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Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool- and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. We recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure, constrain parameters, and prescribe forcing fields.

Microbes influence soil organic matter decomposition and the long-term stabilization of carbon (C) in soils. We contend that by revising the representation of microbial processes and their interactions with the physicochemical soil environment, Earth system models (ESMs) will make more realistic global C cycle projections. Explicit representation of microbial processes presents considerable challenges due to the scale at which these processes occur. Thus, applying microbial theory in ESMs requires a framework to link micro-scale process-level understanding and measurements to macro-scale models used to make decadal- to century-long projections. Here we review the diversity, advantages, and pitfalls of simulating soil biogeochemical cycles using microbial-explicit modeling approaches. We present a roadmap for how to begin building, applying, and evaluating reliable microbial-explicit model formulations that can be applied in ESMs. Drawing from experience with traditional decomposition models, we suggest the following: (1) guidelines for common model parameters and output that can facilitate future model intercomparisons; (2) development of benchmarking and model-data integration frameworks that can be used to effectively guide, inform, and evaluate model parameterizations with data from well-curated repositories; and (3) the application of scaling methods to integrate microbial-explicit soil biogeochemistry modules within ESMs. With contributions across scientific disciplines, we feel this roadmap can advance our fundamental understanding of soil biogeochemical dynamics and more realistically project likely soil C response to environmental change at global scales.

The sensitivity of soil organic matter decomposition to global environmental change is a topic of prominent relevance for the global carbon cycle. Decomposition depends on multiple factors that are being altered simultaneously as a result of global environmental change; therefore, it is important to study the sensitivity of the rates of soil organic matter decomposition with respect to multiple and interacting drivers. In this manuscript, we present an analysis of the potential response of decomposition rates to simultaneous changes in temperature and moisture. To address this problem, we first present a theoretical framework to study the sensitivity of soil organic matter decomposition when multiple driving factors change simultaneously. We then apply this framework to models and data at different levels of abstraction: (1) to a mechanistic model that addresses the limitation of enzyme activity by simultaneous effects of temperature and soil water content, the latter controlling substrate supply and oxygen concentration for microbial activity; (2) to different mathematical functions used to represent temperature and moisture effects on decomposition in biogeochemical models. To contrast model predictions at these two levels of organization, we compiled different data sets of observed responses in field and laboratory studies. Then we applied our conceptual framework to: (3) observations of heterotrophic respiration at the ecosystem level; (4) laboratory experiments looking at the response of heterotrophic respiration to independent changes in moisture and temperature; and (5) ecosystem-level experiments manipulating soil temperature and water content simultaneously.

It is often assumed that daytime patterns of ecosystem carbon assimilation are mostly driven by direct physiological responses to exogenous environmental cues. Under limited environmental variability, little variation in carbon assimilation should thus be expected unless endogenous plant controls on carbon assimilation, which regulate photosynthesis in time, are active. We evaluated this assumption with eddy flux data, and we selected periods when net ecosystem exchange (NEE) was decoupled from environmental variability in seven sites from highly contrasting biomes across a 74° latitudinal gradient over a total of 36 site-years. Under relatively constant conditions of light, temperature, and other environmental factors, significant diurnal NEE oscillations were observed at six sites, where daily NEE variation was between 20% and 90% of that under variable environmental conditions. These results are consistent with fluctuations driven by the circadian clock and other endogenous processes. Our results open a promising avenue of research for a more complete understanding of ecosystem fluxes that integrates from cellular to ecosystem processes. © 2012 Blackwell Publishing Ltd.

The major driving factors of soil CO2 production - substrate supply, temperature, and water content - vary vertically within the soil profile, with the greatest temporal variations of these factors usually near the soil surface. Several studies have demonstrated that wetting and drying of the organic horizon contributes to temporal variation in summertime soil CO2 efflux in forests, but this contribution is difficult to quantify. The objectives of this study were to partition CO2 production vertically in a mixed hardwood stand of the Harvard Forest, Massachusetts, USA, and then to use that partitioning to evaluate how the relative contributions of CO2 production by genetic soil horizon vary seasonally and interannually. We measured surface CO2 efflux and vertical soil profiles of CO2 concentration, temperature, water content, and soil physical characteristics. These data were applied to a model of effective diffusivity to estimate CO2 flux at the top of each genetic soil horizon and the production within each horizon. A sensitivity analysis revealed sources of uncertainty when applying a diffusivity model to a rocky soil with large spatial heterogeneity, especially estimates of bulk density and volumetric water content and matching measurements of profiles and surface fluxes. We conservatively estimate that the O horizon contributed 40-48% of the total annual soil CO2 efflux. Although the temperature sensitivity of CO2 production varied across soil horizons, the partitioning of CO2 production by horizon did not improve the overall prediction of surface CO2 effluxes based on temperature functions. However, vertical partitioning revealed that water content covaried with CO2 production only in the O horizon. Large interannual variations in estimates of O horizon CO2 production indicate that this layer could be an important transient interannual source or sink of ecosystem C. © 2006 Blackwell Publishing Ltd.

