Find research datasets worth reusing

opencc-by-4.0Jun 2020View details →

On-site plant pathogen detection methods and introduction to microfluidics

On June 24, 2020, IPANEMA organized the fourth Scientific online lecture (SOL4). The lesson was held by Dr. Cor Schoen from <a href="https://www.wur.nl/">Wageningen University & Research</a>, who brought us closer to different possible approaches for pathogen detection on the field.

opencc-zeroOct 2020View details →

Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen

Genetic diversity within pathogen populations is critically important for predicting pathogen evolution, disease outcomes, and prevalence. However, we lack a good understanding of the processes maintaining genetic variation and constraints on pathogen life‐history evolution. Here, we analyzed interactions between 12 wheat host genotypes and 145 strains of Zymoseptoria tritici from five global populations to investigate the evolution and maintenance of variation in pathogen virulence and reproduction. We found a strong positive correlation between virulence (amount of leaf necrosis) and reproduction (pycnidia density within lesions), with substantial variation in both traits maintained within populations. On average, highly virulent isolates exhibited higher reproduction, which might increase transmission potential in agricultural fields planted to homogeneous hosts at a high density. We further showed that pathogen strains with a narrow host range (i.e. specialists) for reproduction were on average less virulent, and those with a broader host range (i.e. generalists) were on average less fecund on a given specific host. These costs associated with adaptation to different host genotypes might constrain the emergence of generalists by disrupting the directional evolution of virulence and fecundity. We conclude that selection favoring pathogen strains that are virulent across diverse hosts, coupled with selection that maximizes fecundity on specific hosts, may explain the maintenance of these pathogenicity traits within and among populations.

opencc-zeroDec 2019View details →

An invasive plant rapidly increased the similarity of soil fungal pathogen communities

Background and Aims: Plant invasions can change soil microbial communities and affect subsequent invasions directly or indirectly via foliar herbivory. It has been proposed that invaders promote uniform biotic communities that displace diverse, spatially variable communities ("Biotic Homogenization Hypothesis") but this has not been experimentally tested for soil microbial communities, so the underlying mechanisms and dynamics are unclear. Here, we compared density-dependent impacts of the invasive plant Alternanthera philoxeroides and its native congener A.sessilis on soil fungal communities, and their feedback effects on plants and a foliar beetle. Methods: We conducted a plant-soil feedback (PSF) experiment and a lab bioassay to examine PSFs associated with the native and invasive plants and a beetle feeding on them. We also characterized the soil fungal community using high-throughput sequencing. Key Results: We found locally differentiated soil fungal pathogen assemblages associated with high densities of the native plant Alternanthera sessilis but little variation in those associated with the invasive congener A. philoxeroides regardless of plant density. In contrast, AM fungal assemblages associated with high densities of the invasive plant were more variable. Soil biota decreased plant shoot mass but their effect was weak for the invasive plant growing in native plant conditioned soils. PSFs increased the larval biomass of a beetle reared on leaves of the native plant only. Moreover, PSFs on plant shoot, root and beetle mass were predicted by different pathogen taxa in a plant species-specific manner. Conclusion: Our results suggest that plant invasions can rapidly increase the similarity of soil pathogen assemblages even at low plant densities leading to taxonomically and functionally homogeneous soil communities that may limit negative soil effects on invasive plants.

opencc-zeroDec 2015View details →

Data from: Invasive mutualisms between a plant pathogen and insect vectors in the Middle East and Brazil

Complex multi-trophic interactions in vectorborne diseases limit our understanding and ability to predict outbreaks. Arthropod-vectored pathogens are especially problematic, with the potential for novel interspecific interactions during invasions. Variations and novelties in plant–arthropod–pathogen triumvirates present significant threats to global food security. We examined aspects of a phytoplasma pathogen of citrus across two continents. 'Candidatus Phytoplasma aurantifolia' causes Witches' Broom Disease of Lime (WBDL) and has devastated citrus production in the Middle East. A variant of this phytoplasma currently displays asymptomatic or 'silent' infections in Brazil. We first studied vector capacity and fitness impacts of the pathogen on its vectors. The potential for co-occurring weed species to act as pathogen reservoirs was analysed and key transmission periods in the year were also studied. We demonstrate that two invasive hemipteran insects—Diaphorina citri and Hishimonus phycitis—can vector the phytoplasma. Feeding on phytoplasma-infected hosts greatly increased reproduction of its invasive vector D. citri both in Oman and Brazil; suggesting that increased fitness of invasive insect vectors thereby further increases the pathogen's capacity to spread. Based on our findings, this is a robust system for studying the effects of invasions on vectorborne diseases and highlights concerns about its spread to warmer, drier regions of Brazil.

