C. Wayne Honeycutt

Effects of Different 3-Year Cropping Systems on Soil Microbial Communities and Rhizoctonia Diseases of Potato

ABSTRACT Eight different 3-year cropping systems, consisting of soybean-canola, soybean-barley, sweet corn-canola, sweet corn-soybean, green bean-sweet corn, canola-sweet corn, barley-clover, and continuous potato (non-rotation control) followed by potato as the third crop in all systems, were established in replicated field plots with two rotation entry points in Presque Isle, ME, in 1998. Cropping system effects on soil microbial community characteristics based on culturable soil microbial populations, single carbon source substrate utilization (SU) profiles, and whole-soil fatty acid methyl ester (FAME) profiles were evaluated in association with the development of soilborne diseases of potato in the 2000 and 2001 field seasons. Soil populations of culturable bacteria and overall microbial activity were highest following barley, canola, and sweet corn crops, and lowest following continuous potato. The SU profiles derived from BIOLOG ECO plates indicated higher substrate richness and diversity and greater utilization of certain carbohydrates, carboxylic acids, and amino acids associated with barley, canola, and some sweet corn rotations, indicating distinct differences in functional attributes of microbial communities among cropping systems. Soil FAME profiles also demonstrated distinct differences among cropping systems in their relative composition of fatty acid types and classes, representing structural attributes of microbial communities. Fatty acids most responsible for differentiation among cropping systems included 12:0, 16:1 omega5c, 16:1 omega7c, 18:1 omega9c, and 18:2omega6c. Based on FAME biomarkers, barley rotations resulted in higher fungi-to-bacteria ratios, sweet corn resulted in greater mycorrhizae populations, and continuous potato produced the lowest amounts of these and other biomarker traits. Incidence and severity of stem and stolon canker and black scurf of potato, caused by Rhizoctonia solani, were reduced for most rotations relative to the continuous potato control. Potato crops following canola, barley, or sweet corn provided the lowest levels of Rhizoctonia disease and best tuber quality, whereas potato crops following clover or soybean resulted in disease problems in some years. Both rotation crop and cropping sequence were important in shaping the microbial characteristics, soilborne disease, and tuber qualities. Several microbial parameters, including microbial populations and SU and FAME profile characteristics, were correlated with potato disease or yield measurements in one or both harvest years. In this study, we have demonstrated distinctive effects of specific rotation crops and cropping sequences on microbial communities and have begun to relate the implications of these changes to crop health and productivity.

Ultrahigh Resolution Mass Spectrometry and Indicator Species Analysis to Identify Marker Components of Soil- and Plant Biomass-Derived Organic Matter Fractions

The chemical properties of organic matter affect important soil processes such as speciation, solubilization, and transport of plant nutrients and metals. This work uses ultrahigh resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry to determine the molecular composition of three organic matter fractions of soils and aqueous extracts of crop biomass. Comparison of the van Krevelen plots allowed tracking the changes in organic matter with increasing humification. Aqueous plant biomass extracts contain a diverse mixture of lipids, proteins, and lignins. Soil aqueous extracts were marked by increases in lignin and carbohydrate components and decrease in the protein component as compared to the plant extract. Refractory humic acid fractions were marked by decrease in the lignin component and increases in the lipid and condensed aromatic components. The multivariate indicator species analysis was used to identify marker components of the four organic matter types investigated. The plant extract group had 772 marker components compared to 237 for soil aqueous extract, 92 for mobile humic acid, and 418 for calcium humic acid. This study demonstrates that ultrahigh resolution mass spectrometry and multivariate methods can be used to identify marker components to gain a molecular-scale description and understanding of C dynamics.

