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Verticillium dahliae causes Verticillium wilt, resulting in significant losses to potato production. Benzovindiflupyr, a succinate dehydrogenase inhibitor, effectively controls V. dahliae. However, frequent applications of the chemical may expedite the development of fungicide resistance in the pathogen population. To evaluate the risk of benzovindiflupyr resistance, 38 V. dahliae strains were obtained from diseased potatoes in Maine. The sensitivity of the field population was determined based on effective concentration for 50% inhibition (EC50), which ranged from 0.07 to 11.28 μg ml−1 with a median of 1.08. Segregated clusters of EC50 values indicated that Maine V. dahliae populations have developed benzovindiflupyr resistance. By exposing conidia of V. dahliae to a high concentration of benzovindiflupyr, 18 benzovindiflupyr-resistant mutants were obtained. To examine their fitness, the mutants were continuously subculture-transferred for up to 10 generations. Mycelial growth, conidial production, competitiveness, pathogenicity, and cross resistance of the 10th generation mutants were examined. Results showed that 50% of the resistant mutants retained an adaptive level in mycelial growth, and 60% maintained conidial production similar to their parents. Pathogenicity did not change for any of the mutants. No cross resistance was detected between benzovindiflupyr and either azoxystrobin, boscalid, fluopyram, or pyrimethanil. Thus, the resistance risk in V. dahliae to benzovindiflupyr should be considered in Maine potato production.

Dickeya dianthicola has caused an outbreak of blackleg and soft rot of potato in the eastern half of the United States since 2015. To investigate genetic diversity of the pathogen, a comparative analysis was conducted on genomes of D. dianthicola strains. Whole genomes of 16 strains from the United States outbreak were assembled and compared with 16 previously sequenced genomes of D. dianthicola isolated from potato or carnation. Among the 32 strains, eight distinct clades were distinguished based on phylogenomic analysis. The outbreak strains were grouped into three clades, with the majority of the strains in clade I. Clade I strains were unique and homogeneous, suggesting a recent incursion of this strain into potato production from alternative hosts or environmental sources. The pangenome of the 32 strains contained 6,693 genes, 3,377 of which were core genes. By screening primary protein subunits associated with virulence from all U.S. strains, we found that many virulence-related gene clusters, such as plant cell wall degrading enzyme genes, flagellar and chemotaxis related genes, two-component regulatory genes, and type I/II/III secretion system genes, were highly conserved but that type IV and type VI secretion system genes varied. The clade I strains encoded two clusters of type IV secretion systems, whereas the clade II and III strains encoded only one cluster. Clade I and II strains encoded one more VgrG/PAAR spike protein than did clade III. Thus, we predicted that the presence of additional virulence-related genes may have enabled the unique clade I strain to become predominant in the U.S. outbreak.

Crop rotations and the inclusion of cover crops and green manures are primary tools in the sustainable management of soil-borne diseases in crop production systems. Crop rotations can reduce soil-borne disease through three general mechanisms: (1) serving as a break in the host-pathogen cycle; (2) by altering the soil physical, chemical, or biological characteristics to stimulate microbial activity and diversity; or (3) directly inhibiting pathogens through the release of suppressive or toxic compounds or the enhancement of specific antagonists. Brassicas, sudangrass, and related plant types are disease-suppressive crops well-known for their biofumigation potential but also have other effects on soil microbiology that are important in disease suppression. The efficacy of rotations for reducing soil-borne diseases is dependent on several factors, including crop type, rotation length, rotation sequence, and use of the crop (as full-season rotation, cover crop, or green manure). Years of field research with Brassica and non-Brassica rotation crops in potato cropping systems in Maine have documented the efficacy of Brassica green manures for the reduction of multiple soil-borne diseases. However, they have also indicated that these crops can provide disease control even when not incorporated as green manures and that other non-biofumigant crops (such as barley, ryegrass, and buckwheat) can also be effective in disease suppression. In general, all crops provided better disease control when used as green manure vs. as a cover crop, but the addition of a cover crop can improve control provided by most rotation crops. In long-term cropping system trials, rotations incorporating multiple soil health management practices, such as longer rotations, disease-suppressive rotation crops, cover crops, and green manures, and/or organic amendments have resulted in greater yield and microbial activity and fewer disease problems than standard rotations. These results indicate that improved cropping systems may enhance productivity, sustainability, and economic viability.

An outbreak of blackleg and soft rot of potato, caused primarily by the bacterial pathogen Dickeya dianthicola, has resulted in significant economic losses in the northeastern United States since 2015. The spread of this seedborne disease is highly associated with seed distribution; therefore, the pathogen likely spread with seed tubers. To describe the blackleg epidemic and track inoculum origins, a total of 1,183 potato samples were collected from 11 states associated with blackleg outbreak from 2015 to 2019. Of these samples, 39.8% tested positive for D. dianthicola. Seventeen isolates of D. dianthicola were recovered from these samples and the genetic diversity of these isolates was examined. Fingerprinting with BOX-A1R-based repetitive extragenic palindromic PCR and phylogenetic analysis based on sequences of the 16S rRNA and gapA genes indicated that D. dianthicola isolates were divided into three genotypes, denoted types I, II, and III. Ninety-five percent of samples from Maine were type I. Type II was found in Maine only in 2015 and 2018. Type II was present throughout the 5 years in some states at a lower percentage than type I. Type III was found in Pennsylvania, New Jersey, and Massachusetts, but not in Maine. Therefore, type I appears to be associated with Maine, but type II appeared to be distributed throughout the northeastern United States. The type II and rarer type III strains were closer to the D. dianthicola type strain isolated from the United Kingdom. This work provides evidence that the outbreak of blackleg of potato in the northeastern United States was caused by multiple strains of D. dianthicola. The geographic origins of these strains remain unknown.

Soilborne diseases are persistent problems in potato production and alternative management practices are needed, particularly in organic production, where control options are limited. Selected bioc...

