Remote Sensing Evaluation of CLM4 GPP for the Period 2000-2009*

Remote sensing can provide long-term and large-scale products helpful for ecosystem model evaluation. The authors compare monthly gross primary production (GPP) simulated by the Community Land Model, version 4 (CLM4) at a half-degree resolution with satellite estimates of GPP from the Moderate Resolution Imaging Spectroradiometer (MODIS) GPP product (MOD17) for the 10-yr period January 2000–December 2009. The assessment is presented in terms of long-term mean carbon assimilation, seasonal mean distributions, amplitude and phase of the annual cycle, and intraannual and interannual GPP variability and their responses to climate variables. For the long-term annual and seasonal means, major GPP patterns are clearly demonstrated by both products. Compared to the MODIS product, CLM4 overestimates the magnitude of GPP for tropical evergreen forests. CLM4 has a longer carbon uptake period than MODIS for most plant functional types (PFTs) with an earlier onset of GPP in spring and a later decline of GPP in autumn. Empirical orthogonal function analysis of the monthly GPP changes indicates that, on the intraannual scale, both CLM4 and MODIS display similar spatial representations and temporal patterns for most terrestrial ecosystems except in northeast Russia and in the very dry region of central Australia. For 2000–09, CLM4 simulated increases in annual averaged GPP over both hemispheres; however, estimates from MODIS suggest a reduction in the Southern Hemisphere (−0.2173 PgC yr−1), balancing the significant increase over the Northern Hemisphere (0.2157 PgC yr−1). The evaluations highlight strengths and weaknesses of the CLM4 primary production and illuminate potential improvements and developments

On the hydraulic fracturing in naturally-layered porous media using the phase field method

In the hydraulic fracturing of natural rocks, understanding and predicting crack penetrations into the neighboring layers is crucial and relevant in terms of cost-efficiency in engineering and environmental protection. This study constitutes a phase field framework to examine hydraulic fracture propagation in naturally-layered porous media. Biot's poroelasticity theory is used to couple the displacement and flow field, while a phase field method helps characterize fracture growth behavior. Additional fracture criteria are not required and fracture propagation is governed by the equation of phase field evolution. Thus, penetration criteria are not required when hydraulic fractures reach the material interfaces. The phase field method is implemented within a staggered scheme that sequentially solves the displacement, phase field, and fluid pressure. We consider the soft-to-stiff and the stiff-to-soft configurations, where the layer interface exhibits different inclination angles $\theta$. Penetration, singly-deflected, and doubly-deflected fracture scenarios can be predicted by our simulations. In the soft-to-stiff configuration, $\theta=0^\circ$ exhibits penetration or symmetrical doubly-deflected scenarios, and $\theta=15^\circ$ exhibits singly-deflected or asymmetric doubly-deflected scenarios. Only the singly-deflected scenario is obtained for $\theta=30^\circ$. In the stiff-to-soft configuration, only the penetration scenario is obtained with widening fractures when hydraulic fractures penetrate into the soft layer

Evaluation of simulated soil carbon dynamics in Arctic-Boreal ecosystems

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Huntzinger, D. N., Schaefer, K., Schwalm, C., Fisher, J. B., Hayes, D., Stofferahn, E., Carey, J., Michalak, A. M., Wei, Y., Jain, A. K., Kolus, H., Mao, J., Poulter, B., Shi, X., Tang, J., & Tian, H. Evaluation of simulated soil carbon dynamics in Arctic-Boreal ecosystems. Environmental Research Letters, 15(2), (2020): 025005, doi:10.1088/1748-9326/ab6784.Given the magnitude of soil carbon stocks in northern ecosystems, and the vulnerability of these stocks to climate warming, land surface models must accurately represent soil carbon dynamics in these regions. We evaluate soil carbon stocks and turnover rates, and the relationship between soil carbon loss with soil temperature and moisture, from an ensemble of eleven global land surface models. We focus on the region of NASA's Arctic-Boreal vulnerability experiment (ABoVE) in North America to inform data collection and model development efforts. Models exhibit an order of magnitude difference in estimates of current total soil carbon stocks, generally under- or overestimating the size of current soil carbon stocks by greater than 50 PgC. We find that a model's soil carbon stock at steady-state in 1901 is the prime driver of its soil carbon stock a hundred years later—overwhelming the effect of environmental forcing factors like climate. The greatest divergence between modeled and observed soil carbon stocks is in regions dominated by peat and permafrost soils, suggesting that models are failing to capture the frozen soil carbon dynamics of permafrost regions. Using a set of functional benchmarks to test the simulated relationship of soil respiration to both soil temperature and moisture, we find that although models capture the observed shape of the soil moisture response of respiration, almost half of the models examined show temperature sensitivities, or Q10 values, that are half of observed. Significantly, models that perform better against observational constraints of respiration or carbon stock size do not necessarily perform well in terms of their functional response to key climatic factors like changing temperature. This suggests that models may be arriving at the right result, but for the wrong reason. The results of this work can help to bridge the gap between data and models by both pointing to the need to constrain initial carbon pool sizes, as well as highlighting the importance of incorporating functional benchmarks into ongoing, mechanistic modeling activities such as those included in ABoVE.This work was supported by NASA'S Arctic Boreal Vulnerability Experiment (ABoVE; https://above.nasa.gov); NNN13D504T. Funding for the Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP; https://nacp.ornl.gov/MsTMIP.shtml) activity was provided through NASA ROSES Grant #NNX10AG01A. Data management support for preparing, documenting, and distributing model driver and output data was performed by the Modeling and Synthesis Thematic Data Center at Oak Ridge National Laboratory (MAST-DC; https://nacp.ornl.gov), with funding through NASA ROSES Grant #NNH10AN681. Finalized MsTMIP data products are archived at the ORNL DAAC (https://daac.ornl.gov). We also acknowledge the modeling groups that provided results to MsTMIP. The synthesis of site-level soil respiration, temperature, and moisture data reported in Carey et al 2016a, 2016b) was funded by the US Geological Survey (USGS) John Wesley Powell Center for Analysis and Synthesis Award G13AC00193. Additional support for that work was also provided by the USGS Land Carbon Program. JBF carried out the research at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. California Institute of Technology. Government sponsorship acknowledged

Changes in sulfur in soybean rhizosphere soil and the response of microbial flora in a continuous cropping system mediated by Funneliformis mosseae

Soybean is an S-loving crop, and continuous cropping might cause soil sulfur shortage. The primary objectives of this study are to determine whether Funneliformis mosseae (F. mosseae) can enhance the content of available S in S-deficient soil and thereby improve the sulfur utilization rate in soybean. The experiment used Heinong 48 (HN48), a soybean variety with a vast planting area in Heilongjiang Province, and F. mosseae was inoculated in the soil of soybean that had been continuously cropped for 0 and 3 years. The results of the barium sulfur turbidimetric assay show that the sulfur content in the soil and soybean was reduced by continuous cropping and increased by inoculation with F. mosseae; the results of the macro-genome sequencing technology, show that the diversity and abundance of bacteria in the soil was decreased by continuous cropping and increased by inoculation with F. mosseae. The sulfur-oxidizing bacteria (SOB) activity and sulfur-related gene expression levels were lower in the continuous crop group compared to the control group and higher in the F.mosseae-inoculated group compared to the control group. Continuous cropping reduced the sulfur content and ratio of soybean rhizosphere soil, affecting soil flora activity and thus soybean growth; F. mosseae inoculation increased the sulfur content of soybean root-perimeter soil and plants, increased the diversity and abundance of rhizosphere soil microorganisms, increased the expression of genes for sulfur transport systems, sulfur metabolism, and other metabolic functions related to elemental sulfur, and increased the species abundance and metabolic vigor of most SOB. In summary, continuous cropping inhibits soil sulfur uptake and utilization in soybean while the inoculation with F. mosseae can significantly improve this situation. This study offers a theoretical research foundation for using AMF as a bio-fungal agent to enhance soil sulfur use. It also supports the decrease of chemical fertilizers, their substitution, and the protection of native soil

Comparing Evapotranspiration from Eddy Covariance Measurements, Water Budgets, Remote Sensing, and Land Surface Models over Canada

This study compares six evapotranspiration ET products for Canada’s landmass, namely, eddy covariance EC measurements; surface water budget ET; remote sensing ET from MODIS; and land surface model (LSM) ET from the Community Land Model (CLM), the Ecological Assimilation of Land and Climate Observations (EALCO) model, and the Variable Infiltration Capacity model (VIC). The ET climatology over the Canadian landmass is characterized and the advantages and limitations of the datasets are discussed. The EC measurements have limited spatial coverage, making it difficult for model validations at the national scale. Water budget ET has the largest uncertainty because of data quality issues with precipitation in mountainous regions and in the north. MODIS ET shows relatively large uncertainty in cold seasons and sparsely vegetated regions. The LSM products cover the entire landmass and exhibit small differences in ET among them. Annual ET from the LSMs ranges from small negative values to over 600 mm across the landmass, with a countrywide average of 256 ± 15 mm. Seasonally, the countrywide average monthly ET varies from a low of about 3 mm in four winter months (November–February) to 67 ± 7 mm in July. The ET uncertainty is scale dependent. Larger regions tend to have smaller uncertainties because of the offset of positive and negative biases within the region. More observation networks and better quality controls are critical to improving ET estimates. Future techniques should also consider a hybrid approach that integrates strengths of the various ET products to help reduce uncertainties in ET estimation

Lactational and geographical variation in the concentration of six oligosaccharides in Chinese breast milk: a multicenter study over 13 months postpartum

IntroductionUnderstanding the variations of oligosaccharide in breast milk contribute to better study how human milk oligosaccharides (HMOs) play a role in health-promoting benefits in infants.MethodsSix abundant HMOs, 2’-fucosyllactose (2’-FL), 3-fucosyllactose (3-FL), Lacto-N-tetraose (LNT), Lacto-N-neotetraose (LNnT), 3’-sialyllactose (3’-SL) and 6’-sialyllactose (6’-SL), in breast milk collected at 0–5 days, 10–15 days, 40–45 days, 200–240 days, and 300–400 days postpartum from six locations across China were analyzed using high-performance anion-exchange chromatography-pulsed amperometric detector.ResultsThe concentration of individual HMO fluctuated dynamically during lactational stages. The median ranges of 2’-FL, 3-FL, LNT, LNnT, 3’-SL, and 6’-SL across the five lactational stages were 935–2865 mg/L, 206–1325 mg/L, 300–1473 mg/L, 32–317 mg/L, 106–228 mg/L, and 20–616 mg/L, respectively. The prominent variation was observed in the content of 6’-SL, which demonstrates a pattern of initial increase followed by a subsequent decrease. Among the five lactational stages, the transitional milk has the highest concentration, which was 31 times greater than the concentration in mature milk at 300–400 days postpartum, where the content is the lowest. Geographical location also influenced the content of HMOs. LNT and LNnT were the highest in mature milk of mothers from Lanzhou among the six sites at 40–240 days postpartum. Breast milks were categorized into two groups base on the abundance of 2’-FL (high and low). There was no significant difference in the proportions of high and low 2’-FL phenotypes among the six sites, and the percentages of high and low 2’-FL phenotypes were 79% and 21%, respectively, across all sites in China.DiscussionThis study provided a comprehensive dataset on 6 HMOs concentrations in Chinese breast milk during the extended postpartum period across a wide geographic range and stratified by high and low 2’-FL phenotypes

Hippo dictates signaling for cellular homeostasis and immune defense in Crassostrea hongkongensis hemocytes

IntroductionThe Hippo signaling pathway is an evolutionarily conserved signaling cascade that plays a crucial role in regulating cell proliferation, differentiation, and apoptosis. It has been shown to be a key regulator of cell fate and cellular homeostasis in various immune processes. Despite its well-established functions in vertebrate immunity, its roles in marine invertebrate immunity remain poorly understood. Therefore, our present work provides fresh mechanistic insights into how the Hippo pathway orchestrates hemocytic functions in Crassostrea hongkongensis, with implications for studies on its major forms and modifications in animal evolution.MethodThe complete set of Hippo pathway genes, including SAV1, MOB1, LATS, YAP/TAZ, TEAD, and MST, were identified from the C. hongkongensis genome. Quantitative PCR assays were conducted to examine the mRNA expression levels of these genes in different tissues and the levels of these genes in hemocytes before and after bacterial challenges. The study also examined the crosstalk between the Hippo pathway and other immune pathways, such as the AP-1 and p53-dependent p21 signaling cascades. RNA interference was used to knock down MST and TEAD, and MST is a core orchestrator of non-canonical Hippo signaling, to investigate its impact on phagocytosis and bacterial clearance in hemocytes.ResultThe results demonstrated that members of the Hippo pathway were highly expressed in hemocytes, with their expression levels significantly increasing following bacterial challenges. Crosstalk between the Hippo pathway and other immune pathways triggered hemocytic apoptosis, which functioned similarly to the canonical Mst-Lats-Yap signaling pathway in Drosophila and mammals. Knocking down MST resulted in increased phagocytosis and boosted the efficiency of bacterial clearance in hemocytes, presumably due to mobilized antioxidant transcription by Nrf for maintaining immune homeostasis.DiscussionThis study provides novel insights into the regulatory mechanisms underlying the Hippo pathway in immune responses of C. hongkongensis hemocytes. The study highlights the importance of the Hippo pathway in maintaining immune homeostasis and orchestrating hemocytic functions in oysters. Moreover, this study demonstrates the divergence of the Hippo pathway's roles in marine invertebrate immunity from mammalian observations, indicating the need for further comparative studies across species. These findings have significant implications for future research aimed at elucidating the evolutionary trajectory and functional diversity of the Hippo signaling pathway in animal evolution

Isolation of HIV-1-Neutralizing Mucosal Monoclonal Antibodies from Human Colostrum

BACKGROUND: Generation of potent anti-HIV antibody responses in mucosal compartments is a potential requirement of a transmission-blocking HIV vaccine. HIV-specific, functional antibody responses are present in breast milk, and these mucosal antibody responses may play a role in protection of the majority of HIV-exposed, breastfeeding infants. Therefore, characterization of HIV-specific antibodies produced by B cells in milk could guide the development of vaccines that elicit protective mucosal antibody responses. METHODS: We isolated B cells from colostrum of an HIV-infected lactating woman with a detectable neutralization response in milk and recombinantly produced and characterized the resulting HIV-1 Envelope (Env)-specific monoclonal antibodies (mAbs). RESULTS: The identified HIV-1 Env-specific colostrum mAbs, CH07 and CH08, represent two of the first mucosally-derived anti-HIV antibodies yet to be reported. Colostrum mAb CH07 is a highly-autoreactive, weakly-neutralizing gp140-specific mAb that binds to linear epitopes in the gp120 C5 region and gp41 fusion domain. In contrast, colostrum mAb CH08 is a nonpolyreactive CD4-inducible (CD4i) gp120-specific mAb with moderate breadth of neutralization. CONCLUSIONS: These novel HIV-neutralizing mAbs isolated from a mucosal compartment provide insight into the ability of mucosal B cell populations to produce functional anti-HIV antibodies that may contribute to protection against virus acquisition at mucosal surfaces

The paleoclimatic footprint in the soil carbon stock of the Tibetan permafrost region

Data and code availability The authors declare that the majority of the data supporting the findings of this study are available through the links given in the paper. The unpublished data are available from the corresponding author upon request. The new estimate of Tibetan soil carbon stock and R code are available in a persistent repository (https://figshare.com/s/4374f28d880f366eff6d). Acknowledgements This study was supported by the Strategic Priority Research Program (A) of the Chinese Academy of Sciences (XDA20050101), the National Natural Science Foundation of China (41871104), Key Research and Development Programs for Global Change and Adaptation (2017YFA0603604), International Partnership Program of the Chinese Academy of Sciences (131C11KYSB20160061) and the Thousand Youth Talents Plan project in China. Jinzhi Ding acknowledges the General (2017M620922) and the Special Grade (2018T110144) of the Financial Grant from the China Postdoctoral Science Foundation.Peer reviewedPublisher PD

An Integrative Model for Soil Biogeochemistry and Methane Processes: I. Model Structure and Sensitivity Analysis

Environmental changes are anticipated to generate substantial impacts on carbon cycling in peatlands, affecting terrestrial-climate feedbacks. Understanding how peatland methane (CH4) fluxes respond to these changing environments is critical for predicting the magnitude of feedbacks from peatlands to global climate change. To improve predictions of CH4 fluxes in response to changes such as elevated atmospheric CO2 concentrations and warming, it is essential for Earth system models to include increased realism to simulate CH4 processes in a more mechanistic way. To address this need, we incorporated a new microbial-functional group-based CH4 module into the Energy Exascale Earth System land model (ELM) and tested it with multiple observational data sets at an ombrotrophic peatland bog in northern Minnesota. The model is able to simulate observed land surface CH4 fluxes and fundamental mechanisms contributing to these throughout the soil profile. The model reproduced the observed vertical distributions of dissolved organic carbon and acetate concentrations. The seasonality of acetoclastic and hydrogenotrophic methanogenesis—two key processes for CH4 production—and CH4 concentration along the soil profile were accurately simulated. Meanwhile, the model estimated that plant-mediated transport, diffusion, and ebullition contributed to ∼23.5%, 15.0%, and 61.5% of CH4 transport, respectively. A parameter sensitivity analysis showed that CH4 substrate and CH4 production were the most critical mechanisms regulating temporal patterns of surface CH4 fluxes both under ambient conditions and warming treatments. This knowledge will be used to improve Earth system model predictions of these high-carbon ecosystems from plot to regional scales