A Capture–Recapture Model with Double-Marking,Live and Dead Encounters,and Heterogeneity of Reporting Due to Auxiliary Mark Loss

Capture–recapture (CR) models assume marked individuals remain at risk of capture, which may not be true if individuals lose their mark or emigrate definitively from the study area. Using a double-marking protocol, with a main and auxiliary mark, and both live encounters and dead recoveries at a large scale, partially frees CR models from this assumption. However, the auxiliary mark may fall off and its presence is often not mentioned when dead individuals are reported. We propose a new model to deal with heterogeneity of detection and uncertainty of the presence of an auxiliary mark in a multi-event framework. Our general model, based on a double-marking protocol, uses information from physical captures/recaptures, distant observations and main mark recoveries from dead animals. We applied our model to a 13-year data set of a harvested species, the Greater Snow Goose. We obtained seasonal survival estimates for adults of both sexes. Survival estimates differed between models where the presence of the auxiliary mark upon recovery was ignored versus those where the presence was accounted for. In the multi-event framework, seasonal survival estimates are no longer biased because the heterogeneity due to the presence of an auxiliary mark is accounted for in the estimation of recovery rates.     

Hypothesis Tests on Mixture Model Components with Applications in Ecology and Agriculture

Multiple comparisons are widely used to compare gross features of distributions across populations. However, often a scientific hypothesis is more easily couched in terms of more focused null and alternative statistical hypotheses. For example, among distributions exhibiting clusters of continuous measurements across strata, are there clusters of measurements similar in terms of location, spread, or weight? We propose testing such hypotheses using a sequence of nested finite mixture models. Reasonable, data-driven priors are suggested based on estimates of the sample spreads and midpoints. Formal hypothesis testing is carried out through the computation of Bayes factors. The method is illustrated on Holling’s (Ecological Monographs 62:447–502, 1992) forest and prairie bird body mass data, and data on the time-to-abortion in dairy cows. Supplemental simulations are available online.     

Impact of Supplemental Calcium Chloride on Yield,Quality, Nutrient Status,and Postharvest Attributes of Tomato

Little is known regarding the impact of calcium chloride applications during growth and development on tomato postharvest quality. This trial investigated supplemental calcium chloride applications on yield, nutrient content, texture, and postharvest quality of tomato fruit. Calcium (Ca) nutrient solution concentrations were: 60, 180, and 360 mg·L^?1 calcium, while foliar applications were (0, 1, and 2% calcium chloride w/v). Plants grown with 60 mg·L^?1 Ca had a high incidence of blossom end rot, which was not affected by calcium chloride sprays. Fruit nutrient concentrations were affected by calcium delivered through the nutrient solution. As fruit cluster position increased, fruit nutrient concentrations significantly decreased. Foliar calcium chloride sprays affected fruit soluble solids content and dry weight, but did not affect texture. Pericarp elasticity increased concomitantly with calcium in the nutrient solution. Postharvest disease incidence was not affected by calcium treatment, though weight loss during storage was negatively affected by calcium chloride sprays.     

Soil respiration, N2O, and CH4 emissions from an Andisol under conventional-tillage and no-tillage cultivation for 4 years

No-tillage (NT) management is a promising method to sequester soil C and mitigate global warming caused by agricultural activities. Here, we report 4 years of continuous soil respiration rates and weekly nitrous oxide (N₂O) and methane (CH₄) emissions in NT and conventional-tillage (CT) plots in a typical Japanese volcanic soil. Overall, the soil respiration, N₂O emission, and CH₄ uptake decreased significantly in the NT plot. A difference in soil respiration and N₂O emission between the two plots began after the tillage treatment and the incorporation of crop residues and fertilizers, whereas the CH₄ uptake did not vary significantly during the fallow period after the treatments. The N₂O emission was higher from the CT than from the NT plot during the fall. The overall lower CH₄ uptake in the NT than in the CT plot likely resulted from a combination of decreased soil gas diffusivity and higher mineral N content at the soil surface. Higher soil respiration and N₂O emission occurred in the NT plot in the summer of 2003 and were plausibly caused by an increase in the soil moisture content that resulted from lower temperatures during July and August; the higher soil moisture must have accelerated the decomposition of organic matter accumulated in the topsoil. These results indicate that NT management is generally effective for the mitigation of the total GWP by reducing soil respiration and N₂O emission in temperate regions; however, NT management may increase rather than decrease these emissions when fields experience cool summers with frequent rainfall.     

