The plastid-encoded protein Orf2971 is required for protein translocation and chloroplast quality control.

Photosynthesis and the biosynthesis of many important metabolites occur in chloroplasts. In these semi-autonomous organelles, the chloroplast genome encodes approximately 100 proteins. The remaining chloroplast proteins, close to 3,000, are encoded by nuclear genes whose products are translated in the cytosol and imported into chloroplasts. However, there is still no consensus on the composition of the protein import machinery including its motor proteins and on how newly imported chloroplast proteins are refolded. In this study, we have examined the function of orf2971, the largest chloroplast gene of Chlamydomonas reinhardtii. The depletion of Orf2971 causes the accumulation of protein precursors, partial proteolysis and aggregation of proteins, increased expression of chaperones and proteases, and autophagy. Orf2971 interacts with the TIC (translocon at the inner chloroplast envelope) complex, catalyzes ATP (adenosine triphosphate) hydrolysis, and associates with chaperones and chaperonins. We propose that Orf2971 is intimately connected to the protein import machinery and plays an important role in chloroplast protein quality control.

Synergistic effect of two bacterial strains promoting anaerobic digestion of rice straw to produce methane.

A large amount of agricultural waste causes global environmental pollution. Biogas production by microbial pretreatment is an important way to utilize agricultural waste resources. In this study, Sporocytophaga CG-1 (A, cellulolytic strain) was co-cultured with Bacillus clausii HP-1 (B, non-cellulolytic strain) to analyze the effect of pretreatment of rice straw on methanogenic capacity of anaerobic digestion (AD). The results showed that weight loss rate of filter paper of co-culture combination is 53.38%, which is 29.37% higher than that of A. The synergistic effect of B on A can promote its degradation of cellulose. The cumulative methane production rate of the co-culture combination was the highest (93.04 mL/g VS substrate), which was significantly higher than that of A, B and the control group (82.38, 67.28 and 67.70 mL/g VS substrate). Auxiliary bacteria can improve cellulose degradation rate by promoting secondary product metabolism. These results provide data support for the application of co-culture strategies in the field of anaerobic digestion practices.

Joint analytical hierarchy and metaheuristic optimization as a framework to mitigate fertilizer-based pollution.

The emission of nitrogenous pollution from agricultural lands in form of ammonia volatilization, leaching, runoff, N2O emissions, etc. is still a serious challenge to which agricultural sector faces. In this context, a vast number of decision support systems have been developed and tested to find the best nitrogen application rate. These models are highly dependent on crop simulation models, mathematical and regression models, evolutionary algorithms and artificial intelligent, GIS-based models, etc., while in most cases have ignored to be interfered with regional and national regulations established by experts in the field. In this study, a new framework combining analytical hierarchy (AHP)/modified AHP methods (MAHP) plus metaheuristic optimization techniques has been suggested to find the best nitrogen application rate considering regional capacities and requirements. To reach the objectives of the present study a three yield field experiment was conducted upon which crop yield, nitrogen use efficiency, nitrogen uptake, soil nitrate, ammonia volatilization, N2O emissions, and N leaching were monitored or measured. Using the results from the field experiments and a survey from local experts, the models were developed. AHP-assisted optimization model could cause some biases in the final results due to its intrinsic nature which avoids direct pairwise comparison among indicators (so called sub-criteria) under two different main-criteria. On the contrary, MAHP-assisted model could well reflect the concerns of experts and notably decrease hotspot pollution. Such decision support system can satisfy both farmers and environmentalists' need because of the created high profit and low environmental pollution, while saving resources and ensuring a sustainable production system.

Plastic pollution in croplands threatens long-term food security.

