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Purpose Farmers need alternative approaches to manage nitrogen (N) that meet crop needs while reducing loss to the environment. Identifying crop genotypes that promote positive priming of organic matter in soil could help address this challenge. We aimed to 1) determine whether carrot genotypes differ in their potential to facilitate organic matter decomposition to scavenge N in soil, and 2) identify microbial taxa that are stimulated by carrot roots and thus could play a role in these processes. Methods We grew five genotypes expected to differ in N use efficiency in a nutrient-poor soil amended with 15N-enriched corn residue, tracked changes in carbon (C) and N pools, quantified microbial activity and bacterial community composition, and predicted the potential expression of microbial genes involved in soil C and N cycles. Results Experimental genotypes 8503 and 3999 had the greatest capacity to promote priming. Distinct bacterial communities from the families Micromonosporaceae, Chromatiaceae, and Rhodospirillaceae were enriched in the soils of genotypes most effective in scavenging N and this was correlated with genes responsible for β-glucosidase and nitrification activity. Conclusions Carrot genotypes do differ in the potential to stimulate microbially-mediated decomposition of organic materials indicating that it may be possible to begin selecting for this important trait.

Organic vegetable production continues to increase, while the knowledge about how to best manage foliar diseases in this system has lagged. Several combinations of organically certified products with different modes of action were evaluated for potential to manage foliar diseases of tomato in two field sites with different climatic conditions over two years, and in a greenhouse setting. Early blight, Septoria leaf spot and bacterial spot foliar diseases were naturally present in the field trials, while greenhouse plants were artificially inoculated with a virulent isolate of Alternaria solani, causal agent of early blight. The copper product Badge X2 (23.82% copper oxychloride and 21.49% copper hydroxide), significantly lowered disease levels in all field and greenhouse trials. The biological control product Prestop (Gliocladium catenulatum J1446), significantly lowered early blight disease levels in all field trials and two out of three greenhouse trials. Alternating Serenade Opti (B. amyloliquefaciens QST 713 (syn. B. subtilis QST713), with Regalia (extract of Reynoutria schalinensis) did not consistently lower disease levels compared to the untreated control in field trials. However, Serenade Opti alone lowered early blight disease levels in two out of three greenhouse trials. Sil-Matrix (potassium silicate 29%), and Regalia, applied alone and in combination were generally ineffective in both field and greenhouse trials. An alternation of Oxidate 2.0 (27.1% hydrogen dioxide and 2.0% peroxyacetic acid), which was used to lower the microbe populations on tomato foliage after which Sustane, an aerobically composted turkey litter, was applied to promote colonization by beneficial bacteria, did not consistently lower disease levels compared to the untreated control in greenhouse and field trials. Results of these trials indicate that the biological product Prestop is an effective alternative to copper for the control of early blight, but not necessarily other common foliar diseases in tomato.

Crop domestication events followed by targeted breeding practices have been pivotal for improvement of desirable traits and to adapt cultivars to local environments. Domestication also resulted in a strong reduction in genetic diversity among modern cultivars compared to their wild relatives, though the effect this could have on tripartite relationships between plants, belowground beneficial microbes and aboveground pathogens remains undetermined. We quantified plant growth performance, basal resistance and induced systemic resistance (ISR) by Trichoderma harzianum, a beneficial soil microbe against Botrytis cinerea, a necrotrophic fungus and Phytophthora infestans, a hemi-biotrophic oomycete, in 25 diverse tomato genotypes. Wild tomato related species, tomato landraces and modern commercial cultivars that were conventionally or organically bred, together, representing a domestication gradient were evaluated. Relationships between basal and ISR, plant physiological status and phenolic compounds were quantified to identify potential mechanisms. Trichoderma enhanced shoot and root biomass and ISR to both pathogens in a genotype specific manner. Moreover, improvements in plant performance in response to Trichoderma gradually decreased along the domestication gradient. Wild relatives and landraces were more responsive to Trichoderma, resulting in greater suppression of foliar pathogens than modern cultivars. Photosynthetic rate and stomatal conductance of some tomato genotypes were improved by Trichoderma treatment whereas leaf nitrogen status of the majority of tomato genotypes were not altered. There was a negative relationship between basal resistance and induced resistance for both diseases, and a positive correlation between Trichoderma-ISR to B. cinerea and enhanced total flavonoid contents. These findings suggest that domestication and breeding practices have altered plant responsiveness to beneficial soil microbes. Further studies are needed to decipher the molecular mechanisms underlying the differential promotion of plant growth and resistance among genotypes, and identify molecular markers to integrate selection for responsiveness into future breeding programs.