Soil moisture affects microbial decay of SOM and rhizosphere respiration (RR) in temperate forest soils, but isolating the response of soil respiration (SR) to summer drought and subsequent wetting is difficult because moisture changes are often confounded with temperature variation. We distinguished between temperature and moisture effects by simulation of prolonged soil droughts in a mixed deciduous forest at the Harvard Forest, Massachusetts. Roofs constructed over triplicate 5×5m2 plots excluded throughfall water during the summers of 2001 (168mm) and 2002 (344 mm), while adjacent control plots received ambient throughfall and the same natural temperature regime. In 2003, throughfall was not excluded to assess the response of SR under natural weather conditions after two prolonged summer droughts. Throughfall exclusion significantly decreased mean SR rate by 53mgCm-2h-1 over 84 days in 2001, and by 68mgCm-2h-1 over 126 days in 2002, representing 10-30% of annual SR in this forest and 35-75% of annual net ecosystem exchange (NEE) of C. The differences in SR were best explained by differences in gravimetric water content in the Oi horizon (r250.69) and the Oe/Oa horizon (r250.60). Volumetric water content of the A horizon was not significantly affected by throughfall exclusion. The radiocarbon signature of soil CO2 efflux and of CO2 respired during incubations of O horizon, A horizon and living roots allowed partitioning of SR into contributions from young C substrate (including RR) and from decomposition of older SOM. RR (root respiration and microbial respiration of young substrates in the rhizosphere) made up 43-71% of the total C respired in the control plots and 41-80% in the exclusion plots, and tended to increase with drought. An exception to this trend was an interesting increase in CO2 efflux of radiocarbon-rich substrates during a period of abundant growth of mushrooms. Our results suggest that prolonged summer droughts decrease primarily heterotrophic respiration in the O horizon, which could cause increases in the storage of soil organic carbon in this forest. However, the C stored during two summers of simulated drought was only partly released as increased respiration during the following summer of natural throughfall. We do not know if this soil C sink during drought is transient or long lasting. In any case, differential decomposition of the O horizon caused by interannual variation of precipitation probably contributes significantly to observed interannual variation of NEE in temperate forests. © 2005 Blackwell Publishing Ltd.

Drying and wetting cycles of O horizon in forest soils have not received much attention, partly due to methodological limitations for nondestructive monitoring of the O horizon water content. The objective of this study was to determine the importance of moisture limitations in the O horizon of a temperate forest on summertime soil respiration. We measured soil respiration in three replicated plots in a mixed deciduous forest at Harvard Forest, Massachusetts, weekly from May to October 2001. Direct Current (DC) half-bridge sensors that had been calibrated using destructive samples of the Oi and Oe/ Oa horizons were placed in the Oi and Oe/Oa horizons to record hourly changes of gravimetric water contents. Soil temperature explained 47% of the variation in soil respiration using the Arrhenius equation. The residuals of the temperature model were linearly correlated with gravimetric water content of the Oi horizon (r2 = 0.72, P < 0.0001) and Oe/Oa horizon (r2 = 0.56, P < 0.001), indicating that temporal variation in soil respiration can be partly explained by water content of the O horizon. Additionally, a laboratory study was performed to evaluate drying/wetting cycles of the O horizon at constant temperature. Even small simulated rainfall amounts of 0.5 mm significantly increase CO2 flux from dry O horizon within a few minutes. The duration of CO2 pulses increased with the amount of applied water, lasting from a few hours to days. A strong correlation between CO2 release and water content of the O horizons demonstrates a clear regulatory role of litter water content on decomposition within the O horizons.

Temperate forests of North America are thought to be significant sinks of atmospheric CO2. We developed a below-ground carbon (C) budget for well-drained soils in Harvard Forest Massachusetts, an ecosystem that is storing C. Measurements of carbon and radiocarbon (14C) inventory were used to determine the turnover time and maximum rate of CO2 production from heterotrophic respiration of three fractions of soil organic matter (SOM): recognizable litter fragments (L), humified low density material (H), and high density or mineral-associated organic matter (M). Turnover times in all fractions increased with soil depth and were 2-5 years for recognizable leaf litter, 5-10 years for root litter, 40-100+ years for low density humified material and >100 years for carbon associated with minerals. These turnover times represent the time carbon resides in the plant + soil system, and may underestimate actual decomposition rates if carbon resides for several years in living root, plant or woody material. Soil respiration was partitioned into two components using 14C: recent photosynthate which is metabolized by roots and microorganisms within a year of initial fixation (Recent-C), and C that is respired during microbial decomposition of SOM that resides in the soil for several years or longer (Reservoir-C). For the whole soil, we calculate that decomposition of Reservoir-C contributes approximately 41% of the total annual soil respiration. Of this 41%, recognizable leaf or root detritus accounts for 80% of the flux, and 20% is from the more humified fractions that dominate the soil carbon stocks. Measurements of CO2 and 14CO2 in the soil atmosphere and in total soil respiration were combined with surface CO2 fluxes and a soil gas diffusion model to determine the flux and isotopic signature of C produced as a function of soil depth. 63% of soil respiration takes place in the top 15 cm of the soil (O + A + Ap horizons). The average residence time of Reservoir-C in the plant + soil system is 8±1 years and the average age of carbon in total soil respiration (Recent-C + Reservoir-C) is 44±1 years. The O and A horizons have accumulated 4.4 kgC m-2 above the plow layer since abandonment by settlers in the late-1800's. C pools contributing the most to soil respiration have short enough turnover times that they are likely in steady state. However, most C is stored as humified organic matter within both the O and A horizons and has turnover times from 40 to 100+ years respectively. These reservoirs continue to accumulate carbon at a combined rate of 10-30 gC m-2 yr-1. This rate of accumulation is only 5-15% of the total ecosystem C sink measured in this stand using eddy covariance methods.

