Functional, not Taxonomic, Composition of Soil Fungi Reestablishes to Pre-mining Initial State After 52 Years of Recultivation.

Open-cast mining leads to the loss of naturally developed soils and their ecosystem functions and services. Soil restoration after mining aims to restore the agricultural productivity in which the functions of the fungal community play a crucial role. Whether fungi reach a comparable functional state as in the soil before mining within half a century of recultivation is still unanswered. Here, we characterised the soil fungal community using ITS amplicon Illumina sequencing across a 52-year chronosequence of agricultural recultivation after open-cast mining in northern Europe. Both taxonomic and functional community composition showed profound shifts over time, which could be attributed to the changes in nutrient status, especially phosphorus availability. However, taxonomic composition did not reach the pre-mining state, whereas functional composition did. Importantly, we identified a positive development of arbuscular mycorrhizal root fungal symbionts after the initial three years of alfalfa cultivation, followed by a decline after conversion to conventional farming, with arbuscular mycorrhizal fungi being replaced by soil saprobes. We conclude that appropriate agricultural management can steer the fungal community to its functional pre-mining state despite stochasticity in the reestablishment of soil fungal communities. Nonetheless, conventional agricultural management results in the loss of plant symbionts, favouring non-symbiotic fungi.

Soil microbial community responses to antibiotic-contaminated manure under different soil moisture regimes.

Sulfadiazine (SDZ) is an antibiotic frequently administered to livestock, and it alters microbial communities when entering soils with animal manure, but understanding the interactions of these effects to the prevailing climatic regime has eluded researchers. A climatic factor that strongly controls microbial activity is soil moisture. Here, we hypothesized that the effects of SDZ on soil microbial communities will be modulated depending on the soil moisture conditions. To test this hypothesis, we performed a 49-day fully controlled climate chamber pot experiments with soil grown with Dactylis glomerata (L.). Manure-amended pots without or with SDZ contamination were incubated under a dynamic moisture regime (DMR) with repeated drying and rewetting changes of >20 % maximum water holding capacity (WHCmax) in comparison to a control moisture regime (CMR) at an average soil moisture of 38 % WHCmax. We then monitored changes in SDZ concentration as well as in the phenotypic phospholipid fatty acid and genotypic 16S rRNA gene fragment patterns of the microbial community after 7, 20, 27, 34, and 49 days of incubation. The results showed that strongly changing water supply made SDZ accessible to mild extraction in the short term. As a result, and despite rather small SDZ effects on community structures, the PLFA-derived microbial biomass was suppressed in the SDZ-contaminated DMR soils relative to the CMR ones, indicating that dynamic moisture changes accelerate the susceptibility of the soil microbial community to antibiotics.

Amino acid-sulphur decomposition in agricultural soil profile along a long-term recultivation chronosequence.

The significance of sulphur (S) availability for crop yield and quality is highlighted under the global S deficiency scenario. However, little is known about the temporal trend in belowground organic S mineralisation when restoring land to productive agricultural systems, particularly for the deeper soil parts. Therefore, we investigated the decomposition of 35S-labelled methionine in surface (0-30 cm) and subsurface soil (30-60 cm and 60-90 cm) over a 48-year recultivation chronosequence (sampled after1, 8, 14, 24 and 48 years). Soil total sulphur (TS) significantly (p < 0.05) increased in surface soil but not in subsurface soils after 48 years of recultivation. Overall, the immobilisation of 35S-methionine (35S-MB) in subsurface soils relative to year 1 significantly decreased over the chronosequence but did not change in the surface samples. The 35S-MB values in subsurface soils were positively corrected with soil carbon (C) stoichiometry (Pearson correlation, p < 0.05), suggesting the immobilisation of methionine was likely constrained by microbial C demand in deep soil. Compared to year 1, 35S-SO42- released from 35S-methionine significantly declined throughout the older (≥ 8 years) soil profiles. Significant (p < 0.05) changes in the organic 35S partition (35S immobilisation and 35S released as sulphate) were observed in year 8 after the soil was recultivated with N-fixing alfalfa or fertilisers. Whereas, after that (≥ 14 years), soil organic S partition remained affected when conventional tillage and agricultural crops dominated this site. Indicating that the effect of recultivation on organic S decomposition depends on the manner of recultivation management. Our study contributes to an improved understanding of amino acid S and organic S mineralisation under severe anthropogenic disturbance.

Improving nitrogen retention of cattle slurry with oxidized biochar: An incubation study with three different soils.