opencc-zeroDec 2015View details →

Data from: Compatible and incompatible pathogen-plant interactions differentially affect plant volatile emissions and the attraction of parasitoid wasps

The effects of multiple insect attacks on herbivore-induced plant volatiles and carnivorous arthropods are increasingly studied. Phytopathogens also represent an important threat to plants, and plant defense strategies against pathogens and insects are strongly interconnected, yet the potential impact of pathogens on insect-induced volatiles has been largely overlooked, and degree of pathogenicity rarely considered. We investigated how pathogen challenge, with virulent and avirulent strains of Xanthomonas campestris either alone or with simultaneous Pieris brassicae caterpillar herbivory, affected the volatile emissions of Brassica nigra plants. The impact of these volatiles on the foraging behavior of Cotesia glomerata parasitoids was then assessed. Pathogens themselves induced volatiles that were highly attractive to parasitoids, and enhanced the attractiveness of host-infested plant volatiles. Chemical analyses revealed that virulent and avirulent strains differentially induced plant volatiles, with primarily sesquiterpene, homoterpene and green leaf volatile compounds contributing to the differences. Strong similarities were found in the blends induced by the virulent strain and caterpillar herbivory. Challenge by either virulent or avirulent pathogens has a significant impact on plant chemistry and its interactions with other community members, demonstrating the importance of integrating pathogen- and insect-based research to broaden our knowledge of plant defenses under conditions of increasing complexity.

opencc-zeroDec 2018View details →

Data from: Host plant phylogeny and abundance predict root-associated fungal community composition and diversity of mutualists and pathogens

• Interactions between plants and their root-associated fungi (RAF) may influence the relative abundance of tree species and determine forest community diversity. Such plant-soil feedbacks in turn depend on the degree to which spatial distance and phylogenetic relatedness of host trees structure pathogen and mutualist communities, but research detailing these aspects of RAF communities is lacking. Here, we characterize plant-RAF associations across a diverse plant community, focusing on the degree to which RAF communities are structured by spatial distance, host phylogenetic relatedness, and host abundance. We compare results for different functional groups, including both putative mutualists and pathogens, an aspect poorly examined hitherto. • We collected roots at regular intervals along ten 50 m by 2 m transects, then used DNA barcoding to identify host plants, and characterize the associated fungal community. Variance partitioning was used to measure the relative contributions of host phylogenetic relatedness and spatial distance to explaining RAF community composition. A weighted linear regression was used to measure the correlation between host abundance and RAF diversity. • Phylogenetic distance among hosts was a better predictor of RAF community composition than spatial distance, but this relationship was stronger for putative pathogens than for mutualists, suggesting that pathogens show stronger host preference than mutualists. Across all functional groups, RAF showed similar levels of spatial structure. Additionally, RAF communities of locally abundant plants were less diverse than RAF communities of rare plants. • Synthesis: We found that RAF communities are structured by the phylogenetic relatedness of hosts and, to a lesser extent, by spatial distance, with pathogens showing stronger host preference than mutualists. Abundant hosts had less diverse RAF communities than rare hosts, which is notable because abundant plants tend to experience weaker negative plant-soil feedback. Going forward, mechanisms underlying the host abundance-RAF diversity relationship warrant further investigation. Additionally, the survey approach presented here could be paired with experiments linking RAF community composition to plant recruitment.

opencc-zeroDec 2017View details →

Data from: Trait-based modeling of multi-host pathogen transmission: plant-pollinator networks

Epidemiological models for multi-host pathogen systems often classify individuals taxonomically and use species-specific parameter values, but in species-rich communities, that approach may require intractably many parameters. Trait-based epidemiological models offer a potential solution, but have not accounted for within-species trait variation or between-species trait overlap. Here, we propose and study trait-based models with host and vector communities represented as trait distributions without regard to species identity. To illustrate this approach, we develop SIS models for disease spread in plant-pollinator networks with continuous trait distributions. We model trait-dependent contact rates in two common scenarios: nested networks, and specialized plant-pollinator interactions based on trait matching. We find that disease spread in plant-pollinator networks is impacted the most by selective pollinators, universally attractive flowers, and co-specialized plant-pollinator pairs. When extreme pollinator traits are rare, pollinators with common traits are most important for disease spread, whereas when extreme flower traits are rare, flowers with uncommon traits impact disease spread the most. Greater nestedness and specialization both typically promote disease persistence. Given recent pollinator declines caused in part by pathogens, we discuss how trait-based models could inform conservation strategies for wild and managed pollinators. Furthermore, while we have applied our model to pollinators and pathogens, its framework is general and can be transferred to any kind of species interactions, in any community.

opencc-zeroDec 2012View details →

Data from: Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes

The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including Phytophthora, Pythium and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six Pythium genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as Phytophthora species, Hyaloperonospora arabidopsidis, and Pythium ultimum var. ultimum. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in Phytophthora species and an over-representation of genes involved in proteolytic degradation and signal transduction in Pythium species. A complete lack of classical RxLR effectors was observed in the seven surveyed Pythium genomes along with an overall reduction of pathogenesis-related gene families in H. arabidopsidis. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in Pythium species and H. arabidopsidis as compared to Phytophthora species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven Pythium species with the closely related oomycetes, Phytophthora species and H. arabidopsidis, and distantly related diatoms provide insight into genes that underlie virulence.

