Plant, soil and faunal responses to a contrived pH gradient

© 2021, The Author(s). Purpose: To build a more holistic understanding of soil pH change we assessed the synchronised effects of a contrived soil pH change on soil chemistry, vegetation growth and nutrition, and soil faunal abundance and diversity. Methods: We established a fifteen year old field experiment with a contrived pH gradient (pH 4.3 to 6.3) and measured the effect on soil chemistry, plant biomass and elemental composition and the impact of these changes on soil fauna (earthworms, nematodes, rotifers and tardigrades) and biological indices (based on ecological group structures of earthworms and nematodes). A single 20 × 20 × 20 cm soil block was excavated from each sample site to directly attribute biotic parameters in the block to the abiotic (soil) conditions. Results: Acidification affected the extractable concentrations of Al, Ca, Mn and P and the C:N ratio of the soil and caused a reduction in plant Ca (rs for pH vs Ca = 0.804 p < 0.01), an increase in plant Mn (rs = −0.450 p = 0.019), along with significant decrease in root:shoot ratio (rs = 0.638, p < 0.01). There was a significant positive correlation between pH and earthworm index (rs = 0.606, p < 0.01), and a negative correlation between pH and nematode index (rs = −0.515, p < 0.01). Conclusion: Soil pH influenced the mobility of Ca, Al, Mn and P, which in turn has impacted on plant tissue chemistry and plant biomass ratios. Linked changes in soil chemistry and vegetation had a corresponding effect on the abundance and diversity of nematodes and earthworms in the soil blocks

LEGO® bricks as building blocks for centimeter-scale biological environments

LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil

Plant growth environments with programmable relative humidity and homogeneous nutrient availability

We describe the design, characterization, and use of “programmable”, sterile growth environments for individual (or small sets of) plants. The specific relative humidities and nutrient availability experienced by the plant is established (RH between 15% and 95%; nutrient concentration as desired) during the setup of the growth environment, which takes about 5 minutes and <1$ in disposable cost. These systems maintain these environmental parameters constant for at least 14 days with minimal intervention (one minute every two days). The design is composed entirely of off-the-shelf components (e.g., LEGO® bricks) and is characterized by (i) a separation of root and shoot environment (which is physiologically relevant and facilitates imposing specific conditions on the root system, e.g., darkness), (ii) the development of the root system on a flat surface, where the root enjoys constant contact with nutrient solution and air, (iii) a compatibility with root phenotyping. We demonstrate phenotyping by characterizing root systems of Brassica rapa plants growing in different relative humidities (55%, 75%, and 95%). While most phenotypes were found to be sensitive to these environmental changes, a phenotype tightly associated with root system topology – the size distribution of the areas encircled by roots – appeared to be remarkably and counterintuitively insensitive to humidity changes. These setups combine many of the advantages of hydroponics conditions (e.g., root phenotyping, complete control over nutrient composition, scalability) and soil conditions (e.g., aeration of roots, shading of roots), while being comparable in cost and setup time to Magenta® boxes

Long-term acidification of pH neutral grasslands affects soil biodiversity, fertility and function in a heathland restoration

In the wider context of heathland restoration, we investigated how field scale experimental acidification with sulphur (sulfur)affected soil biodiversity, fertility and function over a period of 17 years. A field experiment was conducted in the Isle of Purbeck, England, using ferrous sulphate and elemental sulphur as acidifying agents. We tested the effects of acidification on soil fertility, plant communities, litter decomposition, microbiology (including fungi bacteria and actinomycetes), arbuscular and ericoid mycorrhizal colonisation, and soil fauna (including earthworms, nematodes, rotifers and tardigrades). We found that elemental sulphur had a considerable and persistent effect on soil pH, lowering it to levels found in the surrounding reference acid grassland and heathland sites. A newly adapted heathland restoration index based on soil chemistry, found that elemental sulphur was by far the most successful treatment leading to soil conditions similar to the heathlands. Overall, acidification caused a loss of base cations and an increase in toxic aluminium compounds. Consequently the more mesotrophic components of soil biology were reduced by acidification during the course of the experiment. This transformed the soil biological system into one typical of acid grasslands and heathlands. Concomitant litter decomposition was similarly inhibited by acidification, with the microbiota more strongly hindered in acidified soil than the macroscopic fauna. Acidification resulted in a reduction in nematode and rotifer abundance and earthworm biomass. The vegetation community was also strongly modified by the elemental sulphur treatments and, where grazing was restricted, soil acidification allowed a restored heathland community to endure. Arbuscular mycorrhizal colonisation of grasses was reduced where heather plants were established, while ericoid mycorrhizas had developed sufficient populations in the acidified pastures to match the colonisation rate in the native heathlands

