Impacts of epigeic, anecic and endogeic earthworms on metal and metalloid mobility and availability

The introduction of earthworms into soils contaminated with metals and metalloids has been suggested to aid restoration practices. Eisenia veneta (epigeic), Lumbricus terrestris (anecic) and Allolobophora chlorotica (endogeic) earthworms were cultivated in columns containing 900 g soil with 1130, 345, 113 and 131 mg kg1 of As, Cu, Pb and Zn, respectively, for up to 112 days, in parallel with earthworm-free columns. Leachate was produced by pouring water on the soil surface to saturate the soil and generate downflow. Ryegrass was grown on the top of columns to assess metal uptake into biota. Different ecological groups affected metals in the same way by increasing concentrations and free ion activities in leachate, but anecic L. terrestris had the greatest effect by increasing leachate concentrations of As by 267%, Cu by 393%, Pb by 190%, and Zn by 429% compared to earthworm-free columns. Ryegrass grown in earthworm-bearing soil accumulated more metal and the soil microbial community exhibited greater stress. Results are consistent with earthworm enhanced degradation of organic matter leading to release of organically bound elements. The degradation of organic matter also releases organic acids which decrease the soil pH. The earthworms do not appear to carry out a unique process, but increase the rate of a process that is already occurring. The impact of earthworms on metal mobility and availability should therefore be considered when inoculating earthworms into contaminated soils as new pathways to receptors may be created or the flow of metals and metalloids to receptors may be elevated

Adult-perpetrated Animal Abuse: Development of a Proclivity Scale

There is a clear discrepancy in the reporting of animal cruelty complaints, prosecutions and convictions suggesting that any prevalence figures of abuse are significant under-representations. Therefore, it can be inferred that there is a large number of animal abusers who are unapprehended. Currently there is no validated tool that assesses the proclivity or propensity to engage in animal abuse amongst members of the general public. Such a tool would enable researchers to study individuals who may think like animal abusers or may be unapprehended offenders themselves. This paper presents the newly developed Animal Abuse Proclivity Scale (AAPS) and some preliminary findings. The results from our two studies show that: (1) the psychometric properties of the AAPS indicate that the scale is a highly reliable measure; (2) the AAPS relates to measures assessing offence-supportive attitudes and reflects the gender differences seen in the literature; and (3) the AAPS demonstrates cross-national validity. These findings support that the AAPS, similar to other offending proclivity measures, is a tool that can be used to examine the factors most related to animal abuse propensity. We discuss how the AAPS can contribute to future developments in theory and practice in the field

Dynamics of Charcoal Alteration in a Tropical Biome: A Biochar-Based Study

Pyrogenic carbon (PyC) is a polyaromatic residue of the incomplete combustion of biomass or fossil fuels. There is a growing recognition that PyC forms an important part of carbon budgets, due to production rates of 116–385 Tg C yr, and the size and ubiquity of PyC stocks in global carbon reservoirs. At least a proportion of PyC exists in a highly recalcitrant chemical form, raising the prospect of long-term carbon sequestration through soil amendment with “biochar,” which is generally produced with the aim of making a particularly recalcitrant form of PyC. However, there is growing evidence that some PyC, including biochar, can be both physically and chemically altered and degraded upon exposure to the environment over annual timescales, yet there is a lack of information concerning the mechanisms and determining factors of degradation. Here, we investigate three main factors; production temperature, feedstock composition, and the characteristics of the environment to which the material is exposed (e.g., pH, organic matter composition, oxygen availability) by analysis of biochar samples in a litterbag experiment before and after a year-long field study in the tropical rainforests of northeast Australia. We find that non-lignocellulosic feedstock has lower aromaticity, plus lower O/C and H/C ratios for a given temperature, and consequently lower carbon sequestration potential. The rate at which samples are altered is production temperature-dependant; however even in the highest temperature samples loss of the semi-labile aromatic carbon component is observed over 1 year. The results of 13C-MAS-NMR measurements suggest that direct oxygenation of aromatic structures may be even more important than carboxylation in environmental alteration of biochar (as a subset of PyC). There is a clear effect of depositional environment on biochar alteration even after the relatively short timescale of this study, as changes are most extensive in the most oxygenated material that was exposed on the soil surface. This is most likely the result of mineral ingress and colonization by soil microbiota. Consequently, oxygen availability and physical or chemical protection from sunlight and/or rainwater is vital in determining the alteration trajectory of this material

