Journal of Plant Nutrition and Soil Science

Antibiotics are highly effective, bioactive substances. As a result of their consumption, excretion, and persistence, they are disseminated mostly via excrements and enter the soils and other environmental compartments. Resulting residual concentrations in soils range from a few μg upto g kg^–1 and correspond to those found for pesticides. Numerous antibiotic molecules comprise of a non‐polar core combined with polar functional moieties. Many antibiotics are amphiphilic or amphoteric and ionize. However, physicochemical properties vary widely among compounds from the various structural classes. Existing analytical methods for environmental samples often combine an extraction with acidic buffered solvents and the use of LC‐MS for determination. In soils, adsorption of antibiotics to the organic and mineral exchange sites is mostly due to charge transfer and ion interactions and not to hydrophobic partitioning. Sorption is strongly influenced by the pH of the medium and governs the mobility and transport of the antibiotics. In particular for the strongly adsorbed antibiotics, fast leaching through soils by macropore or preferential transport facilitated by dissolved soil colloids seems to be the major transport process. Antibiotics of numerous classes are photodegraded. However, on soil surfaces this process if of minor influence. Compared to this, biotransformation yields a more effective degradation and inactivation of antibiotics. However, some metabolites still comprise of an antibiotic potency. Degradation of antibiotics is hampered by fixation to the soil matrix; persisting antibiotics were already determined in soils. Effects on soil organisms are very diverse, although all antibiotics are highly bioactive. The absence of effects might in parts be due to a lack of suitable test methods. However, dose and persistence time related effects especially on soil microorganisms are often observed that might cause shifts of the microbial community. Significant effects on soil fauna were only determined for anthelmintics. Due to the antibiotic effect, resistance in soil microorganisms can be provoked by antibiotics. Additionally, the administration of antibiotics mostly causes the formation of resistant microorganisms within the treated body. Hence, resistant microorganisms reach directly the soils with contaminated excrements. When pathogens are resistant or acquire resistance from commensal microorganisms via gene transfer, humans and animals are endangered to suffer from infections that cannot be treated with pharmacotherapy. The uptake into plants even of mobile antibiotics is small. However, effects on plant growth were determined for some species and antibiotics.

Based on recent findings in the literature, we developed a process‐oriented conceptual model that integrates all three process groups of organic matter (OM) stabilization in soils namely (1) selective preservation of recalcitrant compounds, (2) spatial inaccessibility to decomposer organisms, and (3) interactions of OM with minerals and metal ions. The model concept relates the diverse stabilization mechanisms to active, intermediate, and passive pools. The formation of the passive pool is regarded as hierarchical structured co‐action of various processes that are active under specific pedogenetic conditions.

To evaluate the model, we used data of pool sizes and turnover times of soil OM fractions from horizons of two acid forest and two agricultural soils. Selective preservation of recalcitrant compounds is relevant in the active pool and particularly in soil horizons with high C contents. Biogenic aggregation preserves OM in the intermediate pool and is limited to topsoil horizons. Spatial inaccessibility due to the occlusion of OM in clay microstructures and due to the formation of hydrophobic surfaces stabilizes OM in the passive pool. If present, charcoal contributes to the passive pool mainly in topsoil horizons. The importance of organo‐mineral interactions for OM stabilization in the passive pool is well‐known and increases with soil depth. Hydrophobicity is particularly relevant in acid soils and in soils with considerable inputs of charcoal. We conclude that the stabilization potentials of soils are site‐ and horizon‐specific. Furthermore, management affects key stabilization mechanisms. Tillage increases the importance of organo‐mineral interactions for OM stabilization, and in Ap horizons with high microbial activity and C turnover, organo‐mineral interactions can contribute to OM stabilization in the intermediate pool. The application of our model showed that we need a better understanding of processes causing spatial inaccessibility of OM to decomposers in the passive pool.

