Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time.

BACKGROUND: Soil and phyllosphere (leaves and fruit) microbes play critical roles in the productivity and health of crops. However, microbial community dynamics are currently understudied in orchards, with a limited number incorporating temporal monitoring. We used 16S rRNA gene amplicon sequencing to investigate bacterial community temporal dynamics and community assembly processes on the leaves and fruit, and in the soil of 12 kiwifruit orchards across a cropping season in New Zealand. RESULTS: Community composition significantly differed (P < 0.001) among the three sample types. However, the communities in the phyllosphere substrates more closely resembled each other, relative to the communities in the soil. There was more temporal stability in the soil bacterial community composition, relative to the communities residing on the leaves and fruit, and low similarity between the belowground and aboveground communities. Bacteria in the soil were more influenced by deterministic processes, while stochastic processes were more important for community assembly in the phyllosphere. CONCLUSIONS: The higher temporal variability and the stochastic nature of the community assembly processes observed in the phyllosphere communities highlights why predicting the responsiveness of phyllosphere communities to environmental change, or the likelihood of pathogen invasion, can be challenging. The relative temporal stability and the influence of deterministic selection on soil microbial communities suggests a greater potential for their prediction and reliable manipulation.

Defining the spatial distribution of extracellular adenosine revealed a myeloid-dependent immunosuppressive microenvironment in pancreatic ductal adenocarcinoma.

BACKGROUND: The prognosis for patients with pancreatic ductal adenocarcinoma (PDAC) remains extremely poor. It has been suggested that the adenosine pathway contributes to the ability of PDAC to evade the immune system and hence, its resistance to immuno-oncology therapies (IOT), by generating extracellular adenosine (eAdo). METHODS: Using genetically engineered allograft models of PDAC in syngeneic mice with defined and different immune infiltration and response to IOT and autochthonous tumors in KPC mice we investigated the impact of the adenosine pathway on the PDAC tumor microenvironment (TME). Flow cytometry and imaging mass cytometry (IMC) were used to characterize the subpopulation frequency and spatial distribution of tumor-infiltrating immune cells. Mass spectrometry imaging (MSI) was used to visualize adenosine compartmentalization in the PDAC tumors. RNA sequencing was used to evaluate the influence of the adenosine pathway on the shaping of the immune milieu and correlate our findings to published data sets in human PDAC. RESULTS: We demonstrated high expression of adenosine pathway components in tumor-infiltrating immune cells (particularly myeloid populations) in the murine models. MSI demonstrated that extracellular adenosine distribution is heterogeneous in tumors, with high concentrations in peri-necrotic, hypoxic regions, associated with rich myeloid infiltration, demonstrated using IMC. Protumorigenic M2 macrophages express high levels of the Adora2a receptor; particularly in the IOT resistant model. Blocking the in vivo formation and function of eAdo (Adoi), using a combination of anti-CD73 antibody and an Adora2a inhibitor slowed tumor growth and reduced metastatic burden. Additionally, blocking the adenosine pathway improved the efficacy of combinations of cytotoxic agents or immunotherapy. Adoi remodeled the TME, by reducing the infiltration of M2 macrophages and regulatory T cells. RNA sequencing analysis showed that genes related to immune modulation, hypoxia and tumor stroma were downregulated following Adoi and a specific adenosine signature derived from this is associated with a poorer prognosis in patients with PDAC. CONCLUSIONS: The formation of eAdo promotes the development of the immunosuppressive TME in PDAC, contributing to its resistance to conventional and novel therapies. Therefore, inhibition of the adenosine pathway may represent a strategy to modulate the PDAC immune milieu and improve therapy response in patients with PDAC.

Climatic conditions affect shoot flammability by influencing flammability-related functional traits in nonfire-prone habitats.

