CHARM: COVID-19 Health Action Response for Marines – association of antigen-specific interferon-gamma and IL2 responses with asymptomatic and symptomatic infections after a positive qPCR SARS-CoV-2 test

SARS-CoV-2 T cell responses are associated with COVID-19 recovery, and Class I- and Class II-restricted epitopes have been identified in the spike (S), nucleocapsid (N) and membrane (M) proteins and others. This prospective COVID-19 Health Action Response for Marines (CHARM) study enabled assessment of T cell responses in symptomatic and asymptomatic SARS-CoV-2 infected participants. At enrollment all participants were negative by qPCR; follow-up occurred biweekly and then bimonthly for the next 6 weeks. Study participants who tested positive by qPCR SARS-CoV-2 test were asked to enroll in an immune response sub-study. FluoroSpot interferon-gamma (IFN-γ) and IL2 responses following qPCR-confirmed infection at enrollment (day 0), day 7 and 14 and more than 28 days later were measured using pools of 17mer peptides covering S, N, and M proteins, or CD4+CD8 peptide pools containing predicted epitopes from multiple SARS-CoV-2 antigens. Among 124 asymptomatic and 105 symptomatic participants, SARS-CoV-2 infection generated IFN-γ responses to the S, N and M proteins that persisted longer in asymptomatic cases. IFN-γ responses were significantly (p=0.001) more frequent to the N pool (51.4%) than the M pool (18.9%) among asymptomatic subjects; however, the difference was not statistically significant (p=0.06) for symptomatic subjects (N pool: 44.4%; M pool: 25.9%). In asymptomatic participants IFN-γ responders to the CD4+CD8 pool responded more frequently to the S pool (55.6%) and N pool (57.1%), than the M pool (7.1%), but symptomatic participants, IFN-γ responses were more frequent to the S pool (75.0%) than N pool (33.3%) and M pool (33.3%). The frequencies of IFN-γ responses to the S and N+M pools peaked 7 days after the positive qPCR test among asymptomatic (S pool: 22.2%; N+M pool: 28.7%) and symptomatic (S pool: 15.3%; N+M pool 21.9%) participants and dropped by >28 days. Magnitudes of post-infection IFN-γ and IL2 responses to the N+M pool were significantly correlated with IFN-γ and IL2 responses to the N and M pools. These data further support the central role of Th1-biased cell mediated immunity IFN-γ and IL2 responses, particularly to the N protein, in controlling COVID-19 symptoms, and justify T cell-based COVID-19 vaccines that include the N and S proteins.

Water Supply Increases N Acquisition and N Resorption from Old Branches in the Leafless Shrub Calligonum caput-medusae at the Taklimakan Desert Margin

Irrigation is the main strategy deployed to improve vegetation establishment, but the effects of increasing water availability on N use strategies in desert shrub species have received little attention. Pot experiments with drought-tolerant shrub Calligonum caput-medusae supplied with water at five field capacities in the range of 30–85% were conducted using local soil at the southern margin of the Taklimakan Desert. We examined the changes in plant biomass, soil N status, and plant N traits, and addressed the relationships between them in four- and seven-month-old saplings and mature shrubs after 28 months. Results showed that the growth of C. caput-medusae was highly responsive to increased soil moisture supply, and strongly depleted the soil available inorganic N pools from 16.7 mg kg−1 to an average of 1.9 mg kg−1, although the total soil N pool increased in all treatments. Enhancement of biomass production by increasing water supply was closely linked to increasing total plant N pool, N use efficiency (NUE), N resorption efficiency (NRE), and proficiency (NRP) in four-month saplings, but that to total plant N pool, NRE, and NRP after 28 months. The well-watered plants had lower N concentrations in senesced branches compared to their counterparts experiencing the two lowest water inputs. The mature shrubs had higher NRE and NRP than saplings and the world mean levels, suggesting a higher N conservation. Structural equation models showed that NRE was largely controlled by senesced branch N concentrations, and indirectly affected by water supply, whereas NRP was mainly determined by water supply. Our results indicated that increasing water availability increased the total N uptake and N resorption from old branches to satisfy the N requirement of C. caput-medusae. The findings lay important groundwork for vegetation establishment in desert ecosystems.

Root-Derived Proteases as a Plant Tool to Access Soil Organic Nitrogen; Current Stage of Knowledge and Controversies

Anthropogenic deterioration of the global nitrogen (N) cycle emerges mainly from overuse of inorganic N fertilizers in nutrient-limited cropping systems. To counteract a further dysregulation of the N cycle, we need to improve plant nitrogen use efficiency. This aim may be reached via unravelling all plant mechanisms to access soil N, with special attention to the dominating high-molecular-mass N pool. Traditionally, we believe that inorganic N is the only plant-available N pool, however, more recent studies point to acquisition of organic N compounds, i.e., amino acids, short peptides, and proteins. The least known mechanism of plants to increase the N uptake is a direct increase of soil proteolysis via root-derived proteases. This paper provides a review of the knowledge about root-derived proteases and also controversies behind this phenomenon.