Supplementary material 3 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801

Plant pathogenic bacteria assessment for Zambia

Supplementary material 4 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801

Plant pathogenic protist assessment for Zambia

Supplementary material 2 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801

Guidelines for scoring species

Supplementary material 5 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801

Assessment for vector species

Supplementary material 1 from: Mulema J, Phiri S, Bbebe N, Chandipo R, Chijikwa M, Chimutingiza H, Kachapulula P, Kankuma Mwanda F, Matimelo M, Mazimba-Sikazwe E, Mfune S, Mkulama M, Moonga M, Mphande W, Mufwaya M, Mulenga R, Mweemba B, Ndalamei Mabote D, Nkunika P, Nthenga I, Tembo M, Chowa J, Odunga S, Opisa S, Kasoma C, Charles L, Makale F, Rwomushana I, Phiri NA (2024) Rapid risk assessment of plant pathogenic bacteria and protists likely to threaten agriculture, biodiversity and forestry in Zambia. NeoBiota 91: 145-178. https://doi.org/10.3897/neobiota.91.113801

All data from horizon scanning for Zambia

opencc-zeroDec 2021View details →

Global invasion history of the emerging plant pathogen Phytophthora multivora

Abstract Background: global trade in living plants and plant material has significantly increased the geographic distribution of many plant pathogens. As a consequence, several pathogens have been first found and described in their introduced range where they may cause severe damage on naïve host species. Knowing the center of origin and the pathways of spread of a pathogen is of importance for several reasons, including identifying natural enemies and reducing further spread. Several Phytophthora species are well-known invasive pathogens of natural ecosystems, including Phytophthora multivora. Following the description of P. multivora from dying native vegetation in Australia in 2009, the species was subsequently found to be very common in South Africa where it does not cause any remarkable disease. There are now reports of P. multivora from many other countries worldwide, but not as a commonly encountered species in natural environments. Results: a global collection of 335 isolates from North America, Europe, Africa, Australia, the Canary Islands, and New Zealand was used to unravel the worldwide invasion history of P. multivora, using 10 microsatellite markers for all isolates and sequence data from five loci from 94 representative isolates. Our population genetic analysis revealed an extremely low heterozygosity, significant non-random association of loci and substantial genotypic diversity suggesting the spread of P. multivora readily by both asexual and sexual propagules. The P. multivora populations in South Africa, Australia, and New Zealand show the most complex genetic structure, are well established and evolutionary older than those in Europe, North America and the Canary Islands. Conclusions: according to conducted analyses, the world invasion of P. multivora most likely commenced from South Africa, which can be considered the center of origin of the species. The pathogen was then introduced to Australia, which acted as bridgehead population for Europe and North America. Our study highlighted a complex global invasion pattern of P. multivora, including both direct introductions from the native population and secondary spread/introductions from bridgehead populations.

opencc-zeroDec 2013View details →

Data from: Dynamics of short- and long-term association between a bacterial plant pathogen and its arthropod vector

The dynamics of association between pathogens and vectors can strongly influence epidemiology. It has been proposed that wilt disease epidemics in cucurbit populations are sustained by persistent colonization of beetle vectors (Acalymma vittatum) by the bacterial phytopathogen Erwinia tracheiphila. We developed a qPCR method to quantify E. tracheiphila in whole beetles and frass and used it to assess pathogen acquisition and retention following variable exposure to infected plants. We found that (i) E. tracheiphila is present in frass in as little as three hours after feeding on infected plants and can be transmitted with no incubation period by vectors given brief exposure to infected plants, but also by persistently colonized vectors several weeks following exposure; (ii) duration of exposure influences rates of long-term colonization; (iii) frass infectivity (assessed via inoculation experiments) reflects bacterial levels in frass samples across time; and (iv) vectors rarely clear E. tracheiphila infections, but suffer no apparent loss of fitness. These results describe a pattern conducive to the effective maintenance of E. tracheiphila within cucurbit populations.

opencc-by-4.0Feb 2023View details →

Single-cell profiling of complex plant responses to pathogen infection

Original images for figures and quantifications.