Continuous cropping system altered soil microbial communities and nutrient cycles.

Understanding the response of microbial communities and their potential functions is essential for sustainability of agroecosystems under long-term continuous cropping. However, limited research has focused on investigating the interaction between soil physicochemical factors and microbial community dynamics in agroecosystems under long-term continuous cropping. This study probed into the physicochemical properties, metabolites, and microbial diversity of tobacco rhizosphere soils cropped continuously for 0, 5, and 20 years. The relative abundance of bacterial genera associated with nutrient cycling (e.g., Sphingomonas) increased while potential plant pathogenic fungi and beneficial microorganisms showed synergistic increases with the duration of continuous cropping. Variations in soil pH, alkeline nitrogen (AN) content, and soil organic carbon (SOC) content drove the shifts in soil microbial composition. Metabolites such as palmitic acid, 3-hydroxypropionic acid, stearic acid, and hippuric acid may play a key role in soil acidification. Those results enhance our ability to predict shifts in soil microbial community structure associated with anthropogenic continuous cropping, which can have long-term implications for crop production.

CRISPR/Cas12a-mediated entropy-driven electrochemical biosensor for detection of genetically modified maize Mon810.

Genetically modified crops (GMOs) have led to significant, if not revolutionary, agricultural advances. The development of GMOs requires necessary regulations, which depend on the detection of GMOs. A sensitive and specific biosensor for the detection of transgenic crops is crucial to improve the detection efficiency of GMOs. Here, we developed a CRISPR/Cas12a-mediated entropy-driven electrochemiluminescence (ECL) biosensor for the sensitive and specific detection of MON810, the world's most widely used transgenic insect-resistant maize. We designed two crRNAs to activate CRISPR/Cas12a, allowing it to cut non-specific single strands, and we modified the DNA tetrahedron (DT) on the surface of the gold electrode to diminish non-specific adsorption. The entropy-driven chain displacement reaction with the target DNA takes place for amplification. After optimization, the biosensor has satisfactory accuracy and selectivity, with a linear range of ECL of 1-106 fM and a limit of detection (LOD) of 3.3 fM by the 3σ method. The biosensor does not require polymerase chain reaction (PCR) amplification or complex sample processing, which dramatically improves transgenic crop detection efficiency. This new biosensor achieves rapid, sensitive, and highly specific detection of transgenic crops, and has great potential for large-scale field detection of transgenic crops.

Peroxisome-based metabolic engineering for biomanufacturing and agriculture.

Subcellular compartmentalization of metabolic pathways plays a crucial role in metabolic engineering. The peroxisome has emerged as a highly valuable and promising compartment for organelle engineering, particularly in the fields of biological manufacturing and agriculture. In this review, we summarize the remarkable achievements in peroxisome engineering in yeast, the industrially popular biomanufacturing chassis host, to produce various biocompounds. We also review progress in plant peroxisome engineering, a field that has already exhibited high potential in both biomanufacturing and agriculture. Moreover, we outline various experimentally validated strategies to improve the efficiency of engineered pathways in peroxisomes, as well as prospects of peroxisome engineering.

Characteristics of soil microbial communities in farmland with different comprehensive fertility levels in the Panxi area, Sichuan, China.

Soil bacterial communities are intricately linked to ecosystem functioning, and understanding how communities assemble in response to environmental change is ecologically significant. Little is known about the assembly processes of bacteria communities across agro-ecosystems, particularly with regard to their environmental adaptation. To gain further insights into the microbial community characteristics of agro-ecosystems soil in the Panxi area of Sichuan Province and explore the key environmental factors driving the assembly process of the microbial community, this study conducted field sampling in major farmland areas of Panxi area and used Illumina MiSeq high-throughput sequencing technology to conduct bacterial sequencing. Soil organic matter (SOM), alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), available potassium (AK) and other environmental factors were determined. The membership function method and principal component analysis method were used to evaluate the fertility of the soil. The results revealed minimal differences in alpha diversity index among samples with different comprehensive fertility indices, while NMDS analysis showed that community differences between species were mainly reflected in high fertility and low fertility (R: 0.068, p: 0.011). Proteobacteria, Acidobacteria and Actinobacteria were the main types of microbial communities, accounting for more than 60% of the relative abundance. Proteobacteria accounted for a higher proportion in the high fertility samples, while Acidobacteria and Actinobacteria accounted for a higher proportion in the middle and low fertility samples. Both the neutral theoretical model and zero model analysis showed that the microbial communities in tobacco-planting soil with different comprehensive fertility indices presented a random assembly process. With the increase in environmental distance difference, the diversity of the microbial community in medium and low-fertility soil also increased, but there was no significant change in high-fertility soil. Redundancy analysis showed that pH and SOM were the key factors affecting microbial community composition. The results of this study can provide a theoretical reference for the study of environmental factors and microbial communities in tobacco-growing soil.

Mechanistic basis for mitigating drought tolerance by selenium application in tobacco (Nicotiana tabacum L.): a multi-omics approach.

The lack of irrigation water in agricultural soils poses a significant constraint on global crop production. In-depth investigation into microRNAs (miRNAs) has been widely used to achieve a comprehensive understanding of plant defense mechanisms. However, there is limited knowledge on the association of miRNAs with drought tolerance in cigar tobacco. In this study, a hydroponic experiment was carried out to identify changes in plant physiological characteristics, miRNA expression and metabolite profile under drought stress, and examine the mitigating effects of selenium (Se) application. The shoot dry weight of drought-stressed plants was approximately half (50.3%) of that in non-stressed (control) conditions. However, plants supplied with Se attained 38.8% greater shoot dry weight as compared to plants with no Se supply under drought stress. Thirteen miRNAs were identified to be associated with drought tolerance. These included 7 known (such as nta-miR156b and nta-miR166a) and 6 novel miRNAs (such as novel-nta-miR156-5p and novel-nta-miR209-5p) with the target genes of squamosa promoter-binding-like protein 4 (SPL4), serine/threonine protein phosphatase 2A (PPP2A), cation/calcium exchanger 4-like (CCX4), extensin-1-like (EXT1) and reduced wall acetylation 2 (RWA2). Further investigation revealed that the expression levels of Ext1 and RWA2 were significantly decreased under drought stress but increased with Se addition. Moreover, key metabolites such as catechin and N-acetylneuraminic acid were identified, which may play a role in the regulation of drought tolerance. The integrated analysis of miRNA sequencing and metabolome highlighted the significance of the novel-nta-miR97-5p- LRR-RLK- catechin pathway in regulating drought tolerance. Our findings provide valuable insights into the molecular mechanisms underlying drought tolerance and Se-induced stress alleviation in cigar tobacco.

Identification of low grain cadmium accumulation genotypes and its physiological mechanism in maize (Zea mays L.).

Soil cadmium (Cd) contamination poses adverse impacts on crop yield and quality. Maize is a widely cultivated cereal throughout the world. In this study, field and hydroponic experiments were conducted to investigate the genotypic difference in Cd accumulation and tolerance in maize. There were significant genotypic differences in grain Cd concentrations among 95 genotypes. From these 95 genotypes, L42 which showed a higher grain Cd concentration and L63 which showed a lower grain Cd concentration was selected for further study. Under Cd stress, L63 showed much less reduction in plant growth than L42 compared with the control. Seedlings of L63 recorded higher Cd concentration in roots, but lower in shoots L42, indicating that the low grain Cd concentration in L63 is mainly due to the low rate of transportation of Cd from roots to shoots. Most Cd accumulated in epidermis and xylem vessels of L63, while the green fluorescent was found across almost the entire cross-section of root in L42. Obvious ultrastructural damage was observed in L42 under Cd stress, especially in mesophyll cells, while L63 was less affected. These findings could contribute to developing low Cd accumulation and high tolerance maize cultivars.

HvHOX9, a novel homeobox leucine zipper transcription factor, positively regulates aluminum tolerance in Tibetan wild barley.

Aluminum (Al) toxicity is the primary limiting factor of crop production on acid soils. Tibetan wild barley germplasm is a valuable source of potential genes for breeding barley with acid and Al tolerance. We performed microRNA and RNA sequencing using wild (XZ16, Al-tolerant; XZ61, Al-sensitive) and cultivated (Dayton, Al-tolerant) barley. A novel homeobox-leucine zipper transcription factor, HvHOX9, was identified as a target gene of miR166b and functionally characterized. HvHOX9 was up-regulated by Al stress in XZ16 (but unchanged in XZ61 and Dayton) and was significantly induced only in root tip. Phylogenetic analysis showed that HvHOX9 is most closely related to wheat TaHOX9 and orthologues of HvHOX9 are present in the closest algal relatives of Zygnematophyceae. Barley stripe mosaic virus-induced gene silencing of HvHOX9 in XZ16 led to significantly increased Al sensitivity but did not affect its sensitivity to other metals and low pH. Disruption of HvHOX9 did not change Al concentration in the root cell sap, but led to more Al accumulation in root cell wall after Al exposure. Silencing of HvHOX9 decreased H+ influx after Al exposure. Our findings suggest that miR166b/HvHOX9 play a critical role in Al tolerance by decreasing root cell wall Al binding and increasing apoplastic pH for Al detoxification in the root.

Silicon regulates the expression of vacuolar H+-pyrophosphatase 1 and decreases cadmium accumulation in rice (Oryza sativa L.).

Deciphering the mechanism of Cd accumulation in crops is imperative for minimizing soil-to-plant transfer of Cd to improve safe food production. Hydroponic experiments were performed examining Cd accumulation, growth performance and protein characteristics of two rice genotypes, Xiushui817 and Zheda821, with low and high grain Cd accumulation, respectively, under Cd stress and in the presence of Si. Xiushui817 had lower root-to-shoot Cd translocation and was more sensitive to Cd stress than Zheda821. Si reduced the shoot Cd content in both genotypes but more efficacy in Zheda821. Tandem mass tags (TMT)-based proteomic analysis identified 25 proteins associated with low grain Cd accumulation, including vacuolar H+-pyrophosphatase 1 (OVP1) that was up-regulated after Si addition in Zheda821. The sequence comparison of OVP1 showed one nucleotide difference in Xiushui817 relative to Zheda821 resulting in one amino acid. Overexpression of OVP1 reduced shoot Cd concentration and improved the growth of rice compared with WT under both control and Cd treatment. The results highlight the significant roles of OVP1 in both Cd accumulation and the Si-induced Cd reduction in rice. Our findings provide valuable insights into the molecular mechanism of low Cd accumulation and Si-induced decrease in Cd accumulation in rice. OVP1 could be used for transgenic overexpression in rice or other cereals for safe food production.

Atmospheric heavy metal deposition in agro-ecosystems in China.

Atmospheric deposition has become one of the main sources of heavy metals in crops in developed and industrial zones in China for the past several years. However, lack of data of the agro-ecosystems on the vast areas of China makes it difficult to assess the impacts of air pollution on the heavy metal accumulation in crops. In this study, with deposit samples from 67 sites located at different agro-ecosystems (typical, factory nearby, town nearby, roadside, and remote) of four natural regions [Huanghuai (HH), Southeast (SE), Southwest (SW) and upper-mid Yangzi River (Up-mid YR)], atmospheric heavy metal deposition in agro-ecosystems on a large scale in China was studied. The results showed that during the growing season, the deposition fluxes of Cr, Ni, As, Cd, and Pb in typical agro-ecosystems were 0.60-36.86, 0.65-25.37, 0.05-8.88, 0.12-5.81, and 0.43-35.63 µg m-2 day-1, respectively, which varied greatly between the four different regions. The average deposition fluxes of Cr, Ni, Cd, and Pb in the HH region, as well as the fluxes of As in the SW region, were significantly higher than those in the SE region. Heavy metal deposition rates among agro-ecosystems were very similar, except for the sites around cement factory in flat HH region. In mountainous SW region, however, deposition rates varied widely with sites nearby towns relatively higher and remote regions much lower. Higher correlation coefficients were observed between Cr, As, Pb, and Ni deposition rates, suggesting that they had similar sources. Samples from the SW and SE regions exhibited higher 207Pb/206Pb and 208Pb/206Pb ratios than those from the HH and Up-mid YR regions. Airborne Pb in SW agro-ecosystems were mainly derived from vehicle exhaust and local smelting, whereas that in the HH region from burning of northern Chinese coal.

Physiological and proteomic analysis of selenium-mediated tolerance to Cd stress in cucumber (Cucumis sativus L.).

Selenium can mitigate cadmium toxicity in plants. However, the mechanism of this alleviation has not been fully understood. In the present study, the role of Se in inducing tolerance to Cd stress in cucumber was elucidated. Results showed that Se significantly alleviated Cd-induced growth inhibition, reduced Cd concentration, increased SPAD value and improved photosynthetic performance. Through proteomic analysis by two-dimensional gel electrophoresis (2-DE) coupled with mass spectrometry, 26 protein spots were identified, which were significantly influenced by Cd stress and/or Se application. Among these proteins, the abundance of 21 spots (10 in leaves and 11 in roots) were repressed in Cd-treated and up-accumulated or no-changed in Cd+Se-treated cucumber. These altered proteins were involved in the response to stress, metabolism, photosynthesis and storage, they were including glutathione S-transferase F8, heat shock protein STI-like, peroxidase, ascorbate oxidase, fructose-bisphosphate aldolase 2, NiR, Rieske type