Plant flammability is an important driver of wildfires, and flammability itself is determined by several plant functional traits. While many plant traits are influenced by climatic conditions, the interaction between climatic conditions and plant flammability has rarely been investigated. Here, we explored the relationships among climatic conditions, shoot-level flammability components, and flammability-related functional traits for 186 plant species from fire-prone and nonfire-prone habitats. For species originating from nonfire-prone habitats, those from warmer areas tended to have lower shoot moisture content and larger leaves, and had higher shoot flammability with higher ignitibility, combustibility, and sustainability. Plants in wetter areas tended to have lower shoot flammability with lower combustibility and sustainability due to higher shoot moisture contents. In fire-prone habitats, shoot flammability was not significantly related to any climatic factor. Our study suggests that for species originating in nonfire-prone habitats, climatic conditions have influenced plant flammability by shifting flammability-related functional traits, including leaf size and shoot moisture content. Climate does not predict shoot flammability in species from fire-prone habitats; here, fire regimes may have an important role in shaping plant flammability. Understanding these nuances in the determinants of plant flammability is important in an increasingly fire-prone world.

The soil microbiome: An essential, but neglected, component of regenerative agroecosystems.

Regenerative agriculture (RA) is gaining traction globally as an approach for meeting growing food demands while avoiding, or even remediating, the detrimental environmental consequences associated with conventional farming. Momentum is building for science to provide evidence for, or against, the putative ecosystem benefits of RA practices relative to conventional farming. In this perspective article, we advance the argument that consideration of the soil microbiome in RA research is crucial for disentangling the varied and complex relationships RA practices have with the biotic and abiotic environment, outline the expected changes in soil microbiomes under RA, and make recommendations for designing research that will answer the outstanding questions on the soil microbiome under RA. Ultimately, deeper insights into the role of microbial communities in RA soils will allow the development of biologically relevant monitoring tools which will support land managers in addressing the key environmental issues associated with agriculture.

Decolonizing Indigenous Burial Practices in Aotearoa, New Zealand: A Tribal Case Study.

Before European contact, Maori disposed of the dead in environmentally sustainable ways. Revitalizing pre-colonial burial practices presents an opportunity for Maori to evaluate current practices and reconnect with their ancient tribal customs and practices. The research question asks: What is the decolonizing potential of urupa tautaiao (natural burials)? Paradoxically, environmentally unsustainable modern tangihanga (funerals) retain the ethos of customary funerary traditions. Urupa tautaiao presents an opportunity for iwi (tribes) to retain cultural integrity in the death space, without compromising Papatuanuku (earthmother). Methodologically, a Maori worldview frames an action research mindset. The study captures a tribal community's exploratory journey into urupa tautaiao.

Land-use history impacts spatial patterns and composition of woody plant species across a 35-hectare temperate forest plot.

Land-use history is the template upon which contemporary plant and tree populations establish and interact with one another and exerts a legacy on the structure and dynamics of species assemblages and ecosystems. We use the first census (2010-2014) of a 35-ha forest-dynamics plot at the Harvard Forest in central Massachusetts to describe the composition and structure of the woody plants in this plot, assess their spatial associations within and among the dominant species using univariate and bivariate spatial point-pattern analysis, and examine the interactions between land-use history and ecological processes. The plot includes 108,632 live stems ≥ 1 cm in diameter (2,215 individuals/ha) and 7,595 standing dead stems ≥ 5 cm in diameter. Live tree basal area averaged 42.25 m2/ha, of which 84% was represented by Tsuga canadensis (14.0 m2/ ha), Quercus rubra (northern red oak; 9.6 m2/ ha), Acer rubrum (7.2 m2/ ha) and Pinus strobus (eastern white pine; 4.4 m2/ ha). These same four species also comprised 78% of the live aboveground biomass, which averaged 245.2 Mg/ ha. Across all species and size classes, the forest contains a preponderance (> 80,000) of small stems (<10-cm diameter) that exhibit a reverse-J size distribution. Significant spatial clustering of abundant overstory species was observed at all spatial scales examined. Spatial distributions of A. rubrum and Q. rubra showed negative intraspecific correlations in diameters up to at least a 150-m spatial lag, likely indicative of crowding effects in dense forest patches following intensive past land use. Bivariate marked point-pattern analysis, showed that T. canadensis and Q. rubra diameters were negatively associated with one another, indicating resource competition for light. Distribution and abundance of the common overstory species are predicted best by soil type, tree neighborhood effects, and two aspects of land-use history: when fields were abandoned in the late 19th century and the succeeding forest types recorded in 1908. In contrast, a history of intensive logging prior to 1950 and a damaging hurricane in 1938 appear to have had little effect on the distribution and abundance of present-day tree species. Our findings suggest that current day composition and structure are still being influenced by anthropogenic disturbances that occurred over a century ago.