The importance of soil and vegetation characteristics for establishing ground-nesting bee aggregations

Most bee species are ground-nesters, yet knowledge on the nesting behaviour of this diverse group remains sparse. Evidence on the effectiveness of ground-nesting bee species as crop pollinators is growing, but there is limited information on their nesting habits and preferences and how to manage habitats to enhance populations on farms. In this study, artificially prepared plots of bare soil were constructed with the aim to attract ground-nesting bees to nest in a commercial orchard in Kent, UK. Nine soil parameters were measured to determine their preferred soil properties: hydraulic conductivity, soil compaction, soil moisture, soil temperature, soil stoniness, soil organic matter, soil root biomass, soil texture and vegetation cover. Eighteen non-parasitic ground-nesting bee species (7 Andrena, 9 Lasioglossum, 1 Halictus and 1 Colletes spp.) were recorded in the study plots. Soil stoniness and soil temperature at 10cm depth were positively correlated, and vegetation cover and hydraulic conductivity were negatively correlated with the number of ground-nesting bees on the plots. We show that artificially created habitats can be exploited for nesting by several ground-nesting bee species. This study’s findings can inform management practices to enhance ground-nesting bee populations in agricultural and urban areas

First 20 years of DNDC: Model evolution and GRAMP.

The DNDC (DeNitrification and DeComposition) model was first developed by Li et al. (1992) as a rain event-driven process-orientated simulation model for nitrous oxide, carbon dioxide and nitrogen gas emissions from the agricultural soils in the U.S. Over the last 20 years, the model has been modified and adapted by various research groups around the world to suit specific purposes and circumstances. The Global Research Alliance Modelling Platform (GRAMP) is a UK-led initiative for the establishment of a purposeful and credible web-based platform initially aimed at users of the DNDC model. With the aim of improving the predictions of soil C and N cycling in the context of climate change the objectives of GRAMP are to: 1) to document the existing versions of the DNDC model; 2) to create a family tree of the individual DNDC versions; 3) to provide information on model use and development; and 4) to identify strengths, weaknesses and potential improvements for the model

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care

COVID-19 trajectories among 57 million adults in England: a cohort study using electronic health records

BACKGROUND: Updatable estimates of COVID-19 onset, progression, and trajectories underpin pandemic mitigation efforts. To identify and characterise disease trajectories, we aimed to define and validate ten COVID-19 phenotypes from nationwide linked electronic health records (EHR) using an extensible framework. METHODS: In this cohort study, we used eight linked National Health Service (NHS) datasets for people in England alive on Jan 23, 2020. Data on COVID-19 testing, vaccination, primary and secondary care records, and death registrations were collected until Nov 30, 2021. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity and encompassing five categories: positive SARS-CoV-2 test, primary care diagnosis, hospital admission, ventilation modality (four phenotypes), and death (three phenotypes). We constructed patient trajectories illustrating transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status. FINDINGS: Among 57 032 174 individuals included in the cohort, 13 990 423 COVID-19 events were identified in 7 244 925 individuals, equating to an infection rate of 12·7% during the study period. Of 7 244 925 individuals, 460 737 (6·4%) were admitted to hospital and 158 020 (2·2%) died. Of 460 737 individuals who were admitted to hospital, 48 847 (10·6%) were admitted to the intensive care unit (ICU), 69 090 (15·0%) received non-invasive ventilation, and 25 928 (5·6%) received invasive ventilation. Among 384 135 patients who were admitted to hospital but did not require ventilation, mortality was higher in wave 1 (23 485 [30·4%] of 77 202 patients) than wave 2 (44 220 [23·1%] of 191 528 patients), but remained unchanged for patients admitted to the ICU. Mortality was highest among patients who received ventilatory support outside of the ICU in wave 1 (2569 [50·7%] of 5063 patients). 15 486 (9·8%) of 158 020 COVID-19-related deaths occurred within 28 days of the first COVID-19 event without a COVID-19 diagnoses on the death certificate. 10 884 (6·9%) of 158 020 deaths were identified exclusively from mortality data with no previous COVID-19 phenotype recorded. We observed longer patient trajectories in wave 2 than wave 1. INTERPRETATION: Our analyses illustrate the wide spectrum of disease trajectories as shown by differences in incidence, survival, and clinical pathways. We have provided a modular analytical framework that can be used to monitor the impact of the pandemic and generate evidence of clinical and policy relevance using multiple EHR sources. FUNDING: British Heart Foundation Data Science Centre, led by Health Data Research UK

