Direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry improves appropriateness of antibiotic treatment of bacteremia

Matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows the identification of microorganisms directly from positive blood culture broths. Use of the MALDI-TOF MS for rapid identification of microorganisms from blood culture broths can reduce the turnaround time to identification and may lead to earlier appropriate treatment of bacteremia. During February and April 2010, direct MALDI-TOF MS was routinely performed on all positive blood cultures. During December 2009 and March 2010 no direct MALDI-TOF MS was used. Information on antibiotic therapy was collected from the hospital and intensive care units' information systems from all positive blood cultures during the study period. In total, 253 episodes of bacteremia were included of which 89 during the intervention period and 164 during the control period. Direct performance of MALDI-TOF MS on positive blood culture broths reduced the time till species identification by 28.8-h and was associated with an 11.3% increase in the proportion of patients receiving appropriate antibiotic treatment 24 hours after blood culture positivity (64.0% in the control period versus 75.3% in the intervention period (p0.01)). Routine implementation of this technique increased the proportion of patients on adequate antimicrobial treatment within 24 hours.     

Influence of urea on biological N2 fixation and N transfer from Azolla intercropped with rice

The N₂ fixed by Azolla before and after urea application during the rice cycle, the mineralisation of Azolla-N as well as its availability to rice was studied in two greenhouse experiments conducted in 1996 and 1997 and in June 1998 in Goettingen (Germany). Dry matter production of the various rice parts of experiment 1 showed a clear positive synergism between treatment with Azolla and urea with a resulting apparent N recovery by rice increasing from 40% (without Azolla) to 57% in the presence of Azolla. Part of this increase may be due to N fixed biologically by Azolla and transferred to the rice. The second experiment shed some light on the role of BNF. Using an iterative method of estimation, the daily rate of N fixation was estimated at 0.6 – 0.7 kg N ha^–1. The rate was not so much affected by the age of the Azolla crop. At this rate, the BNF would amount to up to 100 kg N ha^–1 over a 130-day season. Assuming that BNF may be inhibited for a period of 5 – 10 days following urea application due to high levels of N in the floodwater, this might reduce the BNF by between 6 and 14 kg N ha over the season. Using the mean-pool-abundance concept, it was estimated that around 75 – 80% of the Azolla-N mineralized during the growth period was actually absorbed by the rice plants. Of the N taken up by rice around 28% was derived from the biologically fixed Azolla N, the remainder was urea N cycled through the Azolla. Azolla also seems to help sustain the soil N supply by returning N to the soil in quantities roughly equal to those extracted from the soil by the rice plant.     

Carbon storage and root penetration in deep soils under small-farmer land-use systems in the Eastern Amazon region,Brazil

The north-east of Pará state in the Eastern Amazon of Brazil was settled over 100 years ago. Today the region is an agricultural landscape with variously-aged secondary vegetation and fields with annual cultures, plantation crops and pastures. The effect of these different land covers on carbon sequestration as well as on water and nutrient extraction remain subject of debate. Therefore, we assessed the importance of land use on soil carbon stocks by measuring various C fractions and root biomass (0–6 m) in slash-and-burn systems and (semi-) permanent cultures. An extensive root system down to at least 6 m depth was present under various secondary vegetation stands and slashed and burned fields recently taken into cultivation as well as under a primary forest. Shallower rooting patterns were evident under (permanent) oil palm (4.5 m) and (semi-permanent) passion fruit plantations (2.5 m). Carbon storage in soils of traditional slash-and-burn agriculture up to 6 m depth (185 t ha^-1) was not significantly lower than under a primary forest (196 t ha^-1) but declined significantly under (semi-) permanent cultures (to 146–167 t ha^-1). Compared to above-ground C losses, soil C losses due to slash-and-burn agriculture may thus be small. This is an argument for maintaining the secondary vegetation as part of the agricultural land-use system, as the root system of its trees is conserved and thus C is sequestered also at greater depth.     

Effect of urea placement on leaching losses of nitrogen from flooded rice soils

In an effort to provide an explanation for the reported variability in fertilizer N efficiency from deepplaced urea on flooded rice, a set of controlled experiments was conducted to evaluate the effect of water percolation on fertilizer loss and plant uptake from¹⁵N labeled urea supergranules. Three soils of different texture (silt loam-clay) were subjected to various percolation rates (0–20 mm/day) while planted to rice which was harvested after approximately 40 days.The results indicate that moderate to high percolation through silt loam soil will lead to significant fertilizer N losses and drastically decrease the fertilizer uptake by plants. The permeability of the clay soil was too low for any leaching to take place. It is therefore concluded that deep placement of urea supergranules not be recommended in soils where percolation rates may exceed 5 mm/day, particularly if the cation exchange capacity of the soil is low. This experiment points to the need of evaluating and reporting the percolation rates in soils where experiments with supergranular urea are conducted.Contribution from the Agro-Economic Division of the International Fertilizer Development Center (IFDC), Muscle Shoals, Alabama 35660.     

