated to improve our ability to manage the disease using ecologically based approaches. Strategies recommended for management of Phytophthora blight involve integrated approaches that focus first on cultural practices that reduce high soil moisture conditions, but also include monitoring and reduction of propagules of P. capsici that persist in the soil, utilization of cultivars with resistance to the disease, and when necessary, judicious fungicide applications. Symptoms and Life Cycle P. capsici can infect virtually every part of the pepper plant. The pathogen causes a root and crown rot on pepper (Fig. 1) and also forms distinctive black lesions on the stem (Fig. 2). P. capsici can also infect the leaves and causes lesions that are circular, grayish brown, and water-soaked (Fig. 3). Leaf lesions and stem lesions are common when inoculum is splash dispersed from the soil to lower portions of the plant. The pathogen can also infect fruit and causes lesions that are typically covered with white sporangia, a sign of the pathogen (Fig. 4). P. capsici typically causes a fruit rot or stem rot on cucumbers and squash (Fig. 5). P. capsici reproduces by both sexual and asexual means (Fig. 6). The pathogen produces two mating types, known as the A1 and A2. These are actually compatibility types and do not correspond to dimorphic forms. Each mating type produces hormones that are responsible for gametangia differentiation in the opposite mating type. Both A1 and A2 mating types are common in fields in North Carolina and have also been identified within the same plant (59). P. capsici produces a male gametangium, called the antheridium, and a female gametangium, called the oogonium. The antheridium is amphigynous in this species. Meiosis occurs within the gametangia, and plasmogamy and karyogamy result

The Top 10 oomycete pathogens in molecular plant pathology

Late blight, caused by the oomycete plant pathogen Phytophthora infestans, is a devastating disease of potato and was responsible for epidemics that led to the Irish potato famine in 1845 (refs 1,2,3,4,5). Before the 1980s, worldwide populations of P. infestans were dominated by a single clonal lineage, the US-1 genotype or Ib mitochondrial DNA (mtDNA) haplotype, and sexual reproduction was not documented outside Mexico, the centre of diversity of the pathogen. Here we describe the amplification and sequencing of 100-base-pair fragments of DNA from the internal transcribed spacer region 2 from 28 historic herbarium samples including Irish and British samples collected between 1845 and 1847, confirming the identity of the pathogen. We amplified a variable region of mtDNA that is present in modern Ib haplotypes of P. infestans, but absent in the other known modern haplotypes (Ia, IIa and IIb). Lesions in samples tested were not caused by the Ib haplotype of P. infestans, and so theories that assume that the Ib haplotype is the ancestral strain need to be re-evaluated. Our data emphasize the importance of using historic specimens when making inferences about historic populations.

An Andean origin of Phytophthora infestans inferred from mitochondrial and nuclear gene genealogies

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.

Resistance to mefenoxam and metalaxyl among field isolates of Phytophthora capsici causing Phytophthora blight of bell pepper.

Phytophthora infestans (Mont.) de Bary caused the 19th century Irish Potato Famine. We assessed the genealogical history of P. infestans using sequences from portions of two nuclear genes (β-tubulin and Ras) and several mitochondrial loci P3, (rpl14, rpl5, tRNA) and P4 (Cox1) from 94 isolates from South, Central, and North America, as well as Ireland. Summary statistics, migration analyses and the genealogy of current populations of P. infestans for both nuclear and mitochondrial loci are consistent with an “out of South America” origin for P. infestans. Mexican populations of P. infestans from the putative center of origin in Toluca Mexico harbored less nucleotide and haplotype diversity than Andean populations. Coalescent-based genealogies of all loci were congruent and demonstrate the existence of two lineages leading to present day haplotypes of P. infestans on potatoes. The oldest lineage associated with isolates from the section Anarrhichomenun including Solanum tetrapetalum from Ecuador was identified as Phytophthora andina and evolved from a common ancestor of P. infestans. Nuclear and mitochondrial haplotypes found in Toluca Mexico were derived from only one of the two lineages, whereas haplotypes from Andean populations in Peru and Ecuador were derived from both lineages. Haplotypes found in populations from the U.S. and Ireland was derived from both ancestral lineages that occur in South America suggesting a common ancestry among these populations. The geographic distribution of mutations on the rooted gene genealogies demonstrate that the oldest mutations in P. infestans originated in South America and are consistent with a South American origin.

Effect of synthetic and organic soil fertility amendments on southern blight, soil microbial communities, and yield of processing tomatoes.

Incidence of Phytophthora blight in bell pepper fields that were sprayed for the first time with Ridomil Gold (mefenoxam) according to labeled recommendations was higher in North Carolina in 1997 than in previous years. Mefenoxam is the more active enantiomer contained in the racemic fungicide metalaxyl. A total of 150 isolates were obtained from 17 fields at eight grower locations. Among isolates from all locations, 30% were classified as sensitive, 10% as intermediate, and 59% were resistant to mefenoxam. Mefenoxam-resistant isolates were found in 82% of the fields sampled (14 of 17 fields). The proportion of resistant isolates in individual (fields ranged from 28 to 100%. The mean effective concentration (EC50) values for mefenoxam-sensitive isolates was 0.568 μg ml-1 (ranging from 0.12 to 1.1 μg ml-1), whereas the mean EC50 value for mefenoxam-resistant isolates was 366.5 μg ml-1 (ranging from 3 to 863 μg ml-1). The mean EC50 value for metalaxyl-sensitive isolates was 0.27 μg ml-1 (ranging from 0.00002 to 1.3 μg ml-1) and for metalaxyl-resistant isolates was 470.34 μg ml-1 (ranging from 10 to 966 μg ml-1). The greatest proportion of resistant isolates came from fields where mefenoxam was used alone rather than in combination with other fungicides. Both mating types were found among resistant isolates, suggesting that these isolates may persist in soil in subsequent years. Field isolates of Phytophthora capsici resistant to mefenoxam on pepper have not been reported previously and now pose new challenges for management of this important disease.

Influences of organic and synthetic soil fertility amendments on nematode trophic groups and community dynamics under tomatoes

ABSTRACT Soil fertility amendments, including composted cotton-gin trash, swine manure, a rye-vetch green manure, or synthetic fertilizers, were applied to subplots and tillage on bare soil; or tillage followed by surface mulch with wheat straw were applied to main plots to determine the effect on the incidence of southern blight caused by Sclerotium rolfsii, yield of processing tomato, and soil microbial communities. The amendment-tillage interaction was significant in 1997 and disease incidence was 67% in tilled bare soil receiving synthetic fertilizers; whereas disease incidence was 3, 12, and 16% in surface-mulched plots amended with a composted cotton-gin trash, swine manure, or a rye-vetch green manure. The amendment effect was significant in 1998, and disease incidence was 61% in plots receiving synthetic fertilizer and was 23, 44, and 53% in plots receiving cotton-gin trash, swine manure, or rye-vetch green manure, respectively. In 1997, yields were highest in tilled surface-mulched plots amended with synthetic fertilizers, cotton-gin trash, or swine manure, respectively. In 1998, yields were low in all plots and there were no significant differences in yield due to treatment. Propagule densities of antagonistic soil fungi in the genus Trichoderma were highest in soils amended with composted cotton-gin trash or swine manure in both years. Propagule densities of fluorescent pseudomonads in soil were higher in plots amended with organic amendments than with synthetic fertilizers in both years. Propagules densities of enteric bacteria were elevated in soils amended with raw swine manure biosolids in both years. Our research indicates that some organic amendments, such as cotton-gin trash, reduced the incidence of southern blight in processing tomato and also enhanced populations of beneficial soil microbes.