San Joaquin Valley Agricultural Sciences Center

Selenium (Se) is an essential element for humans and animals, which occurs ubiquitously in the environment. It is present in trace amounts in both organic and inorganic forms in marine and freshwater systems, soils, biomass and in the atmosphere. Low Se levels in certain terrestrial environments have resulted in Se deficiency in humans, while elevated Se levels in waters and soils can be toxic and result in the death of aquatic wildlife and other animals. Human dietary Se intake is largely governed by Se concentrations in plants, which are controlled by root uptake of Se as a function of soil Se concentrations, speciation and bioavailability. In addition, plants and microorganisms can biomethylate Se, which can result in a loss of Se to the atmosphere. The mobilization of Se across soil-plant-atmosphere interfaces is thus of crucial importance for human Se status. This review gives an overview of current knowledge on Se cycling with a specific focus on soil-plant-atmosphere interfaces. Sources, speciation and mobility of Se in soils and plants will be discussed as well as Se hyperaccumulation by plants, biofortification and biomethylation. Future research on Se cycling in the environment is essential to minimize the adverse health effects associated with unsafe environmental Se levels.

Although interactions between plants and microbes at the plant-soil interface are known to be important for plant nutrient acquisition, relatively little is known about how root exudates contribute to nutrient exchange over the course of plant development. In this study, root exudates from slow- and fast-growing stages of Arabidopsis thaliana plants were collected, chemically analysed and then applied to a sandy nutrient-depleted soil. We then tracked the impacts of these exudates on soil bacterial communities, soil nutrients (ammonium, nitrate, available phosphorus and potassium) and plant growth. Both pools of exudates shifted bacterial community structure. GeoChip analyses revealed increases in the functional gene potential of both exudate-treated soils, with similar responses observed for slow-growing and fast-growing plant exudate treatments. The fast-growing stage root exudates induced higher nutrient mineralization and enhanced plant growth as compared to treatments with slow-growing stage exudates and the control. These results suggest that plants may adjust their exudation patterns over the course of their different growth phases to help tailor microbial recruitment to meet increased nutrient demands during periods demanding faster growth.

Biochar can be an effective carrier for microbial inoculants because of its favourable properties promoting microbial life. In this review, we assess the effectiveness of biochar as a microbial carrier for agricultural and environmental applications. Biochar is enriched with organic carbon, contains nitrogen, phosphorus, and potassium as nutrients, and has a high porosity and moisture-holding capacity. The large number of active hydroxyl, carboxyl, sulfonic acid group, amino, imino, and acylamino hydroxyl and carboxyl functional groups are effective for microbial cell adhesion and proliferation. The use of biochar as a carrier of microbial inoculum has been shown to enhance the persistence, survival and colonization of inoculated microbes in soil and plant roots, which play a crucial role in soil biochemical processes, nutrient and carbon cycling, and soil contamination remediation. Moreover, biochar-based microbial inoculants including probiotics effectively promote plant growth and remediate soil contaminated with organic pollutants. These findings suggest that biochar can serve as a promising substitute for non-renewable substrates, such as peat, to formulate and deliver microbial inoculants. The future research directions in relation to improving the carrier material performance and expanding the potential applications of this emerging biochar-based microbial immobilization technology have been proposed.

Hopperburn is a non-contagious disease of plants caused by the direct feeding damage of certain leafhoppers and planthoppers. Although long studied, especially with Empoasca spp. leafhoppers (Cicadellidae: Typhlocybinae), the mechanisms underlying hopperburn have only recently been elucidated. Hopperburn is caused by a dynamic interaction between complex insect feeding stimuli (termed hopperburn initiation) and complex plant responses (termed the hopperburn cascade). Herein we review the nature of the feeding stimuli in hopperburn initiation, especially for Empoasca spp., which we also compare with the planthopper Nilaparvata lugens. Contrary to previous reports, Empoasca hopperburn is not caused solely by toxic saliva. Instead, it is caused by a plant wound response triggered by a unique type of stylet movement, which is then exacerbated by saliva. Electrical penetration graph monitoring has revealed that all Empoasca spp. are cell rupture feeders, not sheath feeders, and that certain tactics of that feeding strategy are more damaging than others. Measuring the proportions of the most damaging feeding led to development of a resistance index, the Stylet Penetration Index, which can predict hopperburn severity in different plants or under different environmental conditions and can supplement or replace traditional, field-based resistance indices.

