Meeting the challenge of scaling up processes in the plant–soil–microbe system

The scaling up of processes in the plant–soil–microbe system represents one of the greatest challenges facing environmental scientists and yet is essential for sustainable land management worldwide. The latter encompasses, for example, the mitigation of and adaptation to anthropogenic climate change, the bioremediation of industrially contaminated sites, catchment management of human pathogens such as Escherichia coli O157 and integrated crop management on the farm. Scaling up is also essential for the regional and global biogeochemical modelling that will inform policy-makers of the critical environmental factors driving climate change. Despite increasing understanding of the links between gene expression and process on a microscale, there is still much progress to be made when relating this to processes at the macroscale. In this paper, we explore the challenges this poses and examine key case studies of successful up-scaling.

Heavy metals in the soil–plant system of the Don River estuarine region and the Taganrog Bay coast

Purpose

The aim of this work was to study the level and degree of mobility of heavy metals in the soil–plant system and to perform bioindication observations in the Don River estuarine region and the Russian sector of the Taganrog Bay coast.

Materials and methods

The objects of the study included samples of zonal soils (chernozem) and intrazonal soils (alluvial meadow and alluvial-stratified soils, Solonchak, sandy primitive soil) from monitoring stations of the Don river estuarine region and the Taganrog Bay coast, as well as their higher plants: Phragmites australis Cav., Typha angustifolia L., Carex riparia Curtis, Cichorium intybus L., Bolboschoenus maritimus L. Palla, and Rumex confertus Willd. The total concentrations of Mn, Ni, Cd, Cu, Zn, Pb, and Cr in the soils were determined by X-ray fluorescent scanning spectrometer. The concentration of heavy metal mobile forms exchangeable, complex compounds, and acid-soluble metal were extracted using the following reagents: 1 N NH₄Ac, pH 4.8; 1 % EDTA in NH₄Ac, pH 4.8; 1 N HCl, respectively. Heavy metals in plants were prepared for analysis by dry combustion at 450 °C. The heavy metal concentration in extracts from plants and soils was determined by AAS.

Results and discussion

The total contents of heavy metals in the soil may be described with a successively decreasing series: Mn?>?Cr?>?Zn?>?Ni?>?Cu?>?Pb?>?As?>?Cd. The total concentrations of As, Cd, and Zn in the soil exceed the maximum permissible concentrations levels. Contamination of alluvial soils in the estuarine zone with mobile Сu, Zn, Pb, and Cd has been revealed, which is confirmed by the high bioavailability of Cu and Zn and, to a lesser degree, Cd and Pb accumulating in the tissues of macrophytic plants. Data on the translocation of elements to plant organs have showed their predominant accumulation in the roots. Bioindication by the morphofunctional parameters of macrophytic plants (with a Typha L. species as an example) can be used for revealing the existence of impact zones with elevated contents of metals in aquatic ecosystems.

Conclusions

The results revealed that increased content of Zn, Pb, Cu, Ni, and As in soil have anthropogenic sources. The high content of Cr in the soils is related to the lithogenic factor and, hence, has a natural source.

     

Manganese‐iron interactions in the plant‐soil system

Dicotyledonous plants had significantly higher Mn and Fe intake rates on a near neutral soil, had a significantly higher Mn intake rate on a slightly calcareous soil, but had lower Mn and Fe intake rates on a calcareous soil, than monocotyledonous plants. This dependency on soil reaction suggests that dicots utilize primarily a chemical reduction mechanism, whereas monocots utilize some less pH‐dependent mechanism (possibly Mn(III)‐, Fe(III)‐organic complexation) to mobilize soil Mn and Fe. Soluble soil Mn and Fe fractions in the rhizosphere were consistently positively correlated with each other, as were Mn and Fe intake rates. These results suggest that for soil‐grown plants, Mn and Fe uptake was positively interrelated because both Mn and Fe were mobilized by similar root processes.     

Nanoplastic–plant interaction and implications for soil health

Nanoplastics (NPs) are accumulating in the soil environment at a rapid rate, which may cause serious consequences for ecosystems and human health. However, environmental behaviour and toxicity of NPs in the soil–plant system remain poorly understood. This review summarizes current studies on NP–plant interactions to unravel uptake mechanisms and phytotoxicity of NPs. NPs could be taken up by plant roots and transported upwards through the xylem to all organs of the plant, even to the edible parts such as the grain, thereby threatening human health. The interaction of NPs with plants affects plant transport of water and nutrients. Besides, it induces significant oxidative stress leading to inhibition of physiological and biochemical activities such as photosynthesis, and thus adversely affects plant growth and development. In addition, the co-transport of NPs with other soil pollutants may induce the combined toxic effects. This study also discussed the potential mechanism of NP–plant interactions based on previous experience with engineered nanomaterials. Finally, a comprehensive assessment of the key challenges in each area was presented, and future perspectives are offered.     

