Mechanistic modeling indicates rapid glyphosate dissipation and sorption-driven persistence of its metabolite AMPA in soil.

Residual concentrations of glyphosate and its main transformation product aminomethylphosphonic acid (AMPA) are often observed in soils. The factors controlling their biodegradation are currently not well understood. We analyzed sorption-limited biodegradation of glyphosate and AMPA in soil with a set of microcosm experiments. A mechanistic model that accounts for equilibrium and kinetic sorption facilitated interpretation of the experimental results. Both compounds showed a biphasic dissipation with an initial fast (up to Days 7-10) and subsequent slower transformation rate, pointing to sorption-limited degradation. Glyphosate transformation was well described by considering only equilibrium sorption. Model simulations suggested that only 0.02-0.13% of total glyphosate was present in the soil solution and thus bioavailable. Glyphosate transformation was rapid in solution (time required for 50 % dissipation of the total initially added chemical [DT50 ] = 3.9 min), and, despite strong equilibrium sorption, total glyphosate in soil dissipated quickly (DT50  = 2.4 d). Aminomethylphosphonic acid dissipation kinetics could only be described when considering both equilibrium and kinetic sorption. In comparison to glyphosate, the model simulations showed that a higher proportion of total AMPA was dissolved and directly bioavailable (0.27-3.32%), but biodegradation of dissolved AMPA was slower (DT50  = 1.9 h). The model-based data interpretation suggests that kinetic sorption strongly reduces AMPA bioavailability, leading to increased AMPA persistence in soil (DT50  = 12 d). Thus, strong sorption combined with rapid degradation points to low risks of glyphosate leaching by vertical transport through soil in the absence of preferential flow. Ecotoxicological effects on soil microorganisms might be reduced. In contrast, AMPA persists, rendering these risks more likely.

Spatial Control of Microbial Pesticide Degradation in Soil: A Model-Based Scenario Analysis.

Microbial pesticide degraders are heterogeneously distributed in soil. Their spatial aggregation at the millimeter scale reduces the frequency of degrader-pesticide encounter and can introduce transport limitations to pesticide degradation. We simulated reactive pesticide transport in soil to investigate the fate of the widely used herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) in response to differently aggregated distributions of degrading microbes. Four scenarios were defined covering millimeter scale heterogeneity from homogeneous (pseudo-1D) to extremely heterogeneous degrader distributions and two precipitation scenarios with either continuous light rain or heavy rain events. Leaching from subsoils did not occur in any scenario. Within the topsoil, increasing spatial heterogeneity of microbial degraders reduced macroscopic degradation rates, increased MCPA leaching, and prolonged the persistence of residual MCPA. In heterogeneous scenarios, pesticide degradation was limited by the spatial separation of degrader and pesticide, which was quantified by the spatial covariance between MCPA and degraders. Heavy rain events temporarily lifted these transport constraints in heterogeneous scenarios and increased degradation rates. Our results indicate that the mild millimeter scale spatial heterogeneity of degraders typical for arable topsoil will have negligible consequences for the fate of MCPA, but strong clustering of degraders can delay pesticide degradation.

Heavy rainfall following a summer drought stimulates soil redox dynamics and facilitates rapid and deep translocation of glyphosate in floodplain soils.

We present field data on the effects of heavy rainfall after drought on the mobility of glyphosate and redox conditions in a clayey floodplain soil. By applying glyphosate together with deuterated water as conservative tracer in combination with time resolved in situ redox potential measurements, the spatial and temporal patterns of water infiltration and pesticide transport as well as the concomitant changes of the redox conditions were revealed. Our findings demonstrate that shrinkage cracks in dry soils can serve as effective transport paths for atmospheric oxygen, water and glyphosate. The rain intensity of a typical summer storm event (approx. 25 mm within one hour) was sufficient to translocate deuterated water and glyphosate to the subsoil (50 cm) within 2 hours. Soil wetting induced partial closure of the shrinkage cracks and stimulated microbial activity resulting in pronounced dynamics of in situ soil redox conditions. Redox potentials in 40 to 50 cm depth dropped permanently to strongly reducing conditions within hours to days but fluctuated between reducing and oxidizing conditions in 10 to 30 cm depth. Our findings highlight the close link between the presence of macropores (shrinkage cracks), heavy rainfall after drought, redox dynamics and pesticide translocation to the subsoil and thus call for further studies addressing the effects of dynamic redox conditions as a limiting factor for glyphosate degradation.