The application of livestock slurry in soils can lead to nitrogen (N) losses through ammonia (NH3 ) emission or nitrate (NO3 - ) leaching. Oxidized biochar has great potential to mitigate N losses due to its strong adsorption capacity; however, the effects of oxidized biochar in different soils treated with slurry are currently unclear. Here, we investigated the effect of untreated and oxidized biochar (applied at a rate of 50 kg C m-3 slurry) on reducing N losses in a laboratory experiment with three different soils (loamy sand, sandy loam, loam) amended with cattle slurry at an application rate of 73 kg N ha-1 . Oxidized biochar reduced NH3 emissions by 64-75% in all soils, whereas untreated biochar reduced NH3 emissions by 61% only in the loamy sand. Oxidized biochar significantly reduced the NO3 - content in the soil solution of the loamy sand in the early phase of the incubation and led to a significantly higher NO3 - concentration in the same soil compared with the slurry-only treatment at the end of the experiment, indicating a significant increase in NO3 - retention in this organic C-poor soil. We conclude that oxidized biochar can reduce N losses, both in the form of NH3 emission and NO3 - leaching, from cattle slurry applied to soil, particularly in soil with soil organic carbon content <1% and pH <5 (i.e., oxidized biochar can serve as a means for improving the quality of marginal and acidic soils).

Straw amendment and nitrification inhibitor controlling N losses and immobilization in a soil cooling-warming experiment.

It is common practice in agriculture to apply high­carbon amendments, e.g. straw, or nitrification inhibitors (NI) to reduce soil nitrogen (N) losses. However, little is known on the combined effects of straw and NI and how seasonal soil temperature variations further affect N immobilization. We conducted a 113-day mesocosm experiment with different levels of 15N-fertilizer application (N0: control; N1: 125 kg N ha-1; N2: 250 kg N ha-1) in an agricultural soil, amended with either wheat straw, NI or a combination of both in order to investigate N retention and loss from soil after a cooling-warming phase simulating a seasonal temperature shift, i.e., 30 days cooling phase at 7 °C and 10 days warming phase at 21 °C. Subsequently, soils were planted with barley as phytometers to study 15N-transfer to a following crop. Straw addition significantly reduced soil N-losses due to microbial N immobilization. Although carbon added as straw led to increased N2O emissions at high N fertilization, this was partly counterbalanced by NI. Soil cooling-warming strongly increased ammonification (+77 %), while nitrification was suppressed, and straw-induced microbial N immobilization dominated. N immobilized after straw addition was mineralized at the end of the experiment as indicated by structural equation models. Re-mineralization in N2 was sufficient, but still suboptimal in N0 and N1 at critical times of early barley growth. N-use efficiency of the 15N tracer decreased with fertilization intensity from 50 % in N1 to 35 % in N2, and straw amendment reduced NUE to 25 % at both fertilization rates. Straw amendment was most powerful in reducing N-losses (-41 %), in particular under variable soil temperature conditions, but NI enforced its effects by reducing N2O emission (-40 %) in N2 treatment. Sufficient N-fertilization coupled with straw application is required to adjust the timely re-mineralization of N for subsequent crops.

Fenton oxidation of biochar improves retention of cattle slurry nitrogen.

Nitrogen (N) losses during fertilization with livestock slurry, mainly in the form of ammonia (NH3 ), can cause environmental problems and reduce fertilizer efficiency. Leonardite, which is characterized by oxygen-rich functional groups and low pH, has been found to decrease losses of slurry N. However, leonardite, as a byproduct of open-cast lignite mining, is not a renewable resource. The objective of this study was to modify biochar by chemical surface oxidation in order to find a sustainable but similarly effective substitute for leonardite. Biochar was produced from spruce sawdust in a pyrolysis oven at a maximum temperature of 610 °C. Then the biochar was oxidized using the Fenton reaction, with a ratio of Fe2+ /H2 O2 of 1:1,000, as a source of highly reactive HO· radicals to introduce oxygen-rich functional groups to the biochar surface. The ammonium (NH4 + ) adsorption capacity of biochar, oxidized biochar, and leonardite was tested in ammonium sulfate [(NH4 )2 SO4 ] solution, pH-adjusted (NH4 )2 SO4 solution, and cattle slurry. The results showed that biochar had the highest total NH4 + adsorption of 1.4 mg N g-1 in (NH4 )2 SO4 solution, whereas oxidized biochar had the highest reversible NH4 + adsorption of 0.8 mg N g-1 . In the pH-adjusted ammonium solution, all materials reduced NH3 emissions by ≥90%, and oxidized biochar reduced NH3 emissions by 99.99%. In contrast, leonardite reduced NH3 emissions the most in cattle slurry, and oxidation of biochar increased the reduction in NH3 emissions from 22 to 67% compared with non-oxidized biochar. In conclusion, biochar oxidized by means of the Fenton reaction greatly decreased NH3 emissions by increased adsorption of NH4 + in cattle slurry compared with non-oxidized biochar, indicating the great potential of oxidized biochar for reducing N losses during slurry application.