The future flora of Amazonia will include significant areas of secondary forest as degraded pastures are abandoned and secondary succession proceeds. The rate at which secondary forests regain carbon (C) stocks and re-establish biogeochemical cycles that resemble those of primary forests will influence the biogeochemistry of the region. Most studies have focused on the effects of deforestation on biogeochemical cycles. In this study, we present data on the recuperation of carbon stocks and carbon fluxes within a secondary forest of the eastern Amazon, and we compare these measurements to those for primary forest, degraded pasture, and productive pasture. Along a transect from a 23-y-old degraded pasture, through a 7-y-old secondary forest, through a 16-year-old secondary forest, and to a primary forest, the δ13C values of soil organic matter (SOM) in the top 10 cm of soil were -21.0, -26.5, -27.4, and -27.9‰, respectively, indicating that the isotopic signature of SOM from C3 forest plants was rapidly re-established. The degraded pasture also had significant inputs of C from C3 plants. Radiocarbon data indicated that most of the C in the top 10 cm of soil had been fixed by plants during the last 30 years. Differences in soil C inventory among land use types were small compared to uncertainties in their measurement. Root inputs were nearly identical in primary and secondary forests, and litterfall in the secondary forest was 88% of the litterfall rate of the primary forest. In contrast, the secondary forest had only 17% of the above ground biomass. Because of rapid cycling rates of soil C and rapid recovery of C fluxes to and from the soil, the below ground C cycle in this secondary forest was nearly identical with those of the unaltered primary forest.

DEFORESTATION and logging transform more forest in eastern and southern Amazonia than in any other region of the world1-3. This forest alteration affects regional hydrology4-11 and the global carbon cycle12-14, but current analyses of these effects neglect an important deep-soil link between the water and carbon cycles. Using rainfall data, satellite imagery and field studies, we estimate here that half of the closed forests of Brazilian Amazonia depend on deep root systems to maintain green canopies during the dry season. Evergreen forests in northeastern Pará state maintain evapotranspiration during five-month dry periods by absorbing water from the soil to depths of more than 8m. In contrast, although the degraded pastures of this region also contain deep-rooted woody plants, most pasture plants substantially reduce their leaf canopy in response to seasonal drought, thus reducing dry-season evapotranspiration and increasing potential subsurface runoff relative to the forests they replace. Deep roots that extract water also provide carbon to the soil. The forest soil below 1 m depth contains more carbon than does above-ground biomass, and as much as 15% of this deep-soil carbon turns over on annual or decadal timescales. Thus, forest alteration that affects depth distributions of carbon inputs from roots may also affect net carbon storage in the soil. © 2002 Nature Publishing Group.

Nitrous oxide (N 2 O) emissions from livestock manure contribute significantly to the growth of atmospheric N 2 O, a powerful greenhouse gas and dominant ozone-depleting substance. Here, we estimate global N 2 O emissions from livestock manure during 1890-2020 using the tier 2 approach of the 2019 Refinement to the 2006 IPCC Guidelines. Global N 2 O emissions from livestock manure increased by ~350% from 451 [368-556] Gg N year -1 in 1890 to 2042 [1677-2514] Gg N year -1 in 2020. These emissions contributed ~30% to the global anthropogenic N 2 O emissions in the decade 2010-2019. Cattle contributed the most (60%) to the increase, followed by poultry (19%), pigs (15%), and sheep and goats (6%). Regionally, South Asia, Africa, and Latin America dominated the growth in global emissions since the 1990s. Nationally, the largest emissions were found in India (329 Gg N year -1 ), followed by China (267 Gg N year -1 ), the United States (163 Gg N year -1 ), Brazil (129 Gg N year -1 ) and Pakistan (102 Gg N year -1 ) in the 2010s. We found a substantial impact of livestock productivity, specifically animal body weight and milk yield, on the emission trends. Furthermore, a large spread existed among different methodologies in estimates of global N 2 O emission from livestock manure, with our results 20%-25% lower than those based on the 2006 IPCC Guidelines. This study highlights the need for robust time-variant model parameterization and continuous improvement of emissions factors to enhance the precision of emission inventories. Additionally, urgent mitigation is required, as all available inventories indicate a rapid increase in global N 2 O emissions from livestock manure in recent decades., (© 2024 John Wiley & Sons Ltd.)

