Nitrification,denitrification, and related functional genes under elevated CO2: A meta-analysis in terrestrial ecosystems

Global change may have profound effects on soil nitrogen (N) cycling that can induce positive feedback to climate change through increased nitrous oxide (N₂O) emissions mediated by nitrification and denitrification. We conducted a meta-analysis of the effects of elevated CO₂ on nitrification and denitrification based on 879 observations from 58 publications and 46 independent elevated CO₂ experiments in terrestrial ecosystems. We investigated the effects of elevated CO₂ alone or combined with elevated temperature, increased precipitation, drought, and N addition. We assessed the response to elevated CO₂ of gross and potential nitrification, potential denitrification, and abundances of related functional genes (archaeal amoA, bacterial amoA, nirK, nirS, and nosZ). Elevated CO₂ increased potential nitrification (+28%) and the abundance of bacterial amoA functional gene (+62%) in cropland ecosystems. Elevated CO₂ increased potential denitrification when combined with N addition and higher precipitation (+116%). Elevated CO₂ also increased the abundance of nirK (+25%) and nirS (+27%) functional genes in terrestrial ecosystems and of nosZ (+32%) functional gene in cropland ecosystems. The increase in the abundance of nosZ under elevated CO₂ was larger at elevated temperature and high N (+62%). Four out of 14 two-way interactions tested between elevated CO₂ and elevated temperature, elevated CO₂ and increased precipitation, and elevated CO₂ and N addition were marginally significant and mostly synergistic. The effects of elevated CO₂ on potential nitrification and abundances of bacterial amoA and nirS functional genes increased with mean annual temperature and mean annual precipitation. Our meta-analysis thus suggests that warming and increased precipitation in large areas of the world could reinforce positive responses of nitrification and denitrification to elevated CO₂ and urges the need for more investigations in the tropical zone and on interactive effects among multiple global change factors, as we may largely underestimate the effects of global change on soil N₂O emissions.     

Elevated ozone decreases the multifunctionality of belowground ecosystems

Elevated tropospheric ozone (O₃) affects the allocation of biomass aboveground and belowground and influences terrestrial ecosystem functions. However, how belowground functions respond to elevated O₃ concentrations ([O₃]) remains unclear at the global scale. Here, we conducted a detailed synthesis of belowground functioning responses to elevated [O₃] by performing a meta-analysis of 2395 paired observations from 222 publications. We found that elevated [O₃] significantly reduced the primary productivity of roots by 19.8%, 16.3%, and 26.9% for crops, trees and grasses, respectively. Elevated [O₃] strongly decreased the root/shoot ratio by 11.3% for crops and by 4.9% for trees, which indicated that roots were highly sensitive to O₃. Elevated [O₃] impacted carbon and nitrogen cycling in croplands, as evidenced by decreased dissolved organic carbon, microbial biomass carbon, total soil nitrogen, ammonium nitrogen, microbial biomass nitrogen, and nitrification rates in association with increased nitrate nitrogen and denitrification rates. Elevated [O₃] significantly decreased fungal phospholipid fatty acids in croplands, which suggested that O₃ altered the microbial community and composition. The responses of belowground functions to elevated [O₃] were modified by experimental methods, root environments, and additional global change factors. Therefore, these factors should be considered to avoid the underestimation or overestimation of the impacts of elevated [O₃] on belowground functioning. The significant negative relationships between O₃-treated intensity and the multifunctionality index for croplands, forests, and grasslands implied that elevated [O₃] decreases belowground ecosystem multifunctionality.     

Cover crops do not increase soil organic carbon stocks as much as has been claimed: What is the way forward?

When compared to virgin land (forest and grassland), croplands store significantly lower amounts of organic carbon (OC), mainly as a result of soil tillage, and decreased plant inputs to the soil over the whole year. Doubts have been expressed over how much reduced and zero tillage agriculture can increase OC in soils when the whole soil profile is considered. Consequently, cover-crops that are grown in-between crops instead of leaving soils bare appear as the “last man standing” in our quest to enhance cropland OC stocks. Despite the claim by numerous meta-analyses of a mean carbon sequestration rate by cover crops to be as high as 0.32 ± 0.08 ton C ha⁻¹ year⁻¹, the present analysis showed that all of the 37 existing field studies worldwide only sampled to a depth of 30 cm or less and did not compare treatments on the basis of equivalent soil mass. Thirteen studies presented information on OC content only and not on OC stocks, had inappropriate controls (n = 14), had durations of 3 years or lower (n = 5), considered only one to two data points per treatment (n = 4), or used cover crops as cash crops (i.e., grown longer that in-between two crops) instead of catch crops (n = 2), which in all cases constitutes shortcomings. Of the remaining six trials, four showed non-significant trends, one study displayed a negative impact of cover crops, and one study displayed a positive impact, resulting in a mean OC storage of 0.03 ton ha⁻¹ year⁻¹. Models and policies should urgently adapt to such new figure. Finally, more is to be done not only to improve the design of cover-crop studies for reaching sound conclusions but also to understand the underlying reasons of the low efficiency of cover crops for improved carbon sequestration into soils, with possible strategies being suggested.     

Inoculation with native soil improves seedling survival and reduces non-native reinvasion in a grassland restoration

Losses of grasslands have been largely attributed to widespread land-use changes, such as conversion to row-crop agriculture. The remaining tallgrass prairie faces further losses due to biological invasions by non-native plant species, often with resultant ecosystem degradation. Of critical concern for conservation, restoration of native grasslands has been met with little success following eradication of non-native plants. In addition to the direct and indirect effects of non-native invasive plants on beneficial soil microbes, management practices targeting invasive species may also negatively affect subsequent restoration efforts. To assess mechanisms limiting germination and survival of native species and to improve native species establishment, we established six replicate plots of each of the following four treatments: (1) inoculated with freshly collected prairie soil with native seeds; (2) inoculated with steam-pasteurized soil with native seeds; (3) noninoculated with native seeds; or (4) noninoculated/nonseeded control. Inoculation with whole soil did not improve seed germination; however, addition of whole soil significantly improved native species survival, compared to pasteurized soil or noninoculated treatments. Inoculation with whole soil significantly decreased reestablishment of non-native invasive Bothriochloa bladhii (Caucasian bluestem); at the end of the growing season, plots receiving whole soil consisted of approximately 30% B. bladhii cover, compared to approximately 80% in plots receiving no soil inoculum. Our results suggest invasion and eradication efforts negatively affect arbuscular mycorrhizal hyphal and spore abundances and soil aggregate stability, and inoculation with locally adapted soil microbial communities can improve metrics of restoration success, including plant species richness and diversity, while decreasing reinvasion by non-native species.     

Soil legacy effects of plants and drought on aboveground insects in native and range-expanding plant communities

Soils contain biotic and abiotic legacies of previous conditions that may influence plant community biomass and associated aboveground biodiversity. However, little is known about the relative strengths and interactions of the various belowground legacies on aboveground plant–insect interactions. We used an outdoor mesocosm experiment to investigate the belowground legacy effects of range-expanding versus native plants, extreme drought and their interactions on plants, aphids and pollinators. We show that plant biomass was influenced more strongly by the previous plant community than by the previous summer drought. Plant communities consisted of four congeneric pairs of natives and range expanders, and their responses were not unanimous. Legacy effects affected the abundance of aphids more strongly than pollinators. We conclude that legacies can be contained as soil ‘memories’ that influence aboveground plant community interactions in the next growing season. These soil-borne ‘memories’ can be altered by climate warming-induced plant range shifts and extreme drought.     

CryoRes: Local Resolution Estimation of Cryo-EM Density Maps by Deep Learning

Recent progress in cryo-EM research has ignited a revolution in biological macromolecule structure determination. Resolution is an essential parameter for quality assessment of a cryo-EM density map, and it is known that resolution varies in different regions of a map. Currently available methods for local resolution estimation require manual adjustment of parameters and in some cases necessitate acquisition or de novo generation of so-called “half maps”. Here, we developed CryoRes, a deep-learning algorithm to estimate local resolution directly from a single final cryo-EM density map, specifically by learning resolution-aware patterns of density map voxels through supervised training on a large dataset comprising 1,174 experimental cryo-EM density maps. CryoRes significantly outperforms all of the state-of-the-art competing resolution estimation methods, achieving an average RMSE of 2.26 Å for local resolution estimation relative to the currently most reliable FSC-based method blocres, yet requiring only the single final map as input. Further, CryoRes is able to generate a molecular mask for each map, with accuracy 12.12% higher than the masks generated by ResMap. CryoRes is ultra-fast, fully automatic, parameter-free, applicable to cryo-EM subtomogram data, and freely available at https://cryores.zhanglab.net.     

LDL的氧化修饰和氧化修饰LDL的组成和结构变化

与低密度脂蛋白(LDL)相比,氧化修饰LDL(O-LDL)的组成、结构和生物学特性发生了深刻的变化,而组成和结构的改变是生物学特性改变的基础.本文根据最近文献资料.结合我们实验室的工作.对LDL的氧化修饰、O-LDL的组成、结构改变,以及它们的机理作一简要综述.     

Root traits of perennial C4 grasses contribute to cultivar variations in soil chemistry and species patterns in particulate and mineral-associated carbon pool formation

Recent studies have indicated that the C₄ perennial bioenergy crops switchgrass (Panicum virgatum) and big bluestem (Andropogon gerardii) accumulate significant amounts of soil carbon (C) owing to their extensive root systems. Soil C accumulation is likely driven by inter- and intraspecific variability in plant traits, but the mechanisms that underpin this variability remain unresolved. In this study we evaluated how inter- and intraspecific variation in root traits of cultivars from switchgrass (Cave-in-Rock, Kanlow, Southlow) and big bluestem (Bonanza, Southlow, Suther) affected the associations of soil C accumulation across soil fractions using stable isotope techniques. Our experimental field site was established in June 2008 at Fermilab in Batavia, IL. In 2018, soil cores were collected (30 cm depth) from all cultivars. We measured root biomass, root diameter, specific root length, bulk soil C, C associated with coarse particulate organic matter (CPOM) and fine particulate organic matter plus silt- and clay-sized fractions, and characterized organic matter chemical class composition in soil using high-resolution Fourier-transform ion cyclotron resonance mass spectrometry. C₄ species were established on soils that supported C₃ grassland for 36 years before planting, which allowed us to use differences in the natural abundance of stable C isotopes to quantify C₄ plant-derived C. We found that big bluestem had 36.9% higher C₄ plant-derived C compared to switchgrass in the CPOM fraction in the 0–10 cm depth, while switchgrass had 60.7% higher C₄ plant-derived C compared to big bluestem in the clay fraction in the 10–20 cm depth. Our findings suggest that the large root system in big bluestem helps increase POM-C formation quickly, while switchgrass root structure and chemistry build a mineral-bound clay C pool through time. Thus, both species and cultivar selection can help improve bioenergy management to maximize soil carbon gains and lower CO₂ emissions.     

The legacy effect of biochar application on soil nitrous oxide emissions

Existing studies suggest that biochar application can reduce soil nitrous oxide (N₂O) emissions, mainly based on short-term results. However, it remains unclear what the effects (i.e., legacy effects) and underlying mechanisms are on N₂O emissions after many years of a single application of biochar. Here, we collected intact soil columns from plots without and with biochar application in a subtropical tea plantation 7 years ago for an incubation experiment. We used the N₂O isotopocule analysis combined with ammonia oxidizer-specific inhibitors and molecular biology approaches to investigate how the legacy effect of biochar affected soil N₂O emissions. Results showed that the soil in the presence of biochar had lower N₂O emissions than the control albeit statistically insignificant. The legacy effect of biochar in decreasing N₂O emissions may be attributed to the reduced effectiveness of the soil substrate, nitrification and denitrification activities, and the promotion of the further reduction of N₂O. The legacy effect of biochar reduced the relative contribution of nitrifier denitrification/bacterial denitrification, nitrification-related N₂O production, and the relative abundance of several microorganisms involved in the nitrogen cycle. Our global meta-analysis also showed that the reduction of N₂O by biochar increased with increasing application rate but diminished and possibly even reversed with increasing experimental time. In conclusion, our findings suggest that the abatement capacity of biochar on soil N₂O emissions may weaken over time after biochar application, but this remains under further investigation.     

ACCUMULATION OF ASTAXANTHIN IN HAEMATOCOCCUS LACUSTRIS (CHLOROPHYTA)1

In N-limited continuous chemostat cultures of the green alga Haematococcus lacustris (Gir.) Rostaf. (UTEX 16), the steady-state astaxanthin content of the cells was determined by the specific growth rate of the cultures. The highest, pigment content was obtained at the lowest dilution rate. The specific rate of astaxanthin accumulation was, however, a function of the photon flux density measured at the illuminated culture surface. In nongrowing Haematococcus cultures, the specific rate of astaxanthin accumulation was determined by the growth rate of the culture during growth phase. The highest possible cellular astaxanthin content of all cultures was comparable and independent of the culture parameters.