Does It Pay Off to Explicitly Link Functional Gene Expression to Denitrification Rates in Reaction Models?

Environmental omics and molecular-biological data have been proposed to yield improved quantitative predictions of biogeochemical processes. The abundances of functional genes and transcripts relate to the number of cells and activity of microorganisms. However, whether molecular-biological data can be quantitatively linked to reaction rates remains an open question. We present an enzyme-based denitrification model that simulates concentrations of transcription factors, functional-gene transcripts, enzymes, and solutes. We calibrated the model using experimental data from a well-controlled batch experiment with the denitrifier Paracoccous denitrificans. The model accurately predicts denitrification rates and measured transcript dynamics. The relationship between simulated transcript concentrations and reaction rates exhibits strong non-linearity and hysteresis related to the faster dynamics of gene transcription and substrate consumption, relative to enzyme production and decay. Hence, assuming a unique relationship between transcript-to-gene ratios and reaction rates, as frequently suggested, may be an erroneous simplification. Comparing model results of our enzyme-based model to those of a classical Monod-type model reveals that both formulations perform equally well with respect to nitrogen species, indicating only a low benefit of integrating molecular-biological data for estimating denitrification rates. Nonetheless, the enzyme-based model is a valuable tool to improve our mechanistic understanding of the relationship between biomolecular quantities and reaction rates. Furthermore, our results highlight that both enzyme kinetics (i.e., substrate limitation and inhibition) and gene expression or enzyme dynamics are important controls on denitrification rates.

Gene-Centric Model Approaches for Accurate Prediction of Pesticide Biodegradation in Soils.

Pesticides are widely used in agriculture despite their negative impact on ecosystems and human health. Biogeochemical modeling facilitates the mechanistic understanding of microbial controls on pesticide turnover in soils. We propose to inform models of coupled microbial dynamics and pesticide turnover with measurements of the abundance and expression of functional genes. To assess the advantages of informing models with genetic data, we developed a novel "gene-centric" model and compared model variants of differing structural complexity against a standard biomass-based model. The models were calibrated and validated using data from two batch experiments in which the degradation of the pesticides dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxyacetic acid (MCPA) were observed in soil. When calibrating against data on pesticide mineralization, the gene-centric and biomass-based models performed equally well. However, accounting for pesticide-triggered gene regulation allows improved performance in capturing microbial dynamics and in predicting pesticide mineralization. This novel modeling approach also reveals a hysteretic relationship between pesticide degradation rates and gene expression, implying that the biodegradation performance in soils cannot be directly assessed by measuring the expression of functional genes. Our gene-centric model provides an effective approach for exploiting molecular biology data to simulate pesticide degradation in soils.

Biodegradation of Pesticides at the Limit: Kinetics and Microbial Substrate Use at Low Concentrations.

The objective of our study was to test whether limited microbial degradation at low pesticide concentrations could explain the discrepancy between overall degradability demonstrated in laboratory tests and their actual persistence in the environment. Studies on pesticide degradation are often performed using unrealistically high application rates seldom found in natural environments. Nevertheless, biodegradation rates determined for higher pesticide doses cannot necessarily be extrapolated to lower concentrations. In this context, we wanted to (i) compare the kinetics of pesticide degradation at different concentrations in arable land and (ii) clarify whether there is a concentration threshold below which the expression of the functional genes involved in the degradation pathway is inhibited without further pesticide degradation taking place. We set up an incubation experiment for four weeks using 14C-ring labeled 2-methyl-4-chlorophenoxyacetic acid (MCPA) as a model compound in concentrations from 30 to 20,000 µg kg-1 soil. To quantify the abundance of putative microorganisms involved in MCPA degradation and their degradation activity, tfdA gene copy numbers (DNA) and transcripts (mRNA) were determined by quantitative real-time PCR. Mineralization dynamics of MCPA derived-C were analyzed by monitoring 14CO2 production and 14C assimilation by soil microorganisms. We identified two different concentration thresholds for growth and activity with respect to MCPA degradation using tfdA gene and mRNA transcript abundance as growth and activity indices, respectively. The tfdA gene expression started to increase between 1,000 and 5,000 µg MCPA kg-1 dry soil, but an actual increase in tfdA sequences could only be determined at a concentration of 20,000 µg. Accordingly, we observed a clear shift from catabolic to anabolic utilization of MCPA-derived C in the concentration range of 1,000 to 5,000 µg kg-1. Concentrations ≥1,000 µg kg-1 were mainly associated with delayed mineralization, while concentrations ≤1,000 µg kg-1 showed rapid absolute dissipation. The persistence of pesticides at low concentrations cannot, therefore, be explained by the absence of functional gene expression. Nevertheless, significant differences in the degradation kinetics of MCPA between low and high pesticide concentrations illustrate the need for studies investigating pesticide degradation at environmentally relevant concentrations.