In the eye of the storm: impact of COVID-19 pandemic on admission patterns to paediatric intensive care units in the UK and Eire.

BACKGROUND: The coronavirus disease-19 (COVID-19) pandemic had a relatively minimal direct impact on critical illness in children compared to adults. However, children and paediatric intensive care units (PICUs) were affected indirectly. We analysed the impact of the pandemic on PICU admission patterns and patient characteristics in the UK and Ireland. METHODS: We performed a retrospective cohort study of all admissions to PICUs in children < 18 years during Jan-Dec 2020, using data collected from 32 PICUs via a central database (PICANet). Admission patterns, case-mix, resource use, and outcomes were compared with the four preceding years (2016-2019) based on the date of admission. RESULTS: There were 16,941 admissions in 2020 compared to an annual average of 20,643 (range 20,340-20,868) from 2016 to 2019. During 2020, there was a reduction in all PICU admissions (18%), unplanned admissions (20%), planned admissions (15%), and bed days (25%). There was a 41% reduction in respiratory admissions, and a 60% reduction in children admitted with bronchiolitis but an 84% increase in admissions for diabetic ketoacidosis during 2020 compared to the previous years. There were 420 admissions (2.4%) with either PIMS-TS or COVID-19 during 2020. Age and sex adjusted prevalence of unplanned PICU admission reduced from 79.7 (2016-2019) to 63.1 per 100,000 in 2020. Median probability of death [1.2 (0.5-3.4) vs. 1.2 (0.5-3.4) %], length of stay [2.3 (1.0-5.5) vs. 2.4 (1.0-5.7) days] and mortality rates [3.4 vs. 3.6%, (risk-adjusted OR 1.00 [0.91-1.11, p = 0.93])] were similar between 2016-2019 and 2020. There were 106 fewer in-PICU deaths in 2020 (n = 605) compared with 2016-2019 (n = 711). CONCLUSIONS: The use of a high-quality international database allowed robust comparisons between admission data prior to and during the COVID-19 pandemic. A significant reduction in prevalence of unplanned admissions, respiratory diseases, and fewer child deaths in PICU observed may be related to the targeted COVID-19 public health interventions during the pandemic. However, analysis of wider and longer-term societal impact of the pandemic and public health interventions on physical and mental health of children is required.

Identifying optimal bioinformatics protocols for aerosol microbial community data.

Microbes are fundamental to Earth's ecosystems, thus understanding ecosystem connectivity through microbial dispersal is key to predicting future ecosystem changes in a warming world. However, aerial microbial dispersal remains poorly understood. Few studies have been performed on bioaerosols (microorganisms and biological fragments suspended in the atmosphere), despite them harboring pathogens and allergens. Most environmental microbes grow poorly in culture, therefore molecular approaches are required to characterize aerial diversity. Bioinformatic tools are needed for processing the next generation sequencing (NGS) data generated from these molecular approaches; however, there are numerous options and choices in the process. These choices can markedly affect key aspects of the data output including relative abundances, diversity, and taxonomy. Bioaerosol samples have relatively little DNA, and often contain novel and proportionally high levels of contaminant organisms, that are difficult to identify. Therefore, bioinformatics choices are of crucial importance. A bioaerosol dataset for bacteria and fungi based on the 16S rRNA gene (16S) and internal transcribed spacer (ITS) DNA sequencing from parks in the metropolitan area of Auckland, Aotearoa New Zealand was used to develop a process for determining the bioinformatics pipeline that would maximize the data amount and quality generated. Two popular tools (Dada2 and USEARCH) were compared for amplicon sequence variant (ASV) inference and generation of an ASV table. A scorecard was created and used to assess multiple outputs and make systematic choices about the most suitable option. The read number and ASVs were assessed, alpha diversity was calculated (Hill numbers), beta diversity (Bray-Curtis distances), differential abundance by site and consistency of ASVs were considered. USEARCH was selected, due to higher consistency in ASVs identified and greater read counts. Taxonomic assignment is highly dependent on the taxonomic database used. Two popular taxonomy databases were compared in terms of number and confidence of assignments, and a combined approach developed that uses information in both databases to maximize the number and confidence of taxonomic assignments. This approach increased the assignment rate by 12-15%, depending on amplicon and the overall assignment was 77% for bacteria and 47% for fungi. Assessment of decontamination using "decontam" and "microDecon" was performed, based on review of ASVs identified as contaminants by each and consideration of the probability of them being legitimate members of the bioaerosol community. For this example, "microDecon's" subtraction approach for removing background contamination was selected. This study demonstrates a systematic approach to determining the optimal bioinformatics pipeline using a multi-criteria scorecard for microbial bioaerosol data. Example code in the R environment for this data processing pipeline is provided.

