Deconstructing the microbial necromass continuum to inform soil carbon sequestration

1. Microbial necromass is a large, dynamic and persistent component of soil organic carbon, the dominant terrestrial carbon pool. Quantification of necromass carbon stocks and its susceptibility to global change is becoming standard practice in soil carbon research. However, the typical proxies used for necromass carbon do not reveal the dynamic nature of necromass carbon flows and transformations within soil that ultimately determine necromass persistence. In this review, we define and deconstruct four stages of the necromass continuum: production, recycling, stabilization and destabilization. 2. Current understanding of necromass dynamics is described for each continuum stage. We highlight recent advances, methodological limitations and knowledge gaps which need to be addressed to determine necromass pool sizes and transformations. We discuss the dominant controls on necromass process rates and aspects of soil microscale structure including biofilms and food web interactions. The relative importance of each stage of the continuum is then compared in contrasting ecosystems and for climate change drivers. 3. From the perspective of the continuum, we draw three conclusions to inform future research. First, controls on necromass persistence are more clearly defined when viewed through the lens of the continuum; second, destabilization is the least understood stage of the continuum with recycling also poorly evidenced outside of a few ecosystems; and third, the response of necromass process rates to climate change is unresolved for most continuum stages and ecosystems. 4. Future mechanistic research focused on the role of biotic and abiotic soil microscale structure in determining necromass process rates and the relative importance of organo–mineral and organo–organo interactions can inform necromass persistence in different climate change scenarios. Our review demonstrates that deconstructing the necromass continuum is key to predicting the vulnerability and persistence of necromass carbon in a changing world

Differential contributions of peripheral and central mechanisms to pain in a rodent model of osteoarthritis

The mechanisms underlying the transition from acute nociceptive pain to centrally maintained chronic pain are not clear. We have studied the contributions of the peripheral and central nervous systems during the development of osteoarthritis (OA) pain. Male Sprague-Dawley rats received unilateral intra-articular injections of monosodium iodoacetate (MIA 1mg) or saline, and weight bearing (WB) asymmetry and distal allodynia measured. Subgroups of rats received intra-articular injections of, QX-314 (membrane impermeable local anaesthetic)+capsaicin, QX-314, capsaicin or vehicle on days 7, 14 or 28 post-MIA and WB and PWT remeasured. On days 7&14 post-MIA, but not day 28, QX-314+capsaicin signfcantly attenuated changes in WB induced by MIA, illustrating a crucial role for TRPV1 expressing nociceptors in early OA pain. The role of top-down control of spinal excitability was investigated. The mu-opioid receptor agonist DAMGO was microinjected into the rostroventral medulla, to activate endogenous pain modulatory systems, in MIA and control rats and refex excitability measured using electromyography. DAMGO (3ng) had a signifcantly larger inhibitory effect in MIA treated rats than in controls. These data show distinct temporal contribtuions of TRPV1 expressing nociceptors and opioidergic pain control systems at later timepoints

Microbial community structure mediates response of soil C decomposition to litter addition and warming

Microbial activity has been highlighted as one of the main unknowns controlling the fate and turnover of soil organic matter (SOM) in response to climate change. How microbial community structure and function may (or may not) interact with increasing temperature to impact the fate and turnover of SOM, in particular when combined with changes in litter chemistry, is not well understood. The primary aim of this study was to determine if litter chemistry impacted the decomposition of soil and litter-derived carbon (C), and its interaction with temperature, and whether this response was controlled by microbial community structure and function. Fresh or pre-incubated eucalyptus leaf litter (13C enriched) was added to a woodland soil and incubated at 12, 22, or 32 �C. We tracked the movement of litter and soilderived C into CO2, water-extractable organic carbon (WEOC), and microbial phospholipids (PLFA). The litter additions produced significant changes in every parameter measured, while temperature, interacting with litter chemistry, predominately affected soil C respiration (priming and temperature sensitivity), microbial community structure, and the metabolic quotient (a proxy for microbial carbon use efficiency [CUE]). The direction of priming varied with the litter additions (negative with fresh litter, positive with pre-incubated litter) and was related to differences in the composition of microbial communities degrading soil-C, particularly gram-positive and gram-negative bacteria, resulting from litter addition. Soil-C decomposition in both litter treatments was more temperature sensitive (higher Q10) than in the soil-only control, and soil-C priming became increasingly positive with temperature. However, microbes utilizing soil-C in the litter treatments had higher CUE, suggesting the longer-term stability of soil-C may be increased at higher temperature with litter addition. Our results show that in the same soil, the growth of distinct microbial communities can alter the turnover and fate of SOM and, in the context of global change, its response to temperature

Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Background: In this study, we aimed to evaluate the effects of tocilizumab in adult patients admitted to hospital with COVID-19 with both hypoxia and systemic inflammation. Methods: This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. Those trial participants with hypoxia (oxygen saturation <92% on air or requiring oxygen therapy) and evidence of systemic inflammation (C-reactive protein ≥75 mg/L) were eligible for random assignment in a 1:1 ratio to usual standard of care alone versus usual standard of care plus tocilizumab at a dose of 400 mg–800 mg (depending on weight) given intravenously. A second dose could be given 12–24 h later if the patient's condition had not improved. The primary outcome was 28-day mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936). Findings: Between April 23, 2020, and Jan 24, 2021, 4116 adults of 21 550 patients enrolled into the RECOVERY trial were included in the assessment of tocilizumab, including 3385 (82%) patients receiving systemic corticosteroids. Overall, 621 (31%) of the 2022 patients allocated tocilizumab and 729 (35%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0·85; 95% CI 0·76–0·94; p=0·0028). Consistent results were seen in all prespecified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital within 28 days (57% vs 50%; rate ratio 1·22; 1·12–1·33; p<0·0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (35% vs 42%; risk ratio 0·84; 95% CI 0·77–0·92; p<0·0001). Interpretation: In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes. These benefits were seen regardless of the amount of respiratory support and were additional to the benefits of systemic corticosteroids. Funding: UK Research and Innovation (Medical Research Council) and National Institute of Health Research

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

Background: Many patients with COVID-19 have been treated with plasma containing anti-SARS-CoV-2 antibodies. We aimed to evaluate the safety and efficacy of convalescent plasma therapy in patients admitted to hospital with COVID-19. Methods: This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. The trial is underway at 177 NHS hospitals from across the UK. Eligible and consenting patients were randomly assigned (1:1) to receive either usual care alone (usual care group) or usual care plus high-titre convalescent plasma (convalescent plasma group). The primary outcome was 28-day mortality, analysed on an intention-to-treat basis. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936. Findings: Between May 28, 2020, and Jan 15, 2021, 11558 (71%) of 16287 patients enrolled in RECOVERY were eligible to receive convalescent plasma and were assigned to either the convalescent plasma group or the usual care group. There was no significant difference in 28-day mortality between the two groups: 1399 (24%) of 5795 patients in the convalescent plasma group and 1408 (24%) of 5763 patients in the usual care group died within 28 days (rate ratio 1·00, 95% CI 0·93–1·07; p=0·95). The 28-day mortality rate ratio was similar in all prespecified subgroups of patients, including in those patients without detectable SARS-CoV-2 antibodies at randomisation. Allocation to convalescent plasma had no significant effect on the proportion of patients discharged from hospital within 28 days (3832 [66%] patients in the convalescent plasma group vs 3822 [66%] patients in the usual care group; rate ratio 0·99, 95% CI 0·94–1·03; p=0·57). Among those not on invasive mechanical ventilation at randomisation, there was no significant difference in the proportion of patients meeting the composite endpoint of progression to invasive mechanical ventilation or death (1568 [29%] of 5493 patients in the convalescent plasma group vs 1568 [29%] of 5448 patients in the usual care group; rate ratio 0·99, 95% CI 0·93–1·05; p=0·79). Interpretation: In patients hospitalised with COVID-19, high-titre convalescent plasma did not improve survival or other prespecified clinical outcomes. Funding: UK Research and Innovation (Medical Research Council) and National Institute of Health Research

Changes in soil carbon and nitrogen cycling in response to woody plant encroachment into grasslands

