The nifY product of Klebsiella pneumoniae is associated with apodinitrogenase and dissociates upon activation with the iron-molybdenum cofactor.

Apodinitrogenase, which lacks the iron-molybdenum cofactor at its active site, is an oligomer that contains an additional protein not found in the active dinitrogenase tetramer. This associated protein in Klebsiella pneumoniae is shown to be the product of the nifY gene. When apodinitrogenase is activated by the addition of the iron-molybdenum cofactor, NifY dissociates from the apodinitrogenase complex. The conditions for this dissociation are described. Finally, there are aspects of the dissociation and insertion process in K. pneumoniae that are different from that in Azotobacter vinelandii.     

Short-term effects of biological and physical forces on aggregate formation in soils with different clay mineralogy

The mechanisms resulting in the binding of primary soil particles into stable aggregates vary with soil parent material, climate, vegetation, and management practices. In this study, we investigated short-term effects of: (i) nutrient addition (Hoagland's solution), (ii) organic carbon (OC) input (wheat residue), (iii) drying and wetting action, and (iv) root growth, with or without dry–wet cycles, on aggregate formation and stabilization in three soils differing in weathering status and clay mineralogy. These soils included a young, slightly weathered temperate soil dominated by 2:1 (illite and chlorite) clay minerals; a moderately weathered soil with mixed [2:1 (vermiculite) and 1:1 (kaolinite)] clay mineralogy and oxides; and a highly weathered tropical soil dominated by 1:1 (kaolinite) clay minerals and oxides. Air-dried soil was dry sieved through a 250 m sieve to break up all macroaggregates and 100 g-subsamples were brought to field capacity and incubated for 42 days. After 14 and 42 days, aggregate stability was measured on field moist and air-dried soil, to determine unstable and stable aggregation respectively. In control treatments (i.e., without nutrient or organic matter addition, without roots and at constant moisture), the formation of unstable and stable macroaggregates (> 250 m) increased in the order: 2:1 clay soil < mixed clay soil < 1:1 clay soil. After 42 days of incubation, nutrient addition significantly increased both unstable and stable macroaggregates in the 2:1 and 1:1 clay soils. In all soils, additional OC input increased both unstable and stable macroaggregate formation. The increase in macroaggregation with OC input was highest for the mixed clay soil and lowest for the 1:1 clay soil. In general, drying and wetting cycles had a positive effect on the formation of macroaggregates. Root growth caused a decrease in unstable macroaggregates in all soils. Larger amounts of macroaggregates were found in the mixed clay and oxides soil when plants were grown under 50% compared to 100% field capacity conditions. We concluded that soils dominated by variable charge clay minerals (1:1 clays and oxides) have higher potential to form stable aggregates when OC concentrations are low. With additional OC inputs, the greatest response in stable macroaggregate formation occurred in soils with mixed mineralogy, which is probably a result of different binding mechanisms occurring: i.e., electrostatic bindings between 2:1 clays, 1:1 clays and oxides (i.e. mineral-mineral bindings), in addition to OM functioning as a binding agent between 2:1 and 1:1 clays.     

Soil carbon saturation: concept,evidence and evaluation

Current estimates of soil C storage potential are based on models or factors that assume linearity between C input levels and C stocks at steady-state, implying that SOC stocks could increase without limit as C input levels increase. However, some soils show little or no increase in steady-state SOC stock with increasing C input levels suggesting that SOC can become saturated with respect to C input. We used long-term field experiment data to assess alternative hypotheses of soil carbon storage by three simple models: a linear model (no saturation), a one-pool whole-soil C saturation model, and a two-pool mixed model with C saturation of a single C pool, but not the whole soil. The one-pool C saturation model best fit the combined data from 14 sites, four individual sites were best-fit with the linear model, and no sites were best fit by the mixed model. These results indicate that existing agricultural field experiments generally have too small a range in C input levels to show saturation behavior, and verify the accepted linear relationship between soil C and C input used to model SOM dynamics. However, all sites combined and the site with the widest range in C input levels were best fit with the C-saturation model. Nevertheless, the same site produced distinct effective stabilization capacity curves rather than an absolute C saturation level. We conclude that the saturation of soil C does occur and therefore the greatest efficiency in soil C sequestration will be in soils further from C saturation.