Over the last century, outbreaks and pandemics have occurred with disturbing regularity, necessitating advance preparation and large-scale, coordinated response. Here, we developed a machine learning predictive model of disease severity and length of hospitalization for COVID-19, which can be utilized as a platform for future unknown viral outbreaks. We combined untargeted metabolomics on plasma data obtained from COVID-19 patients (n = 111) during hospitalization and healthy controls (n = 342), clinical and comorbidity data (n = 508) to build this patient triage platform, which consists of three parts: (i) the clinical decision tree, which amongst other biomarkers showed that patients with increased eosinophils have worse disease prognosis and can serve as a new potential biomarker with high accuracy (AUC = 0.974), (ii) the estimation of patient hospitalization length with ± 5 days error (R 2  = 0.9765) and (iii) the prediction of the disease severity and the need of patient transfer to the intensive care unit. We report a significant decrease in serotonin levels in patients who needed positive airway pressure oxygen and/or were intubated. Furthermore, 5-hydroxy tryptophan, allantoin, and glucuronic acid metabolites were increased in COVID-19 patients and collectively they can serve as biomarkers to predict disease progression. The ability to quickly identify which patients will develop life-threatening illness would allow the efficient allocation of medical resources and implementation of the most effective medical interventions. We would advocate that the same approach could be utilized in future viral outbreaks to help hospitals triage patients more effectively and improve patient outcomes while optimizing healthcare resources., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Gastrointestinal symptoms are common in most forms of neurodevelopment disorders (NDDs) such as in autism spectrum disorders (ASD). The current patient-reported outcome measures with validated questionnaires used in the general population of children without NDDS cannot be used in the autistic individuals. We explore here the multifactorial pathophysiology of ASD and the role of genetics and the environment in this disease spectrum and focus instead on possible diagnostics that could provide future objective insight into the connection of the gut-brain-microbiome in this disease entity. We provide our own data from both humans and a zebrafish model of ASD called Phelan-McDermid Syndrome. We hope that this review highlights the gaps in our current knowledge on many of these profound NDDs and that it provides a future framework upon which clinicians and researchers can build and network with other interested multidisciplinary specialties., Competing Interests: BM and J.E.D. regarding patent: Provisional U.S. patent 63/283,665.B.M. has grant funding from Medtronic (Wireless Motility Capsule)., (Thieme. All rights reserved.)

Background: Despite widespread global use of artificial turf fields, there is a paucity of research assessing the presence of potentially harmful chemicals within the field components., Objective: This pilot study aimed to assess the capacity of an adapted extraction-analysis method to identify and quantitate FTOHs, a class of perfluoroalkyl and polyfluoroalkyl substances (PFAS), in artificial turf fiber and crumb rubber infill samples., Methods: FTOHs in artificial turf fibers and crumb rubber infill were extracted using 80:20 methanol:methyl tert- butyl ether, reconstituted in methanol, and analyzed by gas chromatography-mass spectroscopy (GC-MS) operated in scanning ion mode (SIM)., Results: 8:2 FTOH was detected in artificial turf fiber and crumb rubber infill samples at concentrations of 1.0 and 0.71 ng/μL, respectively. This translates to 300ng 8:2 FTOH/g artificial turf fiber and 110ng 8:2 FTOH/g crumb rubber. By contrast, 4:2 FTOH and 6:2 FTOH were not found to be present in detectable levels., Conclusion: Our extraction method with subsequent GC-MS analysis proved useful in detecting FTOHs in artificial turf field samples. 8:2 FTOH may be present in artificial turf fibers and crumb rubber infill. This pilot investigation supports the need for further research into the presence of this class of PFAS in artificial turf field components., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

To meet the growing food demand while addressing the multiple challenges of exacerbating phosphorus (P) pollution and depleting P rock reserves 1-15 , P use efficiency (PUE, the ratio of productive P output to P input in a defined system) in crop production needs to be improved. Although many efforts have been devoted to improving nutrient management practices on farms, few studies have examined the historical trajectories of PUE and their socioeconomic and agronomic drivers on a national scale 1,2,6,7,11,16,17 . Here we present a database of the P budget (the input and output of the crop production system) and PUE by country and by crop type for 1961-2019, and examine the substantial contribution of several drivers for PUE, such as economic development stages and crop portfolios. To address the P management challenges, we found that global PUE in crop production must increase to 68-81%, and recent trends indicate some meaningful progress towards this goal. However, P management challenges and opportunities in croplands vary widely among countries., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

Short-chain fatty acids (SCFAs) are volatile fatty acids produced by gut microbial fermentation of dietary nondigestible carbohydrates. Acetate, propionate, and butyrate SCFA measures are important to clinical and nutritional studies for their established roles in promoting healthy immune and gut function. Additionally, circulating SCFAs may influence the metabolism and allied function of additional tissues and organs. The accurate quantification of SCFAs in plasma/serum is critical to understanding the biological role of SCFAs. The low concentrations of circulating SCFAs and their volatile nature present challenges for quantitative analysis. Herein, we report a sensitive method for SCFA quantification via extraction with methyl tert-butyl ether after plasma/serum acidification. The organic extract of SCFAs is injected directly with separation and detection using a polar GC column coupled to mass spectrometry. The solvent-to-sample ratio, plasma volume, and amount of HCl needed for SCFA protonation were optimized. Method validation shows good within-day and inter-day repeatability. The limit of detection was 0.3-0.6 µg/mL for acetate and 0.03-0.12 µg/mL for propionate and butyrate. Successful application of this method on clinical plasma and serum samples was demonstrated in six datasets. By simplifying the sample preparation procedure, the present method reduces the risk of contamination, lowers the cost of analysis, increases throughput, and offers the potential for automated sample preparation., (© 2021. Springer-Verlag GmbH Germany, part of Springer Nature.)