Plastic pollution is a global concern given its prevalence in aquatic and terrestrial ecosystems. Studies have been conducted on the distribution and impact of plastic pollution in marine ecosystems, but little is known on terrestrial ecosystems. Plastic mulch has been widely used to increase crop yields worldwide, yet the impact of plastic residues in cropland soils to soil health and crop production in the long term remained unclear. In this paper, using a global meta-analysis, we found that the use of plastic mulch can indeed increase crop yields on average by 25%-42% in the immediate season due to the increase of soil temperature (+8%) and moisture (+17%). However, the unabated accumulation of film residues in the field negatively impacts its physicochemical properties linked to healthy soil and threatens food production in the long term. It has multiple negative impacts on plant growth including crop yield (at the mean rate of -3% for every additional 100 kg/ha of film residue), plant height (-2%) and root weight (-5%), and soil properties including soil water evaporation capacity (-2%), soil water infiltration rate (-8%), soil organic matter (-0.8%) and soil available phosphorus (-5%) based on meta-regression. Using a nationwide field survey of China, the largest user of plastic mulch worldwide, we found that plastic residue accumulation in cropland soils has reached 550,800 tonnes, with an estimated 6%-10% reduction in cotton yield in some polluted sites based on current level of plastic residue content. Immediate actions should be taken to ensure the recovery of plastic film mulch and limit further increase in film residue loading to maintain the sustainability of these croplands.

Aluminum relieves fluoride stress through stimulation of organic acid production in Camellia sinensis.

Tea plants (Camellia sinensis O. Kuntze) can hyperaccumulate fluoride (F) in leaves. Although, aluminum (Al) can alleviate F toxicity in C. sinensis, the mechanisms driving this process remain unclear. Here, we measured root length, root activity, soluble proteins content, and levels of peroxidase, superoxide dismutase, catalase, malondialdehyde (MDA), and chlorophyll in tea leaves after treatment with different F concentrations. In addition, we focused on the content of organic acids, the gene transcription of malate dehydrogenase (MDH), glycolate oxidase (GO) and citrate synthase (CS) and the relative enzyme activity involved in the tolerance to F in C. sinensis. We also examined the role of Al in this process by analyzing the content of these physiological indicators in tea leaves treated with F and Al. Our results demonstrate that increased MDA content, together with decreased chlorophyll content and soluble proteins are responsible for oxidative damage and metabolism inhibition at high F concentration. Moreover, increased antioxidant enzymes activity regulates ROS damage to protect tea leaves during F stress. Furthermore, exogenous Al alleviated F stress in tea leaves through the regulation of MDA content and antioxidant enzymes activity. In addition, organic acids in exudate stimulated root growth in tea plants exposed to low F concentrations are regulated by MDH, GO, and CS. In addition, Al can stimulate the exudation of organic acids, and may participate in regulating rhizosphere pH of the roots through the interaction with F, eventually leading to the response to F stress in C. sinensis.

Transcriptome Analysis Reveals the Mechanism of Fluoride Treatment Affecting Biochemical Components in Camellia sinensis.

Tea (Camellia sinensis (L.) O. Kuntze), one of the main crops in China, is high in various bioactive compounds including flavonoids, catechins, caffeine, theanine, and other amino acids. C. sinensis is also known as an accumulator of fluoride (F), and the bioactive compounds are affected by F, however, the mechanism remains unclear. Here, the effects of F treatment on the accumulation of F and major bioactive compounds and gene expression were investigated, revealing the molecular mechanisms affecting the accumulation of bioactive compounds by F treatment. The results showed that F accumulation in tea leaves gradually increased under exogenous F treatments. Similarly, the flavonoid content also increased in the F treatment. In contrast, the polyphenol content, free amino acids, and the total catechins decreased significantly. Special amino acids, such as sulfur-containing amino acids and proline, had the opposite trend of free amino acids. Caffeine was obviously induced by exogenous F, while the theanine content peaked after two day-treatment. These results suggest that the F accumulation and content of bioactive compounds were dramatically affected by F treatment. Furthermore, differentially expressed genes (DEGs) related to the metabolism of main bioactive compounds and amino acids, especially the pivotal regulatory genes of catechins, caffeine, and theanine biosynthesis pathways, were identified and analyzed using high-throughput Illumina RNA-Seq technology and qRT-PCR. The expression of pivotal regulatory genes is consistent with the changes of the main bioactive compounds in C. sinensis leaves, indicating a complicated molecular mechanism for the above findings. Overall, these data provide a reference for exploring the possible molecular mechanism of the accumulation of major bioactive components such as flavonoid, catechins, caffeine, theanine and other amino acids in tea leaves in response to fluoride treatment.

Gene expression profile indicates involvement of NO in Camellia sinensis pollen tube growth at low temperature.