Carbon balances in US croplands during the last two decades of the twentieth century

Carbon (C) added to soil as organic matter in crop residues and carbon emitted to the atmosphere as CO₂ in soil respiration are key determinants of the C balance in cropland ecosystems. We used complete and comprehensive county-level yields and area data to estimate and analyze the spatial and temporal variability of regional and national scale residue C inputs, net primary productivity (NPP), and C stocks in US croplands from 1982 to 1997. Annual residue C inputs were highest in the North Central and Central and Northern Plains regions that comprise ~70% of US cropland. Average residue C inputs ranged from 1.8 (Delta States) to 3.0 (North Central region) Mg?C?ha^?1?year^?1, and average NPP ranged from 3.1 (Delta States) to 5.4 (Far West region) Mg?C?ha^?1?year^?1. Residue C inputs tended to be inversely proportional to the mean growing season temperature. A quadratic relationship incorporating the growing season mean temperature and total precipitation closely predicted the variation in residue C inputs in the North Central region and Central and Northern Plains. We analyzed the soil C balance using the crop residue database and the Introductory Carbon Balance regional Model (ICBMr). Soil C stocks (0–20?cm) on permanent cropland ranged between 3.07 and 3.1?Pg during the study period, with an average increase of ~4?Tg?C?year^?1, during the 1990s. Interannual variability in soil C stocks ranged from 0 to 20?Tg?C (across a mean C stock of 3.08?±?0.01?Pg) during the study period; interannual variability in residue C inputs varied between 1 and 43?Tg C (across a mean input of 220?±?19?Tg). Such interannual variation has implications for national estimates of CO₂ emissions from cropland soils needed for implementation of greenhouse gas (GHG) mitigation strategies involving agriculture.     

Simulation of sugarcane residue decomposition and aboveground growth

Due to the worldwide increase in demand for biofuels, the area cultivated with sugarcane is expected to increase. For environmental and economic reasons, an increasing proportion of the areas are being harvested without burning, leaving the residues on the soil surface. This periodical input of residues affects soil physical, chemical and biological properties, as well as plant growth and nutrition. Modeling can be a useful tool in the study of the complex interactions between the climate, residue quality, and the biological factors controlling plant growth and residue decomposition. The approach taken in this work was to parameterize the CENTURY model for the sugarcane crop, to simulate the temporal dynamics of aboveground phytomass and litter decomposition, and to validate the model through field experiment data. When studying aboveground growth, burned and unburned harvest systems were compared, as well as the effect of mineral fertilizer and organic residue applications. The simulations were performed with data from experiments with different durations, from 12 months to 60 years, in Goiana, Timbaúba and Pradópolis, Brazil; Harwood, Mackay and Tully, Australia; and Mount Edgecombe, South Africa. The differentiation of two pools in the litter, with different decomposition rates, was found to be a relevant factor in the simulations made. Originally, the model had a basically unlimited layer of mulch directly available for decomposition, 5,000 g?m^?2. Through a parameter optimization process, the thickness of the mulch layer closer to the soil, more vulnerable to decomposition, was set as 110 g?m^?2. By changing the layer of mulch at any given time available for decomposition, the sugarcane residues decomposition simulations where close to measured values (R ² ?=?0.93), contributing to making the CENTURY model a tool for the study of sugarcane litter decomposition patterns. The CENTURY model accurately simulated aboveground carbon stalk values (R ² ?=?0.76), considering burned and unburned harvest systems, plots with and without nitrogen fertilizer and organic amendment applications, in different climates and soil conditions.     

Sources of nitrate in rivers draining sixteen watersheds in the northeastern U.S.: Isotopic constraints

The feasibility of using nitrogen and oxygenisotope ratios of nitrate (NO₃ ^–) forelucidating sources and transformations ofriverine nitrate was evaluated in a comparativestudy of 16 watersheds in the northeastern U.S.A. Stream water was sampled repeatedly at theoutlets of the watersheds between January andDecember 1999 for determining concentrations,¹⁵N values, and ¹⁸Ovalues of riverine nitrate.In conjunction with information about land useand nitrogen fluxes,¹⁵N_nitrate and¹⁸O_nitrate values providedmainly information about sources of riverinenitrate. In predominantly forested watersheds,riverine nitrate had mean concentrations ofless than 0.4 mg NO₃ ^–-N L^–1,¹⁵N_nitrate values of lessthan +5, and ¹⁸O_nitratevalues between +12 and +19. This indicatesthat riverine nitrate was almost exclusivelyderived from soil nitrification processes withpotentially minor nitrate contributions fromatmospheric deposition in some catchments. Inwatersheds with significant agricultural andurban land use, concentrations of riverinenitrate were as high as 2.6 mg NO₃ ^–-NL^–1 with ¹⁵N_nitratevalues between +5 and +8 and¹⁸O_nitrate values generallybelow +15. Correlations between nitrateconcentrations, ¹⁵N_nitratevalues, and N fluxes suggest that nitrate inwaste water constituted a major, and nitrate inmanure a minor additional source of riverinenitrate. Atmospheric nitrate deposition ornitrate-containing fertilizers were not asignificant source of riverine nitrate inwatersheds with significant agricultural andurban land use. Although complementary studiesindicate that in-stream denitrification wassignificant in all rivers, the isotopiccomposition of riverine nitrate sampled at theoutlet of the 16 watersheds did not provideevidence for denitrification in the form ofelevated ¹⁵N_nitrate and¹⁸O_nitrate values. Relativelylow isotopic enrichment factors for nitrogenand oxygen during in-stream denitrification andcontinuous admixture of nitrate from theabove-described sources are thought to beresponsible for this finding.     

Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis

Lateral gene transfer is an integral part of genome evolution in most bacteria. Bacteria can readily change the contents of their genomes to increase adaptability to ever-changing surroundings and to generate evolutionary novelty. Here, we report instances of lateral gene transfer in Mycobacterium avium subsp. paratuberculosis, a pathogenic bacteria that causes Johne's disease in cattle. A set of 275 genes are identified that are likely to have been recently acquired by lateral gene transfer. The analysis indicated that 53 of the 275 genes were acquired after the divergence of M. avium subsp. paratuberculosis from M. avium subsp. avium, whereas the remaining 222 genes were possibly acquired by a common ancestor of M. avium subsp. paratuberculosis and M. avium subsp. avium after its divergence from the ancestor of M. tuberculosis complex. Many of the acquired genes were from proteobacteria or soil dwelling actinobacteria. Prominent among the predicted laterally transferred genes is the gene rsbR, a possible regulator of sigma factor, and the genes designated MAP3614 and MAP3757, which are similar to genes in eukaryotes. The results of this study suggest that like most other bacteria, lateral gene transfers seem to be a common feature in M. avium subsp. paratuberculosis and that the proteobacteria contribute most of these genetic exchanges.     

Effects of 13, 14-dehydroprostacyclin methyl ester on the feline intestinal vascular bed.

The effects of a stable PGI2 analog, 13, 14-dehydro-PGI2 methyl ester and several vasoactive hormones were compared in the feline intestinal vascular bed under conditions of controlled blood flow so that changes in perfusion pressure directly reflect changes in vascular resistance. The PGI2 analog decreased perfusion pressure in a dose-dependent fashion when injected in the range of dose of 0.03-3 microgram and was quite similar to PGE2 whereas isoproterenol was somewhat more potent as a vasodilagor in the feline intestinal vascular bed. The present data show that 13, 14-dehydro-PGI2 methyl ester has potent vasodilator activity in the intestinal vascular bed.     

Assessing the Soil Carbon,Biomass Production,and Nitrous Oxide Emission Impact of Corn Stover Management for Bioenergy Feedstock Production Using DAYCENT

Harvesting crop residue needs to be managed to protect agroecosystem health and productivity. DAYCENT, a process-based modeling tool, may be suited to accommodate region-specific factors and provide regional predictions for a broad array of agroecosystem impacts associated with corn stover harvest. Grain yield, soil C, and N₂O emission data collected at Corn Stover Regional Partnership experimental sites were used to test DAYCENT performance modeling the impacts of corn stover removal. DAYCENT estimations of stover yields were correlated and reasonably accurate (adjusted r ²?=?0.53, slope?=?1.18, p?<<?0.001, intercept?=?0.36, p?=?0.11). Measured and simulated average grain yields across sites did not differ as a function of residue removal, but the model tended to underestimate average measured grain yields. Modeled and measured soil organic carbon (SOC) change for all sites were correlated (adjusted r ²?=?0.54, p?<<?0.001), but DAYCENT overestimated SOC loss with conventional tillage. Simulated and measured SOC change did not vary by residue removal rate. DAYCENT simulated annual N₂O flux more accurately at low rates (≤2-kg N₂O-N ha^?1 year^?1) but underestimated when emission rates were >3-kg N₂O-N ha^?1 year^?1. Overall, DAYCENT performed well at simulating stover yields and low N₂O emission rates, reasonably well when simulating the effects of management practices on average grain yields and SOC change, and poorly when estimating high N₂O emissions. These biases should be considered when DAYCENT is used as a decision support tool for recommending sustainable corn stover removal practices to advance bioenergy industry based on corn stover feedstock material.