An outbreak of bacterial soft rot and blackleg of potato has occurred since 2014 with the epicenter being in the northeastern region of the United States. Multiple species of Pectobacterium and Dickeya are causal agents, resulting in losses to commercial and seed potato production over the past decade in the Northeastern and North Central United States. To clarify the pathogen present at the outset of the epidemic in 2015 and 2016, a phylogenetic study was made of 121 pectolytic soft rot bacteria isolated from symptomatic potato, also included were 27 type strains of Dickeya and Pectobacterium species, and 47 historic reference strains. Phylogenetic trees constructed based on multilocus sequence alignments of concatenated dnaJ, dnaX and gyrB fragments revealed the epidemic isolates to cluster with type strains of D. chrysanthemi, D. dianthicola, D. dadantii, P. atrosepticum, P. brasiliense, P. carotovorum, P. parmentieri, P. polaris, P. punjabense, and P. versatile. Genetic diversity within D. dianthicola strains was low, with one sequence type (ST1) identified in 17 of 19 strains. Pectobacterium parmentieri was more diverse, with ten sequence types detected among 37 of the 2015–2016 strains. This study can aid in monitoring future shifts in potato soft rot pathogens within the U.S. and inform strategies for disease management.

The potential benefits of different cover crops, biological control amendments, and vegetable rotation on soil chemical and biological properties, crop development and yield, and disease development in organic vegetable production, as represented by legume (green bean, Phaseolus vulgaris), cucurbit (yellow summer squash, Cucurbita pepo), and solanaceous (sweet pepper, Capsicum annuum) vegetable crops, were evaluated in a multi-year field trial in Maine, USA. Cover crops evaluated included winter rye (Secale cereale)/hairy vetch (Vicia villosa), mustard (Brassica juncea) green manure, a multi-species mixture (8 crops), and a fallow control. Overall, cover crops had only marginal effects on soil chemical properties, but all cover crops improved biological properties (microbial activity, populations, respiration) compared to fallow soil. The multi-species mixture and rye/vetch cover crops were associated with earlier emergence in beans and squash. All cover crops improved yield in beans and squash by 7–13%, but only the cover crop mixture increased yield for pepper (by 7–11%). Minimal crop diseases were observed throughout these studies, and biological control amendments, which included commercial formulations of Streptomyces, Trichoderma, and Bacillus sp., in general, did not positively affect yield, but reduced powdery mildew on squash and leaf necrosis on beans by 10–28%. The vegetable rotation also had significant effects, with beans yielding 8% higher following squash vs. pepper, squash yielding 15% higher following beans vs. pepper, and pepper yielding 11% higher following beans vs. squash. These results help define specific management practices to improve organic vegetable production and provide useful information and options for growers.

Cropping systems and management practices that improve soil health may greatly enhance crop productivity. Four different potato cropping systems designed to address specific management goals of soil conservation (SC), soil improvement (SI), disease suppression (DS), and a status quo (SQ) standard rotation, along with a non-rotation (PP) control, were evaluated for their effects on potato crop growth, nutrient, and yield characteristics under both irrigated and non-irrigated (rainfed) conditions in field trials in Maine, USA, from 2004 to 2010. Both cropping system and irrigation significantly (p < 0.05) affected most potato crop parameters associated with growth and yield. All rotations increased tuber yield relative to the non-rotation PP control, and the SI system, which included yearly compost amendments, resulted in overall higher yields and a higher percentage of large-size tubers than all other systems with no irrigation (increases of 14 to 90%). DS, which contained disease-suppressive green manures and cover crops, produced the highest yields overall under irrigation (increases of 11 to 35%). Irrigation increased tuber yields in all cropping systems except SI (average increase of 27–37%). SI also resulted in significant increases in leaf area duration and chlorophyll content (as indicators of photosynthetic potential) and root and shoot biomass relative to other cropping systems, particularly under non-irrigated conditions. SI also resulted in higher shoot and tuber tissue concentrations of N, P, and K, but not most micronutrients. Overall, cropping systems that incorporate management practices such as increased rotation length and the use of cover crops, green manures, reduced tillage, and particularly, organic amendments, can substantially improve potato crop growth and yield. Irrigation also substantially increased growth and yield under normal field conditions in Maine, but SI, with its large organic amendments, was essentially a substitute for irrigation, producing comparable results without irrigation.

An outbreak of blackleg and soft rot of potato, caused primarily by the bacterial pathogen

Soil health is essential for agricultural sustainability and environmental quality yet may be degraded by intensive cropping practices. Improved cropping systems and management practices may greatly enhance soil properties associated with soil heath. Four different potato cropping systems, designed to address specific management goals of soil conservation (SC), soil improvement (SI), disease suppression (DS), and a status quo standard rotation (SQ), along with a non-rotation (PP) control, were evaluated for their effects on soil physical, chemical, and biological properties in field trials in Maine, USA. The purpose of the study was to determine how and to what extent these different cropping system approaches and practices would affect soil properties. Cropping systems were established in 2004 and actively managed through 2010, with potato crops also planted in subsequent years (2011−12) to examine residual effects. Cropping system significantly affected many parameters associated with soil health, with effects generally increasing over time as well as having lasting residual effects. All rotations increased aggregate stability, water availability, microbial biomass C, and total C and N compared to no rotation (PP), and 3-yr systems (SI, SC, DS) increased aggregate stability relative to the 2-yr system (SQ). The 3-yr systems with reduced tillage (SI and SC) also increased water availability and reduced bulk density relative to the other systems. However, the SI system, which included yearly compost amendments, resulted in greater increases in total and particulate organic matter (POM) C and N, active C, microbial biomass C, water availability, CEC, concentrations of P, K, Ca, Mg, and S, and lower bulk density than all other rotations. Cropping systems that incorporate management practices such as increased rotation length and the use of cover crops, green manures, reduced tillage, and, particularly, organic amendments, can improve soil physical, chemical, and biological properties associated with soil health.

