Plant pathogen forensics: capabilities, needs, and recommendations.

A biological attack on U.S. crops, rangelands, or forests could reduce yield and quality, erode consumer confidence, affect economic health and the environment, and possibly impact human nutrition and international relations. Preparedness for a crop bioterror event requires a strong national security plan that includes steps for microbial forensics and criminal attribution. However, U.S. crop producers, consultants, and agricultural scientists have traditionally focused primarily on strategies for prevention and management of diseases introduced naturally or unintentionally rather than on responding appropriately to an intentional pathogen introduction. We assess currently available information, technologies, and resources that were developed originally to ensure plant health but also could be utilized for postintroduction plant pathogen forensics. Recommendations for prioritization of efforts and resource expenditures needed to enhance our plant pathogen forensics capabilities are presented.     

Role of soil, crop debris, and a plant pathogen in Salmonella enterica contamination of tomato plants

Background

In the U.S., tomatoes have become the most implicated vehicle for produce-associated Salmonellosis with 12 outbreaks since 1998. Although unconfirmed, trace backs suggest pre-harvest contamination with Salmonella enterica. Routes of tomato crop contamination by S. enterica in the absence of direct artificial inoculation have not been investigated.

Methodology/Principal Findings

This work examined the role of contaminated soil, the potential for crop debris to act as inoculum from one crop to the next, and any interaction between the seedbourne plant pathogen Xanthomonas campestris pv. vesicatoria and S. enterica on tomato plants. Our results show S. enterica can survive for up to six weeks in fallow soil with the ability to contaminate tomato plants. We found S. enterica can contaminate a subsequent crop via crop debris; however a fallow period between crop incorporation and subsequent seeding can affect contamination patterns. Throughout these studies, populations of S. enterica declined over time and there was no bacterial growth in either the phyllosphere or rhizoplane. The presence of X. campestris pv. vesicatoria on co-colonized tomato plants had no effect on the incidence of S. enterica tomato phyllosphere contamination. However, growth of S. enterica in the tomato phyllosphere occurred on co-colonized plants in the absence of plant disease.

Conclusions/Significance

S. enterica contaminated soil can lead to contamination of the tomato phyllosphere. A six week lag period between soil contamination and tomato seeding did not deter subsequent crop contamination. In the absence of plant disease, presence of the bacterial plant pathogen, X. campestris pv. vesicatoria was beneficial to S. enterica allowing multiplication of the human pathogen population. Any event leading to soil contamination with S. enterica could pose a public health risk with subsequent tomato production, especially in areas prone to bacterial spot disease.     

Domestication of maize, sorghum, and sugarcane did not drive the divergence of their smut pathogens

We investigated two alternative hypotheses for the origin of crop pathogen species: that human-mediated agricultural practices drove the divergence of many crop plant pathogen species or that coevolutionary processes in natural populations of the crops' ancestors drove divergence of pathogen species. We distinguished between these two hypotheses by constructing a robust multigene phylogeny and estimating the dates of divergence among four, monophyletic species of smut fungi (Ustilago maydis, U. scitaminea, Sporisorium reilianum, S. sorghi) known to specifically infect maize, sorghum, sugarcane, and their wild ancestors. Without a fossil record for smut fungi, we calibrated the pathogen species' divergence times to their plant host divergence times. Specifically, a calibration date of 10,000 years was employed to test the hypothesis that the fungal species originated at the time of domestication of their current hosts and a calibration date of 50 million years was employed to test the hypothesis that the fungal species originated on wild ancestors of their domesticated hosts. Substitution rates at five protein coding genes were calculated and rates obtained for the 10,000 year calibration date were orders of magnitude faster than those commonly reported for eukaryotes, thus rejecting the hypothesis that these smut pathogen species diverged at the time of domestication. In contrast, substitution rates obtained for the 50 million year calibration were comparable to eukaryotic substitution rates. We used the 50 million year calibration to estimate divergence times of taxa in two datasets, one comprised solely the focal species and one comprised the focal species and additional related taxa. Both datasets indicate that all taxa diverged millions of years ago, strongly supporting the hypothesis that smut species diverged before the time of domestication and modern agriculture. Thus, smut species diverged in the ecological context of natural host plant and fungal populations.     

A Rapid and Efficient Method for Assessing Pathogenicity of Ustilago maydis on Maize and Teosinte Lines

Maize is a major cereal crop worldwide. However, susceptibility to biotrophic pathogens is the primary constraint to increasing productivity. U. maydis is a biotrophic fungal pathogen and the causal agent of corn smut on maize. This disease is responsible for significant yield losses of approximately $1.0 billion annually in the U.S.¹ Several methods including crop rotation, fungicide application and seed treatments are currently used to control corn smut². However, host resistance is the only practical method for managing corn smut. Identification of crop plants including maize, wheat, and rice that are resistant to various biotrophic pathogens has significantly decreased yield losses annually^3-5. Therefore, the use of a pathogen inoculation method that efficiently and reproducibly delivers the pathogen in between the plant leaves, would facilitate the rapid identification of maize lines that are resistant to U. maydis. As, a first step toward indentifying maize lines that are resistant to U. maydis, a needle injection inoculation method and a resistance reaction screening method was utilized to inoculate maize, teosinte, and maize x teosinte introgression lines with a U. maydis strain and to select resistant plants.Maize, teosinte and maize x teosinte introgression lines, consisting of about 700 plants, were planted, inoculated with a strain of U. maydis, and screened for resistance. The inoculation and screening methods successfully identified three teosinte lines resistant to U. maydis. Here a detailed needle injection inoculation and resistance reaction screening protocol for maize, teosinte, and maize x teosinte introgression lines is presented. This study demonstrates that needle injection inoculation is an invaluable tool in agriculture that can efficiently deliver U. maydis in between the plant leaves and has provided plant lines that are resistant to U. maydis that can now be combined and tested in breeding programs for improved disease resistance.     

Usefulness and Economic potential of the Rare Plants of the United States: A statistical Survey

The economic usefulness and potential of endangered and rare plants in the United States was surveyed to assess some of the potential impacts of plant extinction on the world’s largest economy. We analyzed relationships between an existing comprehensive database of U.S. rare plants, and a new database that synthesizes available information on worldwide plant uses and U.S. crop values. While few rare plants are directly useful, nearly 80% of the U.S. plant genera with rare taxa contain at least one useful species. Moreover, two-thirds of the 2949 U.S. rare and endangered taxa are congeneric with cultivated species. Examples of this close relationship between rare plants and their economically significant congenerics were translated into dollar values. For instance, the annual U.S. wholesale farm value of food crop congenerics of rare plants is $9 billion. Since many crops require periodic genetic infusions from close relatives to combat threats from climatic change and disease, or to supply features such as improved nutritional value, we conclude that the threats to the rare wild plants of the U.S. also constitute threats to the future of many contemporary crops.     

Interactions between Fusarium verticillioides, Ustilago maydis, and Zea mays: an endophyte, a pathogen, and their shared plant host

Highly diverse communities of microbial symbionts occupy eukaryotic organisms, including plants. While many well-studied symbionts may be characterized as either parasites or as mutualists, the prevalent but cryptic endophytic fungi are less easily qualified because they do not cause observable symptoms of their presence within their host. Here, we investigate the interactions of an endophytic fungus, Fusarium verticillioides with a pathogen, Ustilago maydis, as they occur within maize (Zea mays). We used experimental inoculations to evaluate metabolic mechanisms by which these three organisms might interact. We assessed the impacts of fungal-fungal interactions on endophyte and pathogen growth within the plant, and on plant growth. We find that F. verticillioides modulates the growth of U. maydis and thus decreases the pathogen's aggressiveness toward the plant. With co-inoculation of the endophyte with the pathogen, plant growth is similar to that which would be gained without the pathogen present. However, the endophyte may also break down plant compounds that limit U. maydis growth, and obtains a growth benefit from the presence of the pathogen. Thus, an endophyte such as F. verticillioides may function as both a defensive mutualist and a parasite, and express nutritional modes that depend on ecological context.     