Realizing the full potential of drip irrigation technology requires optimizing the operational parameters that are available to irrigators, such as the frequency, rate, and duration of water application and the placement of drip tubing. Numerical simulation is a fast and inexpensive approach to studying optimal management practices. Unfortunately, little work has been done to investigate the accuracy of numerical simulations, leading some to question the usefulness of simulation as a research and design tool. In this study, we compare HYDRUS-2D simulations of drip irrigation with experimental data. A Hanford sandy loam soil was irrigated using thin-walled drip tubing installed at a depth of 6 cm. Three trials (20, 40, and 60 L⋅m-1 applied water) were carried out. At the end of each irrigation and approximately 24 h later, the water content distribution in the soil was determined by gravimetric sampling. The HYDRUS-2D predictions of the water content distribution are found to be in very good agreement with the data. The results support the use of HYDRUS-2D as a tool for investigating and designing drip irrigation management practices.

Journal Article Insects of Stored Products Get access Insects of Stored ProductsRees David CSIRO Publishing, Collingwood, Victoria, Australia, 2004 190 pp., soft cover, $64.95 ISBN: 0-643-06903-8 Jim Leesch Jim Leesch Commodity Protection & Quality Research Unit USDA-ARS-SJVASC Parlier, CA 93648 E-mail: jleesch@fresno.ars.usda.gov Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 99, Issue 6, 1 December 2006, Pages 2219–2220, https://doi.org/10.1093/jee/99.6.2219a Published: 01 December 2006

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

Novel methodology is presented for indexing the relative potential of hosts to function as resources. A Host Potential Index (HPI) was developed as a practical framework to express relative host potential based on combining results from one or more independent studies, such as those examining host selection, utilization, and physiological development of the organism resourcing the host. Several aspects of the HPI are addressed including: 1) model derivation; 2) influence of experimental design on establishing host rankings for a study type (no choice, two-choice, and multiple-choice); and, 3) variable selection and weighting associated with combining multiple studies. To demonstrate application of the HPI, results from the interactions of spotted wing drosophila (SWD), Drosophila suzukii Matsumura (Diptera: Drosophilidae), with seven "reported" hosts (blackberries, blueberries, sweet cherries, table grapes, peaches, raspberries, and strawberries) in a postharvest scenario were analyzed. Four aspects of SWD-host interaction were examined: attraction to host volatiles; population-level oviposition performance; individual-level oviposition performance; and key developmental factors. Application of HPI methodology indicated that raspberries ( (mean)HPIvaried = 301.9±8.39; rank 1 of 7) have the greatest potential to serve as a postharvest host for SWD relative to the other fruit hosts, with grapes ( (mean)HPIvaried = 232.4±3.21; rank 7 of 7) having the least potential.

In water-stressed soybean primary roots, elongation was maintained at well-watered rates in the apical 4 mm (region 1), but was progressively inhibited in the 4-8 mm region (region 2), which exhibits maximum elongation in well-watered roots. These responses are similar to previous results for the maize primary root. To understand these responses in soybean, spatial profiles of soluble protein composition were analysed. Among the changes, the results indicate that region-specific regulation of phenylpropanoid metabolism may contribute to the distinct growth responses in the different regions. Several enzymes related to isoflavonoid biosynthesis increased in abundance in region 1, correlating with a substantial increase of isoflavonoid content in this region which could contribute to growth maintenance via various potential mechanisms. In contrast, caffeoyl-CoA O-methyltransferase, which is involved in lignin synthesis, was highly up-regulated in region 2. This response was associated with enhanced accumulation of lignin, which may be related to the inhibition of growth in this region. Several proteins that increased in abundance in both regions of water-stressed roots were related to protection from oxidative damage. In particular, an increase in the abundance of ferritin proteins effectively sequestered more iron and prevented excess free iron in the elongation zone under water stress.