Plant litter enhances degradation of the herbicide MCPA and increases formation of biogenic non-extractable residues in soil.

Amendment of soils with plant residues is common practice for improving soil quality. In addition to stimulated microbial activity, the supply of fresh soluble organic (C) from litter may accelerate the microbial degradation of chemicals in soils. Therefore, the aim of this study was to test whether the maize litter enhances degradation of 4-chloro-2-methylphenoxyacetic acid (MCPA) and increases formation of non-toxic biogenic non-extractable residues (bioNERs). Soil was amended with 13C6-MCPA and incubated with or without litter addition on the top. Three soil layers were sampled with increasing distance from the top: 0-2 mm, 2-5 mm and 5-20 mm; and the mass balance of 13C6-MCPA transformation determined. Maize litter promoted microbial activity, mineralization of 13C6-MCPA and bioNER formation in the upper two layers (0-2 and 2-5 mm). The mineralization of 13C6-MCPA in soil with litter increased to 27% compared to only 6% in the control. Accordingly, maize addition reduced the amount of extractable residual MCPA in soil from 77% (control) to 35% of initially applied 13C6-MCPA. While non-extractable residues (NERs) were <6% in control soil, litter addition raised NERs to 21%. Thereby, bioNERs comprised 14% of 13C6-MCPA equivalents. We found characteristic differences of bioNER formation with distance to litter. While total NERs in soil at a distance of 2-5 mm were mostly identified as 13C-bioNERs (97%), only 45-46% of total NERs were assigned to bioNERs in the 0-2 and 5-20 mm layers. Phospholipid fatty acid analysis indicated that fungi and Gram-negative bacteria were mainly involved in MCPA degradation. Maize-C particularly stimulated fungal activity in the adjacent soil, which presumably facilitated non-biogenic NER formation. The plant litter accelerated formation of both non-toxic bioNERs and non-biogenic NERs. More studies on the structural composition of non-biogenic NERs with toxicity potential are needed for future recommendations on litter addition in agriculture.

The impact of chemical pollution on the resilience of soils under multiple stresses: A conceptual framework for future research.

Soils are faced with man-made chemical stress factors, such as the input of organic or metal-containing pesticides, in combination with non-chemical stressors like soil compaction and natural disturbance like drought. Although multiple stress factors are typically co-occurring in soil ecosystems, research in soil sciences on this aspect is limited and focuses mostly on single structural or functional endpoints. A mechanistic understanding of the reaction of soils to multiple stressors is currently lacking. Based on a review of resilience theory, we introduce a new concept for research on the ability of polluted soil (xenobiotics or other chemical pollutants as one stressor) to resist further natural or anthropogenic stress and to retain its functions and structure. There is strong indication that pollution as a primary stressor will change the system reaction of soil, i.e., its resilience, stability and resistance. It can be expected that pollution affects the physiological adaption of organisms and the functional redundancy of the soil to further stress. We hypothesize that the recovery of organisms and chemical-physical properties after impact of a follow-up stressor is faster in polluted soil than in non-polluted soil, i.e., polluted soil has a higher dynamical stability (dynamical stability=1/recovery time), whereas resilience of the contaminated soil is lower compared to that of not or less contaminated soil. Thus, a polluted soil might be more prone to change into another system regime after occurrence of further stress. We highlight this issue by compiling the literature exemplarily for the effects of Cu contamination and compaction on soil functions and structure. We propose to intensify research on effects of combined stresses involving a multidisciplinary team of experts and provide suggestions for corresponding experiments. Our concept offers thus a framework for system level analysis of soils paving the way to enhance ecological theory.

Evidence for the importance of litter as a co-substrate for MCPA dissipation in an agricultural soil.

