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Soil organic carbon (SOC) contributes the most significant portion of carbon storage in the terrestrial ecosystem. The potential for variability in carbon losses from soil can lead to severe consequences such as climate change. While extensive studies have been conducted to characterize how land cover type, soil texture, and topography impact the distribution of SOC stocks across different ecosystems, little is known about in Karst Region. Here, we characterized SOC stocks with intensive sampling at the local scale (495 representative samples) via Random Forest Regression (RF) and Principal Component Analysis (PCA). Our findings revealed significant differences in SOC stock among land cover types, with croplands exhibiting the lowest SOC stocks, indicating that management practices could play a crucial role in SOC stocks. Conversely, there was little correlation between SOC stock and clay percentage, suggesting that soil texture was not a primary factor influencing SOC at a local scale. Further, Annual Precipitation was identified as the key driving factor for the dynamics of SOC stocks with the help of RF and PCA. A substantial SOC deficit was observed in most soils in this study, as evaluated by a SOC/clay ratio, indicating a significant potential in SOC sequestration with practical measures in the karst region. As such, future research focused on simulating SOC dynamics in the context of climate change should consider the controlling factors at a local scale and summarize them carefully during the up-scaling process. [ABSTRACT FROM AUTHOR]

This study aims to address the challenges associated with the conventional "wet process" production of SBS and CRM composite modified asphalt, characterized by complex preparation processes and high energy consumption. Through indoor low-speed mixing (simulating a dry process), we prepared varying amounts of SBS-T modifier (dry process SBS modifier, with concentrations of 0%, 3%, 4%) and CRM (concentrations of 0%, 3%, 6%, 9%, 12%). The research involved testing with three major indicators, dynamic shear rheometer (DSR) tests, and bending beam rheometer (BBR) tests to quantitatively analyze the performance changes in dry process composite modified asphalt. Additionally, atomic force microscopy (AFM) was employed to qualitatively study the microscopic structural morphology and mechanical properties of SBS-T/CRM dry process composite modified asphalt.The results indicate that with the addition of SBS-T and CRM, and an increase in concentration, the dry process composite modified asphalt exhibits improved resistance to rutting, fatigue, and low-temperature cracking. The overall performance of dry process composite asphalt surpasses that of single dry process modified asphalt. Following SBS-T and CRM modification, the asphalt surface roughness decreases, and the asphalt modulus increases, leading to a significant enhancement in microcrack resistance and elasticity. The recommended suitable dosage for dry process composite modified asphalt is 4% SBS-T + 9% CRM. • The composite modified asphalt with different SBS-T and CRM ratio was prepared by indoor simulation dry method. • Under the dry process, the two modifiers can improve the high and low temperature properties of asphalt. • The asphalt surface roughness decreases, and the DMT modulus increases, significantly enhancing crack resistance and stiffness. [ABSTRACT FROM AUTHOR]

Interactions between riverine inputs, internal cycling, and oceanic exchange result in dynamic variations in the partial pressure of carbon dioxide (pCO2) in large estuaries. Here, we report the first bay‐wide, annual‐scale observations of surface pCO2 and air–water CO2 flux along the main stem of the Chesapeake Bay, revealing large annual variations in pCO2 (43–3408 μatm) and a spatial‐dependence of pCO2 on internal and external drivers. The low salinity upper bay was a net source of CO2 to the atmosphere (31.2 mmol m−2 d−1) supported by inputs of CO2‐rich Susquehanna River water and the respiration of allochthonous organic matter, but part of this region was also characterized by low pCO2 during spring and fall phytoplankton blooms. pCO2 decreased downstream due to CO2 ventilation supported by long water residence times, stratification, mixing with low pCO2 water masses, and carbon removal by biological uptake. The mesohaline middle bay was a net CO2 sink (−5.8 mmol m−2 d−1) and the polyhaline lower bay was nearly in equilibrium with the atmosphere (1.0 mmol m−2 d−1). Although the main stem of the bay was a weak CO2 source (3.7 ± 3.3 × 109 mol C) during the dry hydrologic (calendar) year 2016, our observations showed higher river discharge could decrease CO2 efflux. In contrast to many other estuaries worldwide that are strong sources of CO2 to the atmosphere, the Chesapeake Bay and potentially other large estuaries are very weak CO2 sources in dry years, and could even turn into a CO2 sink in wet years. [ABSTRACT FROM AUTHOR]

Aquatic macrophytes in inland lakes provide a wide range of ecosystem services. Management efforts to restore aquatic macrophytes for ecosystem recovery need comprehensive understanding of the interaction between growth and nutrient removal efficiency. In contrasting hydrodynamic environments, we examined the growth and phosphorus accrual of two common submerged (Vallisneria natans) and emergent (Acorus calamus) macrophytes. Both biomass and nutrient storage of two macrophytes were observed with significant increases during the incubation period, suggesting the great potential of selected macrophytes in suppressing eutrophication in shallow lakes. Experimental results showed very opposite impacts of flowing water on two macrophyte types. The flowing water was observed to restrain submerged macrophyte's growth and nutrient accrual, but oppositely to stimulate the emergent type. Specifically, our study demonstrated an average reduction of 33.7% in individual plant biomass and 11.4% in nutrient inventory of V. natans, but an overall increase of 27.2% in biomass and 50.0% in nutrient inventory for A. calamus in flowing-water environments. We estimated a total removal of 470-ton phosphorus assuming the complete comeback of aquatic macrophytes in Lake Taihu, as much as 22% of the annual external loading. The results from this study could inform management of aquatic macrophytes at local and lake-wide scales. [ABSTRACT FROM AUTHOR]

The Arctic Ocean has experienced tremendous changes in recent years. To evaluate temporal and spatial variations of the marine carbonate system, a rigorous evaluation of the quality and internal consistency of Arctic field data and the applicability of existing thermodynamic constants to Arctic conditions is needed. Low Arctic temperatures fall outside the range of conditions used to experimentally determine these constants. Using data collected during the Chinese National Arctic Research Expedition (CHINARE) cruise of summer 2010, we compared underway measurements of the partial pressure of carbon dioxide ( p CO 2 ) to p CO 2 values calculated using measurements of dissolved inorganic carbon (DIC) and total alkalinity (TAlk) and seven sets of dissociation constants. For waters sampled outside areas of active sea ice melt, calculated and measured p CO 2 values agreed best when the calculations incorporated the carbonic acid dissociation constants of Mehrbach et al. (1973) (as refit by Dickson and Millero (1987)) (mean difference of 1.5 μatm ± standard deviation of 5.7 μatm) or Lueker et al. (2000) (2.3 ± 5.4 μatm). Differences between calculated and measured p CO 2 values were related to temperature and salinity and were, for all sets of constants, increasing with increasing T and S over a temperature range of − 1.5 to 10.5 °C and a salinity range of 25.8 to 33.1. In the relatively warm Bering Sea, calculated p CO 2 was higher than measured p CO 2 , but in the colder Canada Basin, calculated values were lower than measured values. This pattern indicates that calculations of p CO 2 in very cold waters may underestimate p CO 2 , with an uncertainty of ~ 5 μatm in accuracy. In areas of active sea ice melt (ice cover < 35%), large differences between calculated and measured p CO 2 values occurred. We explored possible explanations for these large differences and concluded that dissolution of CaCO 3 precipitates from sea ice in samples is the most likely cause. Further research including a comparison of filtered and unfiltered samples is needed to resolve this issue. Many processes influence the marine carbonate system of the Arctic Ocean, and further assessment of their relative roles is needed. [ABSTRACT FROM AUTHOR]

To study the gene expression profile during appressorium developmental process of Magnaphorthe grisea strain Y34 isolated from the rich area of Asia cultivated rice resources, expressed sequence tags (ESTs) and cDNA array analysis were performed. A total of 4756 tentative unique transcripts (TUTs) were obtained from 13 057 ESTs of the 3′ ends of the strain, which was approximately 25% of the total M. grisea EST sequences deposited in the GenBank database. Approximately 84% of these TUTs matched with the published draft genome sequences of strain 70-15. Southern analyses with 12 TUT probes revealed no obvious DNA polymorphism among strains 70-15, Guy11 and Y34. A cDNA array with 4108 TUTs was used to monitor gene expression patterns during appressorium development of M. grisea. Compared with ungerminated conidia, the number of up-regulated and down-regulated genes was almost consistent at any time-points of 2, 8, 20 and 30 h during appressorium development. More genes were differentially expressed during appressorium maturation (20 and 30 h) than during appressorium induction (2 h) and formation (8 h). During appressorium maturation (20–30 h), genes generally seemed to be most actively expressed. [ABSTRACT FROM AUTHOR]