A new soil test method for the determination of plant‐available cadmium in soils

Abstract

A new soil test procedure using 1M NH₄Cl was developed for the extraction of plant‐available cadmium (Cd) from soils. Five grams of soil is weighed into a 50‐mL polyethylene vial to which 30 mL of 1M NH₄Cl solution is added. The soil suspension is then shaken on a horizontal shaker for 16 h at 25°C at 180 cycles per min. The suspension is then centrifuged at 2,500g for 5 min and the supernatant filtered through a 0.45 μm nitrocellulose filter under vacuum. Cadmium in the extract is then determined at 228.8 nm on a graphite furnace equipped atomic absorption spectrophotometer. A highly significant correlation was observed between the natural logarithm (In) of 1M NH₄Cl‐extractable Cd in soils and the Cd content in the grain of durum wheat (Triticum turgidum var. durutn L.) grown on the same soils (r = 0.974, p = 3.8 x 10^‐7). In comparison with several commonly used extradants, such as ABDTPA, CaCl₂, NH₄OAc, and NH₄NO₃, the 1M NH₄Cl‐extracted Cd from soils was found to be a better index of Cd availability.     

Protective mechanism of the soil–plant system with respect to heavy metals

Purpose

The aim of this work was to select and assess the efficiency of different amendments applied to ordinary chernozems artificially contaminated with heavy metals (Zn and Pb).

Materials and methods

The effect of different amendments on ordinary chernozem contaminated with Zn and Pb acetate salts was studied in a long-term 3-year field experiment. Glauconite, chalk, manure, and their combinations were chosen as ameliorating agents. Spring barley (Hordeum sativum) was used as test culture for three successive years. The heavy metal concentration in all the soil samples decomposed by HF?+?HClO₄ was determined by atomic absorption spectrophotometry (AAS). One normal concentration of CH₃COONH₄ at pH 4.8 was used to estimate the actual mobility of metals. The compounds of heavy metals extracted by 1 N HCl are regarded as mobile compounds. The concentration of metals in the plants was determined using the dry combustion in a mixture of HNO₃ and HCl at 450 °C. The content of heavy metals in extracts from soil and plant samples was determined by AAS.

Results and discussion

The content of weakly bound metal compounds increased upon the contamination of the soil with Pb and Zn salts, which led to a low quality of barley grown in these soils. Metal concentrations in the barley grain exceeded the maximum permissible concentrations (MPCs). The content of Zn and Pb in grains was higher than the MPC for at least 3 years after the soil pollution. The application of amendments significantly decreased the mobility of metals, and the simultaneous application of chalk and manure was most significant. The share of weakly bound metal compounds in the contaminated soils decreased to the level typical for the clean soils or even below.

Conclusions

The combined application of chalk and manure to Zn- and Pb-contaminated ordinary chernozems decreased the content of weakly bound metal compounds in the soil and lowered their concentrations in barley plants. The polyfunctional properties of the soil components with respect to their capacity for metal fixation were established. The decrease in the intensity of Zn accumulation in grains of barley shows the presence of a barrier at the root–stalk and stalk–grain interfaces.

     

Changes in δ15N in a soil–plant system under different biochar feedstocks and application rates

The application of biochar in soils has been hypothesised to improve soil quality whilst enhancing carbon (C) sequestration. However, its effect on nitrogen (N) dynamics in the soil–plant system is still not fully understood. In the present work, N isotope composition (δ¹⁵N) was used to facilitate the understanding of the processes involved in the N cycling when biochar is applied. We evaluated, through a wheat pot trial, the effect of different application rates of two types of biochar produced from jarrah and pine woodchips on the wheat biomass at harvest and on the soil and plant C and N contents and δ¹⁵N. In addition, the potential benefit of using nutrient-saturated biochar for the soil–plant system was also investigated. Whilst biochar produced from different feedstocks had similar effects on soil and plant nutrient contents, they induced differences in wheat grain biomass and plant δ¹⁵N. The effect of the biochar application rate was more pronounced, and at rates higher than 29 t ha^?1, the application of biochar decreased grain biomass by up to 39 % and potentially increased N losses. Isotopic analyses indicated that this acceleration of N dynamics had probably occurred before the stage of wheat grain formation. The application of nutrient-enriched biochar resulted in an improved wheat grain production, most likely due to the enhanced nutrient availability, and in reduced N cycling rates in the plant–soil system, which could offset the competition between biochar and plants for nutrients and could decrease adverse environmental impacts due to N losses.     