Soil-borne pahtogens and their interactions with the soil environment

Wheat yields in 13th Century Europe have been estimated at 385 kg ha-1 (1 & 2), more than half a millennium later, by 1939 they had been increased to little more than 2 t ha-1. Subsequently, in the period 1952-1986 scientific and technologically based innovation applied to farming increased yields by an average value of 2.6 % pa. It is predicted that wheat yields will rise to 10.48-13.69 t ha-1 by 2015, with a current theoretical biological ceiling of 19.2 t ha-1 (3). These rising yields have been accompanied by a 10-fold increase in the amount of nitrogen applied to wheat in 1943/1945-1994 (2). They represent one example of what has been achieved by a combination of genotype (plant breeding) and environmental modification increasing the nutrients available to the plant in step with its physiological demands and fending-off consequential invasions by pests and pathogens attendant on rapid growth and high yields. Burgeoning human populations, reaching an estimated 10 billion by 2050, demand that similar yield increases are continued and accelerated. The environmental and climatic consequences arising from a policy of raising yield solely by increasing inputs are becoming apparent as dangerously unsustainable. Dramatic changes in the manner by which crops are husbanded are required with the aim of achieving increased yield but with minimal damage to the World’s ecosystems (4). Concomitant with the need to continue and accelerate yield increases in order to fill empty stomachs and enhance lifestyles far greater control of pests and pathogens using intelligent, integrated and environmentally benign methods based on sound scientific knowledge of the intimate relationships of beneficial microbes, roots, soil and pest and pathogen biology is required for the health of our Planet’s environment and biodiversity. So far, our knowledge of soil microbiology is at best scant and fragmentary and at worst non-existent. Yet as shown in this Book the agronomic opportunities for enhanced productivity offered by the soil and its inhabitants are huge. Soils contain very substantial numbers of phytopathogenic microbes capable of devastating crops worldwide. These include representatives of the bacteria, fungi, mycoplasma, protista and viruses. Some pathogens have very limited and highly specific host ranges while others are generalists, to a lesser or greater degree, causing diseases across many host taxa. Similarly, their geographical ranges may be restricted or alternatively spread around the entire globe. The intensity of pathogenesis varies also from those which devastate crops by ultimately killing their hosts in the processes of colonisation and reproduction to those which are only mildly aggressive and possibly almost commensalists. The forms of disease syndrome generated in crop hosts vary from simple root invasion and rotting through to altered root growth e.g. root galling and clubbing, to collar rotting and damping-off into vascular wilting and colonisation throughout all the aerial organs of the plant. Some pathogens invade early in the host life-cycle and may then enter a quiescent or dormant phase from which they re-emerge devastating maturing flowers and fruit or destroying products stored after harvesting from the crop. Indeed some pathogens are only apparent from the toxins which they elicit in stored products. The extensive range of pathogenic lifestyles available to soil-borne microbes increases the problems facing plant pathologists striving to unravel their biology. These difficulties are compounded by the sheer physical obscurity resulting from dwelling either wholly or at least partially in soil. Attempting to ascribe taxonomic identity and to understand the life-cycle biology of organisms that conduct all or part of their life-cycles and subsequently are enclosed in the bodies of their host plants is a complex and at times confusing task. Adding to these problems are barriers in understanding the physiology and metabolism of host roots which are the primary targets for invasion by soil-borne pathogens. Roots possess a modular structure as described by Hodge (5) permitting responses to their soil environment and adaptation to changes, some of which are a result of the presence of pathogenic microbes. In achieving adaptation the roots differentiate between adopting