Four commercial biocontrol formulations (Bacillus subtilis GB03, Burkholderia ambifaria type Wisconsin isolate J82, Trichoderma virens Gl-21, and Trichoderma harzianum strain T-22), a chemical seed treatment (thiophanate-methyl, mancozeb, and cymoxanil mixture, TMC), and a combination chemical/biological treatment, were compared with no-pathogen and pathogen-treated controls, and monitored in two field seasons in Maine for their effects on the development of Rhizoctonia disease of potato and soil microbial community characteristics. All treatments reduced the incidence and severity of stem canker (37–75% reduction) relative to the pathogen control over both years, with the best control provided by B. subtilis and the combination chemical/biological treatment (TMC/Bamb). Both bacterial treatments (B. subtilis and Bu. ambifaria) reduced severity of black scurf in both years, and T. virens reduced scurf in one year, with reductions of 11–20% relative to the pathogen control. Over both years, the B. subtilis, T. virens, and TMC/Bamb treatments increased total and marketable yield, and Bu. ambifaria increased marketable yield, by 11–15% relative to the pathogen control. Substantial populations of the added fungal agents, but not the bacteria, were detected in bulk soil at the end of the growing season. Biocontrol treatments also significantly (P

Numerous fungi and bacteria, including existing biocontrol strains with known activity against soilborne fungal pathogens as well as isolates collected from the roots and rhizosphere of tomato plants growing in the field, were tested for their efficacy in controlling Fusarium wilt of tomato. Tomato seedlings were treated with the potential biocontrol agents in the greenhouse and transplanted into pathogen-infested field soil. Organisms tested included nonpathogenic strains of Fusarium spp., Trichoderma spp., Gliocladium virens, Pseudomonas fluorescens, Burkholderia cepacia, and others. Specific nonpathogenic isolates of F. oxysporum and F. solani collected from a Fusarium wilt-suppressive soil were the most effective antagonists, providing significant and consistent disease control (50 to 80% reduction of disease incidence) in several repeated tests. These isolates also were equally effective in controlling Fusarium wilt diseases of other crops, including watermelon and muskmelon. Other organisms, including isolates of G. virens, T. hamatum, P. fluorescens, and B. cepacia, also significantly reduced Fusarium wilt compared to disease controls (30 to 65% reduction), but were not as consistently effective as the nonpathogenic Fusarium isolates. Commercially available biocontrol products containing G. virens and T. harzianum (SoilGard and RootShield, respectively) also effectively reduced disease (62 to 68% reduction) when granules were incorporated into potting medium at 0.2% (wt/vol). Several fungal and bacterial isolates collected from the roots and rhizosphere of tomato plants also significantly reduced Fusarium wilt of tomato, but were no more effective than other previously identified biocontrol strains. Combinations of antagonists, including multiple Fusarium isolates, Fusarium with bacteria, and Fusarium with other fungi, also reduced disease, but did not provide significantly better control than the nonpathogenic Fusarium antagonists alone.

Soilborne potato diseases and soil microbial community characteristics were evaluated over 8 years in different potato cropping systems designed to address specific management goals of soil conservation, soil improvement and disease suppression. Results were compared to a standard rotation and non‐rotation control in field trials in Maine. Standard rotation consisted of barley underseeded with red clover, followed by potato (2‐year). Soil‐conserving system (SC) featured an additional year of forage grass and reduced tillage (3‐year, barley/timothy–timothy–potato). Soil‐improving system (SI) added yearly compost amendments to SC, and the disease‐suppressive system (DS) featured crops with known disease‐suppressive capability (3‐year, mustard/rapeseed–sudangrass/rye–potato). Systems were established in 2004, evaluated with and without irrigation, and actively managed until 2010, with potato also planted in 2011 and 2012 to examine residual effects. All rotations reduced soilborne diseases black scurf and common scab, and increased yield after one rotation cycle (3 years), but diseases increased overall after two rotation cycles. DS maintained lower soilborne disease levels than all other rotations, as well as high yields, throughout the study. Cropping system effects became more pronounced after multiple cycles. SI system and irrigation both resulted in higher yields, but also higher levels of soilborne disease. Cropping system and irrigation effects were significant even after systems were no longer maintained. Soil microbial community data showed significant changes associated with cropping system, and differences increased over time. Cropping system strategy had significant and lasting effects on soil microbiology and soilborne diseases, and can be used to effectively enhance potato production.

Potato is an important crop globally and late blight (Phytophthora infestans) often results in severe crop loss. The cost for late blight control can be in excess of $210 million in the United States. We utilised a non-parametric density distribution analysis of local temperature (T) and relative humidity (RH), from 2005 to 2009, to assess and validate sporangia survival potential using survival model and late blight risks during the potato cropping season at Presque Isle, in the northern part of the state of Maine, USA. Modelbased analyses showed that ambient temperatures of 3−30°C and RH values of 45−100% were conducive for sporangia survival. Disease outbreaks and risk periods coincided with a high sporangia survival probability (15−35%). Due to the omission of solar radiation (SR) in the computation of survival potential in previous research, we applied a Cox proportional model to estimate the probability of sporangia survival [i.e. hazard at a specific time H(t)] as a function of baseline hazard (H0) and the influencing parameters. The model is: H(t) = H0(t) × exp(0.067ET + 0.138T + 0.083RH + 0.001SR) where ET is exposure time. The survival model indicated that RH (β = 0.083) and T (β = 0.138) were significant (p < 0.05) factors in sporangia survival in comparison to SR (β = 0.001). The hazard ratio, indicative of sporangia survival risk, varied with the predictors. For the unit increase of T, sporangia survival hazard increased by 1.148 times. The Cox model and sporangia hazard probabilities can be used for short-term disease forecasts based on the risk period most conducive for pathogen survival and targeted fungicide applications for optimum late blight management.

Soil health has been defined as the capacity of soil to function as a vital living system to sustain biological productivity, maintain environmental quality, and promote plant, animal, and human health. Building and maintaining soil health are essential to agricultural sustainability and ecosystem function. Management practices that promote soil health, including the use of crop rotations, cover crops and green manures, organic amendments, and conservation tillage, also have generally positive effects on the management of soilborne diseases through a number of potential mechanisms, including increasing soil microbial biomass, activity, and diversity, resulting in greater biological suppression of pathogens and diseases. However, there also may be particular disease issues associated with some soil health management practices. In this review, research and progress made over the past twenty years regarding soil health, sustainability, and soil health management practices, with an emphasis on their implications for and effects on plant disease and disease management strategies, are summarized.

