Publications

Investment in soil phosphorus (P) capital in the tropics is often constrained by poor availability of mineral fertiliser to small-scale farmers. Consequently, new sustainable agricultural cropping strategies are required to maintain fertility and maximise crop yields. The co-application of Tithonia diversifolia (Tithonia) green manure and mineral fertiliser (KH2PO4) together (integrated nutrient management) in comparison to the addition of one or the other alone has been hypothesized to promote crop P uptake. The aim of this study was to critically evaluate the benefits of integrated nutrient management practices in laboratory experiments. Wheat was grown as a test crop in microcosms to which either 32P-labelled mineral fertiliser or 33P-labelled Tithonia was added either singly or in combination. Exclusion meshes were used to determine the role of arbuscular mycorrhizal (AM) fungi in P uptake from the different P sources. The rate of uptake of both 32P and 33P by mycorrhizas was similar, and the rate of mycorrhizal P capture was comparable to that of roots. Generally, there was little difference in wheat P acquisition under integrated nutrient management treatments in comparison to P acquisition from 32P-mineral fertiliser or the addition of 33P-Tithonia alone. Overall, Tithonia residues were not very effective in supplying P to wheat over a short time evaluation period, suggesting that mineral fertilisers will still be required to satisfy crop demand.

Nitrification inhibitors (NIs) such as dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) provide an opportunity to reduce losses of reactive nitrogen (Nr) from agricultural ecosystems. To understand the fate and efficacy of these two inhibitors, laboratory-scale experiments were conducted with 14C-labelled DCD and DMPP to determine the relative rates of mineralization, recovery in soil extracts and sorption in two agricultural soils with contrasting pH and organic matter content. Concurrently, the net production of soil ammonium and nitrate in soil were determined. Two months after NI addition to soil, significantly greater mineralization of 14C-DMPP (15.3%) was observed, relative to that of 14C-DCD (10.7%), and the mineralization of both NIs increased with temperature, regardless of NI and soil type. However, the mineralization of NIs did not appear to have a major influence on their inhibitory effect (as shown by the low mineralization rates and the divergent average half-lives for mineralization and nitrification, which were 454 and 37days, respectively). The nitrification inhibition efficacy of DMPP was more dependent on soil type than that of DCD, although the efficacy of both inhibitors was lower in the more alkaline, low-organic matter soil. Although a greater proportion of DMPP becomes unavailable, possibly due to physico-chemical sorption to soil or microbial immobilization, our results demonstrate the potential of DMPP to achieve higher inhibition rates than DCD in grassland soils. Greater consideration of the interactions between NI type, soil and temperature is required to provide robust and cost-effective advice to farmers on NI use.

The return of agricultural crop residues are vital to maintain or even enhance soil fertility. However, the influence of application rate of crop residues on denitrification and its related gaseous N emissions is not fully understood. We conducted a fully robotized continuous flow incubation experiment using a Helium/Oxygen atmosphere over 30 days to examine the effect of maize straw application rate on: i) the rate of denitrification, ii) denitrification product stoichiometry N2O/(N2O+N2), and iii) the contribution of fungal denitrification to N2O fluxes. Five treatments were established using sieved, repacked sandy textured soil; i) non-amended control, ii) nitrate only, iii) low rate of straw + nitrate, iv) medium rate of straw + nitrate, and iv) high rate of straw + nitrate (n = 3). We simultaneously measured NO, N2O as well as direct N2 emissions and used the N2O 15N site preference signatures of soil-emitted N2O to distinguish N2O production from fungal and bacterial denitrification. Uniquely, soil NO3 − measurements were also made throughout the incubation. Emissions of N2O during the initial phase of the experiment (0–13 days) increased almost linearly with increasing rate of straw incorporation and with (almost) no N2 production. However, the rate of straw amendment was negatively correlated with N2O, but positively correlated with N2 fluxes later in the experimental period (13–30 days). Soil NO3 − content, in all treatments, was identified as the main factor responsible for the shift from N2O production to N2O reduction. Straw amendment immediately lowered the proportion of N2O from bacterial denitrification, thus implying that more of the N2O emitted was derived from fungi (18 ± 0.7% in control and up to 40 ± 3.0% in high straw treatments during the first 13 days). However, after day 15 when soil NO3 − content decreased to <40 mg NO3 −-N kg−1 soil, the N2O 15N site preference values of the N2O produced in the medium straw rate treatment showed a sharp declining trend 15 days after onset of experiment thereby indicating a clear shift towards a more dominant bacterial source of N2O. Our study singularly highlights the complex interrelationship between soil NO3 − kinetics, crop residue incorporation, fungal denitrification and N2O/(N2O + N2) ratio. Overall we found that the effect of crop residue applications on soil N2O and N2 emissions depends mainly on soil NO3 − content, as NO3 − was the primary regulator of the N2O/(N2O + N2) product ratio of denitrification. Furthermore, the application of straw residue enhanced fungal denitrification, but only when the soil NO3 − content was sufficient to supply enough electron acceptors to the denitrifiers.