BACKGROUND: Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress. RESULTS: Three libraries were generated from C. sinensis cv. 'Longjingchangye' pollen tubes cultured at 25 °C (CsPT-CK) and 4 °C (CsPT-LT) or with 25 µM DEA NONOate (CsPT-NO). The number of unigenes found for the three biological replications were 39,726, 40,440 and 41,626 for CsPT-CK; 36,993, 39,070 and 39,439 for CsPT-LT; and 39,514, 38,298 and 39,061 for CsPT-NO. A total of 36,097 unique assembled and annotated sequences from C. sinensis pollen tube reads were found in a BLAST search of the following databases: NCBI non-redundant nucleotide, Swiss-prot protein, Kyoto Encyclopedia of Genes and Genomes, Cluster of Orthologous Groups of proteins, and Gene Ontology. The absolute values of log2Ratio > 1 and probability > 0.7 were used as the thresholds for significantly differential gene expression, and 766, 497 and 929 differentially expressed genes (DEGs) were found from the comparison analyses of the CK-VS-LT, CK-VS-NO and LT-VS-NO libraries, respectively. Genes related to metabolism and signaling pathways of plant hormones, transcription factors (TFs), vesicle polarized trafficking, cell wall biosynthesis, the ubiquitination machinery of the ubiquitin system and species-specific secondary metabolite pathways were mainly observed in the CK-VS-LT and CK-VS-NO libraries. CONCLUSION: Differentially expressed unigenes related to the inhibition of C. sinensis pollen tube growth under low temperature and NO are identified in this study. The transcriptomic gene expression profiles present a valuable genomic tool to improve studying the molecular mechanisms underlying low-temperature tolerance in pollen tube.

Unveiling the impact of high-pressure processing on anthocyanin-protein/polysaccharide interactions: A comprehensive review.

Anthocyanins, natural plant pigments responsible for the vibrant hues in fruits, vegetables, and flowers, boast antioxidant properties with potential human health benefits. However, their susceptibility to degradation under conditions such as heat, light, and pH fluctuations necessitates strategies to safeguard their stability. Recent investigations have focused on exploring the interactions between anthocyanins and biomacromolecules, specifically proteins and polysaccharides, with the aim of enhancing their resilience. Notably, proteins like soy protein isolate and whey protein, alongside polysaccharides such as pectin, starch, and chitosan, have exhibited promising affinities with anthocyanins, thereby enhancing their stability and functional attributes. High-pressure processing (HPP), emerging as a non-thermal technology, has garnered attention for its potential to modulate these interactions. The application of high pressure can impact the structural features and stability of anthocyanin-protein/polysaccharide complexes, thereby altering their functionalities. However, caution must be exercised, as excessively high pressures may yield adverse effects. Consequently, while HPP holds promise in upholding anthocyanin stability, further exploration is warranted to elucidate its efficacy across diverse anthocyanin variants, macromolecular partners, pressure regimes, and their effects within real food matrices.

Response of food waste anaerobic digestion to the dimensions of micron-biochar under 30 g VS/L organic loading rate: Focus on gas production and microbial community structure.

Biochar modification is an effective approach to enhance its ability to promote anaerobic digestion (AD). Focusing on the physical properties of biochar, the impact of different particle sizes of biochar on AD of food waste (FW) at high organic loading rate (OLR) was investigated. Four biochar with different sizes (40-200 mesh) were prepared and used in AD systems at OLR 30 g VS/L. The research results found that biochar with a volume particle size of 102 µm (RBC-P140) had top-performance in promoting cumulative methane production, increasing by 13.20% compared to the control group. The analysis results of the variety in volatile acids and alkalinity in the system did not show a correlation with the size of biochar, but small size has the potential to improve the environmental tolerance of the system to high acidity. Microbial community analysis showed that the abundance of aceticlastic methanogen and the composition of zoogloea were optimized through relatively small-sized biochar. Through revealing the effect of biochar particle size on AD system at high OLR, this work provided theoretical guidance for regulating fermentation systems using biochar.

Heavy metals drive microbial community assembly process in farmland with long-term biosolids application.

Biosolids are considered an alternative to chemical fertilizers due to their rich nutrients. However, long-term biosolids application can lead to heavy metals accumulation, which severely affects soil microbial community compositions. The factors influencing soil microbial community assembly were explored under a 16-year long-term experiment with biosolids applications. Our results indicated that biosolids application significantly increased fungal richness while not for bacterial and arbuscular mycorrhizal (AM) fungal richness. Besides, biosolids application significantly affected soil bacterial, fungal compositions and AM fungal community. Soil microorganisms were clustered into different modules with bacterial and AM fungal communities were affected by both organic matter and heavy metals, while fungal communities were affected by heavy metals (Cr, Ni, and As). The soil bacterial community assembly was dominated by stochastic processes while the fungal and AM fungal community assemblies were mainly driven by deterministic processes. Random forest analysis showed that heavy metals were identified as major drivers (Hg, Cu, Cd, and Zn for bacteria, Pb and Cr for fungi, and As and Ni for AM fungi) of the community assembly process. Overall, our study highlights the significant role of heavy metals in shaping microbial community dynamics and gives a guide for controlling biosolids application.

Comparison analysis of microbial agent and different compost material on microbial community and nitrogen transformation genes dynamic changes during pig manure compost.

This study aimed to assess the impact of microbial agent and different compost material, on physicochemical parameters dynamic change, nitrogen-transfer gene/bacterial community interaction network during the pig manure composting. Incorporating a microbial agent into rice straw-mushroom compost reduced the NH3 and total ammonia emissions by 25.52 % and 14.41 %, respectively. Notably, rice straw-mushroom with a microbial agent reduced the total ammonia emissions by 37.67 %. NH4+-N and pH emerged as primary factors of phylum-level and genus-level microorganisms. Microbial agent increased the expression of narG, nirK, and nosZ genes. Rice straw-mushroom elevated the content of amoA, nirK, nirS, and nosZ genes. Alcanivorax, Luteimonas, Pusillimonas, Lactobacillus, Aequorivita, Clostridium, Moheibacter and Truepera were identified as eight core microbial genera during the nitrogen conversion process. This study provides a strategy for reducing ammonia emissions and analyzes the potential mechanisms underlying compost processes.

Advancing anaerobic digestion with MnO2-modified biochar: Insights into performance and mechanisms.

The use of bio-based composites to enhance the methane production in anaerobic digestion has attracted considerable attention. Nevertheless, the study of electron transfer mechanisms and the applications of biochar/MnO2 (MBC) in complex systems remains largely unexplored. Biochar composited with MnO2 at 10:1 mass ratio (MBC10) increased the content of volatile fatty acids by 9.09 % during acidogenic phase. During the methanogenic experiments using acetate, cumulative methane production (CMP) rose by 5.83 %, and in the methanogenic experiments using food waste, CMP increased by 24.32 %. Microbial community analysis indicated an enrichment of Syntrophomonas, Bacilli, and Methanosaetaceae in the MBC10 group. This enrichment occurred mainly due to the redox capability of MnO2 enhancing MBC capacitance, thereby facilitating microbial electron transfer processes. Additionally, under 2 g/L ammonia nitrogen concentration and 30 g/L organic load, the CMP of MBC10 increased by 12.74 % and 9.44 %, respectively, compared to the BC600 group. This study illuminates MBC's electron transfer mechanisms and applications, facilitating its wider practical adoption and fostering future innovations.

Architecture of the ATP-driven motor for protein import into chloroplasts.

Thousands of nuclear-encoded proteins are transported into chloroplasts through the TOC-TIC translocon spanning the chloroplast envelope membranes. A motor complex pulls the translocated proteins out of the TOC-TIC complex into the chloroplast stroma by hydrolyzing ATP. The Orf2971-FtsHi complex was suggested to serve as the ATP-hydrolyzing motor in Chlamydomonas reinhardtii, but little is known about its architecture and assembly. Here, we report the 3.2-Å resolution structure of the Chlamydomonas Orf2971-FtsHi complex. The 20-subunit complex spans the chloroplast inner envelope with two bulky modules protruding into the intermembrane space and stromal matrix. Six subunits form a hetero-hexamer potentially providing the pulling force through ATP hydrolysis. The remaining subunits, including potential enzymes/chaperones, likely facilitate the complex assembly and regulate its proper function. Our results provide the structural foundation for mechanistic understanding of chloroplast protein translocation.

Potential and benefits of biochar production: crop straw management and carbon emission mitigation in Shaanxi Province, China.

Shaanxi Province is an important agricultural province in western China. Its profit-oriented management of crop residues remains a concern in the agriculture sector. Aiming to accelerate the valorization of agricultural straw and offer potential solutions for profit-oriented use of crop residues in Shaanxi, this study estimated the quantity of resources and collectable amount of crop straw by using the grain-to-straw ratio, analyzed the carbon emission reduction potential considering biochar energy and soil uses with the help of a life cycle assessment (LCA) model, and calculated the economic benefits of biochar production using waste and abandoned straw in Weinan (a city of Shaanxi). The theoretical resources and collectible amount of crop straw in Shaanxi showed an overall growth trend from 1949 to 2021, reaching 1.47 × 107 and 1.26 × 107 t in 2021 respectively. In 2021, straw from corn, wheat, and other grains accounted for 94.32% of the total straw. Among the 11 cities in Shaanxi, Weinan had the largest straw resources of 2.82 × 106 t, Yulin had the largest per capita straw resources of 0.72 t/person, and Yangling had the highest resource density of 7.60 t/hm2. The total carbon emission reduction was 3.11 × 104 t under scenario A with crop straw used for power generation. The emission reduction ranged from 1.25 × 107 to 1.27 × 107 CO2e t under scenario B with biochar production for energy and soil use. By using waste and abandoned straw in Weinan for biochar production, carbon emissions could be reduced by up to 2.07 × 105 t CO2e. In terms of the economic benefit from straw pyrolysis, the actual income was estimated to range from 0.67 × 108 to 1.33 × 108 ¥/a with different carbon prices. This study sheds light on the economic and environmental benefits of agricultural straw valorization through pyrolysis in Shaanxi, and provided an important basis for promoting the agricultural straw utilization in view of its potential for carbon emission reduction.

Insight into the humification and carbon balance of biogas residual biochar amended co-composting of hog slurry and wheat straw.

The impact of biogas residual biochar (BRB) on the humification and carbon balance process of co-composting of hog slurry (HGS) and wheat straw (WTS) was examined. The 50-day humification process was significantly enhanced by the addition of BRB, particular of 5% BRB, as indicated by the relatively higher humic acid content (67.28 g/kg) and humification ratio (2.31) than other treatments. The carbon balance calculation indicated that although BRB addition increased 22.16-46.77% of C lost in form of CO2-C, but the 5% BRB treatment showed relatively higher C fixation and lower C loss than other treatments. In addition, the BRB addition reshaped the bacterial community structure during composting, resulting in increased abundances of Proteobacteria (25.50%) during the thermophilic phase and Bacteroidetes (33.55%) during the maturation phase. Combined these results with biological mechanism analysis, 5% of BRB was likely an optimal addition for promoting compost humification and carbon fixation in practice.

Recent developments in improving the emulsifying properties of chitosan.

Chitosan is one of the valuable products obtained from crustacean waste. The unique characteristics of chitosan (antimicrobial, antioxidant, anticancer, and anti-inflammatory) have increased its application in various sectors. Besides unique biological properties, chitosan or chitosan-based compounds can stabilize emulsions. Nevertheless, studies have shown that chitosan cannot be used as an efficient stabilizer because of its high hydrophilicity. Hence, this review aims to provide an overview of recent studies dealing with improving the emulsifying properties of chitosan. In general, two different approaches have been reported to improve the emulsifying properties of chitosan. The first approach tries to improve the stabilization property of chitosan by modifying its structure. The second one uses compounds such as polysaccharides, proteins, surfactants, essential oils, and polyphenols with more wettability and emulsifying properties than chitosan's particles in combination with chitosan to create complex particles. The tendency to use chitosan-based particles to stabilize Pickering emulsions has recently increased. For this reason, more studies have been conducted in recent years to improve the stabilizing properties of chitosan-based particles, especially using the electrostatic interaction method. In the electrostatic interaction method, numerous research has been conducted on using proteins and polysaccharides to increase the stabilizing property of chitosan.