Late blight, caused by Phytophthora infestans (Mont.) de Bary, is a devastating disease which is found worldwide. In Maine, United States (US), we recorded late blight on potato and tomato during the 2006-2009 cropping seasons. From 2006 to 2008, over 90% of the diseased samples were collected in potato fields from northern and central Aroostook County in Northern Maine, US. Then, in 2009, an unprecedented influx of inoculum on infected tomato transplants shipped to retail garden centers throughout the Northeast US significantly changed the late blight infection patterns. In 2009, 43% of diseased samples obtained were from tomato, and 57% from potato, and disease was found to occur all over the state. Moran’s index and spatial autocorrelation analysis of disease occurrence, geographical locations, host factors, and infection levels from previous years, were not statistically significant (p > 0.05). Therefore, random distributions of late blight incidences were recorded across locations and years. Nearest neighbor analysis revealed that mean spatial distances for late blight occurrence ranged from 1.51 to 71.4 km from 2006 to 2008, and 7.4 to 126.5 km in 2009. The frequency and locations of late blight outbreaks in 2009 were substantially greater than in 2006, 2007, and 2008, as affected by the influx of inoculum and movement of infected tomato seedlings as well as conducive environmental conditions. All were contributing factors for late blight occurrence in Maine. In 2010, few disease samples were collected, indicating that the influx of inoculum in 2009 did not persist to cause widespread disease in 2010. The reduction of inocula sources, fungicide protection of susceptible hosts, and the removal and destruction of infected tomato seedlings and potato cull piles or volunteer plants, can greatly reduce late blight occurrences and improve potato production. These actions should be considered as an integral part of late blight management programmes in regions where late blight commonly occurs

Soilborne potato diseases are persistent problems in potato production. Use of disease-suppressive rotation crops, such as Brassica spp. (mustards, rapeseed) and sudangrass, has shown potential for management of soilborne diseases and enhanced yield in various crop production systems. However, how to best implement these crops into productive potato cropping systems has not yet been determined. In this research, potential disease-suppressive crops were evaluated under four different types of production management (as a cover crop, green manure, harvested crop-residue incorporated, and harvested crop-residue not incorporated) in potato rotation field trials, and their effects on disease, yield, and economic viability determined. Mustard blend, sudangrass, and rapeseed rotations reduced the tuber disease black scurf (by 16–27 %) and increased yield (by 6–11 %) relative to a barley rotation control, but only mustard blend consistently reduced common scab (by 11 %). All rotation crops managed as green manures produced lower disease (by 15–26 %) and higher yields (by 6–13 %) than other management practices. Overall, the combination of mustard blend managed as a green manure was most effective, reducing scurf by 54 % and increasing yield by 25 % relative to a soybean cover crop. The use of mustard or rapeseed as a harvested crop with incorporation provided the best economic return, increasing net income by more than $860/ha relative to the standard barley rotation, but mustard blend grown as a green manure or non-incorporated harvest crop also substantially increased net income ($600 to $780/ha).

Aims Integrating multiple soil and disease manage- ment practices may improve crop productivity and disease control, but potential interactions and limita- tions need to be determined. Methods Three different potential disease-suppressive management practices, including a Brassica napus (rapeseed) green manure rotation crop, conifer-based compost amendment, and three biological control or- ganisms (Trichoderma virens, Bacillus subtilis, and Rhizoctonia solani hypovirulent isolate Rhs1A1) were evaluated alone and in combination at sites with both organic and conventional management histories for their effects on soilborne diseases and tuber yield. Results Rapeseed rotation reduced all observed soil- borne diseases (stem canker, black scurf, common scab, and silver scurf) by 10 to 52 % in at least one year at both sites. Compost amendment had variable effects on tuber diseases, but consistently increased yield (by 9 to 15 %) at both sites. Biocontrol effects on disease varied, though Rhs1A1 decreased black scurf at the conventional site and T. virens reduced multiple diseases at the organic site in at least one year. Combining rapeseed rotation with compost amend- ment both reduced disease and increased yield, where- as biocontrol additions produced only marginal addi- tive effects. Conclusions Use of these treatments alone, and in combination, can be effective at reducing disease and increasing yield under both conventional and organic production practices.

Soilborne potato diseases are persistent problems in potato production and alternative management practices are needed. In this research, biocontrol agents (Bacillus subtilis GB03 and Rhizoctonia solani hypovirulent isolate Rhs1A1) and compost amendments (from different source material), were evaluated alone and in combination, for their potential to reduce soilborne diseases and increase tuber yield over three field seasons in Maine. Both biocontrol organisms reduced multiple soilborne diseases, stem and stolon canker by 20–38 %, black scurf by 30–58 %, and common scab by 10–34 % relative to the nontreated control treatment, and the combination treatment of both biocontrol organisms together provided nominally better control than individual treatments. However, biocontrol treatments had no direct effect on tuber yield. Compost amendments from different sources all increased total and marketable tuber yield substantially (11–37 % and 17–51 %, respectively) relative to nontreated controls. However, except for some reduction of Rhizoctonia canker, compost amendments did not reduce soilborne diseases (black scurf and commons scab) in any year, and resulted in increased levels of common scab in some years (20–45 % increase). The combination compost-biocontrol treatment, although did not perform significantly better than individual component treatments, still provided indications of combined beneficial effects from both component treatments. This research demonstrated the usefulness of these approaches and combinations as additional options for reduction of soilborne diseases and increased tuber yield and can be implemented for enhanced sustainability and productivity in potato production systems.

Potato productivity in the northeastern US has been relatively constant for over 50 years, raising questions about what factors are limiting productivity. Research was initiated in 2004 to identify key constraints to potato productivity by evaluating Status Quo (SQ), Soil Conserving (SC), and Soil Improving (SI) cropping systems under both rainfed and irrigated management, and it was found that addition of compost or irrigation substantially increased yield. In this study, we employed partial budgeting to determine cost differences and their impact on net revenue for these cropping systems. Differences in systems were primarily associated with rotation length, tillage operations, compost and application expenses, and water management practices. When compost (as composted dairy manure) was annually applied at 19 Mg haf-1 and evaluated over the entire 3-year crop rotation cycle, the compost-amended rainfed SI system was more expensive to maintain than the irrigated SC system if compost cost exceeded $3.63 Mg-1. Average marketable yields were used to calculate gross and net revenue for each system. Because average potato yield for the irrigated SQ system (28.4 Mg·ha-1) equaled that in the rainfed SI system (28.3 Mg·ha-1), we were able to compare cost of irrigation versus compost for achieving comparable yield. The compost-amended SI system under rainfed management generated more net revenue from the potato crop than the irrigated SQ system when compost costs were less than $7.42 Mg-1. When compared to the commonly used rainfed SQ system, rainfed SI achieved higher net revenue as long as compost cost was less than $22.95 Mg-1. The rainfed SI system achieved higher net revenue than the irrigated SC system when compost cost was $9.43 Mg-1or less, but generated greater net revenue than the rainfed SC system regardless of compost costs, due to substantially higher yields associated with compost amendment. This investigation demonstrates that compost is a potentially viable substitute to irrigation for potato in the northeastern US; however, such potential is highly dependent on suitable compost sources and application costs.