Recent reports have challenged the notion that the lens is immune-privileged. However, these studies have not fully identified the molecular mechanism(s) that promote immune surveillance of the lens. Using a mouse model of targeted glutathione (GSH) deficiency in ocular surface tissues, we have investigated the role of oxidative stress in upregulating cytokine expression and promoting immune surveillance of the eye. RNA-sequencing of lenses from postnatal day (P) 1-aged Gclc f/f ;Le-Cre Tg/- (KO) and Gclc f/f ;Le-Cre -/- control (CON) mice revealed upregulation of many cytokines (e.g., CCL4, GDF15, CSF1) and immune response genes in the lenses of KO mice. The eyes of KO mice had a greater number of cells in the aqueous and vitreous humors at P1, P20 and P50 than age-matched CON and Gclc w/w ;Le-Cre Tg/- (CRE) mice. Histological analyses revealed the presence of innate immune cells (i.e., macrophages, leukocytes) in ocular structures of the KO mice. At P20, the expression of cytokines and ROS content was higher in the lenses of KO mice than in those from age-matched CRE and CON mice, suggesting that oxidative stress may induce cytokine expression. In vitro administration of the oxidant, hydrogen peroxide, and the depletion of GSH (using buthionine sulfoximine (BSO)) in 21EM15 lens epithelial cells induced cytokine expression, an effect that was prevented by co-treatment of the cells with N-acetyl-l-cysteine (NAC), a antioxidant. The in vivo and ex vivo induction of cytokine expression by oxidative stress was associated with the expression of markers of epithelial-to-mesenchymal transition (EMT), α-SMA, in lens cells. Given that EMT of lens epithelial cells causes posterior capsule opacification (PCO), we propose that oxidative stress induces cytokine expression, EMT and the development of PCO in a positive feedback loop. Collectively these data indicate that oxidative stress induces inflammation of lens cells which promotes immune surveillance of ocular structures., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Mitigating soil nitrous oxide (N 2 O) emissions is essential for staying below a 2 °C warming threshold. However, accurate assessments of mitigation potential are limited by uncertainty and variability in direct emission factors (EFs). To assess where and why EFs differ, we created high-resolution maps of crop-specific EFs based on 1,507 georeferenced field observations. Here, using a data-driven approach, we show that EFs vary by two orders of magnitude over space. At global and regional scales, such variation is primarily driven by climatic and edaphic factors rather than the well-recognized management practices. Combining spatially explicit EFs with N surplus information, we conclude that global mitigation potential without compromising crop production is 30% (95% confidence interval, 17-53%) of direct soil emissions of N 2 O, equivalent to the entire direct soil emissions of China and the United States combined. Two-thirds (65%) of the mitigation potential could be achieved on one-fifth of the global harvested area, mainly located in humid subtropical climates and across gleysols and acrisols. These findings highlight the value of a targeted policy approach on global hotspots that could deliver large N 2 O mitigation as well as environmental and food co-benefits., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Purpose: The purpose of this study was to elucidate the role and molecular consequences of impaired glutathione (GSH) biosynthesis on eye development., Methods: GSH biosynthesis was impaired in surface ectoderm-derived ocular tissues by crossing Gclc f/f mice with hemizygous Le-Cre transgenic mice to produce Gclc f/f /Le-Cre Tg/- (KO) mice. Control mice included Gclc f/f and Gclc wt/wt /Le-Cre Tg/- mice (CRE). Eyes from all mice (at various stages of eye development) were subjected to histological, immunohistochemical, Western blot, RT-qPCR, RNA-seq, and subsequent Gene Ontology, Ingenuity Pathway Analysis and TRANSFAC analyses. PAX6 transactivation activity was studied using a luciferase reporter assay in HEK293T cells depleted of GSH using buthionine sulfoximine (BSO)., Results: Deletion of Gclc diminished GSH levels, increased reactive oxygen species (ROS), and caused an overt microphthalmia phenotype characterized by malformation of the cornea, iris, lens, and retina that is distinct from and much more profound than the one observed in CRE mice. In addition, only the lenses of KO mice displayed reduced crystallin (α, β), PITX3 and Foxe3 expression. RNA-seq analyses at postnatal day 1 revealed 1552 differentially expressed genes (DEGs) in the lenses of KO mice relative to those from Gclc f/f mice, with Crystallin and lens fiber cell identity genes being downregulated while lens epithelial cell identity and immune response genes were upregulated. Bioinformatic analysis of the DEGs implicated PAX6 as a key upstream regulator. PAX6 transactivation activity was impaired in BSO-treated HEK293T cells., Conclusions: These data suggest that impaired ocular GSH biosynthesis may disrupt eye development and PAX6 function., (Copyright © 2021 Elsevier Inc. All rights reserved.)

