Scoping biological indicators of soil quality Phase II. Defra Final Contract Report SP0534

This report presents results from a field assessment of a limited suite of potential biological indicators of soil quality to investigate their suitability for national-scale soil monitoring

Soil microbial community assembly precedes vegetation development after drastic techniques to mitigate effects of nitrogen deposition

Oligotrophic semi-natural systems are threatened by high levels of nitrogen deposition. To mitigate these effects, drastic techniques such as sod-cutting and topsoil removal are applied to reduce nitrogen loads in existing systems and expand their area on former agricultural fields. We assessed the effects of these techniques along with the influence of previous land-use, isolation and vegetation development on subsequent microbial community assembly in restored agricultural areas. Microbial community phenotypic structure was measured using PLFA-analysis, along with soil chemistry and vegetation development. Differences in soil nitrogen pools due to restoration techniques were the most differentiating factor for both microbial community assembly and vegetation development. Only after topsoil removal was resemblance of both below- and above-ground communities to well-developed heathlands increased within 10–15 years. After sod-cutting both microbial community and vegetation composition remained more similar to agricultural sites. The relative contribution of agricultural sites and heathlands in the direct vicinity had more pronounced effects on local microbial community composition than current land-use in all study sites including agricultural areas and heathlands. Vegetation development was apparently of minor importance for microbial community assembly, since characteristic belowground assembly preceded that of aboveground development in both restoration contexts

On the origin of carbon dioxide released from rewetted soils

When dry soils are rewetted a pulse of CO2 is invariably released, and whilst this phenomenon has been studied for decades, the precise origins of this CO2 remain obscure. We postulate that it could be of chemical (i.e. via abiotic pathways), biochemical (via free enzymes) or biological (via intact cells) origin. To elucidate the relative contributions of the pathways, dry soils were either sterilised (double autoclaving) or treated with solutions of inhibitors (15% trichloroacetic acid or 1% silver nitrate) targeting the different modes. The rapidity of CO2 release from the soils after the drying:rewetting (DRW) cycle was remarkable, with maximal rates of evolution within 6 min, and 41% of the total efflux over 96 h released within the first 24 h. The complete cessation of CO2 eflux following sterilisation showed there was no abiotic (dissolution of carbonates) contribution to the CO2 release on rewetting, and clear evidence for an organismal or biochemical basis to the flush. Rehydration in the presence of inhibitors indicated that there were approximately equal contributions from biochemical (outside membranes) and organismal (inside membranes) sources within the first 24 h after rewetting. This suggests that some of the flux was derived from microbial respiration, whilst the remainder was a consequence of enzyme activity, possibly through remnant respiratory pathways in the debris of dead cells

Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria

The profound negative effect of inorganic chemical fertilizer application on rhizobacterial diversity has been well documented using 16S rRNA gene amplicon sequencing and predictive metagenomics. We aimed to measure the function and relative abundance of readily culturable putative plant growth-promoting rhizobacterial (PGPR) isolates from wheat root soil samples under contrasting inorganic fertilization regimes. We hypothesized that putative PGPR abundance will be reduced in fertilized relative to unfertilized samples. Triticum aestivum cv. Cadenza seeds were sown in a nutrient depleted agricultural soil in pots treated with and without Osmocote⃝R fertilizer containing nitrogen-phosphorous-potassium (NPK). Rhizosphere and rhizoplane samples were collected at flowering stage (10 weeks) and analyzed by culture-independent (CI) amplicon sequence variant (ASV) analysis of rhizobacterial DNA as well as culture- dependent (CD) techniques. Rhizosphere and rhizoplane derived microbiota culture collections were tested for plant growth-promoting traits using functional bioassays. In general, fertilizer addition decreased the proportion of nutrient-solubilizing bacteria (nitrate, phosphate, potassium, iron, and zinc) isolated from rhizocompartments in wheat whereas salt tolerant bacteria were not affected. A “PGPR” database was created from isolate 16S rRNA gene sequences against which total amplified 16S rRNA soil DNA was searched, identifying 1.52% of total community ASVs as culturable PGPR isolates. Bioassays identified a higher proportion of PGPR in non-fertilized samples [rhizosphere (49%) and rhizoplane (91%)] compared to fertilized samples [rhizosphere (21%) and rhizoplane (19%)] which constituted approximately 1.95 and 1.25% in non-fertilized and fertilized total community DNA, respectively. The analyses of 16S rRNA genes and deduced functional profiles provide an in-depth understanding of the responses of bacterial communities to fertilizer; our study suggests that rhizobacteria that potentially benefit plants by mobilizing insoluble nutrients in soil are reduced by chemical fertilizer addition. This knowledge will benefit the development of more targeted biofertilization strategies