Testing a global standard for quantifying species recovery and assessing conservation impact.

Recognizing the imperative to evaluate species recovery and conservation impact, in 2012 the International Union for Conservation of Nature (IUCN) called for development of a "Green List of Species" (now the IUCN Green Status of Species). A draft Green Status framework for assessing species' progress toward recovery, published in 2018, proposed 2 separate but interlinked components: a standardized method (i.e., measurement against benchmarks of species' viability, functionality, and preimpact distribution) to determine current species recovery status (herein species recovery score) and application of that method to estimate past and potential future impacts of conservation based on 4 metrics (conservation legacy, conservation dependence, conservation gain, and recovery potential). We tested the framework with 181 species representing diverse taxa, life histories, biomes, and IUCN Red List categories (extinction risk). Based on the observed distribution of species' recovery scores, we propose the following species recovery categories: fully recovered, slightly depleted, moderately depleted, largely depleted, critically depleted, extinct in the wild, and indeterminate. Fifty-nine percent of tested species were considered largely or critically depleted. Although there was a negative relationship between extinction risk and species recovery score, variation was considerable. Some species in lower risk categories were assessed as farther from recovery than those at higher risk. This emphasizes that species recovery is conceptually different from extinction risk and reinforces the utility of the IUCN Green Status of Species to more fully understand species conservation status. Although extinction risk did not predict conservation legacy, conservation dependence, or conservation gain, it was positively correlated with recovery potential. Only 1.7% of tested species were categorized as zero across all 4 of these conservation impact metrics, indicating that conservation has, or will, play a role in improving or maintaining species status for the vast majority of these species. Based on our results, we devised an updated assessment framework that introduces the option of using a dynamic baseline to assess future impacts of conservation over the short term to avoid misleading results which were generated in a small number of cases, and redefines short term as 10 years to better align with conservation planning. These changes are reflected in the IUCN Green Status of Species Standard.

RESUMEN: Reconociendo que era imperativo evaluar la recuperación de especies y el impacto de la conservación, la Unión Internacional para la Conservación de la Naturaleza (UICN) convocó en 2012 al desarrollo de una "Lista Verde de Especies" (ahora el Estatus Verde de las Especies de la UICN). Un marco de referencia preliminar de una Lista Verde de Especies para evaluar el progreso de las especies hacia la recuperación, publicado en 2018, proponía 2 componentes separados pero interconectados: un método estandarizado (i.e., medición en relación con puntos de referencia de la viabilidad de especies, funcionalidad y distribución antes del impacto) para determinar el estatus de recuperación actual (puntuación de recuperación de la especie) y la aplicación de ese método para estimar impactos en el pasado y potenciales de conservación basados en 4 medidas (legado de conservación, dependencia de conservación, ganancia de conservación y potencial de recuperación). Probamos el marco de referencia con 181 especies representantes de diversos taxa, historias de vida, biomas, y categorías (riesgo de extinción) en la Lista Roja de la IUCN. Con base en la distribución observada de la puntuación de recuperación de las especies, proponemos las siguientes categorías de recuperación de la especie: totalmente recuperada, ligeramente mermada, moderadamente mermada, mayormente mermada, gravemente mermada, extinta en estado silvestre, e inderterminada. Cincuenta y nueve por ciento de las especies se consideraron mayormente o gravemente mermada. Aunque hubo una relación negativa entre el riesgo de extinción y la puntuación de recuperación de la especie, la variación fue considerable. Algunas especies en las categorías de riesgo bajas fueron evaluadas como más lejos de recuperarse que aquellas con alto riesgo. Esto enfatiza que la recuperación de especies es diferente conceptualmente al riesgo de extinción y refuerza la utilidad del Estado Verde de las Especies de la UICN para comprender integralmente el estatus de conservación de especies. Aunque el riesgo de extinción no predijo el legado de conservación, la dependencia de conservación o la ganancia de conservación, se correlacionó positivamente con la potencial de recuperación. Solo 1.7% de las especies probadas fue categorizado como cero en los 4 indicadores de impacto de la conservación, lo que indica que la conservación ha jugado, o jugará, un papel en la mejoría o mantenimiento del estatus de la especie la gran mayoría de ellas. Con base en nuestros resultados, diseñamos una versión actualizada del marco de referencia para la evaluación que introduce la opción de utilizar una línea de base dinámica para evaluar los impactos futuros de la conservación en el corto plazo y redefine corto plazo como 10 años.