The consideration of tariffs on China's imports of US agricultural products has focused on economic impacts, while the environmental consequences have received less attention. Here we use a global computable general equilibrium model to evaluate long-term crop portfolio changes induced by China's retaliatory agricultural tariffs and thereby assess the environmental stresses imposed by different crop production portfolios based on region-specific and crop-specific databases. We show that China's tariffs cause unintended increases in nitrogen and phosphorus pollution and blue water extraction in the United States as farmers shift from soybeans to more pollution-causing crops. If diverted to Brazil, China's soybean demands would reduce Brazilian stresses of nitrogen pollution and water use through crop portfolio changes, but may add additional pressures on phosphorus pollution and deforestation. On a global scale, trade policies could help to reduce nutrient pollution and water source depletion by promoting crop production where it is most efficient in terms of nutrient and water use., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Input-output estimates of nitrogen on cropland are essential for improving nitrogen management and better understanding the global nitrogen cycle. Here, we compare 13 nitrogen budget datasets covering 115 countries and regions over 1961-2015. Although most datasets showed similar spatiotemporal patterns, some annual estimates varied widely among them, resulting in large ranges and uncertainty. In 2010, global medians (in TgN yr -1 ) and associated minimum-maximum ranges were 73 (64-84) for global harvested crop nitrogen; 161 (139-192) for total nitrogen inputs; 86 (68-97) for nitrogen surplus; and 46% (40-53%) for nitrogen use efficiency. Some of the most uncertain nitrogen budget terms by country showed ranges as large as their medians, revealing areas for improvement. A benchmark nitrogen budget dataset, derived from central tendencies of the original datasets, can be used in model comparisons and inform sustainable nitrogen management in food systems., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Research involving autism spectrum disorder (ASD) most frequently focuses on its key diagnostic criteria: restricted interests and repetitive behaviors, altered sensory perception, and communication impairments. These core criteria, however, are often accompanied by numerous comorbidities, many of which result in severe negative impacts on quality of life, including seizures, epilepsy, sleep disturbance, hypotonia, and GI distress. While ASD is a clinically heterogeneous disorder, gastrointestinal (GI) distress is among the most prevalent co-occurring symptom complex, manifesting in upward of 70% of all individuals with ASD. Consistent with this high prevalence, over a dozen family foundations that represent genetically distinct, molecularly defined forms of ASD have identified GI symptoms as an understudied area with significant negative impacts on quality of life for both individuals and their caregivers. Moreover, GI symptoms are also correlated with more pronounced irritability, social withdrawal, stereotypy, hyperactivity, and sleep disturbances, suggesting that they may exacerbate the defining behavioral symptoms of ASD. Despite these facts (and to the detriment of the community), GI distress remains largely unaddressed by ASD research and is frequently regarded as a symptomatic outcome rather than a potential contributory factor to the behavioral symptoms. Allowing for examination of both ASD's impact on the central nervous system (CNS) as well as its impact on the GI tract and the associated microbiome, the zebrafish has recently emerged as a powerful tool to study ASD. This is in no small part due to the advantages zebrafish present as a model system: their precocious development, their small transparent larval form, and their parallels with humans in genetics and physiology. While ASD research centered on the CNS has leveraged these advantages, there has been a critical lack of GI-centric ASD research in zebrafish models, making a holistic view of the gut-brain-microbiome axis incomplete. Similarly, high-throughput ASD drug screens have recently been developed but primarily focus on CNS and behavioral impacts while potential GI impacts have not been investigated. In this review, we aim to explore the great promise of the zebrafish model for elucidating the roles of the gut-brain-microbiome axis in ASD., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 James, Davidson, Yanes, Moshiree and Dallman.)

Nitrogen use efficiency (NUE) is a key indicator with which to study nitrogen cycles and inform nitrogen management. However, different quantification approaches may result in substantially divergent NUE values even for the same production system or for the same experimental plot. Based on our investigation of the differences between and connections among the three principal approaches for NUE quantification, we offer recommendations for choosing the appropriate approach and call for long-term observations to assess the impacts of management practices., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Paired-box (PAX) genes encode a family of highly conserved transcription factors found in vertebrates and invertebrates. PAX proteins are defined by the presence of a paired domain that is evolutionarily conserved across phylogenies. Inclusion of a homeodomain and/or an octapeptide linker subdivides PAX proteins into four groups. Often termed "master regulators", PAX proteins orchestrate tissue and organ development throughout cell differentiation and lineage determination, and are essential for tissue structure and function through maintenance of cell identity. Mutations in PAX genes are associated with myriad human diseases (e.g., microphthalmia, anophthalmia, coloboma, hypothyroidism, acute lymphoblastic leukemia). Transcriptional regulation by PAX proteins is, in part, modulated by expression of alternatively spliced transcripts. Herein, we provide a genomics update on the nine human PAX family members and PAX homologs in 16 additional species. We also present a comprehensive summary of human tissue-specific PAX transcript variant expression and describe potential functional significance of PAX isoforms. While the functional roles of PAX proteins in developmental diseases and cancer are well characterized, much remains to be understood regarding the functional roles of PAX isoforms in human health. We anticipate the analysis of tissue-specific PAX transcript variant expression presented herein can serve as a starting point for such research endeavors.