Understanding the bioavailability of selenium (Se) in the soil–plant system plays a vital role in phytoremediation and agronomic biofortification strategies. This review aimed to (a) discuss the effect of various soil parameters on the bioavailability of Se, its uptake and translocation in relation to plant species, genotypes, growth stages, and management regimes; and (b) examine soil and plant indices associated with Se bioavailability. In addition, we particularly discussed potential methods for regulating the bioavailability of Se. Such methods include the application of agricultural residue, Se fertilizer, or take advantage of the interaction between Se and other nutrient elements.

Broccoli is a food often consumed for its potential health-promoting properties. The health benefits of broccoli are partly associated with secondary plant compounds that have bioactivity; glucosinolates and phenolic acids are two of the most abundant and important in broccoli. In an effort to determine how variety, stress, and production conditions affect the production of these bioactive components broccoli was grown in the greenhouse with and without selenium (Se) fertilization, and in the field under conventional or organic farming procedures and with or without water stress. High-performance liquid chromatography/mass spectrometry was used to separate and identify 12 primary phenolic compounds. Variety had a major effect: There was a preponderance of flavonoids in the Majestic variety, but hydroxycinnamic esters were relatively more abundant in the Legacy variety. Organic farming and water stress decreased the overall production of phenolics. Se fertilization increased glucosinolates in general, and sulforaphane in particular, up to a point; above that Se fertilization decreased glucosinolate production. Organic farming and water stress also decreased glucosinolate production. These data show environmental and genetic variation in phenolics and glucosinolates in broccoli, and warn that not all broccoli may contain all health-promoting bioactive components. They further show that selection for one bioactive component (Se) may decrease the content of other bioactive components such as phenolics and glucosinolates.

Methyl bromide is a widely used fumigant for both pre-plant and post-harvest pest and pathogen control. The Montreal Protocol and the US Clean Air Act mandate a phase-out of the import and manufacture of methyl bromide, beginning in 2001 and culminating with a complete ban, except for quarantine and certain pre-shipment uses and exempted critical uses, in January 2005. In 1995, ARS built on its existing programs in soil-borne plant pathology and post-harvest entomology and plant pathology to initiate a national research program to develop alternatives to methyl bromide. The focus has been on strawberry, pepper, tomato, perennial and nursery cropping systems for pre-plant methyl bromide use and fresh and durable commodities for post-harvest use. Recently the program has been expanded to include research on alternatives for the ornamental and cut flower cropping systems. An overview of the national research program is presented. Results from four specific research trials are presented, ranging from organic to conventional systems. Good progress on short-term alternatives is being made. These will be used as the foundation of integrated management systems which begin with pre-plant management decisions and continue through post-harvest processing.

This study is the rst to statistically analyze the stylet probing/penetration behaviors of Lygus (Hemiptera: Miridae) bugs, and the external body movements associated with both probing and nonprobing, via electrical penetration graph (EPG) and videorecording, respectively. Behavioral quantication allows powerful statistical comparisons among host plants or other treatments. Thus, statistical analysis of data has played an important role in EPG research. However, few attempts have been made to standardize types and terminology used for statistical parameters. We provide here the rst complete system of organization and terminology for nonsequential EPG parameters. Widespread adoption of these terms will allow standardization in EPG research. Our EPG and video data reveal for the rst time the stylet penetration behaviors of nymphal L. hesperus that cause cotton square damage, and the mechanism involved. L. hesperus nymphs spent only 15% of their time on squares probing; the remainder was spent standing motionless in place, grooming, or in sensory exploration. While probing, two thirds of their time was spent in laceration/salivation and one third in ingestion. Thus, L. hesperus nymphs actively spread out numerous, minute injections of their macerating watery saliva, deeply drilled/lacerated into all parts of the developing square. After injection of saliva within the square, the insect then stands and waits for solubilization of the squares cell contents, and then quickly ingests the slurry. The extensive laceration by the stylets may, secondarily, potentiate salivary maceration by mechanically rupturing cell walls. The plant responses to such behavior are thus summarized as "mechanical cell rupture-enhanced maceration.

Plants rely on a variety of ways to protect themselves from being fed upon, including de novo production of specific compounds such as those termed as phenolics. Phenolics are often described as important in plant health and numerous studies have concluded they increase as a result of insect feeding, pathogen infection, or beneficial microorganism colonization. However, there are some studies reaching differing conclusions. Therefore, meta-analyses were conducted to observe whether common trends in phenolic induction in plants can be made when they become hosts to insects or microorganisms. Four hypotheses were tested. The first was that total phenolics increase as a generic response, and meta-analyses confirmed that this occurs when plants are infested with insects or colonized by bacterial or fungal microorganisms, but not for oomycetes. The second hypothesis was that phenolic induction is different when a beneficial microorganism colonizes a plant vs. when a plant is infected by a pathogen. Beneficial bacteria, pathogenic bacteria, and beneficial fungi produced increased phenolic levels in plant hosts, but fungal pathogens did not. The third hypothesis was that insect feeding method on plant hosts determines if phenolics are induced. Chewing induced phenolics but piercing-sucking and wood-boring did not. Lastly, we used meta-analyses to determine if annual or perennials rely on phenolic induction in different amounts, and even though annuals had significantly increased phenolic levels but perennials did not, it was observed that phenolic induction was not statistically different when plant type was considered. These results demonstrate that phenolic induction is a common response in plant hosts exposed to feeding or colonization, with specific exceptions such a pathogenic fungi and piercing-sucking insects.

Insects and mites are common inhabitants and accidental invaders of food, including durable commodities, and their presence can have both direct and indirect effects on human health. The most common direct effect is contamination of food with arthropod fragments and related contaminants, which may be allergenic or even carcinogenic. The most important indirect effect is that their presence can change the storage microenvironment, making durable products suitable for the rapid development of fungi and other microorganisms. Some of these fungi can produce toxins (e.g., aflatoxins) that endanger human health. Insects may actively or passively contribute to the spread of microorganisms, increasing product contamination, and they may host bacteria that have developed antibiotic resistance, contributing to their spread in food. Several species also may host, attract, or transmit tapeworms, predators, or parasitoids that may affect health. This review synthesizes research on these topics and suggests directions for future research.

Genotypic variability in vulnerability of leaf xylem to water-stress-induced cavitation was determined in four sugarcane (Saccharum sp.) clones using detached leaf segments in a hydraulic conductivity apparatus. Vulnerability curves were constructed by plotting the percentage of maximum conductivity versus leaf water potential (psi(I)) and fitting curves using a Weibull function. The psi(I) at which each clone lost 10, 50, and 80% of maximum conductivity was determined. Maximum conductivity per unit of leaf width was positively associated with metaxylem vessel diameter. The commercial clone H65-7052 exhibited the highest and the nondomesticated S. spontaneum exhibited the lowest conductivity. All four clones lost substantial conductivity at values of psi(I) less negative than -1.4 MPa, but H65-7052 was able to maintain 50% conductivity to lower psi(I) than the other clones. S. spontaneum sustained the most negative psi(I) (-1.99 MPa) before reaching the 80% conductivity loss point. Clone H69-8235 was consistently the most vulnerable to initial loss of conductivity. These vulnerability functions were used in conjunction with field measurements of psi(I) to estimate diurnal losses in leaf hydraulic conductivity under irrigated and droughted conditions. H69-8235 lost up to 50% of its conductivity during the day, even when well irrigated, and more than 80% when subjected to drought. The other clones exhibited lower conductivity losses. These losses are apparently reversed overnight by root pressure. Despite their close genetic relationships, these clones exhibited large differences in conductivity, in the vulnerability of their xylem to cavitation, and in gas exchange behavior. The potential for altering water relations by selecting for particular hydraulic characteristics is discussed.