The role of Azolla cover in improving the nitrogen use efficiency of lowland rice

The development of management techniques to improve the poor N use efficiency by lowland rice (Oryza sativa L.) and reduce the high N losses has been an important focus of agronomic research. The potential of an Azolla cover in combination with urea was assessed under field conditions in Laguna, Philippines. Two on-station field experiments were established in the 1998–1999 dry season and eight on-farm experiments per season were carried out in the 2000–2001 wet and dry seasons. Treatment combinations consisting of N levels applied alone or combined with Azolla were evaluated with respect to floodwater chemistry, ¹⁵N recovery, crop growth, and grain yield. A full Azolla cover on the floodwater surface at the time of urea application prevented the rapid and large increase in floodwater pH and floodwater temperature. As a consequence, the partial pressure of ammonia (NH₃), which is an indicator of potential NH₃ volatilization, was significantly depressed. ¹⁵N recovery was higher in plots covered with Azolla where the total ¹⁵N recovery ranged between 77 and 99%, and the aboveground (grain and straw) recovery by rice ranged between 32 and 61%. The tiller count in Azolla-covered plots was significantly increased by 50% more than the uncovered plots at all urea levels. Consequently, the grain yield was likewise improved. Grain yields from the 16 on-farm trials increased by as much as 40% at lower N rates (40 and 50 kg N ha^–1) and by as much as 29% at higher N rates (80 and 100 kg N ha^–1). In addition, response of rice to treatments with lower N rates with an Azolla cover was comparable to that obtained with the higher N rates without a cover. Thus, using Azolla as a surface cover in combination with urea can be an alternative management practice worth considering as a means to reduce NH₃ volatilization losses and improve N use efficiency.     

The significance of denitrification of applied nitrogen in fallow and cropped rice soils under different flooding regimes I. Greenhouse experimènts

The role of nitrification-denitrification in the loss of nitrogen from urea applied to puddled soils planted to rice and subjected to continuous and intermittent flooding was evaluated in three greenhouse pot studies. The loss of N via denitrification was estimated indirectly using the¹⁵N balance, after either first accounting for NH₃ volatilization or by analyzing the¹⁵N balance immediately before and after the soil was dried and reflooded. When urea was broadcast and incorporated the loss of¹⁵N from the soil-plant systems depended on the soil, being about 20%–25% for the silt loams and only 10%–12% for the clay. Ammonia volatilization accounted for an average 20% of the N applied in the silt loam. Denitrification losses could not account for more than 10% of the applied N in any of the continuously flooded soil-plant systems under study and were most likely less than 5%. Intermittent flooding of soil planted to rice did not increase the loss of N. Denitrification appeared to be an important loss mechanism in continuously flooded fallow soils, accounting for the loss of approximately 40% of the applied¹⁵N. Loss of¹⁵N was not appreciably enhanced in fallow soils undergoing intermittent flooding. Apparently, nitrate formed in oxidized zones in the soil was readily denitrified in the absence of plant roots. Extensive loss (66%) of¹⁵N-labeled nitrate was obtained when 100 mg/pot of nitrate-N was applied to the surface of nonflooded soil prior to reflooding. This result suggests that rice plants may not compete effectively with denitrifiers if large quantities of nitrate were to accumulate during intermittent dry periods.     

Traits associated with improved P-uptake efficiency in CIMMYT's semidwarf spring bread wheat grown on an acid Andisol in Mexico