Modelling the impact of soil processes on the N and O isotope signatures of nitrate in groundwater

<p>Stable isotope fingerprinting is widely applied to plant-soil-groundwater systems in an aim to identify and even quantify the sources of nitrates found in groundwater. Frequently, in such studies, the <em>δ</em><sup>15</sup>N and <em>δ</em><sup>18</sup>O values of nitrogen sources, such as inorganic fertilizers and manure, are directly compared to the isotope signatures of nitrate encountered in groundwater bodies below agricultural watersheds. We submit that the underlying assumptions (conservative behavior of isotope composition, rapid transfer from surface to groundwater) may only be realistic under very specific conditions whereas, in most cases, significant isotope effects exerted by the soil-microbial-plant system on the <em>δ</em><sup>15</sup>N and <em>δ</em><sup>18</sup>O values of nitrate need to be taken into account when attempting a quantitative apportionment of sources of groundwater nitrate.</p><p>We hypothesise that the isotopic signature of nitrate exported from below the root zone and migrating towards the groundwater will reflect the nitrogen isotope composition of the soil organic N pool, rather than the isotope composition of source fertilizer or organic amendments, due to processes that reset source isotope compositions within soil N pools. We test this hypothesis using empirical observations from a diversity of settings, in France, Spain and Canada with a relatively constant historic anthropogenic N source or a simple and well constrained landuse history. Furthermore, through the use of a process-based model (SIMSONIC, Billy et al., 2010) we estimate to what extent the isotopic composition of the predominant N input to the soil-microbial-plant system and the soil N pool has been modified in an attempt to consider these changes in source apportionment studies elucidating the sources of groundwater nitrate.</p><p>This research was supported through the Consortium award MUTUAL, by the LE STUDIUM® Loire Valley Institute for Advanced Studies via its SMART LOIRE VALLEY (SLV) fellowship programme, co-funded by the H2020 Marie Sklodowska-Curie programme, Contract No. 665790.</p><p> </p><p>Billy C., Billen G., Sebilo M., Birgand F., Tournebize J. (2010) Nitrogen isotopic composition of leached nitrate and soil organic matter as an indicator of denitrification in a sloping drained agricultural plot and adjacent uncultivated riparian buffer strips. Soil Biology and Biochemistry, 42, 108-117.</p>

Impacts of Arctic Shrubs on Root Traits and Belowground Nutrient Cycles Across a Northern Alaskan Climate Gradient

Deciduous shrubs are expanding across the graminoid-dominated nutrient-poor arctic tundra. Absorptive root traits of shrubs are key determinants of nutrient acquisition strategy from tundra soils, but the variations of shrub root traits within and among common shrub genera across the arctic climatic gradient are not well resolved. Consequently, the impacts of arctic shrub expansion on belowground nutrient cycling remain largely unclear. Here, we collected roots from 170 plots of three commonly distributed shrub genera (Alnus, Betula, and Salix) and a widespread sedge (Eriophorum vaginatum) along a climatic gradient in northern Alaska. Absorptive root traits that are relevant to the strategy of plant nutrient acquisition were determined. The influence of aboveground dominant vegetation cover on the standing root biomass, root productivity, vertical rooting profile, as well as the soil nitrogen (N) pool in the active soil layer was examined. We found consistent root trait variation among arctic plant genera along the sampling transect. Alnus and Betula had relatively thicker and less branched, but more frequently ectomycorrhizal colonized absorptive roots than Salix, suggesting complementarity between root efficiency and ectomycorrhizal dependence among the co-existing shrubs. Shrub-dominated plots tended to have more productive absorptive roots than sedge-dominated plots. At the northern sites, deep absorptive roots (>20 cm depth) were more frequent in birch-dominated plots. We also found shrub roots extensively proliferated into the adjacent sedge-dominated plots. The soil N pool in the active layer generally decreased from south to north but did not vary among plots dominated by different shrub or sedge genera. Our results reveal diverse nutrient acquisition strategies and belowground impacts among different arctic shrubs, suggesting that further identifying the specific shrub genera in the tundra landscape will ultimately provide better predictions of belowground dynamics across the changing arctic.