Effect of sulfadiazine-contaminated pig manure on the abundances of genes and transcripts involved in nitrogen transformation in the root-rhizosphere complexes of maize and clover.

The antibiotic sulfadiazine (SDZ) can enter the environment by application of manure from antibiotic-treated animals to arable soil. Because antibiotics are explicitly designed to target microorganisms, they likely affect microbes in the soil ecosystem, compromising important soil functions and disturbing processes in nutrient cycles. In a greenhouse experiment, we investigated the impact of sulfadiazine-contaminated pig manure on functional microbial communities involved in key processes of the nitrogen cycle in the root-rhizosphere complexes (RRCs) of maize (Zea mays) and clover (Trifolium alexandrinum). At both the gene and transcript level, we performed real-time PCR using nifH, amoA (in both ammonia-oxidizing bacteria and archaea), nirK, nirS, and nosZ as molecular markers for nitrogen fixation, nitrification, and denitrification. Sampling was performed 10, 20, and 30 days after the application. SDZ affected the abundance pattern of all investigated genes in the RRCs of both plant species (with stronger effects in the RRC of clover) 20 and 30 days after the addition. Surprisingly, effects on the transcript level were less pronounced, which might indicate that parts of the investigated functional groups were tolerant or resistant against SDZ or, as in the case of nifH and clover, have been protected by the nodules.

52 years of ecological restoration following a major disturbance by opencast lignite mining does not reassemble microbiome structures of the original arable soils.

Opencast mining for lignite continuously creates areas of land that require restoration. Here we applied a chronosequence approach to investigate the development of soil bacterial communities during 52 years as influenced by the restoration process and subsequent changes in soil physico-chemical conditions starting from the initial reclamation of the sites. By comparison with the unaffected soils near the mine, we were able to address the question if soil bacterial communities have reached a steady state within 52 years, which is comparable to the original soil. Our study revealed three distinct phases of the restoration process, each with a specific bacterial community composition. The effect size of these changes was similar to the one observed for seasonal dynamics at our sites. At the beginning of the restoration process Flavobacteriaceae, Cytophagaceae and Sphingobacteriaceae were found as typical members of the bacterial community as well as Rhizobiales as a result of the cultivation of alfalfa on the restored plots. At later stage the families Peptostreptococcaceae, Desulfurellaceae as well as Streptomycetaceae increased in relative abundance and became dominant members of the bacterial community. Even though overall bacterial abundance and richness exhibited values comparable to the original soil already 5 years after the start of the restoration process, main responder analyses reveal differences in the bacterial community structure even 52 years after the start of the restoration process. Mostly Nitrospirae were reduced in abundance in the soils restored for 52 years compared to the original soils. To broaden the significance of our study, we compared our data bioinformatically with published results from other restored areas, which were previously affected by opencast mining. Despite different durations of the different restoration phase, we could observe a large degree of conformity when bacterial patterns of succession were compared indicating common modes of action of ecological restoration tools for bacterial communities.

Potential of Wheat Straw, Spruce Sawdust, and Lignin as High Organic Carbon Soil Amendments to Improve Agricultural Nitrogen Retention Capacity: An Incubation Study.

Plants like winter wheat are known for their insufficient N uptake between sowing and the following growing season. Especially after N-rich crops like oilseed rape or field bean, nitrogen retention of the available soil N can be poor, and the risk of contamination of the hydrosphere with nitrate (NO3-) and the atmosphere with nitrous oxide (N2O) is high. Therefore, novel strategies are needed to preserve these unused N resources for subsequent agricultural production. High organic carbon soil amendments (HCA) like wheat straw promote microbial N immobilization by stimulating microbes to take up N from soil. In order to test the suitability of different HCA for immobilization of excess N, we conducted a laboratory incubation experiment with soil columns, each containing 8 kg of sandy loam of an agricultural Ap horizon. We created a scenario with high soil mineral N content by adding 150 kg NH4+-N ha-1 to soil that received either wheat straw, spruce sawdust or lignin at a rate of 4.5 t C ha-1, or no HCA as control. Wheat straw turned out to be suitable for fast immobilization of excess N in the form of microbial biomass N (up to 42 kg N ha-1), followed by sawdust. However, under the experimental conditions this effect weakened over a few weeks, finally ranging between 8 and 15 kg N ha-1 immobilized in microbial biomass in the spruce sawdust and wheat straw treatment, respectively. Pure lignin did not stimulate microbial N immobilization. We also revealed that N immobilization by the remaining straw and sawdust HCA material in the soil had a greater importance for storage of excess N (on average 24 kg N ha-1) than microbial N immobilization over the 4 months. N fertilization and HCA influenced the abundance of ammonia oxidizing bacteria and archaea as the key players for nitrification, as well as the abundance of denitrifiers. Soil with spruce sawdust emitted more N2O compared to soil with wheat straw, which in relation released more CO2, resulting in a comparable overall global warming potential. However, this was counterbalanced by advantages like N immobilization and mitigation of potential NO3- losses.