Globally, soils store two to three times as much carbon as currently resides in the atmosphere, and it is critical to understand how soil greenhouse gas (GHG) emissions and uptake will respond to ongoing climate change. In particular, the soil-to-atmosphere CO 2 flux, commonly though imprecisely termed soil respiration (R S ), is one of the largest carbon fluxes in the Earth system. An increasing number of high-frequency R S measurements (typically, from an automated system with hourly sampling) have been made over the last two decades; an increasing number of methane measurements are being made with such systems as well. Such high frequency data are an invaluable resource for understanding GHG fluxes, but lack a central database or repository. Here we describe the lightweight, open-source COSORE (COntinuous SOil REspiration) database and software, that focuses on automated, continuous and long-term GHG flux datasets, and is intended to serve as a community resource for earth sciences, climate change syntheses and model evaluation. Contributed datasets are mapped to a single, consistent standard, with metadata on contributors, geographic location, measurement conditions and ancillary data. The design emphasizes the importance of reproducibility, scientific transparency and open access to data. While being oriented towards continuously measured R S , the database design accommodates other soil-atmosphere measurements (e.g. ecosystem respiration, chamber-measured net ecosystem exchange, methane fluxes) as well as experimental treatments (heterotrophic only, etc.). We give brief examples of the types of analyses possible using this new community resource and describe its accompanying R software package., (© 2020 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Nitrous oxide (N 2 O), like carbon dioxide, is a long-lived greenhouse gas that accumulates in the atmosphere. Over the past 150 years, increasing atmospheric N 2 O concentrations have contributed to stratospheric ozone depletion 1 and climate change 2 , with the current rate of increase estimated at 2 per cent per decade. Existing national inventories do not provide a full picture of N 2 O emissions, owing to their omission of natural sources and limitations in methodology for attributing anthropogenic sources. Here we present a global N 2 O inventory that incorporates both natural and anthropogenic sources and accounts for the interaction between nitrogen additions and the biochemical processes that control N 2 O emissions. We use bottom-up (inventory, statistical extrapolation of flux measurements, process-based land and ocean modelling) and top-down (atmospheric inversion) approaches to provide a comprehensive quantification of global N 2 O sources and sinks resulting from 21 natural and human sectors between 1980 and 2016. Global N 2 O emissions were 17.0 (minimum-maximum estimates: 12.2-23.5) teragrams of nitrogen per year (bottom-up) and 16.9 (15.9-17.7) teragrams of nitrogen per year (top-down) between 2007 and 2016. Global human-induced emissions, which are dominated by nitrogen additions to croplands, increased by 30% over the past four decades to 7.3 (4.2-11.4) teragrams of nitrogen per year. This increase was mainly responsible for the growth in the atmospheric burden. Our findings point to growing N 2 O emissions in emerging economies-particularly Brazil, China and India. Analysis of process-based model estimates reveals an emerging N 2 O-climate feedback resulting from interactions between nitrogen additions and climate change. The recent growth in N 2 O emissions exceeds some of the highest projected emission scenarios 3,4 , underscoring the urgency to mitigate N 2 O emissions.

Production and consumption of nitrous oxide (N 2 O), methane (CH 4 ), and carbon dioxide (CO 2 ) are affected by complex interactions of temperature, moisture, and substrate supply, which are further complicated by spatial heterogeneity of the soil matrix. This microsite heterogeneity is often invoked to explain non-normal distributions of greenhouse gas (GHG) fluxes, also known as hot spots and hot moments. To advance numerical simulation of these belowground processes, we expanded the Dual Arrhenius and Michaelis-Menten model, to apply it consistently for all three GHGs with respect to the biophysical processes of production, consumption, and diffusion within the soil, including the contrasting effects of oxygen (O 2 ) as substrate or inhibitor for each process. High-frequency chamber-based measurements of all three GHGs at the Howland Forest (ME, USA) were used to parameterize the model using a multiple constraint approach. The area under a soil chamber is partitioned according to a bivariate log-normal probability distribution function (PDF) of carbon and water content across a range of microsites, which leads to a PDF of heterotrophic respiration and O 2 consumption among microsites. Linking microsite consumption of O 2 with a diffusion model generates a broad range of microsite concentrations of O 2 , which then determines the PDF of microsites that produce or consume CH 4 and N 2 O, such that a range of microsites occurs with both positive and negative signs for net CH 4 and N 2 O flux. Results demonstrate that it is numerically feasible for microsites of N 2 O reduction and CH 4 oxidation to co-occur under a single chamber, thus explaining occasional measurement of simultaneous uptake of both gases. Simultaneous simulation of all three GHGs in a parsimonious modeling framework is challenging, but it increases confidence that agreement between simulations and measurements is based on skillful numerical representation of processes across a heterogeneous environment., (© 2019 John Wiley & Sons Ltd.)