Knowledge on short‐term and long‐term availability of nitrogen (N) after application of organic fertilizers (e.g., farmyard manure, slurry, sewage sludge, composts) provides an important basis to optimize fertilizer use with benefits for the farmer and the environment. Nitrogen from many organic fertilizers often shows little effect on crop growth in the year of application, because of the slow‐release characteristics of organically bound N. Furthermore, N immobilization after application can occur, leading to an enrichment of the soil N pool. However, this process finally increases the long‐term efficiency of organic fertilizers. Short‐term N release from organic fertilizers, measured as mineral‐fertilizer equivalents (MFE), varies greatly from 0% (some composts) to nearly 100% (urine). The most important indicators to be used for predicting the short‐term availability of N are total and NH$ _4^+ $‐N contents, C : N ratio (especially of the decomposable organic fraction), and stability of the organic substances. Processing steps before organic fertilizers are applied in the field particularly can influence N availability. Composting reduces mineral‐N content and increases the stability of the organic matter, whereas anaerobic fermentation increases NH$ _4^+ $‐N content as well as the stability of organic matter, but decreases the C : N ratio remarkably, resulting in a product with a high content of directly available N. Nevertheless, long‐term effects of organic fertilizers rather slowly releasing N have to be considered to enable optimization of fertilizer use. After long‐term application of organic fertilizers, the overall N‐use efficiency is adequate to a MFE in the range of 40%–70%.

Phosphorus (P) is an indispensable element for all life on Earth and, during the past decade, concerns about the future of its global supply have stimulated much research on soil P and method development. This review provides an overview of advanced state‐of‐the‐art methods currently used in soil P research. These involve bulk and spatially resolved spectroscopic and spectrometric P speciation methods (1 and 2D NMR, IR, Raman, Q‐TOF MS/MS, high resolution‐MS, NanoSIMS, XRF, XPS, (µ)XAS) as well as methods for assessing soil P reactions (sorption isotherms, quantum‐chemical modeling, microbial biomass P, enzymes activity, DGT, ³³P isotopic exchange, ¹⁸O isotope ratios). Required experimental set‐ups and the potentials and limitations of individual methods present a guide for the selection of most suitable methods or combinations.

The use of nitrification inhibitors (NI) is a technique which is able to improve N fertilizer use efficiency, to reduce nitrate leaching and to decrease the emission of the climate‐relevant gas N₂O simultaneously, particularly in moderately fertilized agricultural systems adapted to plant N demand. The ammonia monooxygenase (AMO) is the first enzyme which is involved in the oxidation of NH$ _4^+ $ to NO$ _3^ - $ in soils. The inhibition of the AMO by NIs directly decreases the nitrification rate and it reduces the NO$ _3^- $ concentration which serves as substrate for denitrification. Hence, the two main pathways of N₂O production in soils are blocked or their source strength is at least decreased. Although it has been shown that archaea are also able to oxidize NH₃, results from literature suggest that the enzymatic activity of NH₃ oxidizing bacteria is the most important target for NIs because it was much stronger affected. The application of NIs to reduce N₂O emissions is most effective under conditions in which the NI remains close to the N ‐ fertilizer. This is the case when the NI was sprayed on mineral ‐ N fertilizer granules or thoroughly mixed with liquid fertilizers. Most serious problems of spatial separation of NI and substrate emerge on pasture soils, where N₂O hotspots occur under urine and to a lesser extent under manure patches. From the few studies on the effect of different NI quantities it seems that the amount of NI necessary to reduce N₂O emissions is below the recommendations for NI amounts in practice.