Vegetable growers need high-quality transplants to ensure the success of their crops. Treating seedlings with protein hydrolysates and beneficial fungus Trichoderma atroviride has the potential to improve the health and quality of vegetable transplants via various biostimulant activities, but the best rates and application methods to achieve these benefits are still unclear. Therefore, the aim of the studies described in this manuscript were to: (i) identify the optimal rate of a microgranular-based biostimulant containing vegetal-derived protein hydrolysate (PH) and the beneficial fungus T. atroviride MUCL45632 on lettuce and tomato transplant production (Experiment 1), and (ii) determine whether combining the T. atroviride inoculant with the PH in microgranular or liquid form would best support the synergistic effects of these products using greenhouse and laboratory experiments (Experiments 2, 3 and 4). Mixing the microgranular-based PH directly into the substrate prior to sowing resulted in a significant dose-dependent increase in shoot fresh and dry biomass, root dry weight, root to shoot ratio, leaf N content and chlorophyll content (Soil-Plant Analysis Development index) in both lettuce and tomato transplants up to a biostimulant rate of 2 g L&minus, 1. The positive effect of the microgranular-based PH on plant growth, leaf N and chlorophyll content in both the lettuce and tomato transplants was also observed in the second experiment. However, the PH-mediated enhancement of shoot fresh biomass was more pronounced when Trichoderma was combined with the liquid instead of the microgranule PH. In contrast, the microgranule containing PH and Trichoderma was more effective in increasing the plant root to shoot ratios than the combined application of liquid PH and Trichoderma. In the laboratory experiments, the application of PH to sandy soil enhanced the number of Trichoderma colonies and stimulated Trichoderma-induced respiration for up to two and six days for the liquid and microgranular PHs, respectively. These results demonstrate that mixing microgranules containing PH and Trichoderma in the substrate prior to sowing at a rate of 2 g L&minus, 1 is the best approach to enhance shoot and especially root growth of both tomato and lettuce plantlets, while also ensuring high N uptake and leaf chlorophyll content.

Cadmium (Cd) is a toxic metal that can accumulate in soils and negatively impact crop as well as human health. Amendments like biochar have potential to address these challenges by reducing Cd bioavailability in soil, though reliance on post-harvest wet chemical methods to quantify Cd uptake have slowed efforts to identify the most effective amendments. Hyperspectral imaging (HSI) is a novel technology that could overcome this limitation by quantifying symptoms of Cd stress while plants are still growing. The goals of this study were to: 1) determine whether HSI can detect Cd stress in two distinct leafy green crops, 2) quantify whether a locally sourced biochar derived from hardwoods can reduce Cd stress and uptake in these crops, and 3) identify vegetative indices (VIs) that best quantify changes in plant stress responses. Experiments were conducted in a tightly controlled automated phenotyping facility that allowed all environmental factors to be kept constant except Cd concentration (0, 5 10 and 15 mg kg−1). Symptoms of Cd stress were stronger in basil (Ocimum basilicum) than kale (Brassica oleracea), and were easier to detect using HSI. Several VIs detected Cd stress in basil, but only the anthocyanin reflectance index (ARI) detected all levels of Cd stress in both crop species. The biochar amendment did reduce Cd uptake, especially at low Cd concentrations in kale which took up more Cd than basil. Again, the ARI index was the most effective in quantifying changes in plant stress mediated by the biochar. These results indicate that the biochar evaluated in this study has potential to reduce Cd bioavailability in soil, and HSI could be further developed to identify rates that can best achieve this benefit. The technology also may be helping in elucidating mechanisms mediating how biochar can influence plant growth and stress responses.

Small farms near Arequipa, Peru face many challenges including crop diseases caused by soil-borne fungal pathogens. Identifying fungi in these soils and factors that shift the balance between pathogenic and beneficial lifestyles will aid in the development of more effective and sustainable disease control strategies. In this study, the composition and potential functional roles of soil fungal communities on 12 farms was characterized using SMRT sequencing. Communities were compared with soil physiochemical properties and farms grouped based on location (River vs. Canal), and farm age (Old, New, Very New) to investigate possible drivers of community structure and function. Communities were dominated by the Ascomycota phylum, and Fusarium, Alternaria and Cladosporium genera. The majority of phylotypes were saprotrophs, however, an unusually large fraction were pathotrophs (14-29%), and 10% of the entire community were plant pathogens. There were correlations between saprophytic and pathogenic phylotypes with soil pH, organic matter, nitrogen and phosphorous, though the strongest driver of community structure were cobalt and nickel. Dominant pathogenic phylotypes in river and canal farms differed indicating the need for more site-specific intervention strategies. Age was positively correlated with a decline in saprotrophs and increase in pathotrophs highlighting the need to replenish soil organic matter. Correlations between individual phylotypes could mediate disease outbreaks and should be explored in future studies. Results of this study confirm that soils in this unique agroecosystem are highly conducive to the survival of soil-borne pathogens, though it should be possible to suppress these organisms via more targeted soil management practices.

Foodborne pathogen outbreaks have become an increasing problem in the horticultural industry due to changes in diets, production, processing and distribution practices, as well as greater awareness and detection. Once produce is infected, outbreaks can spread rapidly resulting in illness and even death among large groups of people. Strict new food safety laws have been implemented to reduce risks, but outbreaks are still occurring. Pathogens with the greatest threat in ready-to-eat horticultural crops include Salmonella enterica, Escherichia coli (STEC), and Listeria monocytogenes, with contamination introduced through animal manure, water, seeds and plant debris. While previously thought to be only transient inhabitants of horticultural production systems, it is now clear that enteric pathogens are adapted to survive for prolonged periods outside of their animal hosts, attaching tenaciously to plants via biofilm formation and internalization in plant tissues. Management practices including treating animal manure, water and seeds, increasing soil biological diversity and activity, and limiting damage to plants via pests and equipment can help reduce food safety risks in pre-harvest production systems. Further reducing food safety risks in these systems will require innovative, interdisciplinary research that integrate the fields of soil microbial ecology, plant pathology, plant breeding and engineering. Specifically, we advocate for additional research to: 1) better understand how soil and phyllosphere ecology affects pathogen residence time, 2) identify key traits and markers to integrate selection for enteric pathogens into crop breeding programs, and 3) develop new detection technologies that rapidly and accurately detect enteric pathogens on produce.

The urgent need to increase sustainable crop production has pushed the agricultural sector towards methods based on natural products such as biostimulants. The nursery industry holds strategic importance for modern horticulture because only “high quality” seedlings can guarantee productive success. The aim of our research was to assess the effects of a microgranule plant-derived biostimulant added to the transplants’ substrate. Biometric parameters, mineral composition, total chlorophylls, carotenoids, and total phenols content of eggplant (Solanum melongena L., cv. Mirabelle F1), pepper (Capsicum annuum L., cv. Tarquinio F1), and tomato (Solanum lycopersicum L., cv. Taylor F1) at four different biostimulant doses (0.5, 1, 2, and 4 g L−1) were evaluated. Compared to the untreated control, the use of the highest dose of microgranule biostimulant (4.0 g L−1) increased shoot dry weight by 73%, 61%, and 33% and root dry weight by 37%, 34%, 36%, for eggplant, pepper, and tomato, respectively. Similarly, the nitrogen and potassium contents of eggplant, pepper, and tomato plants were positively affected by biostimulant application. Total chlorophylls content and carotenoids were significantly affected only in tomato leaves with the 2.0 and 4.0 g L−1 doses while no significant differences for total phenols were recorded in transplant leaves of tested vegetable crops. Chlorophyll a/b decreased in eggplant and pepper with increasing microgranular-based PHs rates, indicating a greater accumulation of chlorophyll b than chlorophyll a. Our results show that microgranule biostimulant application directly mixed in the substrate can improve the quali-quantitative traits of nursery seedlings while reducing the excessive use of fertilizers and concomitantly producing vigorous seedlings potentially capable of overcoming easily transplant stress.

Fresh produce, viewed as an essential part of a healthy life style, usually consumed in the form of raw or minimally processed fruits and vegetables, is a potentially important source of food-borne disease including human pathogenic bacteria and viruses. These are passed on to the consumer since the bacteria can form biofilms or otherwise populate plant tissues, thereby using plants as vectors to infect animal hosts. The life cycle of the bacteria in plants differs from those in animals or humans and results in altered physiochemical and biological properties (e.g., physiology, immunity, native microflora, physical barriers, mobility, and temperature). Mechanisms by which healthy plants may become contaminated by microorganisms, develop biofilms, and then pass on their pathogenic burden to people are explored in the context of hollow fiber microfiltration by which plant-derived microorganisms may be recovered and rapidly concentrated to facilitate study of their properties. Enzymes, when added to macerated plant tissues, hydrolyze or alter macromolecules that would otherwise foul hollow-fiber microfiltration membranes. Hence, microfiltration may be used to quickly increase the concentration of microorganisms to detectable levels. This review discusses microbial colonization of vegetables, formation and properties of biofilms, and how hollow fiber microfiltration may be used to concentrate microbial targets to detectable levels when added enzymes help to disintegrate biofilms and minimize hollow fiber membrane fouling, thereby providing a new tool for more time effectively elucidating mechanisms by which biofilms develop and plant tissue becomes contaminated with human pathogens. This article is protected by copyright. All rights reserved

Managing pests in carrot production is challenging. Endophytic microbes have been demonstrated to improve the health and productivity of many crops, but factors affecting endophyte dynamics in carrot is still not well understood. The goal of this study was to determine how crop management system and carrot genotype interact to affect the composition and potential of endophytes to mitigate disease caused by Alternaria dauci, an important carrot pathogen. Twenty-eight unique isolates were collected from the taproots of nine diverse genotypes of carrot grown in a long-term trial comparing organic and conventional management. Antagonistic activity was quantified using an in vitro assay, and potential for individual isolates to mitigate disease was evaluated in greenhouse trials using two carrot cultivars. Results confirm that carrot taproots are colonized by an abundant and diverse assortment of bacteria and fungi representing at least distinct 13 genera. Soils in the organic system had greater total organic matter, microbial biomass and activity than the conventional system and endophyte composition in taproots grown in this system were more abundant and diverse, and had greater antagonistic activity. Carrot genotype also affected endophyte abundance as well as potential for individual isolates to affect seed germination, seedling growth and tolerance to A. dauci. The benefits of endophytes on carrot growth were greatest when plants were subject to A. dauci stress, highlighting the importance of environmental conditions in the functional role of endophytes. Results of this study provide evidence that endophytes can play an important role in improving carrot performance and mediating resistance to A. dauci, and it may someday be possible to select for these beneficial plant-microbial relationships in carrot breeding programs. Implementing soil-building practices commonly used in organic farming systems has potential to promote these beneficial relationships and improve the health and productivity of carrot crops.

To attain Salmonella detection thresholds in spinach suspensions using enrichment media requires at least 24 hr. Separation and concentration of selected microorganisms via microfiltration and microfugation reduce time for sample preparation, especially when working with large volumes of vegetable suspensions. This facilitates accelerated detection of Salmonella in spinach suspensions, and may contribute to effectively monitoring this pathogen before it reaches the consumer. We report a microfiltration-based protocol for accelerated sample preparation to concentrate and recover ≤1 colony forming unit (CFU) Salmonella/g pathogen-free spinach. Store-bought samples of spinach and a spinach plant subjected to two environmental conditions (temperature and light exposure) during its production were tested. The overall procedure involves extraction with buffer, a short enrichment step, prefiltration using a nylon filter, crossflow hollow fiber microfiltration, and retentate centrifugation to bring microbial cells to detection levels. Based on 1 CFU Salmonella/g frozen spinach, and a Poisson distribution statistical analyses with 99% probability, we calculated that 3 hr of incubation, when followed by microfiltration, is sufficient to reach the 2 log concentration required for Salmonella detection within 7 hr. Longer enrichment times (5 hr or more) is needed for concentrations lower than 1 CFU Salmonella/g of ready to eat spinach. The recovered microbial cells were identified and confirmed as Salmonella using both polymerase chain reaction (PCR) and plating methods. Different environmental conditions tested during production did not affect Salmonella viability; this demonstrated the broad adaptability of Salmonella and emphasized the need for methods that enable efficient monitoring of production for the presence of this pathogen.