Here, we present the whole genome sequence of Bt S2160-1, a potential alternative to the mosquitocidal model strain, Bti. One chromosome genome and four mega-plasmids were contained in Bt S2160-1, and 13 predicted genes encoding predicted insecticidal crystal proteins were identified clustered on one plasmid pS2160-1p2 containing two pathogenic islands (PAIs) designed as PAI-1 (Cry54Ba, Cry30Ea4, Cry69Aa-like, Cry50Ba2-like, Cry4Ca1-like, Cry30Ga2, Cry71Aa-like, Cry72Aa-like, Cry70Aa-like, Cyt1Da2-like and Vpb4C1-like) and PAI-2 (Cyt1Aa-like, and Tpp80Aa1-like). The clusters appear to represent mosquitocidal toxin islands similar to pathogenicity islands. Transcription/translation of 10 of the 13 predicted genes was confirmed by whole-proteome analysis using LTQ-Orbitrap LC–MS/MS. In summary, the present study identified the existence of a mosquitocidal toxin island in Bacillus thuringiensis, and provides important genomic information for understanding the insecticidal mechanism of B. thuringiensis. [ABSTRACT FROM AUTHOR]

Examines the extent to which prototypic CHV1-713 hypovirus alters fungal gene transcript accumulation in the chestnut blight fungus. Disruption of CPG-1 pathway as a contributor to the changes; Effect of CHV1-713 infection and CPG-1 suppression on cyclic AMP accumulation.

Sugarcane (Saccharum spp.) is a major sucrose and bioenergy crop in the world. The fungal pathogen Sporisorium scitamineum causes sugarcane smut, a devastating disease that destroys stalks and reduces sugar content in sugarcane. This disease can be controlled most effectively by applying smut-resistant sugarcane varieties. Previous studies have shown that Dirigent (DIR) genes are involved in the synthesis of the lignin precursor pinoresinol, which plays a crucial role in plant resistance to biotic stresses. However, the immune response of the DIR homologs in sugarcane (ScDIR) has not been reported yet. In this study, we found that the lignin content of smut-resistant sugarcane varieties (ZZ1, ZZ6, and ZZ9) was significantly higher than that of smut-susceptible varieties (GT42, ROC22, and FN41), and the lignin content of sugarcane increased after smut infection. The smut-resistant and smut-susceptible clones derived from the same genetic population (ROC25 × YZ89-7) showed similar patterns. Quantitative real-time PCR assays revealed that among the 64 DIR genes in sugarcane, ScDIR5, ScDIR7, ScDIR11, and ScDIR40 showed elevated expression after S. scitamineum infection. In vitro coupling reactions showed that the four corresponding ScDIR proteins could mediate the coupling of coniferyl alcohol and its conversion into the lignin precursor pinoresinol. Overexpression of the four ScDIR genes in Nicotiana benthamiana enhanced disease resistance to the fungal pathogens Sclerotium rolfsii, Rhizoctonia solani, and Botrytis cinerea. Moreover, transgenic sugarcane overexpressing these ScDIR genes showed enhanced resistance to smut disease. Taken together, our findings provide evidence that sugarcane ScDIR genes can improve the resistance of plants to fungal pathogens and highlight their potentials in sugarcane breeding for disease resistance. [ABSTRACT FROM AUTHOR]

Fusarium sacchari, a key pathogen of sugarcane, is responsible for the Pokkah boeng disease (PBD) in China. The 14-3-3 proteins have been implicated in critical developmental processes, including dimorphic transition, signal transduction, and carbon metabolism in various phytopathogenic fungi. However, their roles are poorly understood in F. sacchari. This study focused on the characterization of two 14-3-3 protein-encoding genes, FsBmh1 and FsBmh2, within F. sacchari. Both genes were found to be expressed during the vegetative growth stage, yet FsBmh1 was repressed at the sporulation stage in vitro. To elucidate the functions of these genes, the deletion mutants ΔFsBmh1 and ΔFsBmh2 were generated. The ΔFsBmh2 exhibited more pronounced phenotypic defects, such as impaired hyphal branching, septation, conidiation, spore germination, and colony growth, compared to the ΔFsBmh1. Notably, both knockout mutants showed a reduction in virulence, with transcriptome analysis revealing changes associated with the observed phenotypes. To further investigate the functional interplay between FsBmh1 and FsBmh2, we constructed and analyzed mutants with combined deletion and silencing (ΔFsBmh/siFsBmh) as well as overexpression (O-FsBmh). The combinations of ΔFsBmh1/siFsBmh2 or ΔFsBmh2/siFsBmh1 displayed more severe phenotypes than those with single allele deletions, suggesting a functional redundancy between the two 14-3-3 proteins. Yeast two-hybrid (Y2H) assays identified 20 proteins with pivotal roles in primary metabolism or diverse biological functions, 12 of which interacted with both FsBmh1 and FsBmh2. Three proteins were specifically associated with FsBmh1, while five interacted exclusively with FsBmh2. In summary, this research provides novel insights into the roles of FsBmh1 and FsBmh2 in F. sacchari and highlights potential targets for PBD management through the modulation of FsBmh functions. [ABSTRACT FROM AUTHOR]

Fusarium sacchari is a causal agent of sugarcane Pokkah boeng, an important fungal disease that causes a considerable reduction in yield and sugar content in susceptible varieties of sugarcane worldwide. Despite its importance, the fungal factors that regulate the virulence of this pathogen remain largely unknown. In our previous study, mapping of an insertional mutant defect in virulence resulted in the identification of a cutinase G-box binding protein gene, designated FsCGBP, that encodes a C2H2-type transcription factor (TF). FsCGBP was shown to localize in the nuclei, and the transcript level of FsCGBP was significantly upregulated during the infection process or in response to abiotic stresses. Deletion or silencing of FsCGBP resulted in a reduction in mycelial growth, conidial production, and virulence and a delay in conidial germination in the F. sacchari. Cutinase genes FsCUT2, FsCUT3, and FsCUT4 and the mitogen-activated protein kinase (MAPK) genes FsHOG1, FsMGV1, and FsGPMK1, which were significantly downregulated in ΔFsCGBP. Except for FsHOG1, all of these genes were found to be transcriptionally activated by FsCGBP using the yeast one-hybrid system in vitro. The deletion of individual cutinase genes did not result in any of the phenotypes exhibited in the ΔFsCGBP mutant, except for cutinase activity. However, disruption of the MAPK pathway upon deletion of FsMGV1 or FsGPMK1 resulted in phenotypes similar to those of the ΔFsCGBP mutant. The above results suggest that FsCGBP functions by regulating the MAPK pathway and cutinase genes, providing new insights into the mechanism of virulence regulation in F. sacchari. [ABSTRACT FROM AUTHOR]

In a survey of mycoviruses in Fusarium species that cause sugarcane Pokkah boeng disease, twelve Fusarium strains from three Fusarium species (F. sacchari, F. andiyazi, and F. solani) were found to contain Fusarium sacchari hypovirus 1 (FsHV1), which we reported previously. The genomes of these variants range from 13,966 to 13,983 nucleotides, with 98.6% to 99.9% nucleotide sequence identity and 98.70% to 99.9% protein sequence similarity. Phylogenetic analysis placed these FsHV1 variants within the Alphahypovirus cluster of Hypoviridae. Intriguingly, no clear correlation was found between the geographic origin and host specificity of these viral variants. Additionally, six out of the twelve variants displayed segmental deletions of 1.5 to 1.8 kilobases, suggesting the existence of defective viral dsRNA. The presence of defective viral dsRNA led to a two-thirds reduction in the dsRNA of the wild-type viral genome, yet a tenfold increase in the total viral dsRNA content. To standardize virulence across natural strains, all FsHV1 strains were transferred into a single, virus-free Fusarium recipient strain, FZ06-VF, via mycelial fusion. Strains of Fusarium carrying FsHV1 exhibited suppressed pigment synthesis, diminished microspore production, and a marked decrease in virulence. Inoculation tests revealed varying capacities among different FsHV1 variants to modulate fungal virulence, with the strain harboring the FsHV1-FSA1 showing the lowest virulence, with a disease severity index (DSI) of 3.33, and the FsHV1-FS1 the highest (DSI = 17.66). The identification of highly virulent FsHV1 variants holds promise for the development of biocontrol agents for Pokkah boeng management. [ABSTRACT FROM AUTHOR]

Discusses the reduction of virulence or hypovirulence in the chestnut blight fungus Cryphonectria parasitica, by noninfectious cytoplasmically transmissible viral double-stranded RNAs of the genus Hypovirus. Condition for infectiousness of full-length hypovirus RNA coding strand; Demonstration on the use of synthetic mycovirus transcript.

Fusarium sacchari is one of the primary pathogens causing pokkah boeng disease, which impairs the yield and quality of sugarcane around the world. Understanding the molecular mechanisms of the F. sacchari effectors that regulate plant immunity is of great importance for the development of novel strategies for the persistent control of pokkah boeng disease. In a previous study, Fs00367 was identified to inhibit BAX‐induced cell death. In this study, Fs00367nsp (without signal peptide) was found to suppress BAX‐induced cell death, reactive oxygen species bursts and callose accumulation. The amino acid region 113–142 of Fs00367nsp is the functional region. Gene mutagenesis indicated that Fs00367 is important for the full virulence of F. sacchari. A yeast two‐hybrid assay revealed an interaction between Fs00367nsp and sugarcane ScPi21 in yeast that was further confirmed using bimolecular fluorescence complementation, pull‐down assay and co‐immunoprecipitation. ScPi21 can induce plant immunity, but this effect could be blunted by Fs00367nsp. These results suggest that Fs00367 is a core pathogenicity factor that suppresses plant immunity through inhibiting ScPi21‐induced cell death. The findings of this study provide new insights into the molecular mechanisms of effectors in regulating plant immunity. [ABSTRACT FROM AUTHOR]

Mesotrione is considered as an effective triketone herbicide for the control of major broadleaf grasses and some Gramineae weeds. However, over-application of mesotrione poses significant environmental and ecological hazards. The development of a mesotrione fluorescent sensor is essential for detecting mesotrione. A novel fluorescent probe (nitrogen and sulfur co-doped graphene quantum dots (N, S-GQDs)) was designed for the rapid analysis of mesotrione in real water samples. N, S-GQDs synthesized by pyrolytic carbonation have the multilayer graphene structure with the size range of 9.8–29.1 nm, the average size of 19.2 nm, and the average height of 9.7 nm. The fluorescent probe was capable of emitting high-intensity fluorescence. And when mesotrione was mixed with the fluorescent probe, the fluorescence of the probe was rapidly quenched by static quenching and the internal filter effect. The fluorescent probe provided great sensitivity and selectivity in the linear range of 0.5–15 and 15–700 μM for the detection of mesotrione with the detection limit (LOD) of 0.26 μM. Noticeably, real sample tests illustrated the use of the fluorescent probe for mesotrione was a promising strategy. [ABSTRACT FROM AUTHOR]

Cryphonectria parasitica, the chestnut blight fungus, and hypoviruses are excellent models for examining fungal pathogenesis and virus–host interactions. Increasing evidence suggests that lysine acetylation plays a regulatory role in cell processes and signalling. To understand protein regulation in C. parasitica by hypoviruses at the level of posttranslational modification, a label‐free comparative acetylome analysis was performed in the fungus with or without Cryphonectria hypovirus 1 (CHV1) infection. Using enrichment of acetyl‐peptides with a specific anti‐acetyl‐lysine antibody, followed by high accuracy liquid chromatography–tandem mass spectrometry analysis, 638 lysine acetylation sites were identified on 616 peptides, corresponding to 325 unique proteins. Further analysis revealed that 80 of 325 proteins were differentially acetylated between C. parasitica strain EP155 and EP155/CHV1‐EP713, with 43 and 37 characterized as up‐ and down‐regulated, respectively. Moreover, 75 and 65 distinct acetylated proteins were found in EP155 and EP155/CHV1‐EP713, respectively. Bioinformatics analysis revealed that the differentially acetylated proteins were involved in various biological processes and were particularly enriched in metabolic processes. Differences in acetylation in C. parasitica citrate synthase, a key enzyme in the tricarboxylic acid cycle, were further validated by immunoprecipitation and western blotting. Site‐specific mutagenesis and biochemical studies demonstrated that the acetylation of lysine‐55 plays a vital role in the regulation of the enzymatic activity of C. parasitica citrate synthase in vitro and in vivo. These findings provide a valuable resource for the functional analysis of lysine acetylation in C. parasitica, as well as improving our understanding of fungal protein regulation by hypoviruses from a protein acetylation perspective. [ABSTRACT FROM AUTHOR]

Protein phosphorylation is the process of binding a protein kinase to a specific site in a protein substrate for post-translational modification. Thousands of distinct phosphorylation sites have been identified, but most of them are not annotated with any kinase information. This work proposes a novel kinase-subgrouping propensity method (kiSP) to predict the binding kinases for phosphopeptides. Existing methods do not distinguish the residue conservation properties of the kinase family subgroups for annotation. Our method exploits maximum entropy variance to prune non-conserved sites from the subset of phosphopeptides that bind to the same kinase family. We also use maximal mutual information to estimate an appropriate upstream-downstream window size for this subset. A propensity score for every kinase family is calculated from its positive and negative data, which indicates its effectiveness as a site for each test phosphopeptide. Experimental results demonstrate that our method outperforms current algorithms in specificity and sensitivity under cross-validation. kiSP is also demonstrated to correctly predict kinase families for phosphopeptides with unknown kinase information. [ABSTRACT FROM AUTHOR]

Sugarcane leaf blight (SLB), a major fungal leaf disease of sugarcane (Saccharum spp.), has been attributed to Stagonospora tainanensis. In December 2020 and May 2021, signs of leaf blight were observed on sugarcane in the fields of Chongzuo City, in the Guangxi Province of China. Lesions on the leaves were characterized by yellow or dark red spots in the center. Fungal species were isolated, purified and subjected to pathogenicity evaluation on the sugarcane plants. An isolate that caused symptoms the same as those observed in the field was initially identified as S. tainanensis (Leptosphaeria taiwanensis, perfect state) based on its morphological characteristics both of asexual and sexual stages. Dark brown and nearly spherical pycnidia with conidia of long ellipsoidal, hyaline, one to four cells and 29.27 to 54.39 μm long and 9.03 to 16.12 μm wide were found on corn meal agar medium. Ascomata with asci of cylindrical to clavate, a short stipe and eight spores slightly constricted at the septum, with the size of the spore ranging from 36 to 44 μm long and 8.5 to 12 μm wide, were formed on the sugarcane-leaf-decoction saccharose agar medium. The identity of the species was further confirmed by rDNA ITS and TEF-1α sequencing. The optimal temperature for mycelial growth was 25 °C and the optimal pH was 6.0. The pathogen grew well in a medium with oats as the carbon source and yeast extract as the nitrogen source, but poorly in a medium with urea as the nitrogen source. This study is the first to identify the sugarcane leaf blight pathogen in Guangxi, and the first publication describing the biological characterization of S. tainanensis. The occurrence of sugarcane leaf blight should alert sugarcane breeders and plant pathologists to consider integrating control of this potentially important disease into the agenda of their breeding and disease control programs. [ABSTRACT FROM AUTHOR]

A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector that is able to transmit RTIV and found that RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover. Author summary: Emerging and re-emerging dangerous viruses cause epidemics or pandemics to threaten human and economically important crops and animals. Some of the most dangerous human viruses have zoonotic origins from wild animals. Native plants may also host new endemic viruses that can spread to cause epidemics in cultivated rice, one of the most important staple plants in the world. In the research, we discovered Rice tiller inhibition virus (RTIV), a new insect-borne positive-strand RNA virus, from Asian wild rice plants through metagenomic sequencing, and demonstrated that RTIV could be transmitted by a wide-distributed specific species of aphids to cultivated rice and inhibited tillering, an important agronomic trait of rice plants. We further rescued RTIV by developing infectious clone and confirmed that it can be a dangerous aphid-transmitted viral pathogen of cultivated rice plants. Thus, not only a rare aphid-transmitted viral pathogen of rice plants was discovered in the research, our findings also indicate that novel pathogenic viruses could spread out from native plants to threaten important crop plants. [ABSTRACT FROM AUTHOR]

A fluorescence off-on method for the detection of Sorghum mosaic virus (SrMV) based on fluorescence resonance energy transfer (FRET) was developed in this study. The biosensor was realized by the adsorption of SrMV coat protein (CP) on gold nanoparticle (AuNP) and conjugation of anti-SrMV antibody (Ab) on cadmium telluride quantum dot (CdTe QD). The optimum quenching efficiency was about 50% obtained at a CdTe QD-Ab/AuNP-CP ratio of 1:7. Moreover, the feasibility of the developed biosensor was verified by the detection of purified CP and the limit of detection was estimated as 0.02 μg/mL. This strategy was also successfully applied to monitor SrMV CP in plant sap with a recovery rate between 97.7 and 107.4%. The developed biosensor is a simple, rapid, and efficient technique which does not need excessive washing and separation steps. [ABSTRACT FROM AUTHOR]

DELLA proteins are important repressors of gibberellin signaling, regulating plant development and defense responses through crosstalk with various phytohormones. Sugarcane ScGAI encodes a DELLA protein that regulates culm development. However, it is unclear which transcription factors mediate the transcription of ScGAI. Here, we identified two different ScGAI promoter sequences that cooperatively regulate ScGAI transcription. We also identified a nuclear-localized AP2 family transcription factor, ScAIL1, which inhibits the transcription of ScGAI by directly binding to two ScGAI promoters. ScAIL1 was expressed in all sugarcane tissues tested and was induced by gibberellin and various stressors, including NaCl, polyethylene glycol, and pathogenic fungi and bacteria. Overexpression of ScAIL1 in rice significantly improved resistance to bacterial blight and rice blast, while reducing growth and development. In addition, several genes associated with stress responses were significantly up-regulated in transgenic rice overexpressing ScAIL1. Endogenous phytohormone content and expression analysis further revealed that ScAIL1 -overexpressing lines improved resistance to bacterial blight and rice blast instead of promoting growth, and that this response was associated with increased jasmonic acid synthesis and gibberellin inactivation. These results provide molecular evidence that the role of ScAIL1 in the plant defense response is related to jasmonic acid and gibberellin signaling. [ABSTRACT FROM AUTHOR]

The Arctic Ocean has experienced rapid warming and sea ice loss in recent decades, becoming the first open-ocean basin to experience widespread aragonite undersaturation [saturation state of aragonite (Warag) < 1]. However, its trend toward long-term ocean acidification and the underlying mechanisms remain undocumented. Here, we report rapid acidification there, with rates three to four times higher than in other ocean basins, and attribute it to changing sea ice coverage on a decadal time scale. Sea ice melt exposes seawater to the atmosphere and promotes rapid uptake of atmospheric carbon dioxide, lowering its alkalinity and buffer capacity and thus leading to sharp declines in pH and Warag. We predict a further decrease in pH, particularly at higher latitudes where sea ice retreat is active, whereas Arctic warming may counteract decreases in Warag in the future. [ABSTRACT FROM AUTHOR]

Background: Xanthomonas is a genus of gram-negative bacterium containing more than 35 species. Among these pathogenic species, Xanthomonas albilineans (Xal) is of global interest, responsible for leaf scald disease in sugarcane. Another notable Xanthomonas species is Xanthomonas sachari (Xsa), a sugarcane-associated agent of chlorotic streak disease. Result: The virulence of 24 Xanthomonas strains was evaluated by disease index (DI) and Area Under Disease Progress Curve (AUDPC) in the susceptible inoculated plants (GT 46) and clustered into three groups of five highly potent, seven mild virulent, and twelve weak virulent strains. The highly potent strain (X. albilineans, Xal JG43) and its weak virulent related strain (X. sacchari, Xsa DD13) were sequenced, assembled, and annotated in the circular genomes. The genomic size of JG43 was smaller than that of DD13. Both strains (JG43 and DD13) lacked a Type III secretory system (T3SS) and T6SS. However, JG43 possessed Salmonella pathogenicity island-1 (SPI-1). More pathogen-host interaction (PHI) genes and virulent factors in 17 genomic islands (GIs) were detected in JG43, among which six were related to pathogenicity. Albicidin and a two-component system associated with virulence were also detected in JG43. Furthermore, 23 Xanthomonas strains were sequenced and classified into three categories based on Single Nucleotide Polymorphism (SNP) mutation loci and pathogenicity, using JG43 as a reference genome. Transitions were dominant SNP mutations, while structural variation (SV) is frequent intrachromosomal rearrangement (ITX). Two essential genes (rpfC/rpfG) of the two-component system and another gene related to SNP were mutated to understand their virulence effect. The mutation of rpfG resulted in a decrease in pathogenicity. Conclusion: These findings revealed virulence of 24 Xanthomonas strains and variations by 23 Xanthomonas strains. We sequenced, assembled, and annotated the circular genomes of Xal JG43 and Xsa DD13, identifying diversity detected by pathogenic factors and systems. Furthermore, complete genomic sequences and sequenced data will provide a theoretical basis for identifying pathogenic factors responsible for sugarcane leaf scald disease. [ABSTRACT FROM AUTHOR]

Sporisorium scitamineum is a biotrophic fungus responsible for sugarcane smut disease. To investigate the key genes involved in S. scitamineum infection, we conducted RNA sequencing of sugarcane sprouts inoculated with S. scitamineum teliospores. A weighted gene co-expression network analysis (WGCNA) showed that two co-expressed gene modules, MEdarkturquoise and MEpurple—containing 66 and 208 genes, respectively—were associated with S. scitamineum infection. The genes in these two modules were further studied using Gene Ontology (GO) enrichment analysis, pathogen-host interaction (PHI) database BLASTp, and small secreted cysteine-rich proteins (SCRPs) prediction. The top ten hub genes in each module were identified using the Cytohubba plugin. The GO enrichment analysis found that endoplasmic reticulum-related and catabolism-related genes were expressed during S. scitamineum infection. A total of 83 genes had homologs in the PHI database, 62 of which correlated with pathogen virulence. A total of 21 proteins had the characteristics of small secreted cysteine-rich proteins (SCRPs), a common source of fungal effectors. The top ten hub genes in each module were identified, and seven were annotated as Mig1-Mig1 protein, glycosyl hydrolase, beta-N-acetylglucosaminidase, secreted chorismate mutase, collagen, mRNA export factor, and pleckstrin homology domain protein, while the remaining three were unknown. Two SCRPs—SPSC_06609 and SPSC_04676—and three proteins—SPSC_01958, SPSC_02155, and SPSC_00940—identified in the PHI database were also among the top ten hub genes in the MEdarkturquoise and MEpurple modules, suggesting that they may play important roles in S. scitamineum infection. A S. scitamineum infection model was postulated based on current findings. These findings help to deepen the current understanding of early events in S. scitamineum infection. [ABSTRACT FROM AUTHOR]