Effect of Grinding on Soil Extraction by Aqua Regia, 2 M Nitric Acid,and Mehlich 3

Abstract

The effect of grinding on soil extraction was determined for two soil fractions and three extractants. Arsenic (As), beryllium (Be), cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), vanadium (V), and zinc (Zn) were extracted by aqua regia and 2 M nitric acid. Mehlich 3 extractant was used for determination of potassium (K), magnesium (Mg), calcium (Ca), phosphorus (P), iron (Fe), and aluminum (Al). One hundred forty‐seven agricultural soil samples representing all major soil types, climatic regions, and proportions of agronomic cultures in the Czech Republic were collected for the study. Particle size fractions smaller than 2 mm and smaller than 0.150 mm were chosen for investigation. Extraction of elements by aqua regia was similar for both size fractions of soil. Cold 2 M nitric acid is a weaker extractant than aqua regia, and a statistically significant increase in extractable Be (5%), Cd (6%), Co (11%), Cu (5%), Ni (5%), and V (2%) was measured with the finely ground soils. An increase for the finer fraction for K (10%) and Mn (25%) was found for Mehlich 3. A more complex nonlinear relationship was found for Mehlich 3 extractable Al and Fe. This was probably caused by a more intensive re‐adsorption of Fe and Al to the finely ground soils.     

Comparative Study of Different Soil Amendments and Microbes for Integrated Nutrient Management and Growth Promotion of Jatropha Curcas

Increased alkalinity caused reduction in growth of Jatropha curcas plant. This experiment was designed to test the efficacy of beneficial microbes and vermicompost individually and in combinations to alleviate the stressful effect of alkaline stress on growth of Jatropha. Plants inoculated with bacterial consortia had significantly increase in vegetative growth parameters. Soil analysis showed increase in total organic carbon (TOC) by 68% compared to soil before plantation treated with Bacterial consortia + vermicompost. Nitrogen (N) and phosphorus (P) content in the soil was increased by 25% and 84% before plantation treated with Bacterial consortia. Maximum uptake of potassium (K) and sodium (Na) content was observed in consortia. Plant analysis showed that consortia could increase uptake of micronutrients compared to control and other treatments. It can be concluded that multispecies bacterial consortia alone or in combination with mycorrhiza and vermicompost can reduce alkaline stress and enhances the seed germination potential, vegetative growth, and nutrient status of soil.     

Changes in the composition and diversity of topsoil bacterial,archaeal and fungal communities after 22 years conventional and no-tillage managements in Northern China

A comprehensive comparison about microbial community (bacterial, archaeal and fungal) response to different tillage managements in Northern China remain little studied, in this study we compared no-tillage (NT) versus conventional tillage (CT) management on topsoil microbial community diversity and composition in field experiment. We found that NT practice significantly increased the soil moisture content (SMC), bulk density, stocks of soil organic carbon (SOC), total nitrogen (TN), and microbial biomass carbon and nitrogen (P < 0.05). Moreover, higher levels of bacterial and archaeal alpha diversity were observed in NT relative to CT while unexpectedly, there was no significant difference found in fungal diversity between two treatments. The most pronounced shifts in the composition of the different microbial groups were found for the archaeal community, which followed by bacterial and fungal. NT practice markedly enhanced abundances of Proteobacteria (belongs to bacteria) phyla, Thaumarchaeota phyla (belongs to archaea) and Glomeromycota phyla (belongs to fungi). Redundancy analysis revealed that the factor that most closely correlated with bacterial, archaeal and fungal composition were SMC, TN and SOC, respectively. Considering NT enhanced both microbial composition and C storage in topsoil, we suggest that NT offers significant promise to improve topsoil health in this region.     

The effect of concentrations and properties of phenanthrene, pyrene, and benzo(a)pyrene on desorption in contaminated soil aged for 1 year

Purpose

The choice and timing of microorganisms added to soils for bioremediation is affected by the dominant bioavailable contaminants in the soil. However, changes to the concentration of bioavailable PAHs in soil are not clear, especially when several PAHs coexist. This study investigated the effects of PAH concentration and chemical properties on desorption in meadow brown soil after a 1-year aging period, which could reflect changes of PAH bioavailability during bioremediation.

