Barley stripe mosaic virus γb protein disrupts chloroplast antioxidant defenses to optimize viral replication.

The plant antioxidant system plays important roles in response to diverse abiotic and biotic stresses. However, the effects of virus infection on host redox homeostasis and how antioxidant defense pathway is manipulated by viruses remain poorly understood. We previously demonstrated that the Barley stripe mosaic virus (BSMV) γb protein is recruited to the chloroplast by the viral αa replicase to enhance viral replication. Here, we show that BSMV infection induces chloroplast oxidative stress. The versatile γb protein interacts directly with NADPH-dependent thioredoxin reductase C (NTRC), a core component of chloroplast antioxidant systems. Overexpression of NbNTRC significantly impairs BSMV replication in Nicotiana benthamiana plants, whereas disruption of NbNTRC expression leads to increased viral accumulation and infection severity. To counter NTRC-mediated defenses, BSMV employs the γb protein to competitively interfere with NbNTRC binding to 2-Cys Prx. Altogether, this study indicates that beyond acting as a helicase enhancer, γb also subverts NTRC-mediated chloroplast antioxidant defenses to create an oxidative microenvironment conducive to viral replication.

Disentangling the variability of symbiotic nitrogen fixation rate and the controlling factors.

Symbiotic nitrogen (N) fixation (SNF), replenishing bioavailable N for terrestrial ecosystems, exerts decisive roles in N cycling and gross primary production. Nevertheless, it remains unclear what determines the variability of SNF rate, which retards the accurate prediction for global N fixation in earth system models. This study synthesized 1230 isotopic observations to elucidate the governing factors underlying the variability of SNF rate. The SNF rates varied significantly from 3.69 to 12.54 g N m-2 year-1 across host plant taxa. The traits of host plant (e.g. biomass characteristics and taxa) far outweighed soil properties and climatic factors in explaining the variations of SNF rate, accounting for 79.0% of total relative importance. Furthermore, annual SNF yield contributed to more than half of N uptake for host plants, which was consistent across different ecosystem types. This study highlights that the biotic factors, especially host plant traits (e.g. biomass characteristics and taxa), play overriding roles in determining SNF rate compared with soil properties. The suite of parameters for SNF lends support to improve N fixation module in earth system models that can provide more confidence in predicting bioavailable N changes in terrestrial ecosystems.

Relative importance between nitrification and denitrification to N2 O from a global perspective.

Nitrous oxide (N2 O) is a potent greenhouse gas, and its mitigation is a pressing task in the coming decade. However, it remains unclear which specific process between concurrent nitrification and denitrification dominates worldwide N2 O emission. We snagged an opportunity to ascertain whence the N2 O came and which were the controlling factors on the basis of 1315 soil N2 O observations from 74 peer-reviewed articles. The average N2 O emission derived from nitrification (N2 On ) was higher than that from denitrification (N2 Od ) worldwide. The ratios of nitrification-derived N2 O to denitrification-derived N2 O, hereof N2 On :N2 Od , exhibited large variations across terrestrial ecosystems. Although soil carbon and nitrogen content, pH, moisture, and clay content accounted for a part of the geographical variations in the N2 On :N2 Od ratio, ammonia-oxidizing microorganisms (AOM):denitrifier ratio was the pivotal driver for the N2 On :N2 Od ratios, since the AOM:denitrfier ratio accounted for 53.7% of geographical variations in N2 On :N2 Od ratios. Compared with natural ecosystems, soil pH exerted a more remarkable role to dictate the N2 On :N2 Od ratio in croplands. This study emphasizes the vital role of functional soil microorganisms in geographical variations of N2 On :N2 Od ratio and lays the foundation for the incorporation of soil AOM:denitrfier ratio into models to better predict N2 On :N2 Od ratio. Identifying soil N2 O derivation will provide a global potential benchmark for N2 O mitigation by manipulating the nitrification or denitrification.

Global variations and controlling factors of anammox rates.