Lysis performance of bacteriophages with different plaque sizes and comparison of lysis kinetics after simultaneous and sequential phage addition

Background: Although bacteriophages see a revival for specifically removing undesired bacteria, there is still much uncertainty about how to achieve the most rapid and long-lasting clearance. Materials and Methods: This study investigated the lysis kinetics of three distinct environmental coliphages, reproducibly forming different plaque sizes (big, medium, and small). Lysis performance by individual phages was compared with the one obtained after simultaneous or sequential addition of all three phages. Kinetics was monitored by density absorbance or by flow cytometry, with the latter having the advantage of providing higher sensitivity. Results: Plaque size happened to correlate with lysis kinetics in liquid suspensions, with phages producing big (phage B), medium (phage M), and small (phage S) plaques showing maximal bacterial clearance under the chosen conditions within ∼6, 12, and 18 h, respectively. Use of a phage cocktail (all three phages added simultaneously) resulted in slower initial lysis compared with the fastest lysing phage with the greatest plaque size alone, but it showed longer efficacy in suppression. When adding phages sequentially, overall lysis kinetics could be influenced by administering phages at different time points. The lowest bacterial concentration after 36 h was obtained when administering phages in the sequence S, M, and B although this combination initially took the longest to achieve bacterial clearance. Conclusions: Results support that timing and order of phage addition can modulate strength and duration of bacterial suppression and, thus, influence the overall success of phage treatment

Facilitating ecosystem assembly: plant-soil interactions as a restoration tool

Although plant-soil interactions are increasingly recognized as an important factor in ecosystem restoration, their effects on community assembly during de novo ecosystem establishment are largely unknown. In a heathland restoration trial after topsoil removal we introduced either only aboveground heathland species with fresh herbage or both above- and belowground heathland species with sods to facilitate community assembly. Sod inoculation increased resemblance of the microbial community to the reference system, with a higher fungal and lower bacterial proportion to the community structure. Also densities of bacteriophagous and phytophagous nematodes, Acari and Collembola increased after sod inoculation. The cover of heathland plant species increased by 49% after sod inoculation. The introduction of solely aboveground heathland species increased the cover of these species by only 13%, and did not affect soil community assembly. Additionally, the increase in cover of heathland species over time was inversely correlated to the cover of mesotrophic grassland species. Inverse correlations were also observed between changes in fungal and bacterial abundances. Simultaneous introduction of key species of both above- and below-ground communities had a critical effect on the establishment of both communities, providing a potential shortcut for successful restoration of target ecosystems on disturbed soils

Effect of different organic amendments on actual and achievable yields in a cereal-based cropping system