Materials and methods

Based on the percentage of different molecular weights in a field investigation, high-level contaminated soil (HCS) and low-level contaminated soil (LCS) were prepared by adding phenanthrene (PHE), pyrene (PYR) and benzo(a)pyrene (BaP) to uncontaminated meadow brown soil. The concentrations of HCS and LCS were 250 mg?kg^?1 (PHE, PYR, and BaP: 100, 100, and 50 mg?kg^?1) and 50 mg?kg^?1 (PHE, PYR, and BaP: 20, 20, and 10 mg?kg^?1) respectively. The soils were aged for 1 year, after which desorption was induced by means of a XAD-2 adsorption technique over a 96-h period.

Results and discussion

The range of the rapidly desorbing fraction (F _rap) for PHE, PYR, and BaP in HCS and LCS was from 1.9 to 27.8 %. In HCS, desorption of PYR was most difficult, and the rate constant of very slow desorption (K _vs) of PYR was 8 orders of magnitude lower than that of BaP, which had similar very slow desorbing fractions (49.8 and 50.5 %, respectively). However, in LCS, desorption of PYR was the easiest; the K_vs of PYR was 8–10 orders of magnitude higher than those of PHE and BaP. In HCS, the time scale for release of 50 % of the PAHs was ranked as BaP?>?PYR?>?PHE, while in LCS this was BaP?>?PHE?>?PYR.

Conclusions

The combined effect of PAH concentrations and properties should be taken into account during desorption. The desorption of PAH did not always decrease with increasing molecular weight, and the desorption of four-ring PAHs might be special. These results are useful for screening biodegrading microbes and determining when they should be added to soils based on the dominant contaminants present during different periods, thus improving the efficiency of soil bioremediation.     

Yield and Price Forecasting for Stochastic Crop Decision Planning

The primary objective of this paper is to develop yield and price forecasting models employed in informed crop decision planning—a key aspect of effective farm management. For yearly yield prediction, we introduce a weather-based regression model with time-dependent varying coefficients. In order to allow for within-year climate variations, we predict yearly crop yield using weekly temperature and rainfall summaries resulting in a large number of correlated predictors. To overcome this difficulty, we reduce the space of predictors to a small number of uncorrelated predictors using Functional Principal Component Analysis (FPCA). For detailed price forecasting, we develop a futures-based model for long-range cash price prediction. In this model, the cash price is predicted as a sum of the nearby settlement futures price and the predicted commodity basis. We predict the one-year commodity basis as a mixture of historical basis data using a functional model-based approach. In both forecasting models, we estimate approximate prediction confidence intervals that are further integrated in a decision planning model. We applied our methods to corn yield and price forecasting for Hancock County in Illinois. Our forecasting results are more accurate in comparison to predictions based on existing methods. The methods introduced in this paper generally apply to other locations in the US and other crop types. The supplemental materials for this article are available online.     

Influence of Organic Residue Recycling on Crop Yield,Nutrient Uptake,and Microbial and Nutrient Status of rabi Sorghum (Sorghum bicolor L.) under Dryland Condition

The field experiment was conducted on black soil (Vertic Ustropept) at Zonal Agricultural Research Station farm, Solapur, for successive 30 years from 1987–1988 to 2016–2017 under dryland condition in a randomized block design with 10 treatments and 3 replications. The pooled results of seven years (2010–2011 to 2016–2017) revealed that the application of 25 kg N ha^?1 through crop residue (CR, byre waste) along with 25 kg N ha^-1 through Leucaena lopping (Leucaena leucocephala) to rabi sorghum gave significantly higher grain and stover yield and Sustainable Yield Index (14.61 and 36.11 q ha^?1 and 0.47, respectively) which was on par with T₇, where 25 kg N ha^?1 through farmyard manure (FYM) + 25 kg N ha^?1 through urea was applied for grain and stover yield (13.95 and 34.46 q ha^?1 and 0.44, respectively). The gross and net monetary returns and benefit–cost ratio were also influenced significantly due to integrated nitrogen management (Rs. 59,796, Rs. 47,353 ha^?1, and 3.13, respectively). This was also reflected in residual soil fertility status of soil after harvest of rabi sorghum. The organic carbon content and available nitrogen content of soil, as well as nitrogen uptake and moisture use efficiency for grain, were also increased. The total microbial count of bacteria, fungi, and actinomycetes was more where FYM or CR addition was done. The count of N fixers and P solubilizers was more under Leucaena application either alone or with CR or urea. Application of CR at 4.8 t ha^?1 (25 kg N ha^?1) along with Leucaena lopping at 3.5 t ha^?1 (25 kg N ha^?1) as green leaf manure is the best alternative organic source for fertilizer urea (50 kg N ha^?1) to increase the production of dryland rabi sorghum.     