Phytophthora blight has become one of the most serious threats to the vegetable industry. Managing this disease is challenging, because the oomycete pathogen responsible, Phytophthora capsici, can move rapidly through crop fields, has a wide host range, is resistant to many commonly used fungicides, and produces resilient spores that can survive in soil for up to 10 years. Recent studies have demonstrated that biochar amendments can suppress infection by many soil-borne pathogens—indicating that these amendments could have the potential to help control phytophthora blight. In this study, greenhouse trials were conducted to determine whether two commercially available biochar amendments could suppress P. capsici infection in sweet bell pepper (Capsicum annuum) using three naturally infested field soils. Soil biological and chemical assays were conducted to evaluate whether potential changes induced by biochar amendments were correlated with suppressive activity. Amending soil with a biochar product that included a proprietary mix of beneficial microorganisms and enriched substrates resulted in lower soil P. capsici abundance in all soils, and lower percent root infection in two of the soils tested. This product also resulted in higher soil pH, and lower soil nitrogen availability and leaf chlorophyll content. The other biochar product did not suppress P. capsici, and had few effects on soil chemical and biological properties. Results of this study indicate that some commercially available biochar amendments have the potential to help mediate phytophthora blight, but further trials are needed to confirm that suppressive effects will be observed in field trials. Additional research is also recommended to identify the mechanisms regulating biochar-mediated suppression of phytophthora blight to develop products that can reliably suppress soil-borne diseases in the field.

Increasing nitrogen use efficiency is critical to the productivity and long-term sustainability of vegetable production systems in the US Midwest. Understanding the impact of alternative fertility sources on the ecology of the soil nitrogen cycle has potential to allow for management that will increase crop N uptake and reduce loss. We determined how repeated applications of urea, composted chicken litter, hairy vetch green manure with alfalfa meal, and an unfertilized control affected the structure and potential nitrification activity (PNA) of ammonia oxidizers in bulk and rhizosphere soil when N needs were expected to be high. PNA was greater in animal and green manure treatments relative to urea and the unfertilized control in bulk soil, and greater in the rhizosphere relative to bulk soil regardless of fertility treatment. A strong correlation was observed between PNA and ammonia oxidizing bacteria (AOB) abundance, suggesting that AOB rather than ammonia oxidizing archaea (AOA) controlled nitrification in this system. However, AOB abundance did not differ between bulk and rhizosphere soil, and PNA was lower in the urea treatment despite greater AOB abundance indicating that other factors could have affected PNA. For example, greater availability of labile carbon (C) could have stimulated PNA through various mechanisms, and lower pH and/or specific nitrification potential per AOB cell could have reduced PNA in the urea treatment. AOB community structure was more diverse in all fertility treatments relative to the unfertilized control in bulk soil, and community structure differed between bulk and rhizosphere soil indicating niche differentiation. However, differences in AOB community structure and PNA were only observed in rhizosphere relative to bulk soil indicating that the rhizosphere had a greater effect on nitrification dynamics than fertility practices. These findings indicate that organic fertility amendments stimulate PNA, but they could also increase N loss and should be investigated further. The rhizosphere appears to play a greater role in nitrification dynamics than fertility practices, and more detailed investigations at this key plant-soil interface are warranted.

Salmonella is the most burdensome foodborne pathogen in the USA and a major causal agent of foodborne outbreaks. Detection of a pathogen such as Salmonella can be achieved within a few hours using commercially available rapid methods, but the sample preparation is time consuming and may require multiple days. We have developed and successfully tested an accelerated sample preparation method based on microfiltration, in some cases preceded by a short enrichment step, for the rapid detection of selected pathogens. The time-frame of the overall process, from sample preparation (i.e., food rinse or homogenate preparation, microbial enrichment, and filtration steps) to detection is 8 h or less. While microfiltration has been practiced for 70 years, the complex interactions between food substances and filter membrane surfaces have shown that food pretreatment methods need to be developed on a case by case basis for the recovery of bacteria from food homogenates and/or rinses. We have also demonstrated that addition of protease to treat homogenates of different poultry products prior to microfiltration avoids the rapid decrease in flux that otherwise occurs during microfiltration. This protease treatment minimizes filter clogging, so that the microbial concentration, recovery and detection of 1 to 10 CFU/g of Salmonella in poultry products is possible in less than 8 h.

Salmonella is the most burdensome foodborne pathogen in the USA and a major causal agent of foodborne outbreaks. Detection of a pathogen such as Salmonella can be achieved within a few hours using commercially available rapid methods, but the sample preparation is time consuming and may require multiple days. We have developed and successfully tested an accelerated sample preparation method based on microfiltration, in some cases preceded by a short enrichment step, for the rapid detection of selected pathogens. The time-frame of the overall process, from sample preparation (i.e., food rinse or homogenate preparation, microbial enrichment, and filtration steps) to detection is 8 h or less. While microfiltration has been practiced for 70 years, the complex interactions between food substances and filter membrane surfaces have shown that food pretreatment methods need to be developed on a case by case basis for the recovery of bacteria from food homogenates and/or rinses. We have also demonstrated that addition of protease to treat homogenates of different poultry products prior to microfiltration avoids the rapid decrease in flux that otherwise occurs during microfiltration. This protease treatment minimizes filter clogging, so that the microbial concentration, recovery and detection of 1 to 10 CFU/g of Salmonella in poultry products is possible in less than 8 h.