Rotation and Cover Crop Effects on Soilborne Potato Diseases, Tuber Yield, and Soil Microbial Communities

Seven different 2-year rotations, consisting of barley/clover, canola, green bean, millet/rapeseed, soybean, sweet corn, and potato, all followed by potato, were assessed over 10 years (1997-2006) in a long-term cropping system trial for their effects on the development of soilborne potato diseases, tuber yield, and soil microbial communities. These same rotations were also assessed with and without the addition of a fall cover crop of no-tilled winter rye (except for barley/clover, for which underseeded ryegrass was substituted for clover) over a 4-year period. Canola and rapeseed rotations consistently reduced the severity of Rhizoctonia canker, black scurf, and common scab (18 to 38% reduction), and canola rotations resulted in higher tuber yields than continuous potato or barley/clover (6.8 to 8.2% higher). Addition of the winter rye cover crop further reduced black scurf and common scab (average 12.5 and 7.2% reduction, respectively) across all rotations. The combined effect of a canola or rapeseed rotation and winter rye cover crop reduced disease severity by 35 to 41% for black scurf and 20 to 33% for common scab relative to continuous potato with no cover crop. Verticillium wilt became a prominent disease problem only after four full rotation cycles, with high disease levels in all plots; however, incidence was lowest in barley rotations. Barley/clover and rapeseed rotations resulted in the highest soil bacterial populations and microbial activity, and all rotations had distinct effects on soil microbial community characteristics. Addition of a cover crop also resulted in increases in bacterial populations and microbial activity and had significant effects on soil microbial characteristics, in addition to slightly improving tuber yield (4% increase). Thus, in addition to positive effects in reducing erosion and improving soil quality, effective crop rotations in conjunction with planting cover crops can provide improved control of soilborne diseases. However, this study also demonstrated limitations with 2-year rotations in general, because all rotations resulted in increasing levels of common scab and Verticillium wilt over time.

Effect of swine and dairy manure amendments on microbial communities in three soils as influenced by environmental conditions

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.

Effects of Different Potato Cropping System Approaches and Water Management on Soilborne Diseases and Soil Microbial Communities

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.

Characterization of plant-derived water extractable organic matter by multiple spectroscopic techniques.

Water extractable organic matter (WEOM) derived from fresh- or early-stage decomposing soil amendment materials may play an important role in the process of organic matter accumulation. In this study, eight WEOM samples extracted with a 40:1 (v/w) water to sample ratio from alfalfa (Medicago sativa L.), corn (Zea mays L.), crimson clover (Trifolium incarnatum L.), hairy vetch (Vicia villosa L.), lupin (Lupinus albus L.), soybean (Glycine max L. Merr.), wheat (Triticum aestivum L.), and dairy manure were investigated using ultraviolet (UV)–visible, Fourier transform infrared (FT-IR), solution 31P nuclear magnetic resonance (NMR), and solid state 13C NMR spectroscopies. UV–visible and FT-IR spectra of the plant-derived WEOM samples were typical for natural organic matter, but possessed less humic-like characteristics than dairy manure-derived WEOM. Solution 31P NMR spectra indicated that WEOM samples extracted from alfalfa, corn, and soybean shoots contained both orthophosphate and monoester P. Of the monoester P in WEOM from soybean shoot, 70% was phytate P. WEOM from crimson clover, hairy vetch, lupin, and wheat shoots contained orthophosphate only. The solid-state 13C NMR spectra of the seven plant-derived WEOM samples indicated that they all were primarily composed of sugars, amino acids or peptides, and low molecular mass carboxylic acids. Carbohydrates were dominant components with very few aromatics present in these samples. In addition, WEOM from crimson clover and lupin, but not other three leguminous plant WEOM samples, contained significant asparagine. On the other hand, WEOM from corn and wheat contained less amino acids or peptides. The spectra of WEOM of dairy manure revealed the presence of significant amounts of nonprotonated carbons and lignin residues, suggesting humification of the manure-derived WEOM. Significant carbohydrates as well as aromatics were present in this WEOM. The P and C bonding information for these WEOM samples may be useful for understanding the effects of WEOM on soil nutrient availability to plants.

Phosphorus forms in conventional and organic dairy manure identified by solution and solid state p-31 NMR spectroscopy.

Organic dairy production has increased rapidly in recent years. Organic dairy cows (Bos taurus) generally eat different diets than their conventional counterparts. Although these differences could impact availability, utilization, and cycling of manure nutrients, little such information is available to aid organic dairy farmers in making nutrient and manure management decisions. In this study, we comparatively characterized P in organic and conventional dairy manure using solution and solid state (31)P NMR spectroscopic techniques. Phosphorus in both types of dairy manure was extracted with water, Na acetate buffer (100 mmol L(-1), pH 5.0) plus 20 mg Na dithionite mL(-1), or 0.025 mol L(-1) NaOH with 50 mmolL(-1) EDTA. Solution NMR analysis revealed that organic dairy manure contained about 10% more inorganic phosphate than conventional dairy manure. Whereas organic dairy manure did contain slightly more phytate P, it contained 30 to 50% less monoester P than conventional dairy manure. Solid state NMR spectroscopy revealed that mono-, di-, and trivalent metal P species with different stabilities were present in the two dairy manures. Conventional dairy manure contained relatively higher contents of soluble inorganic P species and stable metal phytate species. In contrast, organic dairy manure contained more Ca and Mg species of P. These results indicate that P transformation rates and quantities should be expected to differ between organic and conventional dairy manures.

Evaluation Of Soil Phosphorus Transformations By Sequential Fractionation And Phosphatase Hydrolysis

Increased understanding is needed on the interconversion among P species when manure and fertilizer are added to soils. To assess changes in P species affected by manure and fertilizer addition, a sandy loam (no established soil series designation; coarseloamy, mixed, frigid, Typic Haplorthod) and a Lamoine silt loam (fine, illitic, nonacid, frigid Aeric Epiaquept) with no P added, with fertilizer P, and with dairy manures were incubated at 22 °C for up to 108 days. Sequential fractionation with H2O, 0.5 M NaHCO3, and 0.1 M NaOH and phosphatase hydrolysis were used to monitor changes in inorganic P and enzymatically hydrolyzable and nonhydrolyzable organic P during the incubation period. Similar patterns of P dynamics were observed in the two soils. Added inorganic P from either chemical fertilizer or animal manure amendments was found mainly in the NaHCO3 and NaOH fractions. Changes in H2O, NaHCO3, and NaOH-extractable P were similar for P fertilizer–amended soils and unamended soils, indicating that soil properties played a major role in controlling P dynamics. In the H2O fraction, inorganic P attained a low and stable level after an initial rapid decrease. Concentrations of P species in other fractions fluctuated during the incubation period. Furthermore, the fluctuations were observed in complementary patterns between inorganic P in the NaHCO3 and NaOH fractions as well as between labile P (inorganic and hydrolyzable organic) and nonhydrolyzable organic P in the NaOH fraction. These complementary fluctuations implied an interchange of P species during incubation. This interchange could be an important mechanism for maintaining balance between labile and immobile P in soils. Further detailed examination of the patterns of interchange among P fractions in soils may provide more accurate prediction of soil P bioavailability, thus improving soil P management.

Phosphorus Distribution in Sequentially Extracted Fractions of Biosolids, Poultry Litter, and Granulated Products

Land application of biosolids and poultry litter can benefit crop production by providing phosphorus (P) and other nutrients and organic matter. However, the bioavailability of applied P in those waste materials is directly dependent on the presence of specific P forms. In this study, we comparatively examined the P forms in biosolids and broiler litter by sequential fractionation (i.e., H2O, 0.5 M NaHCO3, 0.1 M NaOH, and 1 M HCl fractions) coupled with enzymatic hydrolysis. Extractable P in broiler litter was found in the order of HCl > H2O > NaOH > NaHCO3. Biosolid P was found in the four fractions in the following order: HCl > NaOH > NaHCO3 > H2O. Correlation analysis indicated that P was coextracted with Ca, Mn, Zn, Fe, and Al, but not Mg. Whereas most P was Ca bound in broiler litter, Al, Mn, and Zn played more important roles in metal P species in biosolids. The relative abundance of P species was determined to be inorganic P > hydrolyzable organic P > nonhydrolyzable organic P in each fraction. Compared with the P levels in the samples stored in a freezer, storage of the broiler litter sample at room temperature transformed part of the phytate P in the HCl fraction to other forms, resulting in more labile P in the H2O fraction. Granulated products of poultry litter and biosolid could be used as off-farm nutrient sources. Data in this work show that granulation transformed moderate NaHCO3- and NaOH-extractable P bilaterally to labile water-soluble P and stable HCl-extractable P in the granulated poultry litter but did not remarkably change the distribution of H2O-, NaHCO3-, and NaOH-extractable P in granulated products containing both poultry litter and biosolids.

The effect of cropping systems and irrigation management on development of potato early blight

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.