Overlooked nitrous oxide emissions driven by bedrock weathering

Atmospheric nitrous oxide (N2O) contributes directly to global warming, yet current models1-5 overlook bedrock-contained nitrogen (rock-N), the largest terrestrial N pool6, as a N2O source. Although rock-N release rates are large6-9, incomplete understanding on the fate of released rock-N has obscured connections between rock-N and atmospheric N2O. This connection emerged through our field studies of a hillslope underlain by marine shale. Bedrock weathering within the zone of the seasonally fluctuating water table controls the weathering depth, hence the release of rock-N. At this site, rock-N weathering contributes 78% of the subsurface reactive-N, with ~22% derived from atmospheric deposition and biological nitrogen fixation, commonly regarded as the sole sources of reactive-N in pristine environments10,11. About 56% of reactive-N denitrifies, including 14% emitted as N2O into the atmosphere. The remaining reactive-N discharges in porewaters to a floodplain where additional denitrification likely occurs. Using global rock-N releases of 11–18 Tg y-1 8, our measurements extrapolate to a weathering driven efflux of 1.3–2.1 Tg N-N2O y-1, consistent with a flux of 1.0–1.7 Tg N- N2O y-1 solely derived from the literature. Thus, bedrock weathering contributes approximately 10-17 % of nitrous oxide to the current global estimate of ~10 Tg y-1.

Effect of Site Specific Nitrogen Management on Seed Nitrogen—A Driving Factor of Winter Oilseed Rape (Brassica napus L.) Yield

It has been assumed that the management of both soil and fertilizer N in winter oilseed rape (WOSR) is crucial for N accumulation in seeds (Nse) and yield. This hypothesis was evaluated based on field experiments conducted in 2008/09, 2009/10, 2010/11 seasons, each year at two sites, differing in soil fertility, including indigenous N (Ni) supply. The experimental factors consisted of two N fertilizers: N and NS, and four Nf rates: 0, 80, 120, 160 kg ha−1. Yield, as governed by site × Nf rate interaction, responded linearly to Nse at harvest. The maximum Nse (Nsemax), as evaluated by N input (Nin = Ni + Nf) to WOSR at spring regrowth, varied from 95 to 153 kg ha−1, and determined 80% of yield variability. The basic reason of site diversity in Nsemax was Ni efficiency, ranging from 46% to 70%, respectively. The second cause of Nse variability was a shortage of N supply from + 9.5 soil to −8.8 kg ha−1 to the growing seeds during the seed filling period (SFP). This N pool supports the N concentration in seeds, resulting in both seed density and a seed weight increase, finally leading to a yield increase.

Effects of Changing Temperature on Gross N Transformation Rates in Acidic Subtropical Forest Soils

Soil temperature change caused by global warming could affect microbial-mediated soil nitrogen (N) transformations. Gross N transformation rates can provide process-based information about abiotic–biotic relationships, but most previous studies have focused on net rates. This study aimed to investigate the responses of gross rates of soil N transformation to temperature change in a subtropical acidic coniferous forest soil. A 15N tracing experiment with a temperature gradient was carried out. The results showed that gross mineralization rate of the labile organic N pool significantly increased with increasing temperature from 5 °C to 45 °C, yet the mineralization rate of the recalcitrant organic N pool showed a smaller response. An exponential response function described well the relationship between the gross rates of total N mineralization and temperature. Compared with N mineralization, the functional relationship between gross NH4+ immobilization and temperature was not so distinct, resulting in an overall significant increase in net N mineralization at higher temperatures. Heterotrophic nitrification rates increased from 5 °C to 25 °C but declined at higher temperatures. By contrast, the rate of autotrophic nitrification was very low, responding only slightly to the range of temperature change in the most temperature treatments, except for that at 35 °C to 45 °C, when autotrophic nitrification rates were found to be significantly increased. Higher rates of NO3− immobilization than gross nitrification rates resulted in negative net nitrification rates that decreased with increasing temperature. Our results suggested that, with higher temperature, the availability of soil N produced from N mineralization would significantly increase, potentially promoting plant growth and stimulating microbial activity, and that the increased NO3− retention capacity may reduce the risk of leaching and denitrification losses in this studied subtropical acidic forest.

Biochar application significantly affects the N pool and microbial community structure in purple and paddy soils

Background The increasing demand for food production has resulted in the use of large quantities of chemical fertilizers. This has created major environmental problems, such as increased ammonia volatilization, N2O emission, and nitrogen (N) leaching from agricultural soil. In particular, the utilization rate of N fertilizer is low in subtropical southern parts of China due to high rainfall. This causes not only large financial losses in agriculture, but also serious environmental pollution. Methods In this study, 16S rDNA-based analysis and static-chamber gas chromatography were used to elucidate the effects of continuous straw biochar application on the N pool and bacteria environment in two typical soil types, purple and paddy soils, in southern China. Results Straw biochar application (1) improved the soil N pool in both rhizosphere and non-rhizosphere soils; (2) significantly reduced the emission of N2O, with no difference in emission between 1 and 2 years of application; (3) increased the abundance of N-processing bacteria in the soil and altered the bacterial community structure; and (4) improved the tobacco yield and N use efficiency in paddy soil. These findings suggest that, in southern China, the application of straw biochar can promote N transformation in purple and paddy soils and reduce the emission of the greenhouse gas N2O.