The pandemic has left us in a state of flux at work. How can we manage the unknown?

With COVID-19, uncertainty and a state of transition are creating and increasing individual, team, and organisational risk. Feelings of impending change affect recruitment, team development and career ambitions. Catherine Baxendale discusses how leaders can deal with these different levels of risk

The Automated Root Exudate System (ARES): a method to apply solutes at regular intervals to soils in the field.

Root exudation is a key component of nutrient and carbon dynamics in terrestrial ecosystems. Exudation rates vary widely by plant species and environmental conditions, but our understanding of how root exudates affect soil functioning is incomplete, in part because there are few viable methods to manipulate root exudates in situ. To address this, we devised the Automated Root Exudate System (ARES), which simulates increased root exudation by applying small amounts of labile solutes at regular intervals in the field. The ARES is a gravity-fed drip irrigation system comprising a reservoir bottle connected via a timer to a micro-hose irrigation grid covering c. 1 m2; 24 drip-tips are inserted into the soil to 4-cm depth to apply solutions into the rooting zone. We installed two ARES subplots within existing litter removal and control plots in a temperate deciduous woodland. We applied either an artificial root exudate solution (RE) or a procedural control solution (CP) to each subplot for 1 min day-1 during two growing seasons. To investigate the influence of root exudation on soil carbon dynamics, we measured soil respiration monthly and soil microbial biomass at the end of each growing season. The ARES applied the solutions at a rate of c. 2 L m-2 week-1 without significantly increasing soil water content. The application of RE solution had a clear effect on soil carbon dynamics, but the response varied by litter treatment. Across two growing seasons, soil respiration was 25% higher in RE compared to CP subplots in the litter removal treatment, but not in the control plots. By contrast, we observed a significant increase in microbial biomass carbon (33%) and nitrogen (26%) in RE subplots in the control litter treatment. The ARES is an effective, low-cost method to apply experimental solutions directly into the rooting zone in the field. The installation of the systems entails minimal disturbance to the soil and little maintenance is required. Although we used ARES to apply root exudate solution, the method can be used to apply many other treatments involving solute inputs at regular intervals in a wide range of ecosystems

Can digital image classification be used as a standardised method for surveying peatland vegetation cover?

The ability to carry out systematic, accurate and repeatable vegetation surveys is an essential part of long-term scientific studies into ecosystem biodiversity and functioning. However, current widely used traditional survey techniques such as destructive harvests, pin frame quadrats and visual cover estimates can be very time consuming and are prone to subjective variations. We investigated the use of digital image techniques as an alternative way of recording vegetation cover to plant functional type level on a peatland ecosystem. Using an established plant manipulation experimental site at Moor House NNR (an Environmental Change Network site), we compared visual cover estimates of peatland vegetation with cover estimates using digital image classification methods, from 0.5 m × 0.5 m field plots. Our results show that digital image classification of photographs taken with a standard digital camera can be used successfully to estimate dwarf-shrub and graminoid vegetation cover at a comparable level to field visual cover estimates, although the methods were less effective for lower plants such as mosses and lichens. Our study illustrates the novel application of digital image techniques to provide a new way of measuring and monitoring peatland vegetation to the plant functional group level, which is less vulnerable to surveyor bias than are visual field surveys. Furthermore, as such digital techniques are highly repeatable, we suggest that they have potential for use in long-term monitoring studies, at both plot and landscape scales

Can digital image classification be used as a standardised method for surveying peatland vegetation cover?

The ability to carry out systematic, accurate and repeatable vegetation surveys is an essential part of long-term scientific studies into ecosystem biodiversity and functioning. However, current widely used traditional survey techniques such as destructive harvests, pin frame quadrats and visual cover estimates can be very time consuming and are prone to subjective variations. We investigated the use of digital image techniques as an alternative way of recording vegetation cover to plant functional type level on a peatland ecosystem. Using an established plant manipulation experimental site at Moor House NNR (an Environmental Change Network site), we compared visual cover estimates of peatland vegetation with cover estimates using digital image classification methods, from 0.5 m × 0.5 m field plots. Our results show that digital image classification of photographs taken with a standard digital camera can be used successfully to estimate dwarf-shrub and graminoid vegetation cover at a comparable level to field visual cover estimates, although the methods were less effective for lower plants such as mosses and lichens. Our study illustrates the novel application of digital image techniques to provide a new way of measuring and monitoring peatland vegetation to the plant functional group level, which is less vulnerable to surveyor bias than are visual field surveys. Furthermore, as such digital techniques are highly repeatable, we suggest that they have potential for use in long-term monitoring studies, at both plot and landscape scales

Altered litter inputs modify carbon and nitrogen storage in soil organic matter in a lowland tropical forest