The timing of floral transition is essential for reproductive success in flowering plants. In sugarcane, flowering time affects the production of sugar and biomass. Although the function of the crucial floral pathway integrators, FLOWERING LOCUS T (FT), in sugarcane, has been uncovered, the proteins responsible for FT export and the underlying mechanism remain unexplored. In this study, we identified a member of the multiple C2 domain and transmembrane region proteins (MCTPs) family in sugarcane, FT-interacting protein 1 (ScFTIP1), which was localized to the endoplasmic reticulum. Ectopic expression of ScFTIP1 in the Arabidopsis mutant ftip1-1 rescued the late-flowering phenotype. ScFTIP1 interacted with AtFT in vitro and in vivo assays. Additionally, ScFTIP1 interacted with ScFT1 and the floral inducer ScFT3. Furthermore, we found that the NAC member, ScNAC23, could directly bind to the ScFTIP1 promoter and negatively regulate its transcription. Overall, our findings revealed the function of ScFTIP1 and proposed a potential mechanism underlying flowering regulation in sugarcane. • ScFTIP1 promotes flowering in Arabidopsis. • ScFTIP1 interacts with AtFT/ScFT1/ScFT3 in vitro and in vivo. • ScNAC23, a NAC transcription factor, directly represses ScFTIP1 transcription. [ABSTRACT FROM AUTHOR]

High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the 'Saccharum Complex', and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species. [ABSTRACT FROM AUTHOR]

The hormone gibberellin (GA) is crucial for internode elongation in sugarcane. DELLA proteins are critical negative regulators of the GA signaling pathway. ScGAI encodes a DELLA protein that was previously implicated in the regulation of sugarcane culm development. Here, we characterized ScGAI-like (ScGAIL) in sugarcane, which lacked the N-terminal region but was otherwise homologous to ScGAI. ScGAIL differed from ScGAI in its chromosomal location, expression patterns, and cellular localization. Although transgenic Arabidopsis overexpressing ScGAIL were insensitive to GAs, GA synthesis was affected in these plants, suggesting that ScGAIL disrupted the GA signaling pathway. After GA treatment, the expression patterns of GA-associated genes differed between ScGAIL- overexpressing and wild-type Arabidopsis, and the degradation of AtDELLA proteins in transgenic lines was significantly inhibited compared with wild-type lines. A sugarcane GID1 gene (ScGID1) encoding a putative GA receptor was isolated and interacted with ScGAIL in a GA-independent manner. Five ScGAIL-interacting proteins were verified by yeast two-hybrid assays, and only one interacted with ScGAI. Therefore, ScGAIL may inhibit plant growth by modulating the GA signaling pathway. [ABSTRACT FROM AUTHOR]

Dirigent proteins (DIRs) are known to function in lignin biogenesis and to be involved in stress resistance in plants. However, the sugarcane DIRs have not been functionally characterized. In this study, we investigated the DIR−protein−encoding genes in Saccharum spp. (ScDIR) by screening collections of sugarcane databases, monitoring the responses of these genes to drought stress by real−time quantitative PCR, and identifying their heterologous expression in tobacco. Of the 64 ScDIRs identified, four belonging to the DIR−b/d (ScDIR5 and ScDIR11) and DIR−c (ScDIR7 and ScDIR40) subfamilies showed a significant transcriptional response when subjected to drought stress. ScDIR5, ScDIR7, and ScDIR11 are localized in the cell membrane, whereas ScDIR40 is found in the cell wall. The overexpression of these ScDIR genes in tobacco generally increased the drought tolerance of the transgenic lines, with ScDIR7 conferring the highest degree of drought tolerance. The characterization of the physiological and biochemical indicators (superoxide dismutase, catalase, malondialdehyde, and H2O2) confirmed that the ScDIR−overexpressing lines outperformed the wild type. These results demonstrated that specific ScDIRs in sugarcane respond and contribute to tolerance of drought stress, shedding light on potential means of improving drought tolerance in this crop. [ABSTRACT FROM AUTHOR]

Background: When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available. Results: To understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism. Conclusion: Through WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance. [ABSTRACT FROM AUTHOR]

[Display omitted] • A method for detection of sugarcane pathogens using CRISPR/Cas12a and labeled LAMP. • Labeled LAMP relieves the high dependence of the CRISPR/Cas12a system on CrRNA. • Without relying on expensive instruments and professional technical personnel. • The method is simple, fast, sensitive, specific, and cost-effective. Sugarcane diseases are caused by various pathogens, and rapid and accurate identification of these diseases has many challenges. Detection of sugarcane diseases using conventional assays are often handicapped by their low-throughput, high-cost, and low-sensitivity nature. Here, we report a novel method for the multiplexed and visual detection of sugarcane pathogens using CRISPR/Cas12a coupled with labeled loop-mediated isothermal amplification (Cas-mCfLAMP). This method labels the product during LAMP amplification, relieving the high dependence of CRISPR/Cas12a on specific CrRNAs and enabling the detection of multiple target genes in a single reaction. In addition, we have developed a field detection system that allows visual detection of sugarcane diseases in the field without the need for specialized technicians or expensive equipment. This method is simple, efficient, specific, and cost-effective for sugarcane disease detection, and holds potential to be modified for the field detection of other plant diseases. [ABSTRACT FROM AUTHOR]

• Graded adaptable regulation of cane seed transfer flux. • Flexible seed metering device enables orderly and quantitative delivery of irregular stalk-shaped seeds. • Logistics response models address synergistic relationship between seed supply and discharge processes. Considering that the rigid seed metering device has difficulty adapting to the irregular geometry of cane seeds and the gradual change in required conveying capacity, it is very prone to defects as passage blockage, missed sowing and bud damage. In order to achieve continuous and orderly seed supply for quantitative seeding, a novel design methodology of seed metering device underlying the flexible regulation of transfer flux was proposed for the rolling stalk-shaped seed flow. The effective action modes of compliant wall constraint, elastic de-redundancy and vibration-excited blockage relief were dynamically analyzed, and their synergistic utilization was confirmed to generate adaptive control effects for graded cane seed flux. The principle of reducing obstruction by dynamic balance between supply and discharge rates was also clarified. Regarding the interaction process between guided seeds and their restrictive passage, a rigid-flexible coupling DEM-MBD model was established to reveal the combined functional mechanism of various diversion wall properties, including driving, axial and flexible constraints, and elastic boundaries, on particle groups in terms of contact mechanics. Based on bench experiments, the impact of regulatory factors in the diversion structure on the comprehensive seeding performance in terms of smoothness and discharge quantity was further studied, and a logistics response relationship model was created accordingly. Through optimizing the coordinated effects involved in the supply and discharge processes, confirmatory tests indicated that the optimal qualified rate of discharge quantity was increased by 43.7%, while the incidences of blockage and local congestion were reduced by 23.4% and 6.7% respectively. This provided direct evidence for improved control accuracy in terms of seeding rate and smoothness by strengthening the particle deliverability of irregular stalk seeds. [ABSTRACT FROM AUTHOR]

Acidification can present a stress on organisms and habitats in estuaries in addition to hypoxia. Although oxygen and pH decreases are generally coupled due to aerobic respiration, pH dynamics may be more complex given the multiple modes of buffering in the carbonate system. We studied the seasonal cycle of dissolved oxygen (DO), pH, dissolved inorganic carbon, total alkalinity, and calcium ion (Ca2+) along the main channel of Chesapeake Bay from May to October in 2016. Contrary to the expected co‐occurrence of seasonal DO and pH declines in subsurface water, we found that the pH decline ended in June while the DO decline continued until August in mid‐Chesapeake Bay. We discovered that aerobic respiration was strong from May to August, but carbonate dissolution was minor in May and June and became substantial in August, which buffered further pH declines and caused the seasonal DO and pH minima mismatch. The rate of calcium carbonate (CaCO3) dissolution was not primarily controlled by the saturation state in bottom water, but was instead likely controlled by the supply of CaCO3 particles. The seasonal variability of Ca2+ addition in the mid‐bay was connected to Ca2+ removal in the upper bay, and the timing of high carbonate dissolution coincided with peak seasonal biomass of upper Bay submerged aquatic vegetation. This study suggests a mechanism for a novel decoupling of DO and pH in estuarine waters associated with CaCO3, but future studies are needed to fully investigate the seasonality of physical transport and cycling of CaCO3. [ABSTRACT FROM AUTHOR]