Bioaccumulation of total mercury in the earthworm Eisenia andrei

Earthworms are a major part of the total biomass of soil fauna and play a vital role in soil maintenance. They process large amounts of plant and soil material and can accumulate many pollutants that may be present in the soil. Earthworms have been explored as bioaccumulators for many heavy metal species such as Pb, Cu and Zn but limited information is available for mercury uptake and bioaccumulation in earth- worms and very few report on the factors that influence the kinetics of Hg uptake by earthworms. It is known however that the uptake of Hg is strongly influenced by the presence of organic matter, hence the influence of ligands are a major factor contribut - ing to the kinetics of mercury uptake in biosystems. In this work we have focused on the uptake of mercury by earthworms ( Eisenia andrei ) in the presence of humic acid (HA) under varying physical conditions of pH and temperature, done to assess the role of humic acid in the bioaccumulation of mercury by earthworms from soils. The study was conducted over a 5-day uptake period and all earthworm samples were analysed by direct mercury analysis. Mercury distribution profiles as a function of time, bioac- cumulation factors (BAFs), first order rate constants and body burden constants for mercury uptake under selected conditions of temperature, pH as well as via the dermal and gut route were evaluated in one comprehensive approach. The results showed that the uptake of Hg was influenced by pH, temperature and the presence of HA. Uptake of Hg 2 + was improved at low pH and temperature when the earthworms in soil were in contact with a saturating aqueous phase. The total amount of Hg 2 + uptake decreased from 75 to 48 % as a function of pH. For earthworms in dry soil, the uptake was strongly influenced by the presence of the ligand. Calculated BAF values ranged from 0.1 to 0.8. Mercury uptake typically followed first order kinetics with rate constants determined as 0.2 to 1 h ? 1 .Scopus 201

Improvement of soil structure and crop yield by adding organic matter to soil (AHDB Project Report No.576)