A method for the determination of β-glucosidase activity in soil

A method is described for the rapid and simple assay of soil β-glucosidase activity. It involves colorimetric estimation of ρ-nitrophenol released by β-glucosidase activity when soil is incubated in McIlvaine buffer (pH 4.8) with ρnitrophenyl βd-glucoside and toluene at 30°C for 1 hr. The method has been applied to three different soils. The range of β-glucosidase activity in cultivated soils was from 10.1 to 15.2 mµ mole per min per gram of dried soil. K_m value for ρ-nitrophenyl β-d-glucoside was 3.3 × 10^-4 M. Optimum pH was 4.8.     

Cropland soil–plant systems control production and consumption of methane and nitrous oxide and their emissions to the atmosphere

Croplands are an important source of atmospheric methane (CH₄) and nitrous oxide (N₂O), both potent greenhouse gases. Reduction of cropland CH₄ and N₂O emissions is expected to mitigate climate change. However, large uncertainty remains in the assessment and prediction of these emissions, which prevents us from establishing appropriate mitigation options and strategies. The uncertainty is attributed mainly to the high spatiotemporal variability in emissions (e.g., emission spikes of N₂O). Understanding and quantifying how hotspots of CH₄ and N₂O production in soil and then hot moments of their emissions occur would help reduce the uncertainty. This review focuses on soil–plant systems, particularly the rhizosphere, as possible hotspots of production and consumption of CH₄ and N₂O. It is well known that the rhizosphere controls CH₄ emission strongly, though each process of production and consumption remains to be quantified. On the other hand, surprisingly little attention has been paid to N₂O, besides the fact that plant roots strongly control nitrification and denitrification. We review the current knowledge of cropland CH₄ and N₂O emissions, and conclude that soil–plant interactions strongly affect cropland emissions of both gases, in which functions of plant roots affecting biogeochemical factors (e.g., availability of oxygen, labile organic carbon and inorganic nitrogen) in the rhizosphere and phenological changes are particularly important. In relation to the status of current knowledge, we discuss future research needed.     

Evaluation of efficient soil test methods for Zn and their critical vales in salt‐affects soils for rice

Abstract

Soil pot culture experiment was conducted on 22 soils of Balewal‐Phaguwala‐Narike (BPN) and 24 soils of Isri‐Langrian‐Narike (ILN) associations using rice (PR 106) as test crop at 0 and 7.5 ppm Zn levels. Chelating extractants 0.005M DTPA, 0.01M EDTA‐(NH₄)₂CO₃ and 0.05M EDTA, extracted more soil Zn than double‐acid and were significantly correlated with each other as well as with soil pH and clay in BPN and only with clay in ILN soil association. Soil CaCO₃ governed the double‐acid extractable Zn in these soils. Dry matter yield and Zn uptake by rice significantly increased with 7.5 ppm Zn application. The response was higher in ILN than BPN soil association, The DTPA method gave the highest correlation with Bray's yield and Zn uptake (r =0.72 and 0.55) followed by 0.05M EDTA (r ‐ 0.75 and 0.61) or EDTA‐(NH₄)₂CO₃ (r =0.70 and 0.61). The predictability of rice yield improved from 18–27 to 27–35, 32–43, 34–44 and 51–55 percent as a result of stepwise inclusion of pH, CaCO₃, organic carbon (OC) and clay respectively in the regression equation alongwith Zn extracted by chelating agents.

The critical levels of DTPA, EDTA‐(NH₄)₂CO₃ and EDTA extractable Zn significantly differed in the two associations and were 0.69, 0.82 and 1.24 ppm in BPN and O.BC, 1.09 and 1.42 ppm in ILN soil association. Soil properties further affected the critical levels. This for DTPA available Zn was 0.80 and 1.03 ppm in soil containing less and greater than 2% CaCO₃, 1.03 and 0.80 ppm in soils containing less and greater than 0.25% OC. These values for EDTA‐(NH₄)₂CO₃ available Zn were 1.09 and 0.91 ppm Zn in soils containing less and greater than 15% clay suggesting that critical levels of Zn for each category of soil properties should be considered while making recommendations of Zn fertilization of crops.,     

Assessment of soil and plant analysis laboratories in the West Asia‐North Africa Region