Local production of organic tomatoes marketed directly to consumers is growing rapidly in the U.S. Midwest. Growers serving this market need cultivars that are well adapted to local climatic conditions, are competitive under organic management, and have end-use quality characteristics desired by their customers. Participatory plant breeding is a powerful, cost-effective approach with potential to engage growers in development of new cultivars optimally adapted to organic farming systems. To initiate a participatory breeding program for organic tomatoes an online grower survey was conducted to identify key plant traits, and a diverse set of tomato germplasm was evaluated under organic management to better understand horticultural constraints and identify adapted germplasm for further development. Tomato growers rated flavor as their top breeding priority, followed by disease resistance with late blight (LB) (Phytophthora infestans), early blight (EB) (Alternaria solani), and septoria leaf spot (SLS) (Septoria lycopersici) identified as the most problematic diseases. In field trials, foliar diseases were problematic in both years, though many entries exhibited partial resistance. Differences among entries in resistance to insect pests such as hornworms (Manduca sexta) were also observed. Yield varied widely among entries with some of the F1 hybrids and heirloom cultivars performing well despite significant disease pressure. Overall, we identified existing cultivars and F1 hybrids with potential to meet the immediate needs of Midwest organic tomato growers, and segregating breeding populations for further selection to be conducted on working organic farms.

Use of high tunnel crop production is expected to increase to meet the growing demand for locally produced fresh market vegetables. These structures have the potential to offer many production benefits; however, managing soil quality in these structures is challenging and work in the area is limited. In this 3-year study, we compared the impacts of organic and inorganic fertility amendments on soil quality, nutrient availability, and the productivity of chard (Beta vulgaris L.) and sweet peppers (Capsicum annuum L.) produced in high tunnel and open field systems. Fertility amendments included a green manure treatment [hairy vetch (Vicia villosa Roth) and dehydrated alfalfa meal], partially composted and pelletized chicken litter, urea, and an unfertilized control. Chard was grown in 2011, and peppers were grown in 2012 and 2013. Soil nutrients, microbial activity, active carbon, pH, electrical conductivity (EC), total soil organic matter, and yield were quantified. Chard yield was lower in the high tunnel compared with the open field in 2011, but pepper yield was greater in the high tunnel in 2012 and 2013. Productivity of chard was lower in the green manure compared with urea in 2011 across high tunnel and open field production systems, but no difference in pepper yield was observed between plants receiving fertility inputs in either 2012 or 2013. Repeated application of green manure and chicken litter resulted in soils with increased microbial activity and active carbon, but the green manure was the only treatment successful at accruing carbon in the high tunnel over time. High tunnel production resulted in greater EC compared with the open field, but levels were not considered inhibitory for chard or peppers. High tunnels can increase vegetable crop productivity in the midwest United States, and organic fertility amendments can improve soil quality as measured by soil microbial activity and active carbon in high tunnel and open field production systems.

Plant-derived protein hydrolysates (PHs) have gained prominence as plant biostimulants because of their potential to increase the germination, productivity and quality of a wide range of horticultural and agronomic crops. Application of PHs can also alleviate the negative effects of abiotic plant stress due to salinity, drought and heavy metals. Recent studies aimed at uncovering the mechanisms regulating these beneficial effects indicate that PHs could be directly affecting plants by stimulating carbon and nitrogen metabolism, and interfering with hormonal activity. Indirect effects could also play a role as PHs could enhance nutrient availability in plant growth substrates, and increase nutrient uptake and nutrient-use efficiency in plants. Moreover, the beneficial effects of PHs also could be due to the stimulation of plant microbiomes. Plants are colonized by an abundant and diverse assortment of microbial taxa that can help plants acquire nutrients and water and withstand biotic and abiotic stress. The substrates provided by PHs, such as amino acids, could provide an ideal food source for these plant-associated microbes. Indeed, recent studies have provided evidence that plant microbiomes are modified by the application of PHs, supporting the hypothesis that PHs might be acting, at least in part, via changes in the composition and activity of these microbial communities. Application of PHs has great potential to meet the twin challenges of a feeding a growing population while minimizing agriculture’s impact on human health and the environment. However, to fully realize the potential of PHs, further studies are required to shed light on the mechanisms conferring the beneficial effects of these products, as well as identify product formulations and application methods that optimize benefits under a range of agro-ecological conditions.

Fresh produce, viewed as an essential part of a healthy life style is usually consumed in the form of raw or minimally processed fruits and vegetables, and is a potentially important source of food-borne human pathogenic bacteria and viruses. These are passed on to the consumer since the bacteria can form biofilms or otherwise populate plant tissues, thereby using plants as vectors to infect animal hosts. The life cycle of the bacteria in plants differs from those in animals or humans and results in altered physiochemical and biological properties (e.g., physiology, immunity, native microflora, physical barriers, mobility, and temperature). Mechanisms by which healthy plants may become contaminated by microorganisms, develop biofilms, and then pass on their pathogenic burden to people are explored in the context of hollow fiber microfiltration by which plant-derived microorganisms may be recovered and rapidly concentrated to facilitate study of their properties. Enzymes, when added to macerated plant tissues, hydrolyze or alter macromolecules that would otherwise foul hollow-fiber microfiltration membranes. Hence, microfiltration may be used to quickly increase the concentration of microorganisms to detectable levels. This review discusses microbial colonization of vegetables, formation and properties of biofilms, and how hollow fiber microfiltration may be used to concentrate microbial targets to detectable levels. The use of added enzymes helps to disintegrate biofilms and minimize hollow fiber membrane fouling, thereby providing a new tool for more time effectively elucidating mechanisms by which biofilms develop and plant tissue becomes contaminated with human pathogens. Biotechnol. Bioeng. 2017;114: 1403-1418. © 2017 Wiley Periodicals, Inc.