Extreme weather events are increasing in frequency and magnitude with profound effects on ecosystem functioning. Further, there is now a greater likelihood that multiple extreme events are occurring within a single year. Here we investigated the effect of a single drought, flood or compound (flood + drought) extreme event on temperate grassland ecosystem processes in a field experiment. To assess system resistance and resilience, we studied changes in a wide range of above- and below-ground indicators (plant diversity and productivity, greenhouse gas emissions, soil chemical, physical and biological metrics) during the 8 week stress events and then for 2 years post-stress. We hypothesized that agricultural grasslands would have different degrees of resistance and resilience to flood and drought stress. We also investigated two alternative hypotheses that the combined flood + drought treatment would either, (A) promote ecosystem resilience through more rapid recovery of soil moisture conditions or (B) exacerbate the impact of the single flood or drought event. Our results showed that flooding had a much greater effect than drought on ecosystem processes and that the grassland was more resistant and resilient to drought than to flood. The immediate impact of flooding on all indicators was negative, especially for those related to production, and climate and water regulation. Flooding stress caused pronounced and persistent shifts in soil microbial and plant communities with large implications for nutrient cycling and long-term ecosystem function. The compound flood + drought treatment failed to show a more severe impact than the single extreme events. Rather, there was an indication of quicker recovery of soil and microbial parameters suggesting greater resilience in line with hypothesis (A). This study clearly reveals that contrasting extreme weather events differentially affect grassland ecosystem function but that concurrent events of a contrasting nature may promote ecosystem resilience to future stress.

Although it has been hypothesized that soluble organic nitrogen (SON) plays a central role in regulating productivity in some terrestrial ecosystems, the f

This proof of concept study was undertaken to test methodologies to characterize potential environmental risk associated with the presence of microplastics in surface waters. The goals of the study were to determine whether urban New Jersey freshwaters contained microplastic pollutants, and if so, to test analytic techniques that could potentially identify chemical compounds associated with this pollution. A third objective was to test whether identified associated compounds might have physiological effects on an aquatic organism. Using field collected microplastic samples obtained from the heavily urbanized Raritan and Passaic Rivers in New Jersey, microplastic densities, types, and sizes at 15 sampling locations were determined. Three types of plastic polymers were identified using pyrolysis coupled with gas chromatography (Pyr-GC/MS). Samples were further characterized using solid phase micro extraction coupled with headspace gas chromatography/ion trap mass spectrometry (HS-SPME-GC/ITMS) to identify organic compounds associated with the: (i) solid microplastic fraction, and (ii) site water fraction. Identical retention times for GC peaks found in both fractions indicated compounds can move between the two phases, potentially available for uptake by aquatic biota in the dissolved phase. Patterns of tentatively identified compounds were similar to patterns obtained in Pyr-GC/MS. Embryonic zebrafish exposed to PyCG/MS- identified pure polymers in the 1–10 ppm range exhibited altered growth and heart defects. Using two analytic methods (SPME GC/MS and Pyr-GC/MS) allows unambiguous identification of compounds associated with microplastic debris and characterization of the major plastic type(s). Specific “fingerprint” patterns can categorize the class of plastics present in a waterbody and identify compounds associated with the particles. This technique can also be used to identify compounds detected in biota that may be the result of ingesting plastics or plastic-associated compounds.