partnership modes with benign microbes which enhance the potential efficiency for resource capture (see other Chapters in this volume) and adopting defensive modes as a reaction to the presence of pathogens. The root-cap region appears to be the main environmental sensing and response control centre. Recent research indicates apparent root-to-root interactions and the capacity for recognising ‘self’ and non-self’ roots (6). Root exudates possibly form one means for positive communication with benign microbes and negative responses to pathogens (7). Developing husbandries which are both economically and environmentally sustainable demands a thorough understanding of the impact and interactions between host roots, benign microbes and pathogenic organisms. Pathogens are capable of wreaking either rapid crop destruction or causing the long-term degeneration and decline of hosts possibly without their presence being easily obvious. This Chapter discusses the abilities of pathogenic microbes to cause diseases as moderated by the soil environment and influenced by husbandry practices. Soil-borne microbial pathogens are well evolved and efficiently fitted for their ecological niches, for example as described by Dixon (8) for Plasmodiophora brassicae, the causal agent of Clubroot Disease in the Brassicaceae. Ecologically soil-borne microbes exploit their edaphic and in planta environments with high degrees of effectiveness. Their traits of pathogenic success are indicative of organisms with long established and well tested lifestyles. Herein is one of the major mysteries associated with these crop pathogens. The pathogenic microbe is frequently found only sporadically within natural ecosystems or may be apparently entirely absent. They appear to have evolved their current lifestyles in parallel with their hosts as these were domesticated by man. Devastating disease epidemics appear to result from or be associated with extensive and intensive mono-cropping of vulnerable host genotypes. In this context the pathogens cause “iatrogenic diseases of cultivation”. The consequence of this status for sustainable crop production demands environmentally balanced disease control achieved by using husbandry systems which are compatible with host growth and productivity and the maintenance of benign microbe populations which benefit the host. This means integrating husbandry, biological, chemical, genetical and legislative techniques into logical and coherent strategies. Acceptance of this approach reflects changing agronomic attitudes driven at least partially by the withdrawal of toxic chemical agents such as the sterilant methyl bromide (9). Considerable re-appraisal of the importance of cultural controls and the needs for crop protection strategies using integrated systems aiming to stimulate host growth and reproduction, encourage soil health and repress pathogens result from this approach

Colon extended physiologically based extraction test (CE-PBET) increases bioaccessibility of soil-bound PAH

Assessment of the risk to human health posed by contaminated land may be seriously overestimated if reliant on total pollutant concentration. In vitro extraction tests, such as the physiologically based extraction test (PBET), imitate the physicochemical conditions of the human gastro-intestinal tract and offer a more practicable alternative for routine testing purposes. However, even though passage through the colon accounts for approximately 80% of the transit time through the human digestive tract and the typical contents of the colon in vivo are a carbohydrate-rich aqueous medium with the potential to promote desorption of organic pollutants, PBET comprises stomach and small intestine compartments only. Through addition of an eight-hour colon compartment to PBET and use of a carbohydrate-rich fed-state medium we demonstrated that colon-extended PBET (CE-PBET) in- creased assessments of soil-bound PAH bioaccessibility by up to 50% in laboratory soils and a factor of 4 in field soils. We attribute this increased bioaccessibility to a combination of the additional extraction time and the presence of carbohydrates in the colon compartment, both of which favor PAH desorption from soil. We propose that future assessments of the bioaccessibility of organic pollutants in soils using physiologically based extraction tests should have a colon compartment as in CE-PBET