The prediction of land subsidence is a crucial step for early warning of urban infrastructure damage and timely remedy. However, the performance of most mathematical and empirical prediction models is often compromised by their large number of parameters, complex operational processes and sparsely measured values. Currently, the traditional neural network models are popular and effective, but they cannot accurately discover the characteristic changes of time series data. In this paper, a long short-term memory (LSTM) neural network was proposed to predict the land subsidence of time series Interferometric Synthetic Aperture Radar (InSAR). First, the Persistent Scatterer Interferometric Synthetic Aperture Radar (PS-InSAR) technique was utilized to monitor the time series land subsidence at Beijing Capital International Airport (BCIA) from 2005 to 2010 based on ENVISAT ASAR images with a descending orbit. The results were compared with the existing results to verify the reliability and then used to analyse the temporal and spatial characteristics of the time series land subsidence of the BCIA. Based on the time series InSAR deformation data, the LSTM neural network was used to establish the prediction model of time series InSAR, and the results were compared with those of the Multi-Layer Perceptron (MLP) and Recurrent Neural Network (RNN). The comparison results showed that the LSTM neural network was more accurate than the MLP and RNN on the point scale (the root mean square error was 4.60 mm and the mean absolute error was 3.18 mm), the correlation coefficients between the prediction results of the LSTM neural network and the real InSAR measurement results in 2007 and 2008 were 0.93 mm and 0.96 mm, respectively, indicating that LSTM neural network had better prediction performance. Eventually, based on the land subsidence data of time series InSAR from 2006 to 2010, the LSTM neural network was applied to predict the BCIA time series land subsidence in 2011. The results predicted that cumulative subsidence in September 2011 would reach a maximum of 350 mm. Therefore, the LSTM neural network is a potentially effective prediction method, which can replace numerical or empirical models in the absence of detailed hydrogeological data. Moreover, its prediction results can be used to assist decision-making, early warning and hazard relief. [ABSTRACT FROM AUTHOR]

Background: Sugarcane (Saccharum officinarum L.) is an economically important crop with stalks as the harvest organs. Improvement in stalk quality is deemed a promising strategy for enhancing sugarcane production. However, the lack of efficient approaches for systematic evaluation of sugarcane germplasm largely limits improvements in stalk quality. This study is designed to develop a systematic near-infrared spectroscopy (NIRS) assay for high-throughput phenotyping of sugarcane stalk quality, thereby providing a feasible solution for precise evaluation of sugarcane germplasm. Results: A total of 628 sugarcane accessions harvested at different growth stages before and after maturity were employed to take a high-throughput assay to determine sugarcane stalk quality. Based on high-performance anion chromatography (HPAEC-PAD), large variations in sugarcane stalk quality were detected in terms of biomass composition and the corresponding fundamental ratios. Online and offline NIRS modeling strategies were applied for multiple purpose calibration with partial least square (PLS) regression analysis. Consequently, 25 equations were generated with excellent determination coefficients (R2) and ratio performance deviation (RPD) values. Notably, for some observations, RPD values as high as 6.3 were observed, which indicated their exceptional performance and predictive capability. Conclusions: This study provides a feasible method for consistent and high-throughput assessment of stalk quality in terms of moisture, soluble sugar, insoluble residue and the corresponding fundamental ratios. The proposed method permits large-scale screening of optimal sugarcane germplasm for sugarcane stalk quality breeding and beyond. [ABSTRACT FROM AUTHOR]

Sea surface partial pressure of CO2 (pCO2) data with a high spatiotemporal resolution are important in studying the global carbon cycle and assessing the oceanic carbon uptake. However, the observed sea surface pCO2 data are usually limited in spatial and temporal coverage, especially in marginal seas. This study provides an approach to reconstruct the complete sea surface pCO2 field in the South China Sea (SCS) with a grid resolution of 0.5∘×0.5∘ over the period of 2000–2017 using both remote-sensing-derived pCO2 and observed underway pCO2 , among which the gridded underway pCO2 data in 2004, 2005, and 2006 are presented for the first time. Empirical orthogonal functions (EOFs) were computed from the remote-sensing-derived pCO2. Then, a multilinear regression was applied to the observed pCO2 as the response variable with the EOFs as the explanatory variables. EOF1 explains the general spatial pattern of pCO2 in the SCS. EOF2 shows the pattern influenced by the Pearl River plume on the northern shelf and slope. EOF3 is consistent with the pattern influenced by coastal upwelling along the northern coast of the SCS. When pCO2 observations cover a sufficiently large area, the reconstructed fields successfully display a pattern of relatively high pCO2 in the mid and southern basin. The rate of sea surface pCO2 increase in the SCS is 2.4±0.8 µatmyr-1 based on the spatial average of the reconstructed pCO2 over the period of 2000–2017. This is consistent with the temporal trends at Station SEATS (SouthEast Asia Time-series Study; 18 ∘ N, 116 ∘ E) in the northern basin of the SCS and at Station ALOHA (A Long-Term Oligotrophic Habitat Assessment; 22∘45′ N, 158 ∘ W) in the North Pacific. We validated our reconstruction with a leave-one-out cross-validation approach, which yields the root-mean-square error (RMSE) in the range of 2.4–5.2 µatm , smaller than the spatial standard deviation of our reconstructed data and much smaller than the spatial standard deviation of the observed underway data. The RMSE between the reconstructed summer pCO2 and the observed underway pCO2 is no larger than 31.7 µatm , in contrast to (a) the RMSE from 12.8 to 89.0 µatm between the remote-sensing-derived pCO2 and the underway data and (b) the RMSE from 32.6 to 44.5 µatm between the neural-network-produced pCO2 and the underway data. The difference between the reconstructed pCO2 and those calculated from observations at Station SEATS is in the range from -7 to 10 µatm. These comparison results indicate the reliability of our reconstruction method and output. All the data for this paper are openly and freely available at PANGAEA under the link 10.1594/PANGAEA.921210 (Wang et al., 2020). [ABSTRACT FROM AUTHOR]

Background: Sugarcane is an essential crop for sugar and ethanol production. Immediate processing of sugarcane is necessary after harvested because of rapid sucrose losses and deterioration of stalks. This study was conducted to fill the knowledge gap regarding the exploration of fungal communities in harvested deteriorating sugarcane. Experiments were performed on simulating production at 30 °C and 40 °C after 0, 12, and 60 h of sugarcane harvesting and powder-processing. Results: Both pH and sucrose content declined significantly within 12 h. Fungal taxa were unraveled using ITS amplicon sequencing. With the increasing temperature, the diversity of the fungal community decreased over time. The fungal community structure significantly changed within 12 h of bagasse storage. Before stored, the dominant genus (species) in bagasse was Wickerhamomyces (W. anomalus). Following storage, Kazachstania (K. humilis) and Saccharomyces (S. cerevisiae) gradually grew, becoming abundant fungi at 30 °C and 40 °C. The bagasse at different temperatures had a similar pattern after storage for the same intervals, indicating that the temperature was the primary cause for the variation of core features. Moreover, most of the top fungal genera were significantly correlated with environmental factors (pH and sucrose of sugarcane, storage time, and temperature). In addition, the impact of dominant fungal species isolated from the deteriorating sugarcane on sucrose content and pH in the stored sugarcane juice was verified. Conclusions: The study highlighted the importance of timeliness to refine sugar as soon as possible after harvesting the sugarcane. The lessons learned from this research are vital for sugarcane growers and the sugar industry for minimizing post-harvest losses. [ABSTRACT FROM AUTHOR]

We surveyed the carbonate system along the main channel of the Chesapeake Bay in June 2016 to elucidate carbonate dynamics and the associated sources of oxygen‐consuming organic matter. Using a two endmember mixing calculation, chemical proxies, and stoichiometry, we demonstrated that in early summer, dissolved inorganic carbon (DIC) dynamics were controlled by aerobic respiration in the water column (43%), sulfate reduction in the sediment (39%), atmospheric CO2 invasion (13%), and CaCO3 dissolution (5%). A mass balance of the DIC concentration and its stable isotope suggested that the apparent δ13C of oxygen‐consuming organic matter was −19.4 ± 0.3‰. The bulk composition of particulate organic matter also reflected a dominance of algal material (C/N = ~ 6, δ13C > −25‰). Therefore, we concluded that the decomposition of autochthonous organic matter (i.e., eutrophication‐stimulated primary production) was the dominant process consuming oxygen, while allochthonous organic matter (terrestrially derived) made minor contributions to oxygen consumption in the hypoxic zone in June 2016. These findings in the Chesapeake Bay contrast with another hypoxic estuarine ecosystem, the Pearl River Estuary in China where allochthonous organic matter contributed significantly to oxygen consumption. The differences between these two systems in terms of hydrology, quantity and quality of organic matter, and physical characteristics are discussed to yield new insights on the formation and maintenance of hypoxia. In both systems, autochthonous organic matter dominates oxygen depletion, indicating that nutrient management and reduction are useful actions to control and mitigate the occurrence of hypoxia for the restoration of ecosystem. [ABSTRACT FROM AUTHOR]