Photosynthesis acclimation,leaf nitrogen concentration,and growth of four tree species over 3 years in response to elevated carbon dioxide and nitrogen treatment in subtropical China

Purpose  

Up to date, most studies about the plant photosynthetic acclimation responses to elevated carbon dioxide (CO₂) concentration have been performed in temperate areas, which are often N limited under natural conditions and with low ambient N deposition. It is unclear whether photosynthetic downregulation is alleviated with increased N availability, for example, from increased N deposition due to fossil fuel combustion in the tropics and subtropics. Awareness of plant photosynthetic responses to elevated CO₂ concentration will contribute to the better understanding and prediction of future forest productivity under global change.     

Bayesian Inference for Animal Space Use and Other Movement Metrics

The analysis of animal movement and resource use has become a standard tool in the study of animal ecology. Telemetry devices have become quite sophisticated in terms of overall size and data collecting capacity. Statistical methods to analyze movement have responded, becoming ever more complex, often relying on state-space modeling. Estimation of movement metrics such as utilization distributions have not followed suit, relying primarily on kernel density estimation. Here we consider a method for making inference about space use that is free of all of the major problems associated with kernel density estimation of utilization distributions such as autocorrelation, irregular time gaps, and error in observed locations. Our proposed method is based on a data augmentation approach that defines use as a summary of the complete path of the animal which is only partially observed. We use a sample from the posterior distribution of the complete path to construct a posterior sample for the metric of interest. Three basic importance sampling based methods for sampling from the posterior distribution of the path are proposed and compared. We demonstrate the augmentation approach by estimating a spatial map of diving intensity for female northern fur seals in the Pribilof Islands, Alaska.     

Microbial processes and community composition in the rhizosphere of European beech - The influence of plant C exudates

Plant roots strongly influence C and N availability in the rhizosphere via rhizodeposition and uptake of nutrients. This study aimed at investigating the effect of resource availability on microbial processes and community structure in the rhizosphere. We analyzed C and N availability, as well as microbial processes and microbial community composition in rhizosphere soil of European beech and compared it to the bulk soil. Additionally, we performed a girdling experiment in order to disrupt root exudation into the soil. By this novel approach we were able to demonstrate that enhanced resource availability positively affected N mineralization and hydrolytic enzyme activities in the rhizosphere, but negatively affected nitrification rates and oxidative enzyme activities, which are involved in the degradation of soil organic matter. Both rhizosphere effects on N mineralization and oxidative enzyme activities disappeared in the girdling treatment. Microbial community structure in the rhizosphere, assessed by phospholipid fatty acid analysis, differed only slightly from bulk soil but was markedly altered by the girdling treatment, indicating additional effects of the girdling treatment beyond the reduction of root exudation. Differences in oxidative enzyme activities and nitrification rates between rhizosphere soil and bulk soil, however, suggest considerable differences in the (functional) microbial community composition.     

Changes in Fatty Acid Composition and Content of Two Plants (Lolium perenne and Trifolium repens) Grown During 6 and 18 Months in a Metal (Pb, Cd, Zn) Contaminated Field

The aim of this in situ study was to investigate the fatty acid (FA) composition and content in roots and shoots of Lolium perenne and Trifolium repens, grown under heavy metal stress (Cd, Pb, Zn). The composition of FA was quite similar for the two plants and the two organs; main FA were palmitic acid (C16:0), oleic acid (C18:1), linoleic acid (C18:2) and linolenic acid (C18:3). For both plants, the major FA that characterized the roots was C18:2 whereas C18:3 was the prominent FA in shoots. For the first sampling (S1), in the roots of L. perenne and T. repens, polyunsaturated fatty acids (PUFA) were affected by metal contamination while, in the second sampling (S2), PUFA were affected in the shoots of the two plants. This alteration of PUFA was well correlated with the bioaccumulation factor of metals which decreased in roots and increased in shoots with the time. Moreover, a positive correlation was found between the PUFA decrease and the malondialdehyde (MDA) content, indicating the occurrence of a lipid peroxidation induced by the metal stress.     