Urea represents a common form of organic nitrogen (N) which is added to agricultural soils in large quantities in both cropping (e.g. fertiliser) and livestock (e.g. urine) systems. In addition, there is a small, dynamic ambient pool of urea in soil associated with metabolic functioning in the microbial community. The diacetyl monoxime (DAM) colorimetric method is routinely used to quantify urea in soil, however, it lacks specificity due to the potential to react with the ureido group (R1NHCONHR2), a common structural moiety in soil organic matter. The aim of this study was therefore to critically evaluate the accuracy of this method for urea determination in soil. Using the DAM assay, we demonstrated significant cross-reactivity with a range of ureido compounds, many of which are ubiquitous in soil. We conclude therefore that the DAM assay is highly likely to overestimate urea concentrations in environmental materials. Such overestimation was confirmed using high resolution HPLC-Orbitrap MS to quantify urea in grassland soils using standard addition and the concentrations compared with those of the DAM assay. The results obtained show the DAM colorimetric method overestimated urea concentration by between 7.2 and 58 times for the sites studied. This significant overestimation of urea emphasises the need to validate the colorimetric method with reference to the LC-MS assay to ensure the robustness of measured urea concentrations. On this basis we recommend that reporting of the results from the DAM colorimetric method as “urea” concentration be curtailed and reported as “ureido-N” to recognise the contribution of unknown and variable contributions from other compounds. Indeed, given the problems with quantitatively assessing the latter contributions we would recommend the DAM method is now avoided in surveys of urea concentrations in soil and the wider environment.

Corrigendum on: Distaso, M.A., Bargiela, R., Brailsford, F.L., Williams, G.B., Wright, S., Lunev, E.A., Toshchakov, S.V., Yakimov, M.M., Jones, D.L., Golyshin, P.N., Golyshina, O.V. (2020). High representation of archaea across all depths in oxic and low-pH sediment layers underlying an acidic stream. Front. Microbiol. 11:2871. doi: 10.3389/ fmicb.2020.576520.In the original article, there was a mistake: The incorrect Figure 1 was uploaded as published (PCA including all chemical parameters Analysis by Principal Components Analysis (PCA) of the influence of all chemical properties measured on the three cores). The legend is correct as published. The correct Figure 1 appears below. This Figure 1 represents the synthesis of data reflected in Supplementary Figures S2-S4: Figure S2 (PCA for Carbon-Nitrogen chemical properties), Figure S3 (PCA for anions concentrations), and Figure S4. (PCA including elements concentrations as variables). The authors apologize for this error and state that this does not change the scientific conclusions of the article in any way. The original article has been updated.

No abstract is provided for this article.

An accurate assessment of soil respiration is critical for understanding and predicting ecosystem responses to anthropogenic perturbation such as climate change, pollution, and agriculture. Infra‐red gas analyzer (IRGA)–based field measurement is the most widely used technique for assessing soil‐respiration flux rates. In this study, respiration rates obtained with two common IRGA systems (LI‐COR 8100 and PP Systems EGM‐4) were compared across three ecosystem types. Our results showed that both methods were highly comparable in their flux estimates, but the associated methodology used (notably the use or absence of a soil collar) resulted in greater uncertainty in flux rates and a greater degree of intrasite variation. Specifically, the use of collars significantly decreased the flux estimate for both IRGAs compared to the no‐collar estimate. The disturbance caused by collar insertion was assumed to be a major factor in causing the differing flux estimates, with root and mycorrhizal severance likely being the main contributor. We conclude that the two IRGAs used in this study can be reliably compared for overall flux estimates but emphasis is needed to validate a common measurement methodology.

Soil phosphorus (P) improvement is one of the important aims of vegetation restoration. However, the effects of different vegetation restoration types on soil P cycling and the underlying mechanisms remain unclear. Together with vegetation structure and soil properties, we measured the soil P fractions and P transformation rates to evaluate the characteristics of ecologically relevant soil P fraction distributions and their dynamics for the most common vegetation restoration types in a subtropical mountain ecosystem (i.e., PF, Pinus forest; EF, Eucalyptus forest; SL, shrubland; and NSF, natural secondary forest). We found that water-extractable inorganic P (Pi), organic P (Po), and acid phosphatase activity (APA) were significantly higher in NSF than those in the other vegetation types (P < 0.01), together with the highest gross P mineralization rate (Pmin) and net P immobilization rate (Pimm), suggesting biological processes played a more important role in soil P cycling in the NSF. In contrast, the soil showed the lowest values of Pmin, Pimm, and APA in the EF compared to NSF and PF (P < 0.05), together with the highest P loss and the higher net P solubilization rate (Psol), indicating the greater importance of soil geochemical processes. Compared with the NSF and EF, geochemical and biological processes co-regulated soil P cycling in the PF and SL. However, the soil in the PF displayed higher P fluxes (Pmin, Pimm, Psol, and P loss) than those in the SL (P < 0.05), suggesting the soil had higher P flux magnitudes in the PF. Results of correlation analyses showed that the soil microbial community structure and activity played a more important role than plant community attributes and soil physicochemical properties in soil P fraction distribution and fluxes. In conclusion, soil P fraction distributions and their fluxes can be significantly influenced by vegetation restoration types. Land management strategies focusing on restoration of the soil microbial community may enhance soil P cycling and improve soil quality.