Environmental controls of 2-methyl-4-chlorophenoxyacetic acid (MCPA) degradation are poorly understood. We investigated whether microbial MCPA degraders are stimulated by (maize) litter and whether this process depends on concentrations of MCPA and litter. In a microcosm experiment, different amounts of litter (0, 10 and 20 g kg(-1)) were added to soils exposed to three levels of the herbicide (0, 5 and 30 mg kg(-1)). The treated soils were incubated at 20 °C for 6 weeks, and samples were taken after 1, 3 and 6 weeks of incubation. In soils with 5 mg kg(-1) MCPA, about 50 % of the MCPA was dissipated within 1 week of the incubation. Almost complete dissipation of the herbicide had occurred by the end of the incubation with no differences between the three litter amendments. At the higher concentration (30 mg kg(-1)), MCPA endured longer in the soil, with only 31 % of the initial amount being removed at the end of the experiment in the absence of litter. Litter addition greatly increased the dissipation rate with 70 and 80 % of the herbicide being dissipated in the 10 and 20 g kg(-1) litter treatments, respectively. Signs of toxic effects of MCPA on soil bacteria were observed from related phospholipid fatty acid (PLFA) analyses, while fungi showed higher tolerance to the increased MCPA levels. The abundance of bacterial tfdA genes in soil increased with the co-occurrence of litter and high MCPA concentration, indicating the importance of substrate availability in fostering MCPA-degrading bacteria and thereby improving the potential for removal of MCPA in the environment.

Succession of bacterial and fungal 4-chloro-2-methylphenoxyacetic acid degraders at the soil-litter interface.

Phenoxyacetic acids can be degraded by diverse soil microorganisms. Nevertheless, we miss information about the succession of 4-chloro-2-methylphenoxyacetic acid (MCPA) degraders in micro-environments of soils as well as specific functions of different microbial groups during MCPA degradation. We studied MCPA degradation at the soil-litter interface in a microcosm experiment and followed the succession of different degrader populations by quantifying the abundance of 16S rRNA genes as well as, the fungal ITS fragment and the functional genes tfdA (in total and divided into three classes) and cadA. Adjacent to the litter layer, a dynamic depletion zone of MCPA indicated that the litter effect on MCPA degradation depends on substrate availability and the affected soil volume. The increase of the tfdA class III and cadA genes was linked to MCPA mineralisation. Total abundance of tfdA genes was dominated by class I MCPA degraders and did not reflect MCPA degradation potential of the soil. Litter addition induced the development of pioneer and late-stage fungal communities, which were probably both involved in MCPA degradation. The results underline the importance of the ecological behaviour of different degrader populations for the understanding of herbicide degradation in soils.

Is colloid-facilitated phosphorus leaching triggered by phosphorus accumulation in sandy soils?

The leaching of colloidal phosphorus (P(coll)) contributes to P losses from agricultural soils. In an irrigation experiment with undisturbed soil columns, we investigated whether the accumulation of P in soils due to excess P additions enhances the leaching of colloids and P(coll) from sandy soils. Furthermore, we hypothesized that large concentrations of P(coll) occur at the onset of leaching events and that P(coll) mobilized from topsoils is retained in subsoils. Soil columns of different P saturation and depth (0-25 and 0-40 cm) were collected at a former disposal site for liquid manure and at the Thyrow fertilization experiment in northeastern Germany. Concentrations of total dissolved P, P(coll), Fe(coll), Al(coll), optical density, zeta potential, pH, and electrical conductivity of the leachates were determined. Colloidal P concentrations ranged from 0.46 to 10 micromol L(-1) and contributed between 1 and 37% to total P leaching. Large P(coll) concentrations leached from the P-rich soil of the manure disposal site were rather related to a large P-content of colloids than to the mobilization of additional colloids. Concentrations of colloids and P(coll) in leachates from P-poor and P-rich columns from Thyrow did not differ significantly. In contrast, accumulation of P in the Werbellin and the Thyrow soil consistently increased dissolved P concentrations to maximum values as high as 300 micromol L(-1). We observed no first-flush of colloids and P(coll) at the beginning of the leaching event. Concentrations of P(coll) leached from 40-cm soil columns were not smaller than those leached from 25-cm columns. Our results illustrate that an accumulation of P in sandy soils does not necessarily lead to an enhanced leaching of colloids and P(coll), because a multitude of factors independent from the P status of soils control the mobility of colloids. In contrast, P accumulation generally increases dissolved P concentrations in noncalcareous soils due to the saturation of the P sorption capacity. This indicates that leaching of dissolved P might be a more widespread environmental problem in areas with P-saturated sandy soils than leaching of P(coll).