Phosphorus deficiency is a major yield limiting constraint in wheat cultivation on acid soils. The plant factors that influence P uptake efficiency (PUPE) are mainly associated with root characteristics. This study was conducted to analyze the genotypic differences and relationships between PUPE, root length density (RLD), colonization by vesicular arbuscular and arbuscular mycorrhizal (V)AM fungi and root excretion of phosphatases in a P-deficient Andisol in the Central Mexican Highlands. Forty-two semidwarf spring-bread-wheat (Triticum aestivumL.) genotypes from CIMMYT were grown without (−P) and with P fertilization (+P), and subsequently in subsets of 30 and 22 genotypes in replicated field trials over 2 and 3 years, respectively. Acid phosphatase activity at the root surface (APASE) was analyzed in accompanying greenhouse experiments in nutrient solution. In this environment, PUPE contributed more than P utilization efficiency, in one experiment almost completely, to the variation of grain yield among genotypes. Late-flowering genotypes were higher yielding, because the postanthesis period of wheat was extended due to the cold weather at the end of the crop cycles, and postanthesis P uptake accounted for 40–45% of total P uptake. PUPE was positively correlated with the numbers of days to anthesis (at −P r=0.57 and at +P r=0.73). The RLD in the upper soil layer (0–20 cm) of the wheat germplasm tested ranged from 0.5 to 2.4 cm cm^-3 at –P and 0.7 to 7.7 at +P. RLD was the most important root trait for improved P absorption, and it was positively genetically correlated with PUPE (at –P r=0.42 and at +P r=0.63) and the number of spikes m^-2 (at –P r=0.58 and at +P r=0.36). RLD in the upper soil layer was more important with P fertilizer application. Without P fertilization, root proliferation in the deeper soil profile secured access to residual, native P in the deeper soil layer. (V)AM-colonisation and APASE were to a lesser degree correlated with PUPE. Among genoptypes, the level of (V)AM-colonisation ranged from 14 to 32% of the RLD in the upper soil layer, and APASE from 0.5 to 1.1 nmol s^-1 plant^-1 10^-2. This revised version was published online in June 2006 with corrections to the Cover Date.     

The kinetics of ammonium and nitrate uptake by young rice plants

Summary An important process which affects the fate of fertilizer nitrogen (N) applied to a rice crop is crop N uptake. This uptake rate is controlled by many factors including the N-ion species and its concentration. In this study the relation between N concentration at the root surface and N uptake was characterized using Michaelis-Menten kinetics. The equation considers two parameters, Vmax and Km, which are measures of the maximum rate of uptake and the affinity of the uptake sites for the nutrient, respectively. Uptake rates of intact rice plants growing in a continuously flowing nutrient solution system were fitted to the Michaelis-Menten model using a weighted regression analysis. For NH₄−N the Km values for 4- and 9-week-old rice plants indicated a high affinity for the ammonium ions relative to concentrations reported for rice soils after fertilization. The Vmax values expressed on a unit-root-mass basis decreased with plant age, indicating a reduction in the average density of uptake sites on the root surface. The kinetics of NO₃−N uptake was similar to that of NH₄−N when NO₃−N was the only N source. However, if NH₄−N and NO₃−N were present simultaneously in the solution the Vmax for the uptake of NO₃−N was severely reduced, while the Km was affected very little. This inhibition appears to be noncompetitive. Fertilization of young rice plants leading to concentration of N at the root surface above approximately 900 μM will not increase crop uptake and may contribute to inefficient N recovery by the crop. The existence of NH₄−N and NO₃−N simultaneously at the root surface may also lead to inefficient N recovery because of reduced uptake of NO₃−N.     

Influence of seasonal variation on bioassessment of streams using macroinvertebrates

The EU Water Framework Directive requires assessment of the ecological quality of running waters using macroinvertebrates. One of the problems of obtaining representative samples of organisms from streams is the choice of sampling date, as the scores obtained from macroinvertebrate indices vary naturally between seasons, confounding the detection of anthropogenic environmental change. We investigated this problem in a 4th order calcareous stream in the western Carpathian Mountains of central Europe, the Stupavsky potok brook. We divided our 100 m study site into two stretches and took two replicate samples every other month alternately from each stretch for a period of 1 year, sampling in the months of February, April, June, August, October and December. Multivariate analysis of the macroinvertebrate communities (PCA) clearly separated the samples into three groups: (1) April samples (2) June and August samples (3) October, December and February samples. Metric scores were classified into two groups those that were stable with respect to sampling month, and those that varied. Of the metrics whose values increase with amount of allochthonous organic material (ALPHA_MESO, hyporhithral, littoral, PASF, GSI new, DSI, CSI), the highest scores occurred in February, April, October and December, while for metrics whose values decrease with content of organic material (DSII, DIS, GFI D05, PORI, RETI, hypocrenal, metarhithral, RP, AKA, LITHAL, SHRED, HAI) the highest values occurred in February, April, June and December. We conclude that sampling twice a year, in early spring and late autumn, is appropriate for this type of metarhithral mountain stream. Sampling in summer is less reliable due to strong seasonal influences on many of the metrics examined while sampling in winter is inappropriate for logistical reasons. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.