Soil quality is intimately linked with soil biology. Recent research at Rothamsted Research (RRes) has shown that addition of Farm Yard Manure (FYM) can improve barley grain and straw yield within two years by more than 1t ha−1 each. Penetrometer measurements attribute this increase to an improvement in ease of root exploration in the soil, which, in turn, may be attributed to an increase in earthworm biomass and activity. These results suggest benefits from adding the right kind of organic matter can be achieved relatively rapidly in soils by feeding the soil organisms, which then bring about desirable changes in soil condition. We hypothesised crop yields will increase quickly (within four years) as a result of improved soil physical condition that results from feeding soil organisms, especially earthworms, with relatively small amounts of suitable organic matter additions. To test these ideas, we set up field experiments at Rothamsted Research farm (flinty clay loam soil) in Harpenden between 2012 to 2017. The four harvest years of the project allowed three field experiments to run. These covered two tillage regimes, four arable crop rotation combinations, five nitrogen treatments and fourteen organic matter recipes at a range of concentrations. Additionally, two outdoor pot experiments, growing winter wheat under a range of earthworm amendments, seven organic matter recipes and four soil types, were studied. The influence on soil physical properties, crop yields and earthworm populations were examined on selected plots and pots. Different methods were used on selected plots to examine soil physical properties. Methods included bulk density, infiltration, penetrometer, aggregate stability, resistance to ploughing or CT scans of the pores in soil. Earthworm populations were determined on selected plots by handsorting one 20 x 20 x 20cm cube taken from a plot. Microbial biomass, fungal biomass and microbial community composition were also measured. Five commercial growers’ trials were held at Haines Barn, Woodbridge, Butterwick, Terrington and Spalding (England). Data from three independent trials at AFBI (Northern Ireland), three at NIAB (England) and one at JHI (Scotland) were also included. These data included some yield data on cereal or horticulture cultivations, soil physical measurements and an earthworm survey. Crop yields were determined on every plot, with a beneficial yield effect detected on both the Rothamsted trials after two years of amendments. Amended soils in a pot experiment testing the effect of soil type had more tillers and greater grain masses than unamended soils but there was no significant difference between soil types. Yield improvement in a European study did increase with texture in the order clay<silty clay loam<sand. Differences in soil physical properties were not evident after two years. This was linked to the high proportion of flint in these soils (20 % stones by volume) affecting some of the methods. Adding organic amendments to soil in two field experiments was found to change the yield response of four crops (spring barley, winter wheat, oilseed rape, winter oats) to N. Amendments increased yields but by a greater amount in a tilled system than a system with reduced tillage. An increasing amount of amendment increased yield but there is evidence of a maximum in this response to amendment, beyond which the yield response declines. The amendments contained nutrients which helps to explain why crops yield well at low rates of mineral N application but not why they yield more overall. The full benefits from amending soil does not appear immediately and two or three years of application may be needed. Spring crops appear to benefit more than winter crops but in years when yields are good the benefits of amending soil are less clear, both in absolute and relative terms. Quality was either unaffected by amendment (N) or improved (TGW) and to the extent that might attract a premium (oil). A straightforward economic analysis suggests that acquiring and spreading amendments should cost no more than £50 t−1 C spread if amending is to be economic. Several additional pieces of work were undertaken to try to understand why yields respond to organic amendments. Our initial hypothesis was that organisms rearrange the structure of soil to their own benefit while dwelling there and that this in turn improved the environment for crops. Amendments increased microbial biomass, earthworm biomass (g m−2) and numbers (m−2) on certain occasions but there was no overall statistical difference between amendments and no statistically consistent benefit to mass or numbers of organisms. Means to increase earthworm numbers, such as grinding up part of the amendment to make it more easily ingested by earthworms, staging the application four times per year or eliminating fungicide from the earthworm’s diet, all increased earthworm numbers and biomass but did not increase yields in the field. All wheat crops grown with non-crop residue amendments were first wheats in these experiments. However, FYM was found to have altered N response curve of wheat in historic experiments where take-all was additionally present, such that up to 1t extra grain ha−1 was obtained. Infiltration of water through soil was increased by amending soil, but not significantly. The plough draught forces (in kPa) were significantly reduced by amending soil and in proportion to the amount and energy content of the amendments. No significant difference, however, was found in measurements of soil mechanical impedance to a hand-operated penetrometer, nor in bulk density. However, there was no significant relationship between draught forces in autumn with the yield the following summer except, between autumn 2014 and summer 2015. Despite the lack of conclusive evidence, it is surmised that amendments increase yield and that the most plausible mechanism is that the soil organisms have improved the structure or the ease with which the plant can rearrange the soil structure to its own benefit

A simple and versatile 2-dimensional platform to study plant germination and growth under controlled humidity

We describe a simple, inexpensive, but remarkably versatile and controlled growth environment for the observation of plant germination and seedling root growth on a flat, horizontal surface over periods of weeks. The setup provides to each plant a controlled humidity (between 56% and 91% RH), and contact with both nutrients and atmosphere. The flat and horizontal geometry of the surface supporting the roots eliminates the gravitropic bias on their development and facilitates the imaging of the entire root system. Experiments can be setup under sterile conditions and then transferred to a non-sterile environment. The system can be assembled in 1-2 minutes, costs approximately 8.78$per plant, is almost entirely reusable (0.43$ per experiment in disposables), and is easily scalable to a variety of plants. We demonstrate the performance of the system by germinating, growing, and imaging Wheat (Triticum aestivum), Corn (Zea mays), and Wisconsin Fast Plants (Brassica rapa). Germination rates were close to those expected for optimal conditions

Legacy effect of constant and diurnally oscillating temperatures on soil respiration and microbial community structure.

Raw data for the publication 'Legacy effect of constant and diurnally oscillating temperatures on soil respiration and microbial community structure' comprising respiration measurements, soil properties, and phospholipid fatty acid analysis of incubated soils. Abstract: Laboratory incubation studies evaluating the temperature sensitivity of soil respiration often use measurements of respiration taken at a constant incubation temperature from soil that has been pre-incubated at the same constant temperature. However, such constant temperature incubations do not represent the field situation where soils undergo diurnal temperature oscillations. We investigated the effects of constant and diurnally oscillating temperatures on soil respiration and soil microbial community composition. A grassland soil from the UK was either incubated at a constant temperature of 5 ℃, 10 ℃, or 15 ℃, or diurnally oscillated between 5 ℃ and 15 ℃. Soil CO2 flux was measured by temporarily moving incubated soils from each of the abovementioned treatments to 5 ℃, 10 ℃ or 15 ℃, such that soils incubated at each temperature had CO2 flux measured at every temperature. We hypothesised that, irrespective of measurement temperature, CO2 emitted from the 5 ℃ to 15 ℃ oscillating incubation would be most similar to the soil incubated at 10 ℃. The results showed that both incubation and measurement temperatures influence soil respiration. Incubating soil at a temperature oscillating between 5 ℃ and 15 ℃ resulted in significantly greater CO2 flux than constant incubations at 10 ℃ or 5 ℃, but was not significantly different to the 15 ℃ incubation. The greater CO2 flux from soils incubated at 15 ℃, or oscillating between 5 ℃ and 15 ℃, coincided with a depletion of dissolved organic carbon and a shift in the phospholipid fatty acid profile of the soil microbial community, consistent with the thermal adaptation of microbial communities to higher temperatures. However, diurnal temperature oscillation did not significantly alter Q10. Our results suggest that daily maximum temperatures are more important than daily minimum or daily average temperatures when considering the response of soil respiration to warming