NIs can improve the fertilizer value of liquid manure. For instance, the addition of NIs to slurry can increase N uptake and yield of crops when NO$ _3^ - $ ‐ N leaching losses are reduced. It has clearly been demonstrated that NIs added to cattle slurry are very effective in reducing N₂O as well as NO emissions after surface application and injection of slurry into grassland soils. In flooded rice systems NIs can reduce CH₄ emission significantly, whereas the effect on CO₂ emission is varying. On the other hand, as an effect of the delay of nitrification by NIs, NH₃ emission might increase when N fertilizers are not incorporated into the soil. As compared to other measures NIs have a high potential to reduce N₂O emissions from agricultural soils. Further, no other measure has so consistently been proofed according its efficiency to reduce N₂O emissions. From the published data [Akiyama et al. (2010) and more recent data from the years 2010–2013; 140 data sets in total] a reduction potential of approx. 35% seems realistic; however, further measurements in different management systems, particularly in regions with intense frost/thaw cycles seem necessary to confirm this reduction potential. These measurements generally should cover a whole annual cycle.

The present review is focused on microbiological methods used in agricultural soils accustomed to human disturbance. Recent developments in soil biology are analyzed with the aim of highlighting gaps in knowledge, unsolved research questions, and controversial results. Activity rates (basal respiration, N mineralization) and biomass are used as overall indices for assessing microbial functions in soil and can be supplemented by biomass ratios (C : N, C : P, and C : S) and eco‐physiological ratios (soil organic C : microbial‐biomass C, qCO₂, qN_min). The community structure can be characterized by functional groups of the soil microbial biomass such as fungi and bacteria, Gram‐negative and Gram‐positive bacteria, or by biotic diversity. Methodological aspects of soil microbial indices are assessed, such as sampling, pretreatment of samples, and conversion factors of data into biomass values. Microbial‐biomass C (µg (g soil)^–1) can be estimated by multiplying total PLFA (nmol (g soil)^–1) by the F_PLFA‐factor of 5.8 and DNA (µg (g soil)^–1) by the F_DNA‐factor of 6.0. In addition, the turnover of the soil microbial biomass is appreciated as a key process for maintaining nutrient cycles in soil. Examples are briefly presented that show the direction of human impact on soil microorganisms by the methods evaluated. These examples are taken from research on organic farming, reduced tillage, de‐intensification of land‐use management, degradation of peatland, slurry application, salinization, heavy‐metal contamination, lignite deposition, pesticide application, antibiotics, TNT, and genetically modified plants.

The composition of functional light soil organic matter pools of arable Cambisols with a gradient in clay content was investigated. Soil texture differences originate from increasing loess admixture to the parent material (coarse‐grained tertiary sediments). Using density fractionation in combination with ultrasonic dispersion, two types of particulate organic matter (POM) were obtained: (1) free POM and (2) POM occluded in soil aggregates. Both POM fractions were analyzed by elemental analysis (C, N) and CPMAS ¹³C NMR spectroscopy. With increasing clay content the amount of organic carbon stored in the occluded POM fraction increased considerably, whereas the amounts of free POM were not related to the soil clay content. With increasing soil clay contents increasing proportions of O‐alkyl C and decreasing proportions of aryl C were found for both POM fractions. The occluded POM fraction showed a higher degree of degradation as indicated by lower amounts in O‐alkyl carbon. A lower degree of POM degradation was associated with higher clay contents. Higher soil clay contents promoted the conservation of POM with a low degree of alteration. This effect of soil texture was found to be highly significant when the aryl C : O‐alkyl C ratio was used as indicator for POM decomposition rather than the alkyl C : O‐alkyl C ratio.