Soil organic matter (SOM) in tropical forests is an important store of carbon (C) and nutrients. Although SOM storage could be affected by global changes via altered plant productivity, we know relatively little about SOM stabilisation and turnover in tropical forests compared to temperate systems. Here, we investigated changes in soil C and N within particle size fractions representing particulate organic matter (POM) and mineral-associated organic matter (MAOM) after 13 years of experimental litter removal (L−) and litter addition (L+) treatments in a lowland tropical forest. We hypothesized that reduced nitrogen (N) availability in L− plots would result in N-mining of MAOM, whereas long-term litter addition would increase POM, without altering the C:N ratio of SOM fractions. Overall, SOM-N declined more than SOM-C with litter removal, providing evidence of N-mining in the L− plots, which increased the soil C:N ratio. However, contrary to expectations, the C:N ratio increased most in the largest POM fraction, whereas the C:N ratio of MAOM remained unchanged. We did not observe the expected increases in POM with litter addition, which we attribute to rapid turnover of unprotected SOM. Measurements of ion exchange rates to assess changes in N availability and soil chemistry revealed that litter removal increased the mobility of ammonium-N and aluminium, whereas litter addition increased the mobility of nitrate-N and iron, which could indicate SOM priming in both treatments. Our study suggests that altered litter inputs affect multiple processes contributing to SOM storage and we propose potential mechanisms to inform future work

Tropical forest soil carbon stocks do not increase despite 15 years of doubled litter inputs

peer-reviewedSoil organic carbon (SOC) dynamics represent a persisting uncertainty in our understanding of the global carbon cycle. SOC storage is strongly linked to plant inputs via the formation of soil organic matter, but soil geochemistry also plays a critical role. In tropical soils with rapid SOC turnover, the association of organic matter with soil minerals is particularly important for stabilising SOC but projected increases in tropical forest productivity could trigger feedbacks that stimulate the release of stored SOC. Here, we demonstrate limited additional SOC storage after 13–15 years of experimentally doubled aboveground litter inputs in a lowland tropical forest. We combined biological, physical, and chemical methods to characterise SOC along a gradient of bioavailability. After 13 years of monthly litter addition treatments, most of the additional SOC was readily bioavailable and we observed no increase in mineral-associated SOC. Importantly, SOC with weak association to soil minerals declined in response to long-term litter addition, suggesting that increased plant inputs could modify the formation of organo-mineral complexes in tropical soils. Hence, we demonstrate the limited capacity of tropical soils to sequester additional C inputs and provide insights into potential underlying mechanisms

Protective Contributions against Invasive Streptococcus pneumoniae Pneumonia of Antibody and Th17-Cell Responses to Nasopharyngeal Colonisation

The nasopharyngeal commensal bacteria Streptococcus pneumoniae is also a frequent cause of serious infections. Nasopharyngeal colonisation with S. pneumoniae inhibits subsequent re-colonisation by inducing Th17-cell adaptive responses, whereas vaccination prevents invasive infections by inducing antibodies to S. pneumoniae capsular polysaccharides. In contrast, protection against invasive infection after nasopharyngeal colonisation with mutant S. pneumoniae strains was associated with antibody responses to protein antigens. The role of colonisation-induced Th17-cell responses during subsequent invasive infections is unknown. Using mouse models, we show that previous colonisation with S. pneumoniae protects against subsequent lethal pneumonia mainly by preventing bacteraemia with a more modest effect on local control of infection within the lung. Previous colonisation resulted in CD4-dependent increased levels of Th17-cell cytokines during subsequent infectious challenge. However, mice depleted of CD4 cells prior to challenge remained protected against bacteraemia, whereas no protection was seen in antibody deficient mice and similar protection could be achieved through passive transfer of serum. Serum from colonised mice but not antibody deficient mice promoted phagocytosis of S. pneumoniae, and previously colonised mice were able to rapidly clear S. pneumoniae from the blood after intravenous inoculation. Thus, despite priming for a Th17-cell response during subsequent infection, the protective effects of prior colonisation in this model was not dependent on CD4 cells but on rapid clearance of bacteria from the blood by antibody-mediated phagocytosis. These data suggest that whilst nasopharyngeal colonisation induces a range of immune responses, the effective protective responses depend upon the site of subsequent infectio

Outcomes following SARS-CoV-2 infection in patients with primary and secondary immunodeficiency in the UK

In March 2020, the United Kingdom Primary Immunodeficiency Network (UKPIN) established a registry of cases to collate the outcomes of individuals with PID and SID following SARS-CoV-2 infection and treatment. A total of 310 cases of SARS-CoV-2 infection in individuals with PID or SID have now been reported in the UK. The overall mortality within the cohort was 17.7% (n = 55/310). Individuals with CVID demonstrated an infection fatality rate (IFR) of 18.3% (n = 17/93), individuals with PID receiving IgRT had an IFR of 16.3% (n = 26/159) and individuals with SID, an IFR of 27.2% (n = 25/92). Individuals with PID and SID had higher inpatient mortality and died at a younger age than the general population. Increasing age, low pre-SARS-CoV-2 infection lymphocyte count and the presence of common co-morbidities increased the risk of mortality in PID. Access to specific COVID-19 treatments in this cohort was limited: only 22.9% (n = 33/144) of patients admitted to the hospital received dexamethasone, remdesivir, an anti-SARS-CoV-2 antibody-based therapeutic (e.g. REGN-COV2 or convalescent plasma) or tocilizumab as a monotherapy or in combination. Dexamethasone, remdesivir, and anti-SARS-CoV-2 antibody-based therapeutics appeared efficacious in PID and SID. Compared to the general population, individuals with PID or SID are at high risk of mortality following SARS-CoV-2 infection. Increasing age, low baseline lymphocyte count, and the presence of co-morbidities are additional risk factors for poor outcome in this cohort