Succession of arbuscular mycorrhizal fungi along a 52-year agricultural recultivation chronosequence.

Arbuscular mycorrhizal (AM) fungi provide a range of functions in natural and managed ecosystems. However, the trajectory of AM fungal diversity after land degradation is poorly known. We studied the succession of AM fungi along an agricultural recultivation chronosequence after open-cast mining near Cologne, Germany. We used high-throughput sequencing of the large-subunit ribosomal RNA genes to characterize the soil AM fungal communities of 10 agricultural fields spanning 52 years of recultivation. During three years, soils are recultivated with a legume, and then converted to agriculture to be later returned to local farmers implementing conventional agriculture. Our data reveal a quick and strong recovery of AM fungal richness after a few years of recultivation, but also a rapid decline following years of conventional agriculture. The community structure was strongly correlated to mineral nitrogen and phosphorus, richness peaking at high N:P ratio. This work represents the first molecular data documenting temporal patterns of AM fungal communities in agriculture; it shows the deleterious effect of conventional agricultural practices on AM fungal communities developing over time. Nonetheless, the highly dynamic nature of AM fungal communities suggests strategies for site-level management for which considering N:P stoichiometry is crucial.

Non-invasive imaging of plant roots in different soils using magnetic resonance imaging (MRI).

BACKGROUND: Root systems are highly plastic and adapt according to their soil environment. Studying the particular influence of soils on root development necessitates the adaptation and evaluation of imaging methods for multiple substrates. Non-invasive 3D root images in soil can be obtained using magnetic resonance imaging (MRI). Not all substrates, however, are suitable for MRI. Using barley as a model plant we investigated the achievable image quality and the suitability for root phenotyping of six commercially available natural soil substrates of commonly occurring soil textures. The results are compared with two artificially composed substrates previously documented for MRI root imaging. RESULTS: In five out of the eight tested substrates, barley lateral roots with diameters below 300 µm could still be resolved. In two other soils, only the thicker barley seminal roots were detectable. For these two substrates the minimal detectable root diameter was between 400 and 500 µm. Only one soil did not allow imaging of the roots with MRI. In the artificially composed substrates, soil moisture above 70% of the maximal water holding capacity (WHCmax) impeded root imaging. For the natural soil substrates, soil moisture had no effect on MRI root image quality in the investigated range of 50-80% WHCmax. CONCLUSIONS: Almost all tested natural soil substrates allowed for root imaging using MRI. Half of these substrates resulted in root images comparable to our current lab standard substrate, allowing root detection down to a diameter of 300 µm. These soils were used as supplied by the vendor and, in particular, removal of ferromagnetic particles was not necessary. With the characterization of different soils, investigations such as trait stability across substrates are now possible using noninvasive MRI.

Sulfadiazine uptake and effects in common hazel (Corylus avellana L.).

Soil contamination by antibiotics is a possible consequence of animal husbandry waste, sewage sludge, and reclaimed water spreading in agriculture. In this study, 1-year-old hazel plants (Corylus avellana L.) were grown in pots for 64 days in soil spiked with sulfadiazine (SDZ) in the range 0.01-100 mg kg(-1) soil. Leaf gas exchanges, fluorescence parameters and plant growth were measured regularly during the experiment, whereas plant biomass, sulfonamide concentrations in soil and plant tissues, and the quantitative variation of culturable bacterial endophytes in leaf petiole were analyzed at the end of the trial. During the experiment, photosynthesis and leaf transpiration as well as fluorescence parameters were progressively reduced by the antibiotic. Effects were more evident for leaf transpiration and for the highest SDZ spiking concentrations, whereas growth analyses did not reveal negative effects of the antibiotic. At the end of the trial, a high number of culturable endophytic bacteria in the leaf petiole of plants treated with 0.1 and 0.01 mg kg(-1) were observed, and SDZ was extractable from soil and plant roots for spiking concentrations ≥1 mg kg(-1). Inside plants, the antibiotic was mainly stored at the root level with bioconcentration factors increasing with the spiking dose, and the hydroxylated derivate 4-OH-SDZ was the only metabolite detected. Overall results show that 1-year-old hazel plants can contribute to the reduction of sulfonamide concentrations in the environment, however, sensitive reactions to SDZ can be expected at the highest contamination levels.