Evaluating the impact of a continued maternal pertussis immunisation programme in England: A modelling study and cost-effectiveness analysis.

INTRODUCTION: An unexpected resurgence of pertussis cases and infant deaths was observed in some countries that had switched to acellular pertussis vaccines in the primary immunisation schedule. In response to the outbreaks, maternal pertussis vaccination programmes in pregnant women have been adopted worldwide, including the USA in 2011 and the UK in 2012. Following the success of the programme in England, we evaluated the health and economic impact of stopping versus continuing the maternal pertussis immunisation to inform public health policy making. METHODS: We used a mathematical model to estimate the number of infant hospitalisations and deaths related to pertussis in England over 2019-2038. Losses in quality-adjusted life years, QALYs, were considered for infants (aged 0-2 months) who survived or died from pertussis, bereaved parents (of infants who died from pertussis), and women with pertussis (aged 20-44 years). Direct medical costs to the National Health Service included infant hospitalisations, maternal vaccinations, and disease in women. Costs and QALYs were discounted at 3.5%. Changes in the incremental cost-effectiveness ratio, ICER, were explored in sensitivity analyses. RESULTS: The model supports continuing the maternal pertussis immunisation programme as a cost-effective intervention at an ICER of £14,500/QALY (2.5% and 97.5%-quantile: £7,300/QALY to £32,400/QALY). Stopping versus continuing the maternal programme results in an estimated mean of 972 (range 582 to 1489) versus 308 (184 to 471) infant hospitalisations annually. Results were most sensitive to the number of hospitalisations and deaths when stopping the maternal programme. At a cost-effectiveness threshold of £30,000/QALY, the probability of the maternal programme being cost-effective was 96.2%. CONCLUSION: Our findings support continuing the maternal pertussis vaccination programme as otherwise higher levels of disease activity and infant mortality are expected to return. These results have led policy makers to decide to continue the maternal programme in the UK routine immunisation schedule.

High light-induced photoinhibition is not limiting seedling establishment at abrupt treeline ecotones in New Zealand.

Seedlings of New Zealand's treeline-forming Fuscospora cliffortioides (Hook.f.) perform poorly beyond the established canopy, limiting treeline advance. To test the long-standing assumption that photoinhibition impairs regeneration in the subalpine belt of New Zealand's Southern Alps, we assessed photosystem II (PSII) performance of seedling-sized individuals and microclimate variation. We performed diurnal, non-invasive chlorophyll-a-fluorescence measurements on exposed and canopy-sheltered individuals at two sites in New Zealand's Southern Alps during summer and winter. Diurnal recordings of the effective (ΦPSII) and optimal (Fv/Fm) photosynthetic quantum yield were supplemented with light response curves and micro-temperature recordings. ΦPSII returned to near-optimal values around 0.8 after 30 min of shading, which rules out accumulative or long-term photoinhibition effects. The maximum electron transport rate derived from rapid light curves was significantly higher (+12%) in exposed compared with canopy-shaded individuals. Summer temperature fluctuated widely on the scree (-0.5 to 60.5 °C) and near seedlings (-2 to 26.5 °C). Our results revealed a remarkable level of light adaptation and contradict previous studies hinting at high light-induced photoinhibition as a treeline-limiting factor in the Southern Alps. By linking low ΦPSII on winter mornings, and large, sudden temperature drops in summer, we suspect that cold-induced photoinhibition might occur but the rapid recovery of ΦPSII seen across a wide temperature range makes lethal photo-oxidative damage rather unlikely. Given the demonstrably low summer frost tolerance of F. cliffortioides, cold-related damage resulting from frost events during the growing season or embolism induced by frost drought may offer more plausible explanations for the poor seedling establishment. Duration and frequency of these events could diminish with global warming, which may promote treeline advance.