Soil fertility is at risk in intensive cropping systems when using an exclusive regime of inorganic fertilisers without returning sufficient organic matter to the soil. Our objective was to evaluate the long-term effects of commonly used organic amendments interacting with different rates of inorganic nitrogen fertiliser on crop yields of winter wheat. Yield data from winter wheat were collected for five seasons between 2013 and 2019 from a continuous field trial based at Rothamsted Research, SE England. Organic amendments (anaerobic digestate, compost, farmyard manure, and straw at a rate of 0 and 2.5 ton C per hectare) and five rates of inorganic nitrogen fertiliser (NH4NO3 at 0, 80, 150, 190, 220 kg N ha−1) were applied to winter wheat grown in an arable rotation. At the same inorganic N rate, grain yields for the different organic amendment treatments (excluding the straw treatment) were statistically similar but significantly greater than the unamended control treatment. The nitrogen rate required for optimum yields tended to be lower in plots receiving a combination of organic amendments and mineral fertiliser. Based on the observed and modelled response functions, organic amendments excluding straw increased maximum achievable yields compared to non-amended controls. The size of the effect varied between seasons and amendments (+4.6 to +19.0% of the control yield), increasing the mean maximum achievable yield by 8.8% across four seasons. We conclude that the application of organic amendments can increase the yield potential in winter wheat substantially over what is achievable with inorganic fertiliser only

‘Media events’ reconsidered: from ritual theory to simulation and performativity

This paper re-examines the long-established notion of ‘media events’ by contrasting and critically appraising three distinct approaches to the question of media events. These are: ritual theory associated with Daniel Dayan and Elihu Katz, secondly, Jean Baudrillard’s approach rooted in his notions of simulation and ‘non-events’ and, finally, the more recent performative approaches to media and mediation. I take Sarah Kember and Joanna Zylinska’s reading of media events presented in Life After New Media (2012) as exemplary of the performative approach. An argument is made that the accounts of media events offered by performative approaches add very little, and, indeed, lack the critical insightfulness of the earlier approaches. Both ritual theory and Baudrillard’s thought are briefly reappraised and, against Nick Couldry, I try to show that these accounts are not characterised by binary and reductive thinking. The major misunderstandings concern the nature of the sacred and profane dualism and the further dualisms developed in Baudrillard’s thought, particularly the figures of implosion and reversibility. Finally, Baudrillard’s position on technology is addressed and the paper concludes with the suggestion that his account is not solely negative, since technological developments are not only at the mercy of ironic reversals they may also enable new rituals of disappearance

Urban meadows as an alternative to short mown grassland: Effects of composition and height on biodiversity

There are increasing calls to provide greenspace in urban areas, yet the ecological quality, as well as quantity, of greenspace is important. Short mown grassland designed for recreational use is the dominant form of urban greenspace in temperate regions but requires considerable maintenance and typically provides limited habitat value for most taxa. Alternatives are increasingly proposed, but the biodiversity potential of these is not well understood. In a replicated experiment across six public urban greenspaces we used nine different perennial meadow plantings to quantify the relative roles of floristic diversity and height of sown meadows on the richness and composition of three taxonomic groups – plants, invertebrates and soil microbes. We found that all meadow treatments were colonised by plant species not sown in the plots, suggesting that establishing sown meadows does not preclude further locally determined grassland development if management is appropriate. Colonising species were rarer in taller and more diverse plots, indicating competition may limit invasion rates. Urban meadow treatments contained invertebrate and microbial communities that differed from mown grassland. Invertebrate taxa responded to changes in both height and richness of meadow vegetation, but most orders were more abundant where vegetation height was longer than mown grassland. Order richness also increased in longer vegetation and Coleoptera family richness increased with plant diversity in summer. Microbial community composition seems sensitive to plant species composition at the soil surface (0–10 cm), but in deeper soils (11–20 cm) community variation was most responsive to plant height, with bacteria and fungi responding differently. In addition to improving local residents’ satisfaction, native perennial meadow plantings can produce biologically diverse grasslands that support richer and more abundant invertebrate communities, and restructured plant, invertebrate and soil microbial communities compared with short mown grassland. Our results suggest that diversification of urban greenspace by planting urban meadows in place of some mown amenity grassland is likely to generate substantial biodiversity benefits, with a mosaic of meadow types likely to maximise such benefits

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