Peatlands drained for agriculture are among the most intensive sources of greenhouse gas (GHG) emissions from the land-use sector. Policy decisions on the most effective strategies to reduce GHG emissions in line with Paris Agreement goals, alongside strategies that can halt any ongoing soil and biodiversity losses, are hindered by a lack of understanding on how proposed mitigation measures are likely to be received by the farming sector. Research has identified effective GHG reduction measures, but successful on-farm adoption of these measures is contingent upon farmer perceptions of the relative practicality of implementing the measures, and the economic impact that adoption will have on the farm business. In this study, Best–Worst Scaling, a discrete choice survey method, was utilised to elicit expert (climate change, policy and biodiversity) and farmer opinion on the relative effectiveness, practicality and level of economic cost of mitigation measures that can reduce GHG emissions at the farm level. The method enabled individual mitigation measures to be ranked by effectiveness (expert opinion), practicality and economic cost (farmer opinions). There were no measures ranked as both effective and practical, or effective with low cost, but there were measures ranked by farmers as practical and low cost to implement. These included: more effective nutrient management, reduced or no tillage, the installation of buffer zones, increased fossil fuel efficiency and the optimisation of irrigation systems. The strong divergence of 'effective' measures on the one hand, and 'practical' and 'economic' measures on the other, highlights the major challenges involved in reducing high GHG emissions from agricultural organic soils. Resolving these challenges will require a combination of financial mechanisms to compensate farmers for higher costs and/or reduced yields, engagement and advice to support farmers in adopting changes in management practice, and agricultural innovation and adaptation to maintain overall food production and economic viability. If these challenges are overcome, more sustainable landscape management on agricultural lowland peat could make significant contributions to achieve national and international climate change targets.

Wastewater treatment plants are well-known point sources of emissions of antibacterial resistance genes (ARGs) into the environment. Although most work to date has focused on ARG dispersal via effluent, aerial dispersal in bioaerosols is a poorly understood, but likely important vector for ARG dispersal. Recent evidence suggests that ARG profiles of the conifer needle phyllosphere could be used to measure bioaerosol dispersal from anthropogenic sources. Here, we assessed airborne dispersal of ARGs from wastewater treatment plants in Wales, UK and Quebec, Canada, using conifer needles as passive bioaerosol monitors. ARG profiles of wastewater were compared to those of conifer phyllosphere using high-throughput qPCR. ARG richness was significantly lower in conifer phyllosphere samples than wastewater samples, though no differences were observed across the dispersal gradients. Mean copy number of ARGs followed a similar trend. ARG profiles showed limited, but consistent patterns with increasing distance from wastewater treatment plants, but these did not align with those of wastewater samples. For example, proportional abundance of aminoglycosides decreased over the dispersal gradient in Wales, whereas mobile genetic elements showed the inverse relationship. In summary, while distinct ARG profiles exist along dispersal gradients, links to those of wastewater were not apparent.

Summary Simple organic acids seem to be important in many soil processes including nutrient uptake in the rhizosphere and long‐term pedogenic processes such as podzolization. The factors regulating the concentrations of these acids in soil, however, remain poorly understood. We have investigated one set of factors, namely the impact of ectomycorrhizal ( Paxillus involutus ) and non‐mycorrhizal Picea abies seedlings and humic acid on the concentration and dynamics of organic acids in soil solution. We did so over 10 months in laboratory columns containing soil from the E horizon of a sandy forest soil. Several organic acids were identified in the solution extracted from the root zone including oxalic, citric, malonic, succinic, acetic, formic and lactic acids at concentrations ranging from &lt;0.1 to 2.3 µ m . Both plants and ectomycorrhizas had significant effects on the concentration of organic acids in soil solution. In contrast, omitting P from the irrigation water appeared to have little effect on the concentrations. The microbial mineralization kinetics of oxalate conformed well to a single Michaelis–Menten equation. Further, the soil with the mycorrhizas had a significantly faster mineralization of oxalic acid over a wide concentration range than did the soil without ectomycorrhizas and without plants. We conclude that the oxalate flux through the soil with both trees and mycorrhizas is much faster than is evident from measurements of solution concentration at steady state. Humic acid had little effect on the concentrations of organic acids or dynamics in the soil solution. Oxalic acid concentrations in the soil solution were correlated with hyphal length, rate of microbial mineralization, soil respiration, and shoot to root weight ratio. We conclude that both mycorrhizas and plants have a large impact on organic acid cycling in forest soils.