Soil anammox is an environmentally friendly way to eliminate reactive nitrogen (N) without generating nitrous oxide. Nevertheless, the current earth system models have not incorporated the anammox due to the lack of parameters in anammox rates on a global scale, limiting the accurate projection for N cycling. A global synthesis with 1212 observations from 89 peer-reviewed papers showed that the average anammox rate was 1.60 ± 0.17 nmol N g-1 h-1 in terrestrial ecosystems, with significant variations across different ecosystems. Wetlands exhibited the highest rate (2.17 ± 0.31 nmol N g-1 h-1 ), followed by croplands at 1.02 ± 0.09 nmol N g-1 h-1 . The lowest anammox rates were observed in forests and grasslands. The anammox rates were positively correlated with the mean annual temperature, mean annual precipitation, soil moisture, organic carbon (C), total N, as well as nitrite and ammonium concentrations, but negatively with the soil C:N ratio. Structural equation models revealed that the geographical variations in anammox rates were primarily influenced by the N contents (such as nitrite and ammonium) and abundance of anammox bacteria, which collectively accounted for 42% of the observed variance. Furthermore, the abundance of anammox bacteria was well simulated by the mean annual precipitation, soil moisture, and ammonium concentrations, and 51% variance of the anammox bacteria was accounted for. The key controlling factors for soil anammox rates differed from ecosystem type, for example, organic C, total N, and ammonium contents in croplands, versus soil C:N ratio and nitrite concentrations in wetlands. The controlling factors in soil anammox rate identified by this study are useful to construct an accurate anammox module for N cycling in earth system models.

Dryness limits vegetation pace to cope with temperature change in warm regions.

Climate change leads to increasing temperature and more extreme hot and drought events. Ecosystem capability to cope with climate warming depends on vegetation's adjusting pace with temperature change. How environmental stresses impair such a vegetation pace has not been carefully investigated. Here we show that dryness substantially dampens vegetation pace in warm regions to adjust the optimal temperature of gross primary production (GPP) ( T opt GPP ) in response to change in temperature over space and time. T opt GPP spatially converges to an increase of 1.01°C (95% CI: 0.97, 1.05) per 1°C increase in the yearly maximum temperature (Tmax ) across humid or cold sites worldwide (37o S-79o N) but only 0.59°C (95% CI: 0.46, 0.74) per 1°C increase in Tmax across dry and warm sites. T opt GPP temporally changes by 0.81°C (95% CI: 0.75, 0.87) per 1°C interannual variation in Tmax at humid or cold sites and 0.42°C (95% CI: 0.17, 0.66) at dry and warm sites. Regardless of the water limitation, the maximum GPP (GPPmax ) similarly increases by 0.23 g C m-2 day-1 per 1°C increase in T opt GPP in either humid or dry areas. Our results indicate that the future climate warming likely stimulates vegetation productivity more substantially in humid than water-limited regions.

The Barley stripe mosaic virus γb protein promotes viral cell-to-cell movement by enhancing ATPase-mediated assembly of ribonucleoprotein movement complexes.

Nine genera of viruses in five different families use triple gene block (TGB) proteins for virus movement. The TGB modules fall into two classes: hordei-like and potex-like. Although TGB-mediated viral movement has been extensively studied, determination of the constituents of the viral ribonucleoprotein (vRNP) movement complexes and the mechanisms underlying their involvement in vRNP-mediated movement are far from complete. In the current study, immunoprecipitation of TGB1 protein complexes formed during Barley stripe mosaic virus (BSMV) infection revealed the presence of the γb protein in the products. Further experiments demonstrated that TGB1 interacts with γb in vitro and in vivo, and that γb-TGB1 localizes at the periphery of chloroplasts and plasmodesmata (PD). Subcellular localization analyses of the γb protein in Nicotiana benthamiana epidermal cells indicated that in addition to chloroplast localization, γb also targets the ER, actin filaments and PD at different stages of viral infection. By tracking γb localization during BSMV infection, we demonstrated that γb is required for efficient cell-to-cell movement. The N-terminus of γb interacts with the TGB1 ATPase/helicase domain and enhances ATPase activity of the domain. Inactivation of the TGB1 ATPase activity also significantly impaired PD targeting. In vitro translation together with co-immunoprecipitation (co-IP) analyses revealed that TGB1-TGB3-TGB2 complex formation is enhanced by ATP hydrolysis. The γb protein positively regulates complex formation in the presence of ATP, suggesting that γb has a novel role in BSMV cell-to-cell movement by directly promoting TGB1 ATPase-mediated vRNP movement complex assembly. We further demonstrated that elimination of ATPase activity abrogates PD and actin targeting of Potato virus X (PVX) and Beet necrotic yellow vein virus (BNYVV) TGB1 proteins. These results expand our understanding of the multifunctional roles of γb and provide new insight into the functions of TGB1 ATPase domains in the movement of TGB-encoding viruses.