Evaluation of the Accuracy of Diagnostic Tests From Repeated Measurements Without a Gold Standard

A model is presented to evaluate the accuracy of diagnostic tests from data from individuals that are repeatedly tested in time. Repeated measurements from three diagnostic tests for foot-and-mouth disease, applied to vaccinated and experimentally infected cattle, were analyzed. At any time the true disease status of the individuals was unknown, i.e., no gold standard was available. The model allows for correlation between repeated test results, in consequence of the underlying structure for the unknown true disease status, but also by the distribution of the test results conditional upon true disease status. The model also allows for dependence between the different diagnostic tests conditional upon true disease status. Prior information about the structure of the prevalence and the specificity of the tests was incorporated in a Bayesian analysis. Posterior inference was carried out with Markov chain Monte Carlo. Simulated data were analyzed to gain insight into the performance of the posterior Bayesian inference. The simulated data are typical for the expensive and, therefore, modestly sized infection experiments that are conducted under controlled conditions.     

Effects of phosphorus addition with and without ammonium, nitrate, or glucose on N2O and NO emissions from soil sampled under Acacia mangium plantation and incubated at 100 % of the water-filled pore space

An incubation experiment was conducted to examine the effects of phosphorus (P) addition with and without ammonium, nitrate, or glucose on N₂O and NO emissions from soil taken under Acacia mangium plantation and incubated at 100 % water-filled pore space (WFPS). Additions of NO ₃ ^? stimulated the N₂O and NO emissions while NH ₄ ⁺ did not, showing that denitrification was the main process of N₂O and NO production in the study condition. When NO ₃ ^? was added with P significantly (P?<?0.05) increased N₂O emissions regardless of the ratio of the added nitrogen and carbon, suggesting that P addition stimulated denitrification activity. The activation of denitrification by P addition is possibly attributed to two mechanisms: (1) the added-P stimulated denitrification by relieving P shortage for denitrifying bacteria and (2) the added-P stimulated activity of heterotrophic soil microflora with increased O₂ consumption promoting the development of anaerobic conditions with stimulation of denitrification.     

Time of Day Effect on Foliar Nutrient Concentrations in Corn and Soybean

Foliar nutrient concentrations vary during the day. Field research was conducted to quantify and better understand this variation in corn (Zea mays L.) and soybean (Glycine max L. Merr.) with foliar sampling during the vegetative and reproductive stages. Time of day effects occurred inconsistently across nutrients. Nitrogen (N), manganese (Mn), iron (Fe), and zinc (Zn) foliar concentrations were generally high early in the day. Phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) foliar concentrations varied inconsistently with time of day, while concentrations of boron (B) in both crops and copper (Cu) in corn were not affected. Limiting foliar sampling to after 10:00 AM reduced the variation for soybean but not for corn. Interpretation by Diagnosis and Recommendation Integrated System (DRIS) did not reduce the time of day effect. The variation caused by time of day, along with other causes, affects confidence in interpretation of foliar results suggesting use of the information with either additional foliar sampling or soil testing in making nutrient management decisions.     

Rotenone and rotenoids in cubè resins, formulations, and residues on olives

Rotenone and rotenoids (deguelin, beta-rotenolone (12a beta-hydroxyrotenone), tephrosin (12a beta-hydroxydeguelin), 12a alpha-hydroxyrotenone, and dehydrorotenone) were determined in cubè resins and formulations. Cubè resins from Lonchocarpus contain large quantities of deguelin (ca. 21.2%) and smaller quantities of tephrosin (ca. 3.5%) and beta-rotenolone (ca. 3.0%). The composition of commercial formulations may present very different rotenoid contents depending on the extracts used to prepare them. Because these rotenoids also present insecticide activity, the efficacy of these formulations may be very different. The storage stability and photodegradation of some rotenone formulations were studied. Rotenone and rotenoids are very sensitive to solar radiation, which degrades them rapidly, with half-lives in the order of a few tens of minutes. Some formulations show greater disappearance rates than that of cubè resin, indicating that not much attention has been paid to protecting the active ingredients from photodegradation in the formulation. A study on the residues on olives was also carried out to assess not only the rotenone content, but also that of the main rotenoids. At harvest, the residues of deguelin, tephrosin, and beta-rotenolone were 0.10, 0.06, and 0.10 mg/kg, respectively, very similar to rotenone (0.08 mg/kg), and though a few data indicate similar acute toxicity values for deguelin, only rotenone is taken into consideration in the legal determination of the residue.     

From waste to soil—carbon contents,respiration rates and ecotoxicological effects of an uncovered landfill site after 50 years

Purpose  

In this study, the ecotoxicological effects of the soil contaminations at an uncovered landfill site are assessed with two biological tests (earthworm avoidance test and luminous bacteria test). Furthermore, the state of rotting of the organic substance is estimated. Therefore, total organic carbon (TOC) contents and basal respiration rates are measured.