Measuring change in biological communities: multivariate analysis approaches for temporal datasets with low sample size.

Effective and robust ways to describe, quantify, analyse, and test for change in the structure of biological communities over time are essential if ecological research is to contribute substantively towards understanding and managing responses to ongoing environmental changes. Structural changes reflect population dynamics, changes in biomass and relative abundances of taxa, and colonisation and extinction events observed in samples collected through time. Most previous studies of temporal changes in the multivariate datasets that characterise biological communities are based on short time series that are not amenable to data-hungry methods such as multivariate generalised linear models. Here, we present a roadmap for the analysis of temporal change in short-time-series, multivariate, ecological datasets. We discuss appropriate methods and important considerations for using them such as sample size, assumptions, and statistical power. We illustrate these methods with four case-studies analysed using the R data analysis environment.

Changes in the analysis of temporal community dynamics data: a 29-year literature review.

BACKGROUND: Understanding how biological communities change over time is of increasing importance as Earth moves into the Anthropocene. A wide variety of methods are used for multivariate community analysis and are variously applied to research that aims to characterise temporal dynamics in community composition. Understanding these methods and how they are applied is useful for determining best practice in community ecology. METHODOLOGY: We reviewed the ecological literature from 1990 to 2018 that used multivariate methods to address questions of temporal community dynamics. For each paper that fulfilled our search criteria, we recorded the types of multivariate analysis used to characterise temporal community dynamics in addition to the research aim, habitat type, location, taxon and the experimental design. RESULTS: Most studies had relatively few temporal replicates; the median number was seven time points. Nearly 70% of studies applied more than one analysis method; descriptive methods such as bar graphs and ordination were the most commonly applied methods. Surprisingly, the types of analyses used were only related to the number of temporal replicates, but not to research aim or any other aspects of experimental design such as taxon, or habitat or year of study. CONCLUSIONS: This review reveals that most studies interested in understanding community dynamics use relatively short time series meaning that several, more sophisticated, temporal analyses are not widely applicable. However, newer methods using multivariate dissimilarities are growing in popularity and many can be applied to time series of any length.

Epidemiology of Cardiopulmonary Resuscitation in Critically Ill Children Admitted to Pediatric Intensive Care Units Across England: A Multicenter Retrospective Cohort Study.

Background Cardiopulmonary arrests are a major contributor to mortality and morbidity in pediatric intensive care units (PICUs). Understanding the epidemiology and risk factors for CPR may inform national quality improvement initiatives. Methods and Results A retrospective cohort analysis using prospectively collected data from the Paediatric Intensive Care Audit Network database. The Paediatric Intensive Care Audit Network contains data on all PICU admissions in the United Kingdom. We identified children who received cardiopulmonary resuscitation (CPR) in 23 PICUs in England (2013-2017). Incidence rates of CPR and associated factors were analyzed. Logistic regression was used to estimate the size and precision of associations. Cumulative incidence of CPR was 2.2% for 68 114 admissions over 5 years with an incidence rate of 4.9 episodes/1000 bed days. Cardiovascular diagnosis (odds ratio [OR], 2.30; 95% CI, 2.02-2.61), age <1 year (OR, 1.84; 95% CI, 1.65-2.04), the Paediatric Index of Mortality 2 score on admission (OR, 1.045; 95% CI, 1.042-1.047) and longer length of stay (OR, 1.013; 95% CI, 1.012-1.014) were associated with increased odds of receiving CPR. We also found a higher risk of CPR associated with a history of preadmission cardiac arrest (OR, 20.69; [95% CI, 18.16-23.58) and for children with a cardiac condition admitted to a noncardiac PICU (OR, 2.75; 95% CI, 1.91-3.98). Children from Black (OR, 1.68; 95% CI, 1.36-2.07) and Asian (OR, 1.49; 95% CI, 1.28-1.74) racial/ethnic backgrounds were at higher risk of receiving CPR in PICU than White children. Conclusions Data from this first multicenter study from England provides a foundation for further research and evidence for benchmarking and quality improvement for prevention of cardiac arrests in PICU.