The use of green manures, which involves the incorporation of fresh plant material, has traditionally been primarily for the purpose of soil enrichment through the addition of plant organic matter and nutrients. However, green manures produce many changes in soil physical, chemical and biological properties, and may also result in suppression of specific plant pathogens and diseases. Green manures increase soil microbial biomass and activity, and cause distinct changes in soil microbial populations that may be partially responsible for suppression of diseases. However, green manures of different crops and cultivars may vary considerably in their activity or efficacy against different pathogens and diseases. In particular, green manures of Brassica and related crops have emerged as most effective for management of multiple plant diseases due to their biofumigation potential, which refers to the suppression of pathogens and disease through the release of volatile toxic breakdown products, as well as other unique effects on soil microbial ecology. Brassica crops and other green manures have been used to control a variety of plant pathogens, including species of Rhizoctonia , Verticillium , Sderotinia , Phythophthora , Pythium , Aphanomyces and Macrophomina , in various crop production systems, such as for the management of multiple soilborne diseases of potato, including black scurf, common scab and Verticillium wilt. Although disease reduction with green manures can be variable and provides only partial control, it is a versatile and readily-implementable additional management strategy that should be used as an important component within a larger integrated disease management program to provide improved sustainable production systems.

This work evaluated the level and nature of water-extractable soil organic matter (WEOM) from a 6-yr potato ( L.) crop rotation field experiment. The content of WEOM was higher in continuous potato soils than in the 2-yr and 3-yr crop rotation soils except for those crop rotation soils with soil improvement management by composted manure. Irrigation increased the level of WEOM in crop rotation soils. Ultraviolet–visible and fluorescence parameters indicated that WEOM in continuous potato soil possessed a high degree of humification and that crop rotation increased the aromatic and low molecular mass portions. In most irrigated soils, WEOM contained less aromatic but higher humified components. Characterization of the WEOM samples with crop rotation and irrigation suggests that these management practices stimulate the decomposition of the humic fraction in soil organic matter pools, implying healthier soil conditions with these management practices than with continuous potato growth.

Maine consistently ranks in the top ten potato (Solanum tuberosum L.) production areas though yields are substantially lower than the mid- and western USA. Geospatial frameworks help resolve patterns and trends in production environments (at multiple scales) that may enable improvements in adaptive management strategies which enhance yield, increase whole-farm profitability, and foster sustainable land use. Results from geospatial integration of remotely-sensed cropland (2008–2010) and soil datasets for Maine indicate an estimated 61,900 ha in potato production with 62 % and 27 % on prime farmland (PF) and farmland of statewide importance (FSI), respectively. Geospatial analyses of other agri-environmental indicators indicate close to 85 % of these potato production soils are classified as either “potentially highly erodible” (PHEL) or “highly erodible” (HEL). Therefore, at least 52,300 ha require the highest standards in soil conservation practices. Crop rotation patterns for potato, derived from the time-series geo-referenced datasets, help resolve actual cropping practices and facilitated evaluation of the benefits and economic impacts for select alternate crops.

Cultural practices such as organic amendments, rotations, and use of biological control organisms are regularly investigated for their effects on controlling plant diseases but their effects on soil microbial populations are often unexplored. In this study, three different sustainable disease management practices, use of compost amendment, biocontrol organisms, and a potentially disease-suppressive rotation, were established in potato field trials at two sites under different management regimes and histories, and evaluated over three potato cropping seasons for their effects on soil microbial communities. Specific management factors assessed included the presence or absence of a conifer-based compost amendment, addition of one of three different biocontrol organisms (Trichoderma virens, Bacillus subtilis, and Rhizoctonia solani isolate Rhs1A1), and a Brassica napus (rapeseed) green manure rotation crop preceding potato, and treatments were assessed in all factorial combinations. The two farm sites represented organic and conventional potato production practices in Aroostook County, Maine. Compost amendment and rapeseed rotation had the greatest impacts on soil microbial communities, with both treatments increasing total populations of culturable bacteria at both sites over the course of the study, as well as causing detectable shifts in soil microbial community characteristics as determined by sole carbon-source substrate utilization and fatty acid methyl ester (FAME) profiles. Compost amendment generally led to increased utilization of complex substrates and increased levels of Gram-positive bacteria and fungi, and compost effects were more pronounced at the conventional site. Rapeseed rotation often resulted in somewhat different effects at the two different sites. Consistent overall effects were observed with the biocontrol amendments Rhs1A1 and T. virens, including increased microbial activity and bacterial populations. Combined effects of multiple treatments were greater than those of individual treatments and were generally additive. These results indicate that each treatment factor had significant and specific effects on soil microbial communities, and that combined effects tended to be complementary, suggesting the potential of combining multiple compatible management practices and their associated changes in soil microbial communities.

Phosphorus (P) fertilization is frequently needed for profitable crop production. Modified Morgan P (MMP) is a soil test P used to estimate plant available P in soils. The critical values of MMP for P fertilization and maintenance recommendations are based on the P concentrations measured by a common colorimetric molybdenum blue method although other P quantification methods have also been used for MMP measurements. In this study, we collected 120 surface soil samples of Caribou Sandy loam under potato cultivation or its rotation crops from Maine, USA, and 72 soil samples of Cecil sandy loam with cotton/corn crops under conventional tillage and no-till management with chemical and poultry litter fertilization in Georgia, USA. The MMP levels in all 192 dry samples were greater when they were measured by an inductively coupled plasma (ICP)-based method, compared to the corresponding data produced from colorimetry. Our results show the two sets of data were positively and significantly correlated (r = 0.93, P –1 with standard deviation of 12.9, compared to the average of colorimetric MMP level of 14.9 mg P kg–1 with standard deviation of 8.8. Based on the observations in this work, both colorimetric and ICP-based methods can be used for P fertilizer recommendation, but a conversion factor should be applied for ICP data as the current recommendation systems are based on colorimetric M&R data.