The effects of plant population size on the interactions between the endangered plant Scorzonera humilis, a specialised herbivore, and a phytopathogenic fungus

We studied the effects of population size on the interactions between Scorzonera humilis (Asteraceae), its specialised seed-feeding fly Heterostylodes macrurus (Anthomyidae) and its specific systemic smut fungus Ustilago scorzonerae (Ustilaginales). The number of seeds developing per plant (potential seed production) strongly increased with population size in S. humilis. However, because seed predation by the seed feeding fly H. macrurus and the negative impact of the pathogen U. scorzonerae also increased, realised seed production was not related to population size. The probability of occurrence of H. macrurus increased with the population size of its host plant and its abundance increased more than proportionally. This suggests that Allee effects reduce insect abundance in small populations of S. humilis . The probability of occurrence of the fungus U. scorzonerae also increased with plant population size. Within populations, large genets were more likely to be infected than small ones. The systemic pathogen U. scorzonerae reduces the effective population size of its host because all flowers of an infected individual are sterilised. Nevertheless, in most populations the impact of the fly on reproduction was stronger than that of the pathogen, because most genets were not infected. Both parasites were rarer than the host plant itself, supporting the trophic-level hypothesis of island biogeography. Our results suggest that habitat fragmentation may release plants from parasites and pathogens. These positive effects of isolation and small population size may mask negative effects of fragmentation on, for instance, the quantity and quality of pollination.     

高寒草地珠芽蓼内生拮抗固氮菌Z19的鉴定及其固氮功能

【目的】从东祁连山高寒草地珠芽蓼内生细菌中筛选和鉴定具有固氮能力和拮抗能力的内生细菌。【方法】采用16S rRNA基因序列同源性分析和生理生化指标测定方法对该菌株进行鉴定。【结果】从珠芽蓼中分离获得的21株内生细菌中6株内生菌具有固氮能力,76.2%具有抑菌能力,其中5株内生细菌对5种以上的病原菌有抑制作用;菌株Z19具有较强固氮能力和分解纤维素的能力,其纤维素溶解圈直径与菌落直径比达3.33,产生的纤维素酶活性为0.31 U,且对辣椒立枯丝核病菌(Rhizoctonia solani)、油菜菌核病菌(Sclerotinia sclerotiorum)、番茄灰霉病菌(Botrytis cinerea)、小麦根腐病菌(Bipolaris sorokiniana)和番茄早疫病菌(Alternaria solani)具有较强拮抗能力;经PCR扩增和测序,获得了菌株Z19的固氮基因(nifH)序列和16S rRNA基因序列,在GenBank中的登录号分别为EU693340和EU236746;菌株Z19呈革兰氏阳性,杆状,产芽孢。【结论】结合生理生化特征及16S rRNA基因序列同源性比较,鉴定其为枯草芽孢杆菌(Bacillus subtilis)。     

On the trail of a cereal killer: recent advances in Fusarium graminearum pathogenomics and host resistance

The ascomycete fungal pathogen Fusarium graminearum (sexual stage: Gibberella zeae) causes the devastating head blight or scab disease on wheat and barley, and cob or ear rot disease on maize. Fusarium graminearum infection causes significant crop and quality losses. In addition to roles as virulence factors during pathogenesis, trichothecene mycotoxins (e.g. deoxynivalenol) produced by this pathogen constitute a significant threat to human and animal health if consumed in respective food or feed products. In the last few years, significant progress has been made towards a better understanding of the processes involved in F. graminearum pathogenesis, toxin biosynthesis and host resistance mechanisms through the use of high-throughput genomic and phenomic technologies. In this article, we briefly review these new advances and also discuss how future research can contribute to the development of sustainable plant protection strategies against this important plant pathogen.     