Chitosan nanocarriers containing essential oils as a green strategy to improve the functional properties of chitosan: A review.

Large amounts of agricultural waste, especially marine product waste, are produced annually. These wastes can be used to produce compounds with high-added value. Chitosan is one such valuable product that can be obtained from crustacean wastes. Various biological activities of chitosan and its derivatives, especially antimicrobial, antioxidant, and anticancer properties, have been confirmed by many studies. The unique characteristics of chitosan, especially chitosan nanocarriers, have led to the expansion of using chitosan in various sectors, especially in biomedical sciences and food industries. On the other hand, essential oils, known as volatile and aromatic compounds of plants, have attracted the attention of researchers in recent years. Like chitosan, essential oils have various biological activities, including antimicrobial, antioxidant, and anticancer. In recent years, one of the ways to improve the biological properties of chitosan is to use essential oils encapsulated in chitosan nanocarriers. Among the various biological activities of chitosan nanocarriers containing essential oils, most studies conducted in recent years have been in the field of antimicrobial activity. It was documented that the antimicrobial activity was increased by reducing the size of chitosan particles in the nanoscale. In addition, the antimicrobial activity was intensified when essential oils were in the structure of chitosan nanoparticles. Essential oils can increase the antimicrobial activity of chitosan nanoparticles with synergistic effects. Using essential oils in the structure of chitosan nanocarriers can also improve the other biological properties (antioxidant and anticancer activities) of chitosan and increase the application fields of chitosan. Of course, using essential oils in chitosan nanocarriers for commercial use requires more studies, including stability during storage and effectiveness in real environments. This review aims to overview recent studies on the biological effects of essential oils encapsulated in chitosan nanocarriers, with notes on their biological mechanisms.

Composting pig manure with nano-zero-valent iron amendment: Insights into the carbon cycle and balance.

The effectiveness of nano-zero-valent-iron (NZVI) addition during composting of pig manure (PM) was investigated. Different dosages of NZVI were mixed with PM substrate during a 50 days composting process. The results revealed that the higher share of NZVI addition, the higher OM degradation rate is. On contrary, it was observed that the higher share of NZVI addition, the lower the fulvic acid and the humin degradation rate is. Meanwhile, NZVI amendment increased the CO2 and CH4 emissions by 29-47 % and 53-57 %, respectively. The in-depth analysis showed that NZVI addition increased the activity of Sphaerobacter and Luteimonas, which eventually led to the degradation of hard-to-degrade OM faster. Additionally, NZVI was found to increase the filtration of microorganisms, reducing the toxicity and hygiene of compost products. No significant improvement in humic substance enhancement was observed during composting with NZVI addition but improved OM degradation.

Tuning chitosan's chemical structure for enhanced biological functions.

Chitosan, an amino polysaccharide mostly derived from crustaceans, has been recently highlighted for its biological activities that depend on its molecular weight (MW), degree of deacetylation (DD), and acetylation pattern (AP). More importantly, for some advanced biomaterials, the homogeneity of the chitosan structure is an important factor in determining its biological activity. Here we review emerging enzymes and cell factories, respectively, for in vitro and in vivo preparation of chitosan oligosaccharides (COSs), focusing on advances in the analysis of the AP and structural modification of chitosan to tune its functions. By 'mapping' current knowledge on chitosan's in vitro and in vivo activity with its MW and AP, this work could pave the way for future studies in the field.

Topological charge-density-vector method of identifying filaments of scroll waves.

Scroll waves have been found in a variety of three-dimensional excitable media, including physical, chemical, and biological origins. Scroll waves in cardiac tissue are of particular significance as they underlie ventricular fibrillation that can cause sudden death. The behavior of a scroll wave is characterized by a line of phase singularity at its organizing center, known as a filament. A thorough investigation into the filament dynamics is the key to further exploration of the general theory of scroll waves in excitable media and the mechanisms of ventricular fibrillation. In this paper, we propose a method to identify filaments of scroll waves in excitable media. From the definition of the topological charge of filaments, we obtain the discrete expression of the topological charge-density vector, which is useful in calculating the topological charge vectors at each grid in the space directly. The set of starting points of these topological charge vectors represents a set of phase singularities, thereby forming a line of phase singularity, that is, a filament of a scroll wave.