The ability of disease-suppressive rotation crops to reduce potato disease problems and increase crop productivity in a field with prior severe Verticillium wilt, as well as the potential influence of previous cropping history on disease suppression, was evaluated over three field seasons in Maine. Disease-suppressive rotations consisted of: (i) a high-glucosinolate mustard blend (‘Caliente 119’) as a mixture of white mustard (Sinapis alba) and oriental mustard (Brassica juncea) with known biofumigation potential and (ii) a sorghum-sudangrass hybrid. Each were grown as single-season green manures followed by a subsequent potato crop. These rotations were compared with a standard barley rotation and a barley rotation followed by chemical fumigation with metam sodium as controls. Both green manure rotations significantly reduced (average reductions of 25 and 18%, respectively) Verticillium wilt in the subsequent potato crop compared with the standard barley control but were not as effective as chemical fumigation (35% reduction). The mustard blend also reduced other soilborne diseases (black scurf and common scab) better than all other rotations. Mustard blend and chemical fumigation treatments increased tuber yield relative to the barley control by 12 and 18%, respectively. However, by the second rotation cycle, disease levels were high in all rotations, and only chemical fumigation resulted in substantial disease reduction (35%). Rotations also had significant effects on soil microbiology, including soil bacterial and fungal populations and microbial community characteristics based on fatty acid profiles. However, only chemical fumigation significantly reduced soil populations of Verticillium spp. and increased general soil microbial activity. Previous cropping history did not significantly affect disease reduction, tuber yield, or soil microbial communities. This research indicates the potential for using disease-suppressive rotations for managing Verticillium wilt and other soilborne diseases but also indicates that multiple years of disease-suppressive crops may be needed to substantially reduce disease in heavily infested fields.

Four different potato cropping systems, designed to address specific management goals of soil conservation, soil improvement, disease suppression, and a status quo standard rotation control, were evaluated for their effects on soilborne diseases of potato and soil microbial community characteristics. The status quo system (SQ) consisted of barley underseeded with red clover followed by potato (2-year). The soil-conserving system (SC) featured an additional year of forage grass and reduced tillage (3-year, barley/timothy–timothy–potato). The soil-improving system (SI) added yearly compost amendments to the SC rotation, and the disease-suppressive system (DS) featured diverse crops with known disease-suppressive capability (3-year, mustard/rapeseed–sudangrass/rye–potato). Each system was also compared with a continuous potato control (PP) and evaluated under both irrigated and nonirrigated conditions. Data collected over three potato seasons following full rotation cycles demonstrated that all rotations reduced stem canker (10 to 50%) relative to PP. The SQ, SC, and DS systems reduced black scurf (18 to 58%) relative to PP; SI reduced scurf under nonirrigated but not irrigated conditions; and scurf was lower in DS than all other systems. The SQ, SC, and DS systems also reduced common scab (15 to 45%), and scab was lower in DS than all other systems. Irrigation increased black scurf and common scab but also resulted in higher yields for most rotations. SI produced the highest yields under nonirrigated conditions, and DS produced high yields and low disease under both irrigation regimes. Each cropping system resulted in distinctive changes in soil microbial community characteristics as represented by microbial populations, substrate utilization, and fatty acid methyl-ester (FAME) profiles. SI tended to increase soil moisture, microbial populations, and activity, as well result in higher proportions of monounsaturated FAMEs and the FAME biomarker for mycorrhizae (16:1 ω6c) relative to most other rotations. DS resulted in moderate microbial populations and activity but higher substrate richness and diversity in substrate utilization profiles. DS also resulted in relatively higher proportions of FAME biomarkers for fungi (18:2 ω6c), actinomycetes, and gram-positive bacteria than most other systems, whereas PP resulted in the lowest microbial populations and activity; substrate richness and diversity; proportions of monounsaturated and polyunsaturated FAME classes; and fungal, mycorrhizae, and actinomycete FAME biomarkers of all cropping systems. Overall, soil water, soil quality, and soilborne diseases were all important factors affecting productivity, and cropping systems addressing these constraints improved production. Cropping system approaches will need to balance these factors to achieve sustainable production and disease management.

Soilborne diseases are persistent problems in potato production, resulting in reductions in tuber quality and yield. Brassica rotation crops may reduce soilborne potato diseases, but how to best utilize Brassica crops in potato cropping systems has not been established. In this research, two two-year trials were established at three different sites with histories of soilborne diseases, and up to six different Brassica crops (canola, winter rapeseed, yellow and brown condiment mustards, oriental mustard, oilseed radish, and a mustard blend) and standard rotation crops (ryegrass and buckwheat) were evaluated as rotation and green manure crops. Tuber yield did not vary substantially among the rotation crops, but rotation treatments significantly affected incidence and severity of soilborne diseases at all sites. However, results were variable among sites and years. Perennial ryegrass and mustard blend rotations reduced powdery scab disease by 31&ndash, 55% relative to other rotations in the only field where powdery scab was a serious problem. Mustard blend, ryegrass, and other Brassica rotations also reduced common scab, silver scurf, and black scurf at various sites, but not consistently at all sites. At one site, mustard blend and barley/ryegrass rotations reduced black scurf (by 21&ndash, 58%) and common scab (by 13&ndash, 34%) relative to no rotation. Overall, disease control was not correlated with biofumigation potential or rotation crop biomass production. Although both Brassica and non-Brassica rotations provided disease reduction in potato cropping systems, no single rotation crop performed consistently better than several others.

Crop and soil management may modify canopy and belowground microclimate, but their effects on potential development and control of early blight are not well documented. Several management systems (Status Quo, Soil Conserving, Soil Improving (SI), Disease Suppressive, and Continuous Potato) were evaluated for their effects on early blight potential under irrigated and rainfed conditions. In 2006 and 2007, microclimatic data at the canopy level were recorded with a data logger. Early blight incidence and severity was determined by visually assessing symptoms. Disease incidence and lesion numbers varied among cropping systems and between years. Disease incidence ranged from 31 to 64% (2006) and 12 to 43% (2007), and was significantly higher with the Continuous Potato system than with Disease Suppressive, Status Quo, Soil Conserving, and SI systems. The relationships of incidence and disease severity with microclimate varied and were mostly non-significant, suggesting that the chosen variables were not reflective of pathogen development. Incidence was significantly associated with cropping systems. Disease prediction based on the Tom-Cast model was not correlated with observed disease levels. This research demonstrated that early blight disease is enhanced through continuous potato production.