Terrestrial ecosystems represent the largest pool of actively cycling carbon on the Earth. Within terrestrial ecosystems, grasslands and savannas cover 20% of the Earth\u27s land surface and store 30% of global soil organic carbon (Field et al., 1998). Woody plant encroachment into grasslands and savannas is a globally relevant land cover change, (Archer, 1995) driven primarily by shifts in land use, which impacts the biogeochemical cycling of soil carbon and nutrients. The overarching purpose of this dissertation is to examine the biogeochemical cycling of carbon (C) and nitrogen (N) in response to woody plant encroachment of grasslands in southern Texas. Using a combination of approaches, including soil physical fractionation, long-term incubations, and plant and microbial biopolymer analyses, we attempt to elucidate the relationships between plant input chemistry, microbial community structure and function, and the biogeochemical cycling of carbon and nitrogen. A series of year-long soil incubations were conducted of the whole soil and size (\u3e250 μm) and density (\u3c1.0 g cm-3) separated soil fractions. The quantity and isotopic composition of CO2 respired by soil microorganisms was measured throughout the year-long incubations, allowing us to determine the source (C3 vs. C4) and amount of CO2 respired in soils possessing different soil organic carbon protection mechanisms. The results from these incubations suggested that altered carbon chemistry as a result of the grassland to woodland land cover change slowed microbial respiration in the soil fractions. However, in the whole soil the overall greater allocation of C into these more physically unprotected soil fractions allowed for greater respiration of newer, C 3-derived carbon in well-established woody stands. Amino acids, amino sugars, and carbohydrates were extracted from the soils prior to and after the incubation to determine if there were differences in C and N losses between the remnant grassland and established woody stand soils. These data indicated preferential losses of plant-derived (over microbial-derived) carbohydrate-C during the incubation, and higher carbohydrate-C losses in grasslands and recently established woody stands than older woody stands. Amino acid and amino sugar data from this incubation indicated the formation of non-hydrolysable amino-N in older woody stand soils. This data is consistent with results from amino acids and amino sugars extracted along the chronosequence of woody encroachment and N enzyme activity, which suggested that organic N may be less available for microbial degradation as woody encroachment progresses. In general, these results show that soil organic matter (SOM) accessibility is more important than chemistry in determining SOM degradation and accrual, even in these soils with limited capacity for physical protection of SOM

Greater soil carbon stocks and faster turnover rates with increasing agricultural productivity

Devising agricultural management schemes that enhance food security and soil carbon levels is a high priority for many nations. However, the coupling between agricultural productivity, soil carbon stocks and organic matter turnover rates is still unclear. Archived soil samples from four decades of a long-term crop rotation trial were analyzed for soil organic matter (SOM) cycling-relevant properties: C and N content, bulk composition by nuclear magnetic resonance (NMR) spectroscopy, amino sugar content, short-term C bioavailability assays, and long-term C turnover rates by modeling the incorporation of the bomb spike in atmospheric 14C into the soil. After > 40 years under consistent management, topsoil carbon stocks ranged from 14 to 33MgCha-1 and were linearly related to the mean productivity of each treatment. Measurements of SOM composition demonstrated increasing amounts of plant- and microbially derived SOM along the productivity gradient. Under two modeling scenarios, radiocarbon data indicated overall SOM turnover time decreased from 40 to 13 years with increasing productivity - twice the rate of decline predicted from simple steady-state models or static three-pool decay rates of measured C pool distributions. Similarly, the half-life of synthetic root exudates decreased from 30.4 to 21.5 h with increasing productivity, indicating accelerated microbial activity. These findings suggest that there is a direct feedback between accelerated biological activity, carbon cycling rates and rates of carbon stabilization with important implications for how SOM dynamics are represented in models.We would like to thank our predecessors at the Waite Research Institute for having the foresight to archive soil samples from this long-term trial, T. Carter for laboratory assistance, and J. McGowan for assistance in running NMR analyses. Funds for this research were provided by the CSIRO Sustainable Agriculture National Research Flagship and New Zealand public research funding through GNS Science (540GCT82). Mark Farrell was supported by a CSIRO Julius Career Award

Degree of woody encroachment into grasslands controls soil carbohydrate and amino compound changes during long term laboratory incubation

Up to 50% of organic C and 80% of organic N within soil can exist as amino acids, amino sugars and carbohydrates. To determine how potential microbial accessibility and turnover of these compounds is impacted by encroachment of woody plants into grasslands, we investigated changes in evolved CO2 during thermal analysis and in carbohydrate and amino compound chemistry after long term laboratory incubation of sandy loam grassland woodland soils from southern Texas, USA. Thermal analysis showed that incubation increased the amount of soil organic matter (SOM) released at higher temperatures and that evolved CO2 profiles correlated with increases in amino C. During incubation, total carbohydrate C decreased slightly faster than bulk soil C, with preferential loss of plant-derived carbohydrates and/or production of microbial carbohydrates most strongly expressed in grassland and younger woodland soils. Total N content did not change during incubation, so the reduction in extractable amino N in older woodland soils suggested that N became more resistant to extraction during incubation. These data, along with previous measurements of respired CO2, indicate that changes in carbohydrate C and amino C did not predict mineralized CO2 yields and that amino compounds and microbial carbohydrate C were not selectively lost during incubation. The differing response in SOM loss (or enrichment) during incubation of the older woodland soils revealed a system with altered SOM dynamics due to woody encroachment, confirming that the short term ‘lability’ or ‘recalcitrance’ of SOM components is dependent on a number of interacting variables

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste

Abstract Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy