Incorporation of crop phenology in Simple Biosphere Model (SiBcrop) to improve land-atmosphere carbon exchanges from croplands

Croplands are man-made ecosystems that have high net primary productivity during the growing season of crops, thus impacting carbon and other exchanges with the atmosphere. These exchanges play a major role in nutrient cycling and climate change related issues. An accurate representation of crop phenology and physiology is important in land-atmosphere carbon models being used to predict these exchanges. To better estimate time-varying exchanges of carbon, water, and energy of croplands using the Simple Biosphere (SiB) model, we developed crop-specific phenology models and coupled them to SiB. The coupled SiB-phenology model (SiBcrop) replaces remotely-sensed NDVI information, on which SiB originally relied for deriving Leaf Area Index (LAI) and the fraction of Photosynthetically Active Radiation (fPAR) for estimating carbon dynamics. The use of the new phenology scheme within SiB substantially improved the prediction of LAI and carbon fluxes for maize, soybean, and wheat crops, as compared with the observed data at several AmeriFlux eddy covariance flux tower sites in the US mid continent region. SiBcrop better predicted the onset and end of the growing season, harvest, interannual variability associated with crop rotation, day time carbon uptake (especially for maize) and day to day variability in carbon exchange. Biomass predicted by SiBcrop had good agreement with the observed biomass at field sites. In the future, we will predict fine resolution regional scale carbon and other exchanges by coupling SiBcrop with RAMS (the Regional Atmospheric Modeling System)

On the Long-Term Hydroclimatic Sustainability of Perennial Bioenergy Crop Expansion over the United States

Large-scale cultivation of perennial bioenergy crops (e.g., miscanthus and switchgrass) offers unique opportunities to mitigate climate change through avoided fossil fuel use and associated greenhouse gas reduction. Although conversion of existing agriculturally intensive lands (e.g., maize and soy) to perennial bioenergy cropping systems has been shown to reduce near-surface temperatures, unintended consequences on natural water resources via depletion of soil moisture may offset these benefits. The hydroclimatic impacts associated with perennial bioenergy crop expansion over the contiguous United States are quantified using the Weather Research and Forecasting Model dynamically coupled to a land surface model (LSM). A suite of continuous (2000–09) medium-range resolution (20-km grid spacing) ensemble-based simulations is conducted using seasonally evolving biophysical representation of perennial bioenergy cropping systems within the LSM based on observational data. Deployment is carried out only over suitable abandoned and degraded farmlands to avoid competition with existing food cropping systems. Results show that near-surface cooling (locally, up to 5°C) is greatest during the growing season over portions of the central United States. For some regions, principal impacts are restricted to a reduction in near-surface temperature (e.g., eastern portions of the United States), whereas for other regions deployment leads to soil moisture reduction in excess of 0.15–0.2 m3 m−3 during the simulated 10-yr period (e.g., western Great Plains). This reduction (~25%–30% of available soil moisture) manifests as a progressively decreasing trend over time. The large-scale focus of this research demonstrates the long-term hydroclimatic sustainability of large-scale deployment of perennial bioenergy crops across the continental United States, revealing potential hot spots of suitable deployment and regions to avoid

\u3ci\u3eCorrigendum to\u3c/i\u3e “Incorporation of crop phenology in Simple Biosphere Model (SiBcrop) to improve land-atmosphere carbon exchanges from croplands” published in Biogeosciences, 6, 969–986, 2009

In the above mentioned manuscript a mistake in Fig. 11 occured. The corrected version of the figure is as follows

Substantial carbon loss respired from a corn-soybean agroecosystem highlights the importance of careful management as we adapt to changing climate

Understanding agroecosystem carbon (C) cycle response to climate change and management is vital for maintaining their long-term C storage. We demonstrate this importance through an in-depth examination of a ten-year eddy covariance dataset from a corn-corn-soybean crop rotation grown in the Midwest United States. Ten-year average annual net ecosystem exchange (NEE) showed a net C sink of -0.39 Mg C ha-1 yr-1. However, NEE in 2014 and 2015 from the corn ecosystem was 3.58 and 2.56 Mg C ha-1 yr-1, respectively. Most C loss occurred during the growing season, when photosynthesis should dominate and C fluxes should reflect a net ecosystem gain. Partitioning NEE into gross primary productivity (GPP) and ecosystem respiration (ER) showed this C \u27burp\u27 was driven by higher ER, with a 51% (2014) and 57% (2015) increase from the ten-year average (15.84 Mg C ha-1 yr-1). GPP was also higher than average (16.24 Mg C ha-1 yr-1) by 25% (2014) and 37% (2015), but this was not enough to offset the C emitted from ER. This increased ER was likely driven by enhanced soil microbial respiration associated with ideal growing season climate, substrate availability, nutrient additions, and a potential legacy effect from drought

Nucleic Acids Res

The HIV-1 viral infectivity factor (Vif) is required for productive infection of non-permissive cells, including most natural HIV-1 targets, where it counteracts the antiviral activities of the cellular cytosine deaminases APOBEC-3G (A3G) and A3F. Vif is a multimeric protein and the conserved proline-rich domain (161)PPLP(164) regulating Vif oligomerization is crucial for its function and viral infectivity. Here, we expressed and purified wild-type Vif and a mutant protein in which alanines were substituted for the proline residues of the (161)PPLP(164) domain. Using dynamic light scattering, circular dichroism and fluorescence spectroscopy, we established the impact of these mutations on Vif oligomerization, secondary structure content and nucleic acids binding properties. In vitro, wild-type Vif formed oligomers of five to nine proteins, while Vif AALA formed dimers and/or trimers. Up to 40% of the unbound wild-type Vif protein appeared to be unfolded, but binding to the HIV-1 TAR apical loop promoted formation of beta-sheets. Interestingly, alanine substitutions did not significantly affect the secondary structure of Vif, but they diminished its binding affinity and specificity for nucleic acids. Dynamic light scattering showed that Vif oligomerization, and interaction with folding-promoting nucleic acids, favor formation of high molecular mass complexes. These properties could be important for Vif functions involving RNAs

HIV-1 replication and the cellular eukaryotic translation apparatus

Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1) uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication

Phenological corrections to a field-scale, ET-based crop stress indicator: An application to yield forecasting across the U.S. Corn Belt

Soil moisture deficiency is a major factor in determining crop yields in water-limited agricultural production regions. Evapotranspiration (ET), which consists of crop water use through transpiration and water loss through direct soil evaporation, is a good indicator of soil moisture availability and vegetation health. ET therefore has been an integral part of many yield estimation efforts. The Evaporative Stress Index (ESI) is an ET-based crop stress indicator that describes temporal anomalies in a normalized evapotranspiration metric as derived from satellite remote sensing. ESI has demonstrated the capacity to explain regional yield variability in water-limited regions. However, its performance in some regions where the vegetation cycle is intensively managed appears to be degraded due to interannual phenological variability. This investigation selected three study sites across the U.S. Corn Belt – Mead, NE, Ames, IA and Champaign, IL – to investigate the potential operational value of 30-m resolution, phenologically corrected ESI datasets for yield prediction. The analysis was conducted over an 8-year period from 2010 to 2017, which included both drought and pluvial conditions as well as a broad range in yield values. Detrended yield anomalies for corn and soybean were correlated with ESI computed using annual ET curves temporally aligned based on (1) calendar date, (2) crop emergence date, and (3) a growing degree day (GDD) scaled time axis. Results showed that ESI has good correlations with yield anomalies at the county scale and that phenological corrections to the annual temporal alignment of the ET timeseries improve the correlation, especially when the time axis is defined by GDD rather than the calendar date. Peak correlations occur in the silking stage for corn and the reproductive stage for soybean – phases when these crops are particularly sensitive to soil moisture deficiencies. Regression equations derived at the time of peak correlation were used to estimate yields at county scale using a leave-one-out cross-validation strategy. The ESI-based yield estimates agree well with the USDA National Agricultural Statistics Service (NASS) county-level crop yield data, with correlation coefficients ranging from 0.79 to 0.93 and percent root-mean-square errors of 5–8%. These results demonstrate that remotely sensed ET at high spatiotemporal resolution can convey valuable water stress information for forecasting crop yields across the Corn Belt if interannual phenological variability is considered

Leaf photosynthesis and respiration of three bioenergy crops in relation to temperature and leaf nitrogen: how conserved are biochemical model parameters among crop species?

Given the need for parallel increases in food and energy production from crops in the context of global change, crop simulation models and data sets to feed these models with photosynthesis and respiration parameters are increasingly important. This study provides information on photosynthesis and respiration for three energy crops (sunflower, kenaf, and cynara), reviews relevant information for five other crops (wheat, barley, cotton, tobacco, and grape), and assesses how conserved photosynthesis parameters are among crops. Using large data sets and optimization techniques, the C3 leaf photosynthesis model of Farquhar, von Caemmerer, and Berry (FvCB) and an empirical night respiration model for tested energy crops accounting for effects of temperature and leaf nitrogen were parameterized. Instead of the common approach of using information on net photosynthesis response to CO2 at the stomatal cavity (An–Ci), the model was parameterized by analysing the photosynthesis response to incident light intensity (An–Iinc). Convincing evidence is provided that the maximum Rubisco carboxylation rate or the maximum electron transport rate was very similar whether derived from An–Ci or from An–Iinc data sets. Parameters characterizing Rubisco limitation, electron transport limitation, the degree to which light inhibits leaf respiration, night respiration, and the minimum leaf nitrogen required for photosynthesis were then determined. Model predictions were validated against independent sets. Only a few FvCB parameters were conserved among crop species, thus species-specific FvCB model parameters are needed for crop modelling. Therefore, information from readily available but underexplored An–Iinc data should be re-analysed, thereby expanding the potential of combining classical photosynthetic data and the biochemical model

Regional disparities in the beneficial effects of rising CO2 concentrations on crop water productivity

Rising atmospheric CO2 concentrations ([CO2]) are expected to enhance photosynthesis and reduce crop water use1. However, there is high uncertainty about the global implications of these effects for future crop production and agricultural water requirements under climate change. Here we combine results from networks of field experiments1, 2 and global crop models3 to present a spatially explicit global perspective on crop water productivity (CWP, the ratio of crop yield to evapotranspiration) for wheat, maize, rice and soybean under elevated [CO2] and associated climate change projected for a high-end greenhouse gas emissions scenario. We find CO2 effects increase global CWP by 10[0;47]%–27[7;37]% (median[interquartile range] across the model ensemble) by the 2080s depending on crop types, with particularly large increases in arid regions (by up to 48[25;56]% for rainfed wheat). If realized in the fields, the effects of elevated [CO2] could considerably mitigate global yield losses whilst reducing agricultural consumptive water use (4–17%). We identify regional disparities driven by differences in growing conditions across agro-ecosystems that could have implications for increasing food production without compromising water security. Finally, our results demonstrate the need to expand field experiments and encourage greater consistency in modelling the effects of rising [CO2] across crop and hydrological modelling communities