Delayed tillage and the inclusion of cover crops can substantially reduce erosion in intensively tilled potato systems. Both of these practices can potentially impact potato (Solanum tuberosum L.) yield and quality via changes in soil temperature and soil water status, and suppression or enhancement of soil-borne diseases. Research was conducted over six rotation cycles at two Maine locations to evaluate the effects of timing of primary tillage (fall vs. spring) and cover crop [none, red clover (Trifolium pratense L.), ryegrass (Lolium perenne L.), or winter rapeseed (Brassica napus L.)] on grain yield, ground cover, and tuber yield and quality within the context of 2-year barley (Hordeum vulgare L.)]–potato rotations. Delaying primary tillage until spring, immediately before planting potato, resulted in higher soil water content early in the growing season (before or immediately after planting) in some rotation cycles, and also provided nearly complete ground cover during potentially erosive periods in fall and early spring. The inclusion of clover or ryegrass cover crops had small, positive effects on the proportion of the soil surface covered by crop residue (determined by the line intercept method) in both tillage systems. A significant tillage effect on total tuber yield was seen in only one rotation cycle, when delaying tillage until spring reduced yield by about 12%. Cover crop treatments had no effect on total tuber yield, and neither tillage or cover crop affected the proportion of marketable tubers. Tillage did not affect black scurf (Rhizoctonia solani Kuhn) and common scab [Streptomyces scabiei (Thaxter) Lambert & Loria], which were significantly reduced by red clover in some rotation cycles. This research shows that conservation practices can be implemented, including delaying primary tillage until spring and including underseeded cover crops during the grain phase of the rotation, while maintaining potato yield.

Various biological amendments, including commercial biocontrol agents, microbial inoculants, mycorrhizae, and an aerobic compost tea (ACT), were evaluated, alone and in conjunction with different crop rotations, for their efficacy in introducing beneficial microorganisms, affecting soil microbial community characteristics (SMCC), and reducing soilborne diseases of potato in greenhouse and field trials in Maine. Most amendments successfully delivered microorganisms into the soil, altering microbial populations and activity in accordance with the particular organisms added, and significantly altering SMCC (as determined by FAME analysis) to various degrees from 2 to 24 weeks. Amendment effects were greatest early on (2 weeks after amendment), but effects associated with crop treatment became more dominant at subsequent assessments (10 and 24 weeks after amendment). In field trials, effects on microbial characteristics, soilborne diseases and tuber yield were variable, with some microbial inoculants and a biostimulant producing no significant effects, whereas arbuscular mycorrhizae, reduced stem canker and black scurf by 17–28%. When used in three different 2 yr crop rotations (barley/ryegrass, barley/clover, and potato, all followed by potato), biological amendments reduced soilborne disease and improved yield in some rotations, but not others. Soil-applied ACT and the combination of ACT with a mixture of beneficial microorganisms (Mix) reduced stem canker, black scurf, and common scab on tubers by 18–33% and increased yield 20–23% in the barley/ryegrass rotation, but not in the other rotations. Mix also reduced disease (20–32%) in the barley/clover rotation only. None of the amendments significantly reduced disease in continuous potato plots. Both crop rotation and amendment treatments significantly affected SMCC, but rotation effects were more dominant. These results indicate that certain rotations were better able to support the added beneficial organisms from amendments and enable more effective biological control, and also that favorable crop rotations may be more effective than amendments in manipulating or altering SMCC. Establishment and persistence of amendment effects may depend on many factors, but an effective and supportive crop rotation is apparently important.

Soil borne diseases can greatly reduce marketable yields and are a major concern to Maine potato (Solanum tuberosum L.) producers. Control of these organisms is difficult as they can persist in the soil for several years and symptoms typically worsen each year. Depending on the specific pathogen, different mechanisms for moderating soil borne disease can be employed, such as breaking the hostpathogen cycle, stimulating beneficial microbial activity, and direct inhibition of the pathogens. Current research at the USDA-ARS New England Plant, Soil, and Water Laboratory is investigating the effect of rotation crops and rotation sequences on the incidence and severity of soil-borne diseases in the following potato crop. These results (incidence, severity, and potato yield) are incorporated into an economic simulation model to determine the impact of rotations on profitability, level of income risk, and probability of economic loss for different rotation sequences and rotation lengths. The results show that several rotation sequences can increase profitability and reduce economic risk when compared to continuous potato or to the standard barley-potato rotations.

Brassica crops used in crop rotations and as green manures have been associated with reductions in soilborne pests and pathogens. These reductions have been attributed to the production of volatile sulfur compounds through a process known as biofumigation, and to changes in soil microbial community structure. In this study, selected Brassica crops, including canola, rapeseed, radish, turnip, yellow mustard, and Indian mustard, were evaluated for control of various soilborne potato pathogens and diseases in culture, in greenhouse trials, and in field trials on commercial potato farms. In in vitro assays, volatiles released from chopped leaf material of Brassica crops and barley inhibited growth of a variety of soilborne pathogens of potato, including Rhizoctonia solani , Phytophthora erythroseptica , Pythium ultimum , Sclerotinia sclerotiorum , and Fusarium sambucinam , with Indian mustard resulting in nearly complete inhibition (80–100%). All Brassica crops and barley reduced inoculum levels of R. solani (20–56% reduction) in greenhouse tests, and radish, rapeseed, and Indian mustard reduced subsequent potato seedling disease by 40–83%. In an on-farm field trial at a site with a substantial powdery scab problem, Indian mustard, rapeseed, canola, and ryegrass grown as green manure rotation crops reduced powdery scab in the subsequent potato crop by 15–40%, and canola and rapeseed reduced black scurf by 70–80% relative to a standard oats rotation. At another field site where common scab was the primary disease problem, an Indian mustard green manure reduced common scab by 25%, and rapeseed, yellow mustard, and ‘Lemtal’ ryegrass also reduced black scurf relative to a standard ryegrass rotation. Disease reductions were not always associated with higher glucosinolate-producing crops, and were also observed with non- Brassica crops (barley and ryegrass), indicating other mechanisms and interactions are important, particularly for control of R. solani . Overall, Indian mustard was most effective for reducing powdery scab and common scab diseases, whereas rapeseed and canola were most effective in reducing Rhizoctonia diseases. These results indicate that Brassica crops have potential for use as green manures for the control of multiple soilborne disease problems.