Accumulating evidences have shown that the deregulation of circRNA has close association with many human cancers. However, these experimental verified circRNA–cancer associations are not collected in any database. Here, we develop a manually curated database (circR2Cancer) that provides experimentally supported associations between circRNAs and cancers. The current version of the circR2Cancer contains 1439 associations between 1135 circRNAs and 82 cancers by extracting data from existing literatures and databases. In addition, circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase. At the same time, circR2Cancer provides a simple and friendly interface for users to conveniently browse, search and download the data. It will be a useful and valuable resource for researchers to understanding the regulation mechanism of circRNA in cancers. Database URL http://www.biobdlab.cn:8000 [ABSTRACT FROM AUTHOR]

The vacuolar H+-ATPases (V-ATPases) are conserved ATP-dependent proton pumps that acidify intracellular compartments in eukaryotic cells. The role of Cpvmal, a V-ATPase catalytic subunit A of Cryphonectria parasitica, was investigated by generating c/wmai-overexpressing and cpvmal-silenced strains. The mutant strains were evaluated for phenotypic characteristics, V-ATPase activity, response to elevated pH and Ca2+ in the medium, virulence on chestnut, and accumulation of hypovirus RNA in the cells. Compared with the wild-type strain, cpvmuf-overexpressing strains showed no significant difference in phenotype; however, cpvmal-silenced strains exhibited a phenotype of reduced growth rate, lower level of sporulation, and a marked decrease in V-ATPase activity and virulence. In addition, silencing of cpvmal increased sensitivity to elevated pH and Ca2+, implicating an important role for Cpvmal in pH adaptation and Ca2+ homeostasis. Furthermore, silencing of cpvmal resulted in significantly decreased accumulation of hypoviral RNA. Taken together, our results indicate that Cpvmal plays an important role in the regulation of phenotypic traits and virulence and the accumulation of hypovirus RNA in C. parasitica. [ABSTRACT FROM AUTHOR]

• Interannual variability of air-water CO2 flux in large estuaries are significant. • The mainstem interannual flux was most sensitive to tributary nutrient inputs. • The flux is highly related to the ratio of OC turnover time to water residence time. Air-water CO 2 fluxes in estuarine environments are characterized by high interannual variability, in part due to hydrological variability that alters estuarine carbonate chemistry through multiple physical and biogeochemical processes. To understand the relative contributions of these varied controls on interannual air-water CO 2 fluxes in the mainstem Chesapeake Bay, we implemented both hindcast and scenario simulations using a coupled physical-biogeochemical model. Significant spatiotemporal variability in bay-wide fluxes was found over a 10-year period (1996-2005), where the mainstem Bay was primarily a net CO 2 sink, except in drought periods. Sensitivity scenario results suggested substantial effects of riverine nutrient and organic matter (OM) inputs to CO 2 flux variations. The high correlations between riverine inputs and upper-Bay fluxes were due to elevated respiration under increased OM inputs. The interannual flux variations in the lower Bay was mostly regulated by the nutrient inputs. Both nutrient and OM inputs contributed to the flux variability in the mid Bay. It is found that the interannual CO 2 flux of the mainstem was most sensitive to riverine nutrient inputs associated with the hydrological changes. For each hindcast simulation we computed the ratio of organic carbon turnover time to water residence time (λ), a proxy for CO 2 efflux potential, and found that the wetter periods had a relatively lower λ. The variability of mainstem CO 2 fluxes can be well represented using a generic function of λ. The model results showed that higher river flows would lead to enhanced CO 2 sinks into a large eutrophic estuary by promoting net autotrophy. [Display omitted] [ABSTRACT FROM AUTHOR]

Summary: The fungal pathogen Sporisorium scitamineum causes sugarcane smut disease. The formation and growth of dikaryotic hypha after sexual mating is critical for S. scitamineum pathogenicity, however regulation of S. scitimineum mating has not been studied in detail. We identified and characterized the core components of the conserved cAMP/PKA pathway in S. scitamineum by reverse genetics. Our results showed that cAMP/PKA signalling pathway is essential for proper mating and filamentation, and thus critical for S. scitamineum virulence. We further demonstrated that an elevated intracellular ROS (reactive oxygen species) level promotes S. scitamineum mating‐filamentation, via transcriptional regulation of ROS catabolic enzymes, and is under regulation of the cAMP/PKA signalling pathway. Furthermore, we found that fungal cAMP/PKA signalling pathway is also involved in regulation of host ROS response. Overall, our work displayed a positive role of elevated intracellular ROS in fungal differentiation and virulence. [ABSTRACT FROM AUTHOR]

Background: Pokkah boeng is one of the most serious and devastating diseases of sugarcane and causes significant loss in cane yield and sugar content. Although carbendazim is widely used to prevent fungal diseases, the molecular basis of Fusarium species complex (FSC) resistance to carbendazim remains unknown. Results: The EC50 (fungicide concentration that inhibits 50% of mycelial growth) values of carbendazim for 35 FSC isolates collected in cane growing regions of China were ranged from 0.5097 to 0.6941 μg mL− 1 of active ingredient (a.i.), in an average of 0.5957 μg a.i. mL− 1. Among carbendazim-induced mutant strains, SJ51M (F. verticillioides) had a CTG rather than CAG codon (Q134L) at position 134 of the FVER_09254 gene, whereas in the mutant strain HC30M (F. proliferatum) codon ACA at position 351 of the FPRO_07779 gene was replaced by ATA (T351I). Gene expression profiling analysis was performed for SJ51M and its corresponding wild type strain SJ51, with and without carbendazim treatment. The gene expression patterns in SJ51 and SJ51M changed greatly as evidenced by the detection of 850 differentially expressed genes (DEGs). Functional categorization indicated that genes associated with oxidation-reduction process, ATP binding, integral component of membrane, transmembrane transport and response to stress showed the largest expression changes between SJ51M and SJ51. The expression levels of many genes involved in fungicide resistance, such as detoxification enzymes, drug efflux transporters and response to stress, were up-regulated in SJ51M compared to SJ51 with and without carbendazim treatment. Conclusion: FSC was sensitive to carbendazim and had the potential for rapid development of carbendazim resistance. The transcriptome data provided insight into the molecular pathways involved in FSC carbendazim resistance. [ABSTRACT FROM AUTHOR]

Low temperature at the seedling stage is a major damaging factor for rice production in southern China. To better understand the cold response of cultivated and wild rice, cold-sensitive cultivar 93–11 (Oryza sativa L. ssp. Indica) and cold-resistant hybrid wild rice DC907 with a 93–11 genetic background were used for a quantitative proteomic analysis with tandem mass tags (TMT) in parallel. Rice seedlings grown for four weeks at a normal temperature (25°C) were treated at 8–10°C for 24, 72 and 120 h. The number of differentially expressed proteins increased gradually over time in the cold-exposed rice in comparison with the untreated rice. A total of 366 unique proteins involved in ATP synthesis, photosystem, reactive oxygen species, stress response, cell growth and integrity were identified as responding to cold stress in DC907. While both DC907 and 93–11 underwent similar alterations in proteomic profiles in response to cold stress, DC907 responded in a prompter manner in terms of expressing cold-responding proteins, maintained a higher level of photosynthesis to power the cells, and possessed a stable and higher level of DIR proteins to prevent the plant from obtaining irreversible cell structure damage. The observations made in this study may lay a new foundation for further investigation of cold sensitivity or tolerance mechanisms in rice. [ABSTRACT FROM AUTHOR]