Data for: Differential Temperature Sensitivity of Intracellular and Extracellular Soil Enzyme Activities

We pre-incubated soils at 5 °C, 15 °C or 26 °C to acclimatise the microbial communities to different thermal regimes for 60 days before measuring potential activities of β-glucosidase and chitinase (extracellular enzymes), glucose-induced respiration (intracellular enzymes), and basal respiration at a range of assay temperatures (5 °C, 15 °C, 26 °C, 37 °C, and 45 °C). There are four datasets provided here:Soil properties measured after the pre-incubation (pH, C, N, C/N ratio, and microbial biomass C)β-glucosidase potential activity (pNP µg g dry soil h-1)Chitinase potential activity (pNP µg g dry soil h-1)CO2 flux (respiration) (mg C g soil h-1

Data for: Feedstock nitrogen content mediates maximum possible Pb sorption capacity of biochars

Biochars were produced from four different feedstock materials: hay, wheat straw, coco coir, and pine bark. The feedstock materials were packed in steel containers with a small hole cut into the lid to avoid pressure build up. The containers were heated to the desired temperature for one hour using a Gallenkamp Muffle furnace to pyrolyse the feedstocks and then allowed to cool overnight before the biochar was removed. Biochars were made from each of the four feedstocks at 300 °C, 350 °C, 400 °C, 450 °C, 500 °C, 550 °C, 600 °C, 650 °C, 700 °C, and 750 °C, resulting in a total of 40 different biochars. The biochars were each ground to a fine powder using a TEMA T100ACH Laboratory Disc Mill.Biochar pH was determined in triplicate by shaking 1g of biochar with 20ml of ultra-pure water for 30 minutes and measuring the pH of the biochar/water slurry. Approximately 4 mg of each ground biochar and feedstock sample was analysed for total carbon and nitrogen content by dry combustion using a Thermo Scientific Flash 2000 Organic Elemental Analyser. Biochars and feedstocks were digested in nitric acid prior to determination of Ca, Mg, K, P, S, Na, Cu, Pb, Mn, Zn, Al, and Fe by the ICP-OES (Inductively Coupled Plasma Optical Emission Spectroscopy). Pb batch adsorption isotherms were carried out for each of the 40 biochars using five Pb solutions (100, 200, 500, 1000, and 5000 mg Pb L-1) prepared by serial dilution of a 5000 mg L-1 stock solution of lead nitrate made by dissolving Analytical grade Pb (NO3)2 in &gt; 18.2 MΩ.cm water. Milled biochar (1 g ± 0.05 g) was weighed into a 50 ml centrifuge tube and 30 ml of Pb solution was added to each sample. Samples were placed in a rotary end-over-end shaker at 20 inversions per minute, at a controlled temperature of 20 °C for 24 hours for to ensure equilibrium between biochar surfaces and the Pb in solution. After 24 hours, samples were removed from the shaker and the pH was measured and recorded. Samples were then centrifuged at 3600 rpm for 15 minutes to separate the biochar particles from solution using a Mistral 3000i centrifuge. The supernatant was filtered through a Whatman no. 5 filter paper. Further filtration was carried out using a 0.2 µm cellulose membrane syringe filter. Samples were then diluted and acidified using concentrated nitric acid (HNO3) and analysed for Pb concentration using an ICP-OES.Cs is the Pb concentration on biochar (mg g-1), Ci is the initial solution Pb concentration (mg L-1), Caq is the final solution Pb concentration (mg L-1), V is the solution volume (L), and Sm is the mass of biochar (g)