That the health of soils, plants, animals, and people are linked is an ancient idea that still resonates. Growing evidence links farm management, soil health, and plant health but relationships among soil health, food crop nutritional quality, and human health are less understood. Numerous studies compare organic with conventional farming in order to shed light on these links. Organic farming systems utilize carbon-based amendments, diverse crop rotations, and cover crops to build soil fertility. These practices increase biologically available soil organic matter and beneficial soil microbe and invertebrate activities, improve soil physical properties, reduce disease potential, and increase plant health. To date, comparisons of nutrient content between organic and conventional foods have been inconsistent. Recent evidence suggests that organically grown fruits and vegetables contain higher levels of health promoting phytochemicals, possibly linked to greater plant stress, rhizosphere microbial communities, and/or lower available nitrogen. But the overlap in management practices among farming systems make broad generalizations difficult. Moreover, environmental and crop species and/or cultivar interactions may exert stronger effects than management. Here we summarize the known factors influencing soil and plant health and link these with food-crop quality and human health. Though this paper draws primarily from research on organic farming, management practices that enhance soil, plant, and human health remain an important goal for all sustainable food production systems.

The nitrogen (N) dynamics of nine rotation systems designed to transition dryland cereal to organic production in eastern Washington State were examined. Systems combined cereal and legumes for grain, forage (FOR), and green manure (GRM). Few differences in N balances and soil inorganic N levels were found among transition systems when poor spring crop establishment resulted in competition from weeds. However, FOR and winter GRM crops produced adequate stands that were competitive with weeds and increased residual soil inorganic N in the final year of the transition. Winter legumes and continuous FOR systems demonstrated the greatest potential to provide a sustainable inorganic N source to subsequent organic cereal crops.

Published in Agron. J. 103:1645–1654 (2011) Posted online 14 Sep 2011 doi:10.2134/agronj2011.0131 Available freely online through the author-supported open access option. Copyright © 2011 by the American Society of Agronomy, 5585 Guilford Road, Madison, WI 53711. All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. T first use of hops—with the tender shoots and young leaves used as a salad (Burgess, 1964)—was described in the fi rst century A.D. in Pliny’s Natural History. Th e earliest records of hop cultivation date back to the 8th century, when French and German monks grew hops, presumably for their medicinal value (Burgess, 1964). Hops have a long history of use for medicinal purposes, and they have most oft en been used as a mild sedative due to their anti-anxiety properties. It was not until the 12th century that hops became widely used as a preservative and clarifying component in the beer-brewing process (Burgess, 1964). Hop cultivation and brewing have been an important part of American culture since the fi rst colonists arrived. By the mid1600s, widespread cultivation of hops was becoming commonplace, with farms up to 18 ha in size. Hop production had spread from New York to Wisconsin, and fi nally to the Washington Territory and California by the late 1800s (Steiner, 1973). Th e Humulus genus is made up of dioecious (rarely monoecious), perennial, short-day fl owering plants of the family Cannabaceae and is indigenous to northern temperate climates (Mahaff ee and Pethybridge, 2009; Small, 1978). Th e Humulus genus has three distinct species: H. japonicas Siebold & Zucc., H. yunnanensis Hu, and H. lupulus L. Humulus japonicas is an annual species native to China, Japan, and Taiwan and is cultivated primarily for its ornamental value. It has been introduced to Europe and North America and is now considered a semi-invasive species in some areas of the eastern United States (Mahaff ee and Pethybridge, 2009). Humulus yunnanensis is a relatively unknown species thought to have originated at high elevations in the Yunnan province of southern China (Mahaff ee and Pethybridge, 2009). Humulus yunnanensis is not widely cultivated, and, according to Small (1978), is oft en confused with H. lupulus, while other, more recent sources report that it is a rare species (Mahaff ee and Pethybridge, 2009). Humulus yunnanensis is not found in the USDA’s national plant germplasm system (Mahaff ee and Pethybridge, 2009). Humulus lupulus, widely known as the common hop plant, is the species that possesses marketable traits used for brewing. It consists of a number of taxonomic varieties: H. lupulus var. neomexicanus A. Nelson & Cockerell adapted to western cordilleran conditions; H. lupulus var. cordifolius (Miguel) Maximowicz distributed in eastern Asia, most notably Japan; H. lupulus var. pubescens E. Small of the Midwestern United States; H. lupulus var. lupuloides E. Small of eastern and central North America; and H. lupulus var. lupulus, which originated in Europe but has spread to Asia, Africa, and eastern North America and is the taxonomic variety responsible for retaining most of the favorable brewing characteristics (Hampton et al., 2001; Mahaff ee and Pethybridge, 2009). One other taxonomic variety, H. lupulus var. fengxianensis J.Q. Fu, has also been described (Peredo et al., 2009). Overlapping and introgression is evident for some varieties (Mahaff ee and Pethybridge, 2009). Th ough wild hops cannot be used directly for brewing due to ABSTRACT Hop cones grown on the female plant of the perennial crop (Humulus lupulus L.) are an integral component of the brewing process and provide fl avor, bitterness, aroma, and antimicrobial properties to beer. Demand for organically grown hops from consumers via the brewing industry is on the rise; however, due to high N requirements and severe disease, weed, and arthropod pressures, hops are an extremely diffi cult crop to grow organically. Currently, the majority of the world’s organic hops are grown in New Zealand, while other countries, including China, are beginning to increase organic hop production. Land under organic hop production in Washington State, where 75% of the hops in the United States are grown, increased from 1.6 ha to more than 26 ha from 2004 to 2010, and other hop-producing states demonstrate a similar trend. Removing hops from the USDA Organic Exemption list in January 2013 is expected to greatly increase organic hop demand and will require corresponding increases in organic hop hectarage. Current challenges, including weed management, fertility and irrigation management, insect and disease pressures, and novel practices that address these issues will be presented. Here, we discuss current and future research that will potentially impact organic hop production in the United States.