Zebra Chip (ZC) is an emerging plant disease that causes aboveground decline of potato shoots and generally results in unusable tubers. This disease has led to multi-million dollar losses for growers in the central and western United States over the past decade and impacts the livelihood of potato farmers in Mexico and New Zealand. ZC is associated with 'Candidatus Liberibacter solanacearum', a fastidious alpha-proteobacterium that is transmitted by a phloem-feeding psyllid vector, Bactericera cockerelli Sulc. Research on this disease has been hampered by a lack of robust culture methods and paucity of genome sequence information for 'Ca. L. solanacearum'. Here we present the sequence of the 1.26 Mbp metagenome of 'Ca. L. solanacearum', based on DNA isolated from potato psyllids. The coding inventory of the 'Ca. L. solanacearum' genome was analyzed and compared to related Rhizobiaceae to better understand 'Ca. L. solanacearum' physiology and identify potential targets to develop improved treatment strategies. This analysis revealed a number of unique transporters and pathways, all potentially contributing to ZC pathogenesis. Some of these factors may have been acquired through horizontal gene transfer. Taxonomically, 'Ca. L. solanacearum' is related to 'Ca. L. asiaticus', a suspected causative agent of citrus huanglongbing, yet many genome rearrangements and several gene gains/losses are evident when comparing these two Liberibacter. species. Relative to 'Ca. L. asiaticus', 'Ca. L. solanacearum' probably has reduced capacity for nucleic acid modification, increased amino acid and vitamin biosynthesis functionalities, and gained a high-affinity iron transport system characteristic of several pathogenic microbes.

BACKGROUND: Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning. RESULTS: Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.

Abstract Prebiotics are compounds that selectively stimulate the growth and activity of beneficial microorganisms. The use of prebiotics is a well-established strategy for managing human gut health. This concept can also be extended to plants where plant rhizosphere microbiomes can improve the nutrient acquisition and disease resistance. However, we lack effective strategies for choosing metabolites to elicit the desired impacts on plant health. In this study, we target the rhizosphere of tomato ( Solanum lycopersicum ) suffering from wilt disease (caused by Ralstonia solanacearum ) as source for potential prebiotic metabolites. We identify metabolites (ribose, lactic acid, xylose, mannose, maltose, gluconolactone, and ribitol) exclusively used by soil commensal bacteria (not positively correlated with R . solanacearum ) but not efficiently used by the pathogen in vitro. Metabolites application in the soil with 1 µmol g −1 soil effectively protects tomato and other Solanaceae crops, pepper ( Capsicum annuum ) and eggplant ( Solanum melongena ), from pathogen invasion. After adding prebiotics, the rhizosphere soil microbiome exhibits enrichment of pathways related to carbon metabolism and autotoxin degradation, which were driven by commensal microbes. Collectively, we propose a novel pathway for mining metabolites from the rhizosphere soil and their use as prebiotics to help control soil-borne bacterial wilt diseases.

In vitro, spores of Penicillium digitatum germinated without inhibition between pH 4 and 7, but were inhibited at higher pH. Estimated concentrations of imazalil (IMZ) in potato-dextrose broth-Tris that caused 50% reduction in the germination of spores (ED 50 ) of an IMZ-sensitive isolate M6R at pH 4, 5, 6, and 7 were 0.16, 0.11, 0.015, and 0.006 μg/ml, respectively. ED 50 IMZ concentrations of an IMZ-resistant isolate D201 at pH 4, 5, 6, and 7 were 5.9, 1.4, 0.26, and 0.07 μg/ml, respectively. The natural pH within 2-mm-deep wounds on lemon was 5.6 to 5.1 and decreased with fruit age. IMZ effectiveness to control green mold and its residues increased with pH. The pH in wounds on lemon fruit 24 h after immersion in 1, 2, or 3% NaHCO 3 increased from pH 5.3 to 6.0, 6.3, and 6.7, respectively. NaHCO 3 dramatically improved IMZ performance. Green mold incidence among lemon fruit inoculated with M6R and treated 24 h later with IMZ at 10 μg/ml, 1% NaHCO3, or their combination was 92, 55, and 22%, respectively. Green mold among lemon fruit inoculated with D201 and treated 24 h later with water, IMZ at 500 μg/ml, 3% NaHCO 3 , or their combination was 96.3, 63.0, 44.4, and 6.5%, respectively. NaHCO 3 did not influence IMZ fruit residue levels.