Livestock exclusion reduces the spillover effects of pastoral agriculture on soil bacterial communities in adjacent forest fragments.

Forest-to-pasture conversion is known to cause global losses in plant and animal diversity, yet impacts of livestock management after such conversion on vital microbial communities in adjoining natural ecosystems remain poorly understood. We examined how pastoral land management practices impact soil microorganisms in adjacent native forest fragments, by comparing bacterial communities sampled along 21 transects bisecting pasture-forest boundaries. Our results revealed greater bacterial taxon richness in grazed pasture soils and the reduced dispersal of pasture-associated taxa into adjacent forest soils when land uses were separated by a boundary fence. Relative abundance distributions of forest-associated taxa (i.e., Proteobacteria and Nitrospirae) and a pasture-associated taxon (i.e., Firmicutes) also suggest a greater impact of pastoral land uses on forest fragment soil bacterial communities when no fence is present. Bacterial community richness and composition were most related to changes in soil physicochemical variables commonly associated with agricultural fertilization, including concentrations of Olsen P, total P, total Cd, delta 15 N and the ratio of C:P and N:P. Overall, our findings demonstrate clear, and potentially detrimental effects of agricultural disturbance on bacterial communities in forest soils adjacent to pastoral land. We provide evidence that simple land management decisions, such as livestock exclusion, can mitigate the effects of agriculture on adjacent soil microbial communities.

Characteristics of Severe Acute Respiratory Syndrome Coronavirus-2 Infection and Comparison With Influenza in Children Admitted to U.K. PICUs.

OBJECTIVES: Severe acute respiratory syndrome coronavirus-2 affects adults disproportionately more than children. A small proportion of children with severe acute respiratory syndrome coronavirus-2 required admission to a PICU. We describe the nationwide U.K. PICU experience of severe acute respiratory syndrome coronavirus-2 infection during the first wave of the pandemic and compare this with the critical care course of the 2019 influenza cohort. DESIGN: Prospective nationwide cohort study of characteristics of severe acute respiratory syndrome coronavirus-2-positive children. Data collection utilized routine Pediatric Intensive Care Audit Network and severe acute respiratory syndrome coronavirus-2-specific data. SETTING: All U.K. PICUs. PATIENTS: Children less than 18 years old, admitted to U.K. PICUs between March 14, 2020, and June 13, 2020, and a positive severe acute respiratory syndrome coronavirus-2 polymerase chain reaction. Children admitted to U.K. PICUs in 2019 with influenza provided comparison. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: We identified 76 PICU admissions among 73 children with a positive severe acute respiratory syndrome coronavirus-2 polymerase chain reaction test. Prevalence of PICU admissions per million was 5.2 for children versus 260 for adults. Ten children (14%) were identified on routine screening. Seventeen children (23%) had pediatric inflammatory multisystem syndrome temporally associated with severe acute respiratory syndrome coronavirus-2. Seventeen (23%) had coinfections. Invasive ventilation was required in seven of 17 children (41%) with pediatric inflammatory multisystem syndrome temporally associated with severe acute respiratory syndrome coronavirus-2 versus 38 of 56 other severe acute respiratory syndrome coronavirus-2 positive children (68%), with 77% requiring vasoactive support versus 43%, respectively. Seven children (10%) died. In comparison with influenza children, severe acute respiratory syndrome coronavirus-2 children were older (median [interquartile range]: 10 [1-13] vs 3 yr [1-8 yr]), more often Black or Asian (52% v 18%), higher weight z score (0.29 [-0.80 to 1.62] vs -0.41 [-1.37 to 0.63]), and higher deprivation index (3.3 [-1 to 6.3] vs 1.2 [-1.8 to 4.4]). Comorbidities, frequency of organ supports, and length of stay were similar. CONCLUSIONS: This nationwide study confirms that PICU admissions with severe acute respiratory syndrome coronavirus-2 infections were infrequent. We have reported similarities and differences in sociodemographic characteristics, organ support interventions, and outcomes of children affected by severe acute respiratory syndrome coronavirus-2 compared with influenza.