The trend towards crop specialization and increased farm size in U.S. agricultural systems has had negative economic and environmental impacts. On large, specialized farms, bottlenecks in labor occur, and a significant amount of seasonal labor is underutilized. This study was conducted to determine if this labor could be allocated to the production of supplemental enterprises. A linear programming analysis confirmed that 2,807 hours of underutilized labor exists in a typical corn-soybean rotation and that integration of the supplemental crops evaluated in our study are feasible. Grazing of stalk residues alone did not make use of the underutilized labor, however, integration of two alternative cabbage production scenarios as well as an agroforestry alternative that included decorative woody florals made use of an additional 357 and 306 hours of the underutilized labor, respectively. The integration of supplemental alternative crops into an existing corn–soybean rotation has the ability to make use of unde...

Organic grain production is not common to eastern Washington, but offers attractive market opportunities if systems can be developed that are compatible with regional production constraints. Erodible soils make tillage-intensive systems unsustainable, and there are limited alternative fertility options. Given these constraints, the objective of this study was to evaluate nine cropping systems during the transition to organic grain production under reduced tillage and relying on legumes as the primary source of crop nitrogen. The experimental transition systems ranged in the degree in which legume grain crops or legume green manures/forages were present in the rotation. We found that spring pea grown for grain to be a poor choice for organic production due to the susceptibility of this crop to insect pests and weeds, which generally resulted in crop failure. Likewise, bell bean was poorly suited as a legume green manure crop due to its low productivity in our region. In contrast, alfalfa and winter pea-bas...

Soil erosion due to annual cropping on highly erodible farmland is a major ecological concern in the wheat growing regions of Washington State. In response to requests from farmers, the winter wheat breeding program at Washington State University has been developing perennial wheat selected from crosses between wild wheatgrass species and commonly grown annual wheat cultivars. In 2005/06, we conducted field trials of the most promising perennial wheat breeding lines derived from interspecific crosses between tall wheatgrass (Thinopyrum elongatum) and bread wheat (Triticum aestivum). Thirty-one perennial breeding lines and two annual winter wheat cultivars were evaluated for nutritional value in the form of grain mineral concentration, multiple baking and milling quality traits, and ease of grain threshability. The objective of this study was to identify the strengths and weaknesses of these post-harvest traits in the perennial wheat lines derived from these interspecific crosses. Mineral nutrient concentrations in the perennial lines were 44, 40, 24, 23, 32, 30 and 33% higher than the annual control cultivars for calcium, copper, iron, magnesium, manganese, phosphorus and zinc, respectively. The annual cultivars had a higher grain mineral content per unit area of land than the perennial lines, due primarily to the higher grain yields of the annual cultivars. Compared to the annual wheat cultivars, the perennial lines produced grain with smaller seed size, lower test weight and reduced flour yield, mix time and loaf volume. Protein content was 3.5–4.5% higher in the perennial lines than in the annual cultivars. The threshability index (TI) ranged from 0.63 to 0.89 in the perennials (μ=0.75); significantly lower than the mean TI of the annual cultivars (μ=0.97). The significant genotype×location interaction found for TI suggests that the variation in annual precipitation positively influenced some perennial lines to express greater threshability. In addition to transferring traits important to the perennial growth habit in wheat, the wild wheatgrass species also introduced beneficial characteristics (i.e. increased protein and mineral concentration) and deleterious traits (poor threshing grain and inferior baking qualities). This research gives researchers a platform from which to direct further research and selection in the development of perennial wheat.

Biologically based weed control strategies are needed in organic and low-input systems. One promising practice is the application of Brassicaceous seed meal (BSM) residue, a byproduct of biodiesel production. When applied as a soil amendment, BSM residue has exhibited potential bioherbicide activity. In this study, tree fruit orchard soils were treated with various BSMs and the impact of Pythium on weed suppression was examined in field and greenhouse studies. Although weed control obtained in response to Brassicaceous residue amendments has been repeatedly attributed solely to release of allelopathic phytochemicals, multiple lines of evidence acquired in these studies indicate the involvement of a microbiological component. Reduced weed emergence and increased weed seedling mortality were not related to BSM glucosinolate content but were correlated with significant increases in resident populations of Pythium spp. in three different orchard soils. Seed meal of Brassica juncea did not amplify resident Pythium populations and did not suppress weed emergence. Application of Glycine max SM did stimulate Pythium spp. populations and likewise suppressed weed emergence. Application of a mefenoxam drench to Pythium -enriched soil significantly reduced weed suppression. These studies indicate that a microbial mechanism is involved in SM-induced weed suppression and that selective enhancement of resident pathogenic Pythium spp. can be utilized for the purpose of weed control.