The aim of this work is to review the current knowledge on the effects of plant metabolism (C₃, C₄, and CAM) on root exudation and on the methods of exudate collection as well as the use of such exudates for analyses, testing of microbial response, degradation of pollutants, enzymatic activities, and occurrence of allelochemicals. We examine the advantages and disadvantages of each method as related to the downstream use of the exudates. The use of continuous percolation of solid cultivation medium with adjustment of nutrient‐solution strength appears to be a promising methodology for the determination of root exudation rates and qualitative composition of exuded compounds. The method mimics rhizosphere conditions, minimizing the artificial accumulation of compounds, alteration of plasma‐membrane permeability, ATPase activity, and the impacts of inhibitors or stimulators of root enzymes. Of particular significance is the fact that the adjustment of strength of nutrient solution and percolation enables universal and also long‐term use of the method, allowing high exudation yield by minimizing influx and maximizing efflux rates of exuded compounds at high nutrient‐solution strength. Furthermore, it facilitates assessment of the effect on soil microbial populations and their ability to degrade pollutants. Enzymatic activities can be assessed when a low strength of nutrient solution is used, with percolation of the exudates directly into tested soils. Composition of root exudates, regulation of root enzymes, and plant response to nutrient deficiency can be assessed by measuring net efflux or influx rates. The impact of heavy metals and other type of mechanical, chemical, and biological stresses differs according to the type of plant metabolism. This has significant consequences on transformations in plant communities, both structurally and functionally, and impacts upon crop nutrition, with respect to global climate change, and the use of plants for phytoremediation purposes. Understanding the effects of different types of plant metabolism on root exudation with respect to genetic regulation of synthetic pathways through root enzymes and transport systems presents an important direction for future research.

Before hydrochars can be applied as soil amendments in agriculture, information about how hydrochar application affects soil nutrient cycles and plant growth are necessary. In this study, incubation experiments were performed to investigate hydrochar effects on N concentrations (NO$ _3^- $, NH$ _4^+ $) in soils with different N pools (soil N, fertilizer N). A set of pot trials with three crop species (barley, phaseolus bean, leek) was conducted to determine hydrochar effects on plant N availability and biomass production after mineral‐N fertilization. Results of the incubation experiments show that hydrochar reduced the concentration of mineral N in soil within the first week after incorporation, especially that of nitrate. This was particularly evident, when hydrochars with high C : N ratio, high DOC and low mineral‐N contents were applied. Hydrochars promoted biomass production of barley and phaseolus bean in pot trials, which can be partly attributed to an increase in soil pH after hydrochar incorporation. Dry‐matter yield of leek tended to decrease after hydrochar application. Hydrochars with high C : N ratio decreased the plant's N content, an effect that was strongest with increased hydrochar concentration. Hydrochars with low C : N ratio did not affect the crop's N uptake. Our results show that the use of hydrochars as amendment in arable field or horticultural pot production will require an adjustment of N‐mineral‐fertilization strategies.

The nations that have ratified the Kyoto Protocol must set up an appropriate national inventory on N₂O emissions from agricultural land use, in order to report properly on the achievements made in reducing greenhouse‐gas emissions. The search for the appropriate method is a controversial topic as it is subject to high uncertainty in particular associated to the upscaling from site measurements. In this study, all available data from Germany on annual N₂O‐emission rates derived from field experiments of at least an entire year are summarized. From each study, only differences in soil properties on N input qualified as an individual data set. Under these premises, 101 treatments from 27 sites were found equally spread across Germany. The annual N application ranged from 0 to 400 kg N ha^–1 and the annual emission rates from 0.04 to 17.1 kg ha^–1. Annual emission factors (EFs), uncorrected for background emission, varied considerably from 0.18% to 15.54% of N applied. There was no nationwide correlation found for the relationship between N₂O losses and N application, soil C, soil N, soil texture, or soil pH. However, site‐specific trends in the relationship between emission factor and mean soil aeration status, as expressed by the soil type and/or mean climatic conditions, were revealed. Regularly water‐logged soils were characterized by low emission factors as were soils from the drier regions (<600 mm y^–1), whereas well‐aerated soils from the frost‐intensive regions showed exceptionally high emission factors. Since purely physical and chemical parameterization failed to describe N₂O emissions from agricultural land use on the national scale, there must be a biological adaptation to mean site conditions, i.e., different microbial communities react differently to similar actual conditions in terms of N₂O dynamics. Regardless of the point of view, the chapter on N₂O soil dynamics cannot be closed yet, and new additional model concepts, process studies, and field measurements are needed.