A simple river-ocean mixing approach has been frequently used to examine estuarine and coastal carbonate system speciation. Coastal areas receiving significant nutrient inputs, however, can have the carbonate chemistry greatly deviated from this mixing-only scheme because of disparate, but spatially coupled biogeochemical processes, i.e., intense primary production in surface waters and elevated respiration in bottom waters; the latter often leads to bottom-water hypoxia (dissolved oxygen or DO concentration < 2 mg L − 1 ) and acidification. As a result of land use change, riverine TA input is known to enhance coastal water buffer capacity, although this effect in eutrophic coastal water has not been systematically studied. The physical disturbances of shallow coastal waters by storms can disrupt bottom hypoxia through overturning the water column. This overturn has been proposed to exacerbate bottom water acidification, because of the different exchange rates of oxygen and CO 2 , which could lead to a ‘reset’ of oxygen concentration but little change in the total dissolved inorganic carbon concentration. We used data from the summer 2010 hypoxia cruise in the northern Gulf of Mexico shelf, during which a tropical depression (Bonnie) perturbed the bottom water. Carbonate buffer capacity in both surface and subsurface waters along the salinity gradient suggested that eutrophication-induced surface production and bottom respiration far outweighed the influence of river TA variation and temperature changes in determining carbonate changes on centennial time scales. We propose, based on literature-based CO 2 flux reported in this area, that the benthic (both aerobic and anaerobic) respiration-produced CO 2 flux (with a lesser flux of alkalinity), instead of bottom water reset by storms, could be responsible for further acidifying hypoxic bottom water in addition to water column aerobic respiration. [ABSTRACT FROM AUTHOR]

Marine carbonate system monitoring programs often consist of multiple observational methods that include underway cruise data, moored autonomous time series, and discrete water bottle samples. Monitored parameters include all, or some of the following: partial pressure of CO 2 of the water ( p CO 2w ) and air, dissolved inorganic carbon (DIC), total alkalinity (TA), and pH. Any combination of at least two of the aforementioned parameters can be used to calculate the others. In this study at the Gray's Reef (GR) mooring in the South Atlantic Bight (SAB) we: examine the internal consistency of p CO 2w from underway cruise, moored autonomous time series, and calculated from bottle samples (DIC-TA pairing); describe the seasonal to interannual p CO 2w time series variability and air-sea flux ( F CO 2 ), as well as describe the potential sources of p CO 2w variability; and determine the source/sink for atmospheric p CO 2 . Over the ~8.5 years of GR mooring time series, mooring-underway and mooring-bottle calculated- p CO 2w strongly correlate with r -values > 0.90. p CO 2w and F CO 2 time series follow seasonal thermal patterns; however, seasonal non-thermal processes, such as terrestrial export, net biological production, and air-sea exchange also influence variability. The linear slope of time series p CO 2w increases by 5.2 ± 1.4 µatm y −1 with F CO 2 increasing 51–70 mmol m −2 y −1 . The net F CO 2 sign can switch interannually with the magnitude varying greatly. Non-thermal p CO 2w is also increasing over the time series, likely indicating that terrestrial export and net biological processes drive the long term p CO 2w increase. [ABSTRACT FROM AUTHOR]

The near-infrared spectroscopy (NIRS) has been used for efficient characterization and rapid assay of biomass saccharification in other energy plants, but its application in sugarcane is not reported yet. The current study collected a total of 541 sugarcane accessions to take an online NIRS assay. Among these sugarcane collections, we observed large variations in biomass digestibility, particularly for fermentable hexose and total sugar yield from fresh sugarcane stalks, which were detected ranging from 69.88 to 239.86 kg t-1 and 66.56–228.55 kg t-1 respectively. Using the modified partial least squares method, six reliable NIRS models were obtained with a high coefficient of determination (R 2 ) and the ratio of prediction to deviation (RPD) values during calibration, internal-cross validation and external validation. Notably, the equation for fermentable hexose exhibited the most consistently high R 2 (0.98) and RPD (6.62) values, as well as retaining relatively low root mean square error during calibration (3.74 kg t-1) and validation (4.19 kg t-1), indicating excellent predictive capacity. All models demonstrated accurate and stable prediction performance in the two-year large-scale germplasm resources evaluation, and the optima accessions with high or low biomass digestibility can be screened out consistently. Therefore, this study provides a precise and consistent NIRS assay for high throughput scanning of biomass digestibility in sugarcane. [Display omitted] • Sugarcane is one of the significant bioenergy crops. • Diverse sugarcane germplasm collections allowing for reliable NIRS calibration. • Six excellent equations were generated for biomass digestibility characterization. • Fermentable hexoses and total sugar displayed the best prediction performance. • Model-based NIRS application screened out optima genotypes consistently from large-scale sugarcane germplasm. [ABSTRACT FROM AUTHOR]

Mulberry vein banding associated virus (MVBaV) that infects mulberry plants with typical vein banding symptoms had been identified as a tentative species of the genus Tospovirus based on the homology of N gene sequence to those of tospoviruses. In this study, the complete sequence of the tripartite RNA genome of MVBaV was determined and analyzed. The L RNA has 8905 nucleotides (nt) and encodes the putative RNA-dependent RNA polymerase (RdRp) of 2877 aa amino acids (aa) in the viral complementary (vc) strand. The RdRp of MVBaV shares the highest aa sequence identity (85.9%) with that of Watermelon silver mottle virus (WSMoV), and contains conserved motifs shared with those of the species of the genus Tospovirus. The M RNA contains 4731 nt and codes in ambisense arrangement for the NSm protein of 309 aa in the sense strand and the Gn/Gc glycoprotein precursor (GP) of 1,124 aa in the vc strand. The NSm and GP of MVBaV share the highest aa sequence identities with those of Capsicum chlorosis virus (CaCV) and Groundnut bud necrosis virus (GBNV) (83.2% and 84.3%, respectively). The S RNA is 3294 nt in length and contains two open reading frames (ORFs) in an ambisense coding strategy, encoding a 439-aa non-structural protein (NSs) and the 277-aa nucleocapsid protein (N), respectively. The NSs and N also share the highest aa sequence identity (71.1% and 74.4%, respectively) with those of CaCV. Phylogenetic analysis of the RdRp, NSm, GP, NSs, and N proteins showed that MVBaV is most closely related to CaCV and GBNV and that these proteins cluster with those of the WSMoV serogroup, and that MVBaV seems to be a species bridging the two subgroups within the WSMoV serogroup of tospoviruses in evolutionary aspect, suggesting that MVBaV represents a distinct tospovirus. Analysis of S RNA sequence uncovered the highly conserved 5’-/3’-ends and the coding regions, and the variable region of IGR with divergent patterns among MVBaV isolates. [ABSTRACT FROM AUTHOR]

Subtilisin-like proteases are widely distributed and reported to be required for virulence in pathogenic fungi. In chestnut blight fungus Cryphonectria parasitica, prb1, encoding a putative subtilisin-like protease, was expressed and recombinant Prb1 protein was shown to have a protease activity in vitro. prb1-deleted mutants exhibited reduced total protease activity by 60%. The Δ prb1 mutants showed a phenotype of reduced aerial hyphae, lower level of sporulation, and a significant reduction in virulence. Additionally, site-directed mutagenesis of Prb1 protein revealed that D195, H227, and S393 are critical for C. parasitica Prb1 function in vivo. Transcriptional analysis showed that deletion of prb1 also reduced the transcript accumulation levels for genes encoding key components of the heterotrimeric G-protein signaling pathway, including cpga1, cpgb1, cpgc1, and ste12. Furthermore, deletion of prb1 results in the accumulation of autophagic bodies in the fungus. Taken together, our results showed that prb1-encoded protease functions in the regulation of virulence, phenotypical traits, and autophagy in C. parasitica. [ABSTRACT FROM AUTHOR]

Background: Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. Methods: A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. Result: Two Fusarium species (F. verticillioides and F. proliferatum) that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. Conclusions/Significance: This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng. [ABSTRACT FROM AUTHOR]