This study addresses the often-competing goals of organic fertility and weed control by evaluating alternative orchard floor management strategies for their impact on N cycling, tree performance, and soil biological activity in a newly established apple (Malus domestica Borkh.) orchard. The standard tillage weed control practice resulted in satisfactory tree growth with desirable levels of leaf N and most other nutrients; however, soil biological activity did not improve. Maintenance of a living cover understory increased soil N concentration and availability and improved soil biological activity; however, tree growth was less than in other treatments likely in response to competition with the living cover understory for space and water. Application of wood chip mulch resulted in exceptional tree growth which may have resulted from greater water availability, but available soil N was lower, and consequently, tree leaf N concentration was low; in addition, soil biological activity was not improved. Clove oil organic herbicide provided poor weed control resulting in lower leaf N and tree growth and did not improve soil biological activity. Brassicaceae seed meal applications enhanced N availability and soil nematode abundance, but leaf N and many other nutrients were below desirable levels, and additional research is needed to optimize this treatment. We conclude that meeting the multiple objectives of weed control, optimal tree health, and increased soil biological activity may require employment of different orchard floor management strategies at different times during the life of the orchard.

Organic orchards represent a significant and growing component of Washington state agriculture. Comparison studies have shown that organic apple systems can be equally profitable yet more environmentally sustainable than their conventional counterparts. Despite this success, sustainable methods of weed control, fertility, and soil quality stabilization and improvement have remained a challenge. Intensive cultivation is commonly used to control weeds in organic orchards. This can lead to reduced or degraded soil organic matter, structure, water infiltration, aerated pore space, and other soil productivity parameters. In addition, tillage accelerates nutrient cycling and can result in the loss of valuable nutrients from the system. To address the need for sustainable organic methods of weed management, an integrated study of alternative understory management options was established in a newly planted orchard in 2005. Weed control measures included efficient tillage using a Wonder weeder, organically approved herbicide, wood chip mulch, and living cover mulches. Three rates of nitrogen (low, medium, and high) were applied across the Wonder weeder, wood chip, and living cover mulch plots in order to determine ideal N fertility rate. Analyses of total C and N and N-15 in organic fertilizers, soil pools, living cover biomass, and tree leaves are being used to track N and C cycling and partitioning, N-use efficiency, soil quality, and to determine optimal fertility guidelines. Preliminary results indicate intense competition between living mulch understory and orchard trees, and a trade-off may exist between maximizing soil quality and orchard productivity.

Synchronizing the supply of plant-available nitrogen (N) from organic materials with the N needs of apple trees is essential to cost-effective organic apple production. Tree growth and organic matter mineralization are affected by orchard floor management. This study examines the effects of three orchard floor management systems, cultivation, wood chip mulch, and a legume cover crop, on the accumulation and partitioning of compost-derived N in young apple (Malus domestica Borkh.) trees at different compost application dates across two growing seasons. Compost enriched with 15N was applied to apple trees in April, May, and June of 2006 and 2007, and trees were excavated in Sept. 2007 to determine the fate of labeled compost N. Trees with wood chip mulch had significantly greater dry weight and N accumulation in vegetative tree components than trees with cultivation or legume cover. Fruit yields were similar between cultivation and wood chip treatments despite less vegetative growth under cultivation, as these trees partitioned more dry weight into fruit (44%) than wood chip mulch trees (31%). Nitrogen-use efficiency by trees was lower with a living legume cover crop than in other treatments due to competition for resources. In the cover crop aboveground biomass, 20% to 100% of the N was derived from compost. In comparison, only 5% to 40% of N in the decomposing wood chip mulch originated from compost. Tree reserves were an important source of N for spring fruit and leaf growth in all treatments, but significantly more so for trees in the cultivation treatment. Fruit and leaves were strong sinks for compost N early in the season, with trees allocating 72% of spring N uptake into leaves and fruit. In the summer, N uptake increased improving compost N-use efficiency. Summer N was preferentially allocated to perennial tissues (71%), bolstering N reserves. Trees with wood chip mulch performed well and had greater capacity to build N reserves, making wood chips ideal for establishing young organic apple orchards. However, as the orchard matures, it may be beneficial to switch to a groundcover that reduces tree vegetative growth.

This study evaluated the effects of in-row groundcovers (bare ground, brassica seed meal, cultivation, wood chip mulch, legume cover crop, and non-legume cover crop) and three compost rates (48, 101, and 152 kg available nitrogen (N)/ha/year) on soil carbon (C) pools, biological activity, N supply, fruit yield, and tree growth in a newly planted apple (Malus domestica Borkh.) orchard. We used nonlinear regression analysis of C mineralization curves to differentiate C into active and slow soil C pools. Bare ground and cultivation had large active soil C pools, 1.07 and 0.89 g C/kg soil, respectively, but showed little stabilization of C into the slow soil C pool. The use of brassica seed meal resulted in increased soil N supply, the slow soil C pool, and earthworm activity but not total soil C and N, fruit yield, or tree growth. Legume and non-legume cover crops had increased microbial biomass and the slow soil C pool but had lower fruit yield and tree growth than all other groundcovers regardless of compost rate. Soils under wood chip mulch had elevated earthworm activity, total soil C and N, and the slow soil C pool. Wood chip mulch also had the greatest cumulative C mineralization and a high C:N ratio, which resulted in slight N immobilization. Nevertheless, trees in the two wood chip treatments ranked in the top four of the 13 treatments in both fruit yield and tree growth. Wood chip mulch offered the best balance of tree performance and soil quality of all treatments.