Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry.

Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha(-1). Periodically, subsamples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity, and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates, and the release of inorganic N. Nitrogen mineralization, nitrification potentials, and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure-derived ammonium with soil properties.

Use of primer selection and restriction enzymes to assess bacterial community diversity in an agricultural soil used for potato production via terminal restriction fragment length polymorphism.

Terminal restriction fragment length polymorphism (T-RFLP) can be used to assess how land use management changes the dominant members of bacterial communities. We compared T-RFLP profiles obtained via amplification with forward primers (27, 63F) each coupled with the fluorescently labeled reverse primer (1392R) and multiple restriction enzymes to determine the best combination for interrogating soil bacterial populations in an agricultural soil used for potato production. Both primer pairs provide nearly universal recognition of a 1,400-bp sequence of the bacterial domain in the V(1)-V(3) region of the 16S ribosomal RNA (rRNA) gene relative to known sequences. Labeling the reverse primer allowed for direct comparison of each forward primer and the terminal restriction fragments' relative migration units obtained with each primer pair and restriction enzyme. Redundancy analysis (RDA) and nested multivariate analysis of variance (MANOVA) were used to assess the effects of primer pair and choice of restriction enzyme on the measured relative migration units. Our research indicates that the 63F-1392R amplimer pair provides a more complete description with respect to the bacterial communities present in this potato (Solanum tuberosum L.)-barley (Hordeum vulgare L.) rotation over seeded to crimson clover (Trifolium praense L.). Domain-specific 16S rRNA gene primers are rigorously tested to determine their ability to amplify across a target region of the gene. Yet, variability within or between T-RFLP profiles can result from factors independent of the primer pair. Therefore, researchers should use RDA and MANOVA analyses to evaluate the effects that additional laboratory and environmental variables have on bacterial diversity.

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.

Management of Verticillium Wilt of Potato with Disease-Suppressive Green Manures and as Affected by Previous Cropping History.

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.

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.

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.

Comparison of phosphorus forms in wet and dried animal manures by solution phosphorus-31 nuclear magnetic resonance spectroscopy and enzymatic hydrolysis.

Both enzymatic hydrolysis and solution (31)P nuclear magnetic resonance (NMR) spectroscopy have been used to characterize P compounds in animal manures. In this study, we comparatively investigated P forms in 0.25 M NaOH/0.05 M EDTA extracts of dairy and poultry manures by the two methods. For the dairy manure, enzymatic hydrolysis revealed that the majority of extracted P was inorganic P (56%), with 10% phytate-like P, 9% simple monoester P, 6% polynucleotide-like P, and 18% non-hydrolyzable P. Similar results were obtained by NMR spectroscopy, which showed that inorganic P was the major P fraction (64-73%), followed by 6% phytic acid, 14 to 22% other monoesters, and 7% phosphodiesters. In the poultry manure, enzymatic hydrolysis showed that inorganic P was the largest fraction (71%), followed by 15% phytate-like P and 1% other monoesters, and 3% polynucleotide-like P. NMR spectroscopy revealed that orthophosphate was 51 to 63% of extracted P, phytic acid 24 to 33%, other phosphomonoesters 6 to 12%, and phospholipids and DNA 2% each. Drying process increased orthophosphate (8.4% of total P) in dairy manure, but decreased orthophosphate (13.3% of total P) in poultry manure, suggesting that drying treatment caused the hydrolysis of some organic P to orthophosphate in dairy manure, but less recovery of orthophosphate in poultry manure. Comparison of these data indicates that the distribution patterns of major P forms in animal manure determined by the two methods were similar. Researchers can utilize the method that best fits their specific research goals or use both methods to obtain a full spectrum of manure P characterization.

Influence of decomposition on chemical properties of plant- and manure-derived dissolved organic matter and sorption to goethite.

Sorption of dissolved organic matter (DOM) plays an important role in maintaining the fertility and quality of soils in agricultural ecosystems. Few studies have examined the effects of decomposition on DOM sorption and chemical characteristics. This study investigated the sorption to goethite (alpha-FeOOH) of fresh and decomposed hydrophilic (HPL) and hydrophobic (HPB) DOM fractions extracted from the shoots and roots of crimson clover (Trifolium incarnatum L.), corn (Zea mays L.), soybean [Glycine max (L.) Merr.], hairy vetch (Vicia villosa L.), and dairy and poultry manures. Sorption was positively related to apparent molecular weight (MWAP), aromaticity as measured by absorptivity at 280 nm, and phenolic acid content. A 10-d laboratory microbial decomposition of the source organic matter generally increased the sorption of the extracted DOM onto goethite. The decomposition effect on sorption was greater for the HPL fractions than for the HPB fractions. There was a decrease in the MWAP values of the DOM samples following sorption to goethite. In many cases the reduction in MWAP was large, indicating a strong preference by goethite for the higher MWAP DOM fractions. The results of this laboratory-based research demonstrate that microbial processes affect the chemical characteristics of DOM which may affect the distribution of soil organic C pools.

Preparation and FT-IR characterization of metal phytate compounds.

Phytic acid (inositol hexaphosphoric acid, IP6) has long been recognized as the predominant organic P form in soil and animal manure. Whereas many studies have investigated the wet chemistry of IP6, there is little information on the characterization of solid metal IP6 compounds. This information is essential for further understanding and assessing the chemical behavior of IP6 in diverse soil-plant-water ecosystems. As the first step in full characterization, we synthesized eight metal phytate compounds and investigated their structural features using Fourier transform infrared spectroscopy (FT-IR). The absorption features from 900 to 1200 cm(-1) in FT-IR could be used to identify these phytates as: (i) light divalent metal (Ca and Mg) compounds with a sharp band and a broad band, (ii) heavy divalent metal (Cu and Mn) compounds with splitting broad bands, and (iii) trivalent metal (Al and Fe) compounds with a broad band and a shoulder band. Three different types of chemical structures of metal-phytate compounds were presented based on the FT-IR information. We further demonstrated that metal orthophosphates possessed different FT-IR spectral characteristics from their IP6 counterparts. The unique spectral features of metal phytates from 1000 to 700 cm(-1) could be used to distinguish phytate compounds from metal phosphate compounds. Thus, FT-IR analysis after fine tuning could provide an analytical tool to investigate the basic metal phytate chemistry in molecular levels, such as the competitive interactions between phosphate and phytate with a specific metal ion, and the conversion (or hydrolysis) of metal phytate to metal phosphate under various conditions.

An enzymatic hydrolysis approach for characterizing labile phosphorus forms in dairy manure under mild assay conditions.

Characterizing labile P forms in animal manure is a challenge due to their susceptibility to hydrolysis. In this study, we enzymatically characterized P forms in dairy manure (no bedding), collected from a representative dairy farm in New York, by separating into soluble and residual components under mild assay conditions using water and sodium acetate buffer (pH 5.0). About 75% of total manure P in the fresh manure was characterized, with the remainder (25%) regarded as recalcitrant or biochemically unidentified P. The hydrolyzable organic P in soluble and residual fractions was then characterized by using phosphatase enzymes to simple monoester P, polynucleotide P, phytate-like P, and non-hydrolyzable P. Of the total P in water extracts, 77% was inorganic P, 11% hydrolyzable organic P and 12% non-hydrolyzable P. In the residual resuspension, the distribution of characterized P was 25% spontaneous labile P, 32% simple monoester P, 7% polynucleotide P, 9% phytate-like P, and 26% non-hydrolyzable P. Ultrasonication increased the P(i) release from the manure residues, but the deviation in Pi concentrations due to the sampling variance was greater that the increase in P(i) due to sonication. Autoclaving sped up the release of both spontaneously labile P and enzymatically hydrolyzable P trapped in the manure residual matrix. Quantifying labile P forms by this approach may advance our ability to predict amount of manure P that will be hydrolyzed and eventually become bioavailable. The information obtained by our modified method would be complementary to that obtained by other methods (such as P-31 NMR and sequential fractionation) for a full spectrum of P species in animal manure.

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.

Phosphorus distribution in dairy manures.

The chemical composition of manure P is a key factor determining its potential bioavailability and susceptibility to runoff. The distribution of P forms in 13 dairy manures was investigated with sequential fractionation coupled with orthophosphate-releasing enzymatic hydrolysis. Among the 13 dairy manures, manure total P varied between 4100 and 18,300 mg kg(-1) dry matter (DM). Water-extractable P was the largest fraction, with inorganic phosphorus (P(i)) accounting for 12 to 44% of manure total P (1400-6800 mg kg(-1)) and organic phosphorus (P(o)) for 2 to 23% (130-1660 mg kg(-1)), respectively. In the NaHCO(3) fraction, P(i) varied between 740 and 4200 mg P kg(-1) DM (4-44% of total manure P), and P(o) varied between 340 and 1550 mg P kg(-1) DM (2-27% of total manure P). In the NaOH fraction, P(i) fluctuated around 200 mg P kg(-1) DM, and P(o) ranged from 130 to 630 mg P kg(-1) DM. Of the enzymatically hydrolyzable P(o) in the three fractions, phytate-like P dominated, measuring 26 to 605 mg kg(-1) DM, whereas monoester P and DNA-like P were relatively low and less variable. Although concentrations of various P forms varied considerably, significant correlations between manure total P and certain P forms were observed. For example, H(2)O-extracted P(i) was correlated with total manure P (R(2) = 0.62), and so was NaOH-extracted P(o) (R(2) = 0.81). Data also show that the amount of P released by a single extraction with sodium acetate (100 mM, pH 5.0) was equivalent to the sum of P in all three fractions (H(2)O-, NaHCO(3)-, and NaOH-extractable P). Thus, a single extraction by sodium acetate buffer could provide an efficient evaluation of plant-available P in animal manure, while the sequential fractionation approach provides more detailed characterization of manure P.

Enzymatic hydrolysis of organic phosphorus in swine manure and soil.

Organic phosphorus (Po) exists in many chemical forms that differ in their susceptibility to hydrolysis and, therefore, bioavailability to plants and microorganisms. Identification and quantification of these forms may significantly contribute to effective agricultural P management. Phosphatases catalyze reactions that release orthophosphate (Pi) from Po compounds. Alkaline phosphatase in tris-HCl buffer (pH 9.0), wheat (Triticum aestivum L.) phytase in potassium acetate buffer (pH 5.0), and nuclease P1 in potassium acetate buffer (pH 5.0) can be used to classify and quantify Po in animal manure. Background error associated with different pH and buffer systems is observed. In this study, we improved the enzymatic hydrolysis approach and tested its applicability for investigating Po in soils, recognizing that soil and manure differ in numerous physicochemical properties. We applied (i) acid phosphatase from potato (Solanum tuberosum L.), (ii) acid phosphatases from both potato and wheat germ, and (iii) both enzymes plus nuclease P1 to identify and quantify simple labile monoester P, phytate (myo-inositol hexakis phosphate)-like P, and DNA-like P, respectively, in a single pH/buffer system (100 mM sodium acetate, pH 5.0). This hydrolysis procedure released Po in sequentially extracted H2O, NaHCO3, and NaOH fractions of swine (Sus scrofa) manure, and of three sandy loam soils. Further refinement of the approach may provide a universal tool for evaluating hydrolyzable Po from a wide range of sources.