Caring for critically ill adults in paediatric intensive care units in England during the COVID-19 pandemic: planning, implementation and lessons for the future.

OBJECTIVE: To describe the experience of paediatric intensive care units (PICUs) in England that repurposed their units, equipment and staff to care for critically ill adults during the first wave of the COVID-19 pandemic. DESIGN: Descriptive study. SETTING: Seven PICUs in England. MAIN OUTCOME MEASURES: (1) Modelling using historical Paediatric Intensive Care Audit Network data; (2) space, staff, equipment, clinical care, communication and governance considerations during repurposing of PICUs; (3) characteristics, interventions and outcomes of adults cared for in repurposed PICUs. RESULTS: Seven English PICUs, accounting for 137 beds, repurposed their space, staff and equipment to admit critically ill adults. Neighbouring PICUs increased their bed capacity to maintain overall bed numbers for children, which was informed by historical data modelling (median 280-307 PICU beds were required in England from March to June). A total of 145 adult patients (median age 50-62 years) were cared for in repurposed PICUs (1553 bed-days). The vast majority of patients had COVID-19 (109/145, 75%); the majority required invasive ventilation (91/109, 85%). Nearly, a third of patients (42/145, 29%) underwent a tracheostomy. Renal replacement therapy was provided in 20/145 (14%) patients. Twenty adults died in PICU (14%). CONCLUSION: In a rapid and unprecedented effort during the first wave of the COVID-19 pandemic, seven PICUs in England were repurposed to care for adult patients. The success of this effort was underpinned by extensive local preparation, close collaboration with adult intensivists and careful national planning to safeguard paediatric critical care capacity.

Tracheostomy trends in paediatric intensive care.

Paediatric tracheostomy is most commonly performed in children on the paediatric intensive care unit (PICU) to facilitate long-term ventilation. We sought to identify trends in UK tracheostomy practice in PICUs. Data were analysed from 250 261 admissions, including 4409 children tracheostomised between 2003 and 2017. The incidence of tracheostomy in 2017 was approximately half that in 2003 (incidence rate ratio=0.48, 95% CI 0.40 to 0.57). The percentage of patients tracheostomised during a PICU admission, as a proportion of all admissions, was 2.44% (n=319) in 2003 and reduced to 0.97% (n=180) in 2017. Nevertheless, we identified great variability in practice between different PICUs with tracheostomy rates between 0.0% and 4.0% of all admissions. Risk-adjusted PICU mortality was comparable between tracheostomised children and all admissions to PICU.

Temporal variation in soil bacterial communities can be confounded with spatial variation.

Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13-24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.

Using soil bacterial communities to predict physico-chemical variables and soil quality.

BACKGROUND: Soil ecosystems consist of complex interactions between biological communities and physico-chemical variables, all of which contribute to the overall quality of soils. Despite this, changes in bacterial communities are ignored by most soil monitoring programs, which are crucial to ensure the sustainability of land management practices. We applied 16S rRNA gene sequencing to determine the bacterial community composition of over 3000 soil samples from 606 sites in New Zealand. Sites were classified as indigenous forests, exotic forest plantations, horticulture, or pastoral grasslands; soil physico-chemical variables related to soil quality were also collected. The composition of soil bacterial communities was then used to predict the land use and soil physico-chemical variables of each site. RESULTS: Soil bacterial community composition was strongly linked to land use, to the extent where it could correctly determine the type of land use with 85% accuracy. Despite the inherent variation introduced by sampling across ~ 1300 km distance gradient, the bacterial communities could also be used to differentiate sites grouped by key physico-chemical properties with up to 83% accuracy. Further, individual soil variables such as soil pH, nutrient concentrations and bulk density could be predicted; the correlations between predicted and true values ranged from weak (R2 value = 0.35) to strong (R2 value = 0.79). These predictions were accurate enough to allow bacterial communities to assign the correct soil quality scores with 50-95% accuracy. CONCLUSIONS: The inclusion of biological information when monitoring soil quality is crucial if we wish to gain a better, more accurate understanding of how land management impacts the soil ecosystem. We have shown that soil bacterial communities can provide biologically relevant insights on the impacts of land use on soil ecosystems. Furthermore, their ability to indicate changes in individual soil parameters shows that analysing bacterial DNA data can be used to screen soil quality. Video Abstract.