Abstract

Although limited amount of water is the primary constraint to agricultural productivity in the rainfed area of West Asia and North Africa (WANA), yields are also low because of the poor mineral nutrient status of soils. Yields can, therefore, be considerably increased by judicious fertilizer use. Laboratories for soil and plant analysis are essential for identifying nutrient constraints and providing a basis for efficient fertilizer use, through correlation studies to establish suitable soil testing extractants and calibration studies with crop responses. The Soils Laboratory at the International Center for Agricultural Research in the Dry Areas (ICARDA) has initiated a quality control program among the national agricultural research systems (NARS) in the countries of the WANA region. The efforts include linkages with the Wageningen International Soil Analytical Exchange Program, in‐country training courses, and a laboratory analysis manual. Continued improvement in laboratory performance is dependent upon knowledge of the capabilities of such laboratories and identification of their constraints. This presentation reports a fact‐finding survey of laboratories from 16 countries of the WANA region—mainly public, from universities and ministries of agriculture, and some private or commercial ones—based on a questionnaire about analyses, facilities, methodologies, quality assurance, personnel training, and management. Future efforts to improve the quantity and quality output from of these laboratories will address such deficiencies.     

A computer program to determine the soil textural class in 1–2–3 for windows and excel

Abstract

Spreadsheets are now widely used for data entry and analysis. Therefore, Texture AutoLookup (TAL) is a computer program designed to work within 1–2–3 for Windows and EXCEL to determine the USDA soil textural class. TAL determines the textural class without having to repeat data entry because data is taken directly from the spreadsheet itself. Moreover, TAL works even with two particle size data or with imperfect data (that is, the sum of the three particle sizes being unequal to 100%). TAL is independent of the particle‐size analysis method, and TAL allows textural class names to be modified or be translated into another language.     

Farmers’ perceptions of earthworms and their role in soil

Farmers’ perceptions of earthworms were surveyed based on the criteria they use to identify them, i.e., use of common names, knowledge of morphological characteristics, presence in various land uses, soil layers, as well as direct and indirect use. A total of 39 farmers of the La Vieja River watershed in Colombia were interviewed and the data submitted to chi-square test and multiple correspondence analysis. Significant differences (p < 0.1) were found in farmers’ replies in relation to recognition and use of earthworms depending on gender, level of schooling, and age. According to the interviewees, earthworm abundance was highest in plantain and coffee crops, in places where harvest residues accumulate, and in soil layers from 0 to 20 cm depth. The topsoil was identified as the main area of recognition, which can be attributed to soil preparation tasks. Farmers differentiated earthworms by shape and color and in 97% of the cases, by size and how they react when captured. They recognized nine species and used several common names to differentiate them. Most (95%) farmers considered earthworms as soil quality indicators and many (38–49%) of them recognized their use for recreation and medicinal purposes and as important for soil organic matter decomposition. This study showed the value of local farmer knowledge for scientists as part of research aiming to facilitate communication between farmers and scientists and generate complementary means of addressing and interpreting natural processes and dynamics at the ecosystem level. It also highlights the need to draw from farmers’ perceptions in informal education processes and to link the contributions of scientists to traditional knowledge in order to consolidate proposals related to biodiversity conservation and use in rural development programs.     

Shannon–Weaver index as an integrated indicator of metal differentiation in soil and plant samples

The degree of contrast (differentiation) in the distribution of metals in background and contaminated soils is one of the most important geochemical indicators. The Shannon–Weaver index (H) can be a suitable criterion for the distribution of metals in soil and plant samples. A procedure for calculating the Shannon–Weaver index is described. An index scale of five gradations, from no differentiation (H_rel = 1.0–0.9) to very high differentiation (H_rel = 0.3–0.1), is proposed. The background soils in different regions of Russia have low or even no differentiation of metals. Aerial pollution of soils with heavy metals appreciably increases the degree of metal differentiation, especially near the source of pollution. The parameter value decreases with increasing distance from the pollution source, probably due to the mechanical dilution of dust in the large soil volume.     

Losses of 15N-nitrogen by plant–soil system after herbicide application on black oat

Recent studies have demonstrated that the use of glyphosate or glufosinate-ammonium herbicides for some cover crop desiccation in conservationist systems could favor nitrogen (N) losses from the soil–plant system. In this context, the objective of this study was to evaluate the losses of N by the plant–soil system after the desiccation of black oat (Avena strigosa Schreb.) with the application of herbicides glyphosate, glufosinate-ammonium, or paraquat. Two greenhouse experiments were implemented using black oat plants fertilized with labeled (¹⁵N) ammonium nitrogen, and the N loss of the plant–soil system was quantified. The desiccation of black oat with glyphosate caused a reduction in root dry mass by approximately 60% in both experiments. The glyphosate and glufosinate-ammonium reduced the amount of N present in the aboveground portion; however, the paraquat herbicide did not modify it. None of the herbicides applied affected N losses in the black oat plant–soil system. However, 5–15% of the N applied as fertilizer was lost up to harvest. The results suggest that black oat can be used as a cover crop in direct sowing in order to avoid nitrogen losses in the soil–plant system.