Understanding the impacts of manure amendments on soil microorganisms can provide valuable insight into nutrient availability and potential crop and environmental effects. Soil microbial community characteristics, including microbial populations and activity, substrate utilization (SU) profiles, and fatty acid methyl ester (FAME) profiles, were compared in three soils amended or not amended with dairy or swine manure at two temperatures (18 and 25°C) and two soil water regimes (constant and fluctuating) in laboratory incubation assays. Soil type was the dominant factor determining microbial community characteristics, resulting in distinct differences among all three soil types and some differing effects of manure amendments. Both dairy and swine manures generally increased bacterial populations, substrate diversity, and FAME biomarkers for gram-negative organisms in all soils. Microbial activity was increased by both manures in an Illinois soil but only by dairy manure in two Maine soils. Dairy manure had greater effects than swine manure on SU and FAME parameters such as increased activity, utilization of carbohydrates and amino acids, substrate richness and diversity, and fungal FAME biomarkers. Temperature and water regime effects were relatively minor compared with soil type and amendment, but both significantly affected some microbial responses to manure amendments. Overall, microbial characteristics were more highly correlated with soil physical factors and soil and amendment C content than with N levels. These results indicate the importance of soil type, developmental history, and environmental factors on microbial community characteristics, which may effect nutrient availability from manure amendments and should be considered in amendment evaluations.

Twenty-eight potential biocontrol organisms were tested for efficacy against Rhizoctonia solani on potato in a series of greenhouse trials. Organisms tested consisted of field isolates of Paenibacillus polymyxa, Pseudomonas fluorescens, Penicillium sp., Trichoderma sp., and Rhizoctonia zeae; known biocontrol isolates including Laetisaria arvalis, Verticillium biguttatum, Cladorrhinum foecundissimum, and Stilbella aciculosa; and commercial products of Bacillus subtilis (Kodiak), Trichoderma virens (SoilGard), and T. harzianum (RootShield). Different formulations and rates of several fungal isolates and the efficacy of combinations of effective antagonists were also investigated. None of the treatments, including a chemical control (azoxystrobin), effectively controlled stem canker and black scurf in all trials. However, B. subtilis GB03, R. zeae LRNE17E, S. aciculosa 112-B, and the chemical control were most effective in reducing stem canker severity (40–49% reduction) relative to the infested controls over all trials. L. arvalis ZH-1, R. zeae LRNE17E, and the chemical control reduced black scurf severity 54–60% relative to the infested control. Other treatments also significantly reduced stem canker and black scurf, however they were slightly less effective. Biocontrol amendment rate was not correlated with disease control, although the higher rates usually provided the best control. One combination of biocontrol organisms, B. subtilis and T. virens, demonstrated somewhat better control of stem canker than each organism alone, suggesting that this approach may provide improved biocontrol efficacy.

The effects of 11 different 2- and 3-yr potato crop rotations on soil microbial communities were characterized over three field seasons using several techniques. Assessments included microbial populations determined by soil dilution plate counts on various general and selective culture media, microbial activity by fluorescein diacetate (FDA) hydrolysis, single carbon source substrate utilization (SU) profiles, and fatty acid methyl ester (FAME) profiles. Potato rotation crops evaluated in research plots at Newport, ME, included barley/clover, canola, green bean, millet, soybean, sweet corn, and a continuous potato control. Soil populations of culturable bacteria and overall microbial activity tended to be highest following barley, canola, and sweet corn rotations, and lowest with continuous potato. Differences among rotations were less apparent during the potato phase of the rotations. Populations of actinomycetes and fluorescent pseudomonads tended to be greater in barley rotations than in most other rotations. SU profiles derived from BIOLOG GN2 plates indicated that certain rotations, including barley, canola, and sweet corn tended to have higher overall microbial activity, and barley and sweet corn rotations averaged higher substrate richness and diversity. Soybean and potato rotations tended to have lower substrate richness and diversity. Principal component analyses of SU data revealed differences among rotation soil communities in their utilization of individual carbon sources and substrate guilds, including carbohydrates, carboxylic acids, amines/amides, and amino acids. Analyses of soil FAME profiles demonstrated distinct differences among all the rotation soils in their relative composition of fatty acids, indicating differences in their microbial community structure. Fatty acids most responsible for differentiation among rotation soils included 16:1 ω5c, 16:1 ω7c, 18:2 ω6c, 18:1 ω9c, 12:0, and 13:0 anteiso, with 16:1 ω5c being the single greatest determinant. Overall, monounsaturated fatty acids, particularly 16:1 ω5c, were most prevalent in sweet corn rotations and polyunsaturates were highest in barley and millet rotations. Straight chain saturated fatty acids comprised the greatest proportion of fatty acids in soils under continuous potato. FAME biomarkers for microorganism groups indicated barley and millet rotations had the highest ratio of fungi to bacteria, and soybean and continuous potato had the lowest ratio. This research has demonstrated that different crop rotations have distinctive effects on soil microbial communities that are detectable using a variety of techniques. Further studies will identify more specific changes associated with particular rotations and relate these changes to potential effects on disease management, crop health, and crop productivity.

The utility of fatty acid profiles for characterization and differentiation of isolates of P. infestans was investigated. Two libraries of fatty acid methyl ester (FAME) profiles (one representing average genotype characteristics and one representing individual isolate characteristics) were established from at least eight replicate samples of each of 25 different isolates of P. infestans, including representative isolates of US-1, US-6, US-7, US-8, US-11, US-14, and US-17 genotypes. These libraries then were used to identify and characterize additional unknown isolates. Fatty acid profile characteristics also were compared with cultural and genetic characteristics of the isolates. FAME profiles for isolates of P. infestans were consistent over multiple extractions and distinctly different from profiles for isolates of other Phytophthora species, such as P. capsici and P. erythroseptica, as well as isolates of Pythium spp. and various other fungal groups. Overall, profiles from different isolates within the same genotype shared similar characteristics, although there was overlap among some genotypes. Incubation temperature, growth medium, and prolonged storage on agar media all significantly affected fatty acid profiles; however, when these conditions were kept constant, profiles were distinct, consistent, and reproducible over time. Isolate profiles were sufficiently specific that individual isolates could be distinctly identified by FAME profiles. In general, individual isolate characteristics were more determinant than genotype group characteristics, although genotype could be determined for most isolates tested. Results indicated that FAME profiles can be an additional tool useful for characterizing isolates and populations of P. infestans.