Carbon dioxide (CO 2 ), methane (CH 4 ), and nitrous oxide (N 2 O) are the greenhouse gases largely responsible for anthropogenic climate change. Natural plant and microbial metabolic processes play a major role in the global atmospheric budget of each. We have been studying ecosystem-atmosphere trace gas exchange at a sub-boreal forest in the northeastern United States for over two decades. Historically our emphasis was on turbulent fluxes of CO 2 and water vapor. In 2012 we embarked on an expanded campaign to also measure CH 4 and N 2 O. Here we present continuous tower-based measurements of the ecosystem-atmosphere exchange of CO 2 and CH 4 , recorded over the period 2012-2018 and reported at a 30-minute time step. Additionally, we describe a five-year (2012-2016) dataset of chamber-based measurements of soil fluxes of CO 2 , CH 4 , and N 2 O (2013-2016 only), conducted each year from May to November. These data can be used for process studies, for biogeochemical and land surface model validation and benchmarking, and for regional-to-global upscaling and budgeting analyses.

High rates of land conversion and land use change have vastly increased the proportion of secondary forest in the lowland tropics relative to mature forest. As secondary forests recover following abandonment, nitrogen (N) and phosphorus (P) must be present in sufficient quantities to sustain high rates of net primary production and to replenish the nutrients lost during land use prior to secondary forest establishment. Biogeochemical theory and results from individual studies suggest that N can recuperate during secondary forest recovery, especially relative to P. Here, we synthesized 23 metrics of N and P in soil and plants from 45 secondary forest chronosequences located in the wet tropics to empirically explore (1) whether there is a consistent change in nutrients and nutrient cycling processes during secondary succession in the biome; (2) which metrics of N and P in soil and plants recuperate most consistently; (3) if the recuperation of nutrients during succession approaches similar nutrient concentrations and fluxes as those in mature forest in ~100 yr following the initiation of succession; and (4) whether site characteristics, including disturbance history, climate, and soil order are significantly related to nutrient recuperation. During secondary forest succession, nine metrics of N and/or P cycling changed consistently and substantially. In most sites, N concentrations and fluxes in both plants and soil increased during secondary succession, and total P concentrations increased in surface soil. Changes in nutrient concentrations and nutrient cycling processes during secondary succession were similar whether mature forest was included or excluded from the analysis, indicating that nutrient recuperation in secondary forest leads to biogeochemical conditions that are similar to those of mature forest. Further, of the N and P metrics that recuperated, only soil total P and foliar δ 15 N were strongly influenced by site characteristics like climate, soils, or disturbance history. Predictable nutrient recuperation across a diverse and productive ecosystem may support future forest growth and could provide a means to quantify successful restoration of ecosystem function in secondary tropical forest beyond biomass or species composition., (© 2019 by the Ecological Society of America.)

Our understanding and quantification of global soil nitrous oxide (N 2 O) emissions and the underlying processes remain largely uncertain. Here, we assessed the effects of multiple anthropogenic and natural factors, including nitrogen fertilizer (N) application, atmospheric N deposition, manure N application, land cover change, climate change, and rising atmospheric CO 2 concentration, on global soil N 2 O emissions for the period 1861-2016 using a standard simulation protocol with seven process-based terrestrial biosphere models. Results suggest global soil N 2 O emissions have increased from 6.3 ± 1.1 Tg N 2 O-N/year in the preindustrial period (the 1860s) to 10.0 ± 2.0 Tg N 2 O-N/year in the recent decade (2007-2016). Cropland soil emissions increased from 0.3 Tg N 2 O-N/year to 3.3 Tg N 2 O-N/year over the same period, accounting for 82% of the total increase. Regionally, China, South Asia, and Southeast Asia underwent rapid increases in cropland N 2 O emissions since the 1970s. However, US cropland N 2 O emissions had been relatively flat in magnitude since the 1980s, and EU cropland N 2 O emissions appear to have decreased by 14%. Soil N 2 O emissions from predominantly natural ecosystems accounted for 67% of the global soil emissions in the recent decade but showed only a relatively small increase of 0.7 ± 0.5 Tg N 2 O-N/year (11%) since the 1860s. In the recent decade, N fertilizer application, N deposition, manure N application, and climate change contributed 54%, 26%, 15%, and 24%, respectively, to the total increase. Rising atmospheric CO 2 concentration reduced soil N 2 O emissions by 10% through the enhanced plant N uptake, while land cover change played a minor role. Our estimation here does not account for indirect emissions from soils and the directed emissions from excreta of grazing livestock. To address uncertainties in estimating regional and global soil N 2 O emissions, this study recommends several critical strategies for improving the process-based simulations., (© 2018 John Wiley & Sons Ltd.)