SAMDC3 enhances resistance to Barley stripe mosaic virus by promoting the ubiquitination and proteasomal degradation of viral γb protein.

Posttranslational modifications (PTMs) play important roles in virus-host interplay. We previously demonstrated that Barley stripe mosaic virus (BSMV) γb protein is phosphorylated by different host kinases to support or impede viral infection. However, whether and how other types of PTMs participate in BSMV infection remains to be explored. Here, we report that S-adenosylmethionine decarboxylase 3 (SAMDC3) from Nicotiana benthamiana or wheat (Triticum aestivum) interacts with γb. BSMV infection induced SAMDC3 expression. Overexpression of SAMDC3 led to the destabilization of γb and reduction in viral infectivity, whereas knocking out NbSAMDC3 increased susceptibility to BSMV. NbSAMDC3 positively regulated the 26S proteasome-mediated degradation of γb via its PEST domain. Further mechanistic studies revealed that γb can be ubiquitinated in planta and that NbSAMDC3 promotes the proteasomal degradation of γb by increasing γb ubiquitination. We also found evidence that ubiquitination occurs at nonlysine residues (Ser-133 and Cys-144) within γb. Together, our results provide a function for SAMDC3 in defence against BSMV infection through targeting of γb abundance, which contributes to our understanding of how a plant host deploys the ubiquitin-proteasome system to mount defences against viral infections.

Variations and controlling factors of soil denitrification rate.

The denitrification process profoundly affects soil nitrogen (N) availability and generates its byproduct, nitrous oxide, as a potent greenhouse gas. There are large uncertainties in predicting global denitrification because its controlling factors remain elusive. In this study, we compiled 4301 observations of denitrification rates across a variety of terrestrial ecosystems from 214 papers published in the literature. The averaged denitrification rate was 3516.3 ± 91.1 µg N kg-1  soil day-1 . The highest denitrification rate was 4242.3 ± 152.3 µg N kg-1  soil day-1 under humid subtropical climates, and the lowest was 965.8 ± 150.4 µg N kg-1 under dry climates. The denitrification rate increased with temperature, precipitation, soil carbon and N contents, as well as microbial biomass carbon and N, but decreased with soil clay contents. The variables related to soil N contents (e.g., nitrate, ammonium, and total N) explained the variation of denitrification more than climatic and edaphic variables (e.g., mean annual temperature (MAT), soil moisture, soil pH, and clay content) according to structural equation models. Soil microbial biomass carbon, which was influenced by soil nitrate, ammonium, and total N, also strongly influenced denitrification at a global scale. Collectively, soil N contents, microbial biomass, pH, texture, moisture, and MAT accounted for 60% of the variation in global denitrification rates. The findings suggest that soil N contents and microbial biomass are strong predictors of denitrification at the global scale.

Ecosystem restoration and belowground multifunctionality: A network view.

Ecological restoration is essential to reverse land degradation worldwide. Most studies have assessed the restoration of ecosystem functions individually, as opposed to a holistic view. Here we developed a network-based ecosystem multifunctionality (EMF) framework to identify key functions in evaluating EMF restoration. Through synthesizing 293 restoration studies (2900 observations) following cropland abandonment, we found that individual soil functions played different roles in determining the restoration of belowground EMF. Soil carbon, total nitrogen, and phosphatase were key functions to predict the recovery of belowground EMF. On average, abandoned cropland recovered ~19% of EMF during 18 years. The restoration of EMF became larger with longer recovery time and higher humidity index, but lower with increasing soil depth and initial soil carbon. Overall, this study presents a network-based EMF framework, effectively helping to evaluate the success of ecosystem restoration and identify the key functions.

Synergistically mitigating nitric oxide emission by co-applications of biochar and nitrification inhibitor in a tropical agricultural soil.

Agricultural soils are the hotspots of nitric oxide (NO) emissions, which are related to atmospheric pollution and greenhouse effect. Biochar application has been recommended as an important countermeasure, however, its mitigation efficiency is limited as biochar, under certain conditions, can stimulate soil nitrification. Therefore, biochar co-applied with nitrification inhibitor could optimize the mitigation potential of biochar. Herein, a laboratory-scale experiment was conducted to investigate the effects of co-application of biochar and nitrification inhibitor on NO emission, nitrogen cycling function and bacterial community in a tropical vegetable soil. Results showed that a single application of biochar or nitrification inhibitor significantly decreased NO emissions, and this mitigation effectiveness was amplified by their co-applications. Soil NO2--N intensity, along with abundances of AOB-amoA and nirK were significantly and positively correlated with cumulative NO emissions. The stimulated activity of ammonia monooxygenase and growths of AOB and total comammox Nitrospira by biochar were weakened by nitrification inhibitor, implying decreased nitrification-driven NO production. The nitric oxide reductase activity and related qnorB abundance in nitrification inhibitor-added soils were increased by biochar, indicating promoted NO consumption during denitrification. The nirK abundance and NO2--N intensity were decreased more by co-applications of biochar or nitrification inhibitor. Moreover, both biochar and nitrification inhibitor changed bacterial ß-diversity, and their co-application synergistically enriched Armatimonadetes and Verrucomicrobia abundances and decreased WPS-2 abundance. This study highlights that co-applications of biochar and nitrification inhibitor can make their respective advantages complementary to each other, thereby achieving a larger mitigation of NO emissions from agricultural soils in tropical regions.

Fine-root functional trait responses to experimental warming: a global meta-analysis.

Whether and how warming alters functional traits of absorptive plant roots remains to be answered across the globe. Tackling this question is crucial to better understanding terrestrial responses to climate change as fine-root traits drive many ecosystem processes. We carried out a detailed synthesis of fine-root trait responses to experimental warming by performing a meta-analysis of 964 paired observations from 177 publications. Warming increased fine-root biomass, production, respiration and nitrogen concentration as well as decreased root carbon : nitrogen ratio and nonstructural carbohydrates. Warming effects on fine-root biomass decreased with greater warming magnitude, especially in short-term experiments. Furthermore, the positive effect of warming on fine-root biomass was strongest in deeper soil horizons and in colder and drier regions. Total fine-root length, morphology, mortality, life span and turnover were unresponsive to warming. Our results highlight the significant changes in fine-root traits in response to warming as well as the importance of warming magnitude and duration in understanding fine-root responses. These changes have strong implications for global soil carbon stocks in a warmer world associated with increased root-derived carbon inputs into deeper soil horizons and increases in fine-root respiration.

Vital roles of soil microbes in driving terrestrial nitrogen immobilization.

Nitrogen immobilization usually leads to nitrogen retention in soil and, thus, influences soil nitrogen supply for plant growth. Understanding soil nitrogen immobilization is important for predicting soil nitrogen cycling under anthropogenic activities and climate changes. However, the global patterns and drivers of soil nitrogen immobilization remain unclear. We synthesized 1350 observations of gross soil nitrogen immobilization rate (NIR) from 97 articles to identify patterns and drivers of NIR. The global mean NIR was 8.77 ± 1.01 mg N kg-1  soil day-1 . It was 5.55 ± 0.41 mg N kg-1  soil day-1 in croplands, 15.74 ± 3.02 mg N kg-1  soil day-1 in wetlands, and 15.26 ± 2.98 mg N kg-1  soil day-1 in forests. The NIR increased with mean annual temperature, precipitation, soil moisture, soil organic carbon, total nitrogen, dissolved organic nitrogen, ammonium, nitrate, phosphorus, and microbial biomass carbon. But it decreased with soil pH. The results of structural equation models showed that soil microbial biomass carbon was a pivotal driver of NIR, because temperature, total soil nitrogen, and soil pH mostly indirectly influenced NIR via changing soil microbial biomass. Moreover, microbial biomass carbon accounted for most of the variations in NIR among all direct relationships. Furthermore, the efficiency of transforming the immobilized nitrogen to microbial biomass nitrogen was lower in croplands than in natural ecosystems (i.e., forests, grasslands, and wetlands). These findings suggested that soil nitrogen retention may decrease under the land use change from forests or wetlands to croplands, but NIR was expected to increase due to increased microbial biomass under global warming. The identified patterns and drivers of soil nitrogen immobilization in this study are crucial to project the changes in soil nitrogen retention.

Changes in plant nutrient utilization during ecosystem recovery after wildfire.

Wildfire is the primary natural disturbance in boreal forest ecosystems. It substantially changes soil nutrient conditions and plant nutrient dynamics. After a wildfire, various plant strategies of nutrient utilization are fundamental to ecosystem recovery processes. Stability of plant nutrients reflects the ability of plants possessing relatively constant elemental concentrations in the face of nutrient changes, which can be calculated by the value of "nutrient homeostasis". However, the mechanism of how nutrient homeostasis mediates plant community recovery in post-fire ecosystems remains unknown. The dominant tree species that survived after fire and the new emergence of regenerated tree species are the important components of a plant community during the recovery process. Our primary objective was to elucidate the nutrient homeostasis trade-off between dominant and regenerated species over years after recovery. Five treatments, namely, 2 year, 10 year, 20 year, 30 years after moderate burning severity, and unburned forests, were designed in the boreal forests of Great Xing'an Mountains, Northeast China. Compared with unburned forests, wildfire lowered the average value of homeostasis of plant nutrients (N and P). Moreover, the mean homeostasis value of the dominant species (i.e., Larix gmelinii) was higher than that of the regenerated species (i.e., Betula platyphylla). The slope of relationship between nutrient homeostasis and recovery years of the regenerated species was higher than that of the dominant species, suggesting that the nutrient homeostasis in the regenerated species recovered more quickly than dominant species after recovery. Compared with the dominant species, changes in the regenerated species' homeostasis can explained more to the changes of species diversity during the years after recovery. This study revealed plant nutrient adaptation in different species and different plant organs with years after wildfire and highlighted the importance of nutrient homeostasis in plant adaptation strategies and the recovery of plant community.

Global patterns and controlling factors of soil nitrification rate.

Soil nitrification, an important pathway of nitrogen transformation in ecosystems, produces soil nitrate that influences net primary productivity, while the by-product of nitrification, nitrous oxide, is a significant greenhouse gas. Although there have been many studies addressing the microbiology, physiology, and impacting environment factors of soil nitrification at local scales, there are very few studies on soil nitrification rate over large scales. We conducted a global synthesis on the patterns and controlling factors of soil nitrification rate normalized at 25°C by compiling 3,140 observations from 186 published articles across terrestrial ecosystems. Soil nitrification rate tended to decrease with increasing latitude, especially in the Northern Hemisphere, and varied largely with ecosystem types. The soil nitrification rate significantly increased with mean annual temperature (MAT), soil nitrogen content, microbial biomass carbon and nitrogen, soil ammonium, and soil pH, but decreased with soil carbon:nitrogen and carbon:nitrogen of microbial biomass. The total soil nitrogen content contributed the most to the variations of global soil nitrification rate (total coefficient = 0.29) in structural equation models. The microbial biomass nitrogen (MBN; total coefficient = 0.19) was nearly of equivalent importance relative to MAT (total coefficient = 0.25) and soil pH (total coefficient = 0.24) in determining soil nitrification rate, while soil nitrogen and pH influenced soil nitrification via changing soil MBN. Moreover, the emission of soil nitrous oxide was positively related to soil nitrification rate at a global scale. This synthesis will advance our current understanding on the mechanisms underlying large-scale variations of soil nitrification and benefit the biogeochemical models in simulating global nitrogen cycling.

Construction of an Infectious Poa semilatent virus cDNA Clone and Comparisons of Hordeivirus Cytopathology and Pathogenicity.

Poa semilatent virus (PSLV), Lychnis ringspot virus (LRSV), and Barley stripe mosaic virus (BSMV) are members of the genus Hordeivirus in the family Virgaviridae. However, the biological properties and molecular genetics of PSLV have not been compared with other hordeiviruses. Here, we have constructed an infectious cDNA clone of the PSLV Canadian strain and provided evidence that PSLV differs from BSMV and LRSV. First, unlike the other two hordeiviruses that replicate in chloroplasts, PSLV induces dramatic structural changes in peroxisome during its infection in barley. The αa replication protein also localizes to peroxisomes, suggesting that PSLV replication occurs in peroxisomes. Second, PSLV encodes a γb protein that shares 19 to 23% identity with those of other hordeiviruses, and its activity as a viral suppressor of RNA (VSR) silencing is distinct from those of BSMV and LRSV. Substitution of the BSMV γb protein with that of PSLV or LRSV revealed a negative correlation between VSR activity and symptom severity of the recombinant BSMV derivatives. Intriguingly, the Ser-Lys-Leu (SKL) peroxisome-targeting signals differ among γb proteins of various hordeiviruses, including some BSMV strains. The presence of the C-terminal SKL motif in the γb protein impairs its silencing suppressor activity and influences symptoms. Finally, we developed a PSLV-based virus-induced gene silencing vector that induced strong and effective silencing phenotypes of endogenous genes in barley, wheat, and millet. Our results shed new light on hordeivirus pathogenesis and evolution, and provide an alternative tool for genomics studies of model hosts and economically important monocots.

Microbes drive global soil nitrogen mineralization and availability.

Soil net nitrogen mineralization rate (Nmin ), which is critical for soil nitrogen availability and plant growth, is thought to be primarily controlled by climate and soil physical and/or chemical properties. However, the role of microbes on regulating soil Nmin has not been evaluated on the global scale. By compiling 1565 observational data points of potential net Nmin from 198 published studies across terrestrial ecosystems, we found that Nmin significantly increased with soil microbial biomass, total nitrogen, and mean annual precipitation, but decreased with soil pH. The variation of Nmin was ascribed predominantly to soil microbial biomass on global and biome scales. Mean annual precipitation, soil pH, and total soil nitrogen significantly influenced Nmin through soil microbes. The structural equation models (SEM) showed that soil substrates were the main factors controlling Nmin when microbial biomass was excluded. Microbe became the primary driver when it was included in SEM analysis. SEM with soil microbial biomass improved the Nmin prediction by 19% in comparison with that devoid of soil microbial biomass. The changes in Nmin contributed the most to global soil NH4+ -N variations in contrast to climate and soil properties. This study reveals the complex interactions of climate, soil properties, and microbes on Nmin and highlights the importance of soil microbial biomass in determining Nmin and nitrogen availability across the globe. The findings necessitate accurate representation of microbes in Earth system models to better predict nitrogen cycle under global change.

Effects of water management practices on residue decomposition and degradation of Cry1Ac protein from crop-wild Bt rice hybrids and parental lines during winter fallow season.

Rice is the staple diet of over half of the world's population and Bacillus thuringiensis (Bt) rice expressing insecticidal Cry proteins is ready for deployment. An assessment of the potential impact of Bt rice on the soil ecosystem under varied field management practices is urgently required. We used litter bags to assess the residue (leaves, stems and roots) decomposition dynamics of two transgenic rice lines (Kefeng6 and Kefeng8) containing stacked genes from Bt and sck (a modified CpTI gene encoding a cowpea trypsin inhibitor) (Bt/CpTI), a non-transgenic rice near-isoline (Minghui86), wild rice (Oryza rufipogon) and crop-wild Bt rice hybrid under contrasting conditions (drainage or continuous flooding) in the field. No significant difference was detected in the remaining mass, total C and total N among cultivars under aerobic conditions, whereas significant differences in the remaining mass and total C were detected between Kefeng6 and Kefeng8 and Minghui86 under the flooded condition. A higher decomposition rate constant (km) was measured under the flooded condition compared with the aerobic condition for leaf residues, whereas the reverse was observed for root residues. The enzyme-linked immunosorbent assay (ELISA), which was used to monitor the changes in the Cry1Ac protein in Bt rice residues, indicated that (1) the degradation of the Cry1Ac protein under both conditions best fit first-order kinetics, and the predicted DT50 (50% degradation time) of the Cry1Ac protein ranged from 3.6 to 32.5 days; (2) the Cry1Ac protein in the residue degraded relatively faster under aerobic conditions; and (3) by the end of the study (~154 days), the protein was present at a low concentration in the remaining residues under both conditions. The degradation rate constant was negatively correlated with the initial carbon content and positively correlated with the initial Cry1Ac protein concentration, but it was only correlated with the mass decomposition rate constants under the flooded condition. No Cry1Ac protein was detected in the soils surrounding the buried residue. Our results did not reveal any evidence that the stacked genes (Bt/CpTI) or the presence of the Cry1Ac protein influenced the decomposition dynamics of the rice residues. Furthermore, our results suggested that field drainage after residue incorporation would promote Cry1Ac protein degradation.

m6A modification of plant virus enables host recognition by NMD factors in plants.

N6-methyladenosine (m6A) is the most abundant eukaryotic mRNA modification and is involved in various biological processes. Increasing evidence has implicated that m6A modification is an important anti-viral defense mechanism in mammals and plants, but it is largely unknown how m6A regulates viral infection in plants. Here we report the dynamic changes and functional anatomy of m6A in Nicotiana benthamiana and Solanum lycopersicum during Pepino mosaic virus (PepMV) infection. m6A modification in the PepMV RNA genome is conserved in these two species. Overexpression of the m6A writers, mRNA adenosine methylase A (MTA), and HAKAI inhibit the PepMV RNA accumulation accompanied by increased viral m6A modifications, whereas deficiency of these writers decreases the viral RNA m6A levels but enhances virus infection. Further study reveals that the cytoplasmic YTH-domain family protein NbECT2A/2B/2C as m6A readers are involved in anti-viral immunity. Protein-protein interactions indicate that NbECT2A/2B/2C interact with nonsense-mediated mRNA decay (NMD)-related proteins, including NbUPF3 and NbSMG7, but not with NbUPF1. m6A modification-mediated restriction to PepMV infection is dependent on NMD-related factors. These findings provide new insights into the functionality of m6A anti-viral activity and reveal a distinct immune response that NMD factors recognize the m6A readers-viral m6A RNA complex for viral RNA degradation to limit virus infection in plants.

A Negative Feedback Loop Compromises NMD-Mediated Virus Restriction by the Autophagy Pathway in Plants.

Nonsense-mediated decay (NMD) and autophagy play pivotal roles in restricting virus infection in plants. However, the interconnection between these two pathways in viral infections has not been explored. Here, it is shown that overexpression of NbSMG7 and NbUPF3 attenuates cucumber green mottle mosaic virus (CGMMV) infection by recognizing the viral internal termination codon and vice versa. NbSMG7 is subjected to autophagic degradation, which is executed by its interaction with one of the autophagy-related proteins, NbATG8i. Mutation of the ATG8 interacting motif (AIM) in NbSMG7 (SMG7mAIM1) abolishes the interaction and comprises its autophagic degradation. Silencing of NbSMG7 and NbATG8i, or NbUPF3 and NbATG8i, compared to silencing each gene individually, leads to more virus accumulations, but overexpression of NbSMG7 and NbATG8i fails to achieve more potent virus inhibition. When CGMMV is co-inoculated with NbSMG7mAIM1 or with NbUPF3, compared to co-inoculating with NbSMG7 in NbATG8i transgene plants, the inoculated plants exhibit milder viral phenotypes. These findings reveal that NMD-mediated virus inhibition is impaired by the autophagic degradation of SMG7 in a negative feedback loop, and a novel regulatory interplay between NMD and autophagy is uncovered, providing insights that are valuable in optimizing strategies to harness NMD and autophagy for combating viral infections.

Nitrifying niche in estuaries is expanded by the plastisphere.

The estuarine plastisphere, a novel ecological habitat in the Anthropocene, has garnered global concerns. Recent geochemical evidence has pointed out its potential role in influencing nitrogen biogeochemistry. However, the biogeochemical significance of the plastisphere and its mechanisms regulating nitrogen cycling remain elusive. Using 15N- and 13C-labelling coupled with metagenomics and metatranscriptomics, here we unveil that the plastisphere likely acts as an underappreciated nitrifying niche in estuarine ecosystems, exhibiting a 0.9 ~ 12-fold higher activity of bacteria-mediated nitrification compared to surrounding seawater and other biofilms (stone, wood and glass biofilms). The shift of active nitrifiers from O2-sensitive nitrifiers in the seawater to nitrifiers with versatile metabolisms in the plastisphere, combined with the potential interspecific cooperation of nitrifying substrate exchange observed among the plastisphere nitrifiers, collectively results in the unique nitrifying niche. Our findings highlight the plastisphere as an emerging nitrifying niche in estuarine environment, and deepen the mechanistic understanding of its contribution to marine biogeochemistry.