Modeling the impact of a biocontrol agent, Puccinia lagenophorae, on interactions between a crop, Daucus carota, and a weed, Senecio vulgaris

The impact of a biocontrol agent spreading from a point source on crop–weed interactions was modeled. The model encompassed: (i) severity of crop–weed competition as affected by a rust pathogen, (ii) velocity of spread of the rust pathogen, and (iii) density of infected plants introduced in the weed population as starting points (inoculum sources) for an epidemic. The model was parameterized for a study system encompassing the crop Daucus carota (carrot), the weed Senecio vulgaris (common groundsel), and its antagonist Puccinia lagenophorae. The parameters of (i) were estimated in a greenhouse study using a response-surface design. Estimates of the parameter of (ii) were obtained from the literature. The density of infected plants (iii) was varied to simulate crop loss as function of density. Simulations were run for various densities of the weed and various velocities of rust pathogen spread. The results of the simulations indicated a crop-loss ranging from 5 to 10% at levels of relatively weak D. carota–S. vulgaris competition. Density of inoculum sources and velocity of P. lagenophorae spread had only minor effects on crop loss. In contrast, density of inoculum sources and velocity of spread had major effects on crop loss at levels of intermediate (range of 10–35% loss) and severe competition (range of 30–70% loss). The results are discussed both with respect to biological control of S. vulgaris using P. lagenophorae as biocontrol agent and as a general model describing the impact of the spatial dynamics of a pathogen (natural enemy) on plant competition.     

The rhizosphere microbiome and plant health

The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production.     

The impact of invasive fungi on agricultural ecosystems in the United States

Invasive fungi and other non-indigenous plant pathogens have had a significant effect on American agriculture for hundreds of years. At present crop loss due to invasive plant pathogens, especially fungi, is estimated at $21 billion per year in the United States, greater than the loss caused by non-indigenous insects. Plant pathogenic fungi are difficult to detect and identify. Thus knowledge of which fungi pose a threat is essential to prevent their entry by means others than inspection. In this paper, examples are presented of invasive fungi on agricultural commodities introduced into the United States. In all cases two factors have been crucial: first, the pathway through which these fungi have entered, and second, systematic knowledge to prevent and respond to the new invasive species. Historically important plant pathogens such as black stem rust of wheat still cause considerable damage while others such as late blight of potato appear to be having a resurgence. Known previously in Australia, then moving to Africa and South America, the virulent species of soybean rust appeared in the U.S. in 2004 but has not been as devastating as anticipated. Plant pathogenic fungi on specialty crops such as daylily, gladiola and chrysanthemum are threatened by rust fungi recently found in the U.S. apparently brought in on infected germplasm. A crisis in the export of U.S. wheat occurred in the late 1990’s when the molecular diagnostic test for Karnal bunt gave a false positive response to a closely related but previously unknown species. Many potentially dangerous plant pathogens of crop plants have not yet been introduced into the U.S. It is critical that meticulous surveillance be conducted as plant material enters the country as well as where crops are grown prior to shipment. In addition, the scientific infrastructure is needed to be able to respond quickly to new invasive fungi. This requires sound systematic knowledge of plant pathogenic fungi both in the U.S. and around the world and a cadre of systematic experts who can characterize invasive fungi.     

Genetic and molecular basis of nonhost disease resistance: complex, yes; silver bullet, no

Nonhost resistance (NHR), in which a successful pathogen on some plants fails to overcome host barriers on others, has attracted much attention owing to its potential for robust crop improvement. Recent advances reveal that a multitude of underlying mechanisms contribute to NHR, ranging from components shared with recognition-based defenses up to recessive susceptibility factors involved in plant primary metabolism. Most NHR appears multi-factorial and quantitative. This implies that there is no single, 'silver bullet' NHR mechanism that can be used to broadly restrict pathogens in many or all crops.     

The use of laser capture microdissection to study the infection of Glycine max (soybean) by Heterodera glycines (soybean cyst nematode)

The soybean cyst nematode (Heterodera glycines) is an obligate parasite of soybean (Glycine max). It is the most destructive pathogen of G. max, accounting for approximately 0.46–0.82 billion dollars in crop losses, annually, in the U.S. Part of the infection process involves H. glycines establishing feeding sites (syncytia) that it derives its nourishment from throughout its lifecycle. Microscopic methods (i.e., laser capture microdissection [LCM]) that faithfully dissect out those feeding sites are important improvements to the study of this significant plant pathogen. Our isolation of developing feeding sites during an incompatible or a compatible reaction is providing new ways by which this important plant-pathogen interaction can be studied. We have used these methods to create cDNA libraries, clone genes and perform microarray analyses. Importantly, it is providing insight not only into how the root is responding at the organ level to H. glycines, but also how the syncytium is responding during its maturation into a functional feeding site.Key words: soybean, Glycine max, soybean cyst nematode, SCN, Heterodera glycines, microarray, gene expression, plant pathogen, parasite, laser capture microdissection     

Fast life histories,not pathogens,account for state-level variation in homicide,child maltreatment,and family ties in the U.S.

Parasite stress theory has recently been used to account for an array of cross-cultural differences in human cognition and social behavior, including in-group bias, interpersonal violence, child maltreatment, and religious adherence. Here, we re-assess the apparently ubiquitous effects of parasite stress on behavior observed in the U.S., using the cross-sectional, cross-population approach implemented by prior pathogen stress studies. Our results raise two challenges to previous findings. First, we show that the observed effects of pathogen stress in the U.S. data are due exclusively to one type of infectious disease – sexually transmitted diseases (STD) – while non-STD infections have no effect. Second, we find that controlling for life history measures of extrinsic risk and a fast life history erases the observed associations with family ties, interpersonal violence, child fatalities, and religious adherence. Thus, after appropriate variable specification, stratification, and control, U.S. cross-state population differences provide no support for the pathogen stress hypothesis in these various domains of behavior. Rather, the findings are more consistent with predictions from life history theory.     

Role of Ubiquitination in Plant Innate Immunity and Pathogen Virulence

Plant diseases are a major constraint for stable crop production in the world. Plants are constantly threatened by different pathogens and have developed an array of mechanisms to defend themselves. A growing body of evidence indicates that ubiquitination, which is one of the most important cellular processes for protein modification in eukaryotic organisms, is involved in the regulation of host defense signaling. Pathogens also exploit ubiquitination to block or interfere with plant defenses. Recent studies in a few model plants have demonstrated that ubiquitination plays a critical role in plant–pathogen interactions that lead either to plant resistance or to successful pathogen invasion of the plant host. This review discusses recent findings about the functions of ubiquitination in host defense and pathogen invasion.     

Genetic diversity in major farm crops on the farm and in reserve

Genetic vulnerability does not at this time present a major threat to production of United States field crops, according to a 1981 survey of U.S. crop breeding directors. But plant breeders do regard genetic vulnerability as an important and potentially dangerous problem. The 1981 survey indicated that although the genetic base of U.S. field crop production is not as narrow as in 1970, it still is concentrated on a relatively small number of favored cultivars. Genetic diversity is provided, nevertheless, in other and less obvious ways. Survey responses indicated that the genetic base of the elite germplasm pool is wider and provides more useful diversity than is usually supposed. However, breeders also value the national germplasm repositories as indispensable sources of needed diversity.     

Towards Defining Nutrient Conditions Encountered by the Rice Blast Fungus during Host Infection

Fungal diseases cause enormous crop losses, but defining the nutrient conditions encountered by the pathogen remains elusive. Here, we generated a mutant strain of the devastating rice pathogen Magnaporthe oryzae impaired for de novo methionine biosynthesis. The resulting methionine-requiring strain grew strongly on synthetic minimal media supplemented with methionine, aspartate or complex mixtures of partially digested proteins, but could not establish disease in rice leaves. Live-cell-imaging showed the mutant could produce normal appressoria and enter host cells but failed to develop, indicating the availability or accessibility of aspartate and methionine is limited in the plant. This is the first report to demonstrate the utility of combining biochemical genetics, plate growth tests and live-cell-imaging to indicate what nutrients might not be readily available to the fungal pathogen in rice host cells.     

Microbial Ecology of the Hive and Pollination Landscape: Bacterial Associates from Floral Nectar,the Alimentary Tract and Stored Food of Honey Bees (Apis mellifera)

Nearly all eukaryotes are host to beneficial or benign bacteria in their gut lumen, either vertically inherited, or acquired from the environment. While bacteria core to the honey bee gut are becoming evident, the influence of the hive and pollination environment on honey bee microbial health is largely unexplored. Here we compare bacteria from floral nectar in the immediate pollination environment, different segments of the honey bee (Apis mellifera) alimentary tract, and food stored in the hive (honey and packed pollen or “beebread”). We used cultivation and sequencing to explore bacterial communities in all sample types, coupled with culture-independent analysis of beebread. We compare our results from the alimentary tract with both culture-dependent and culture-independent analyses from previous studies. Culturing the foregut (crop), midgut and hindgut with standard media produced many identical or highly similar 16S rDNA sequences found with 16S rDNA clone libraries and next generation sequencing of 16S rDNA amplicons. Despite extensive culturing with identical media, our results do not support the core crop bacterial community hypothesized by recent studies. We cultured a wide variety of bacterial strains from 6 of 7 phylogenetic groups considered core to the honey bee hindgut. Our results reveal that many bacteria prevalent in beebread and the crop are also found in floral nectar, suggesting frequent horizontal transmission. From beebread we uncovered a variety of bacterial phylotypes, including many possible pathogens and food spoilage organisms, and potentially beneficial bacteria including Lactobacillus kunkeei, Acetobacteraceae and many different groups of Actinobacteria. Contributions of these bacteria to colony health may include general hygiene, fungal and pathogen inhibition and beebread preservation. Our results are important for understanding the contribution to pollinator health of both environmentally vectored and core microbiota, and the identification of factors that may affect bacterial detection and transmission, colony food storage and disease susceptibility.     

Antimicrobial activity of a porcine myeloperoxidase against plant pathogenic bacteria and fungi

Porcine myeloperoxidase was evaluated for its antimicrobial activity against plant pathogenic bacteria and fungi. The results indicated that the enzyme, in the presence of a small amount of hydrogen peroxide, was effective against a broad spectrum of plant pathogens. The growth of seven bacterial species, including nine pathovars, from the genera Erwinia , Pseudomonas and Xanthomonas , was significantly inhibited by the enzyme at a concentration as low as 0·4 U ml⁻¹, while 4·0 U ml⁻¹ was lethal to all plant pathogenic bacteria examined. Myeloperoxidase, at 40 U ml⁻¹, was lethal to germinating spores from three isolates of the fungal plant pathogen Fusarium solani and two isolates from each of Colletotrichum gloeosporioides and C. malvarum . The enzyme's antifungal effects on the rice blast pathogen Magnaporthe grisea were studied both in vitro and on host plants. The enzyme significantly inhibited spore germination of two isolates of M. grisea races IC17 and IB49 at concentrations over 16 U ml⁻¹, and disintegration of fungal spore walls was caused by 80 U ml⁻¹. The enzyme was even more effective in reducing disease incidence of blast on young rice plants treated with 0·5 U ml⁻¹, while 2·5 U ml⁻¹ resulted in complete inhibition of infection. These results support and further extend the suggestion that myeloperoxidase could be used as a broad-spectrum biocontrol agent or as a transgenically expressed protein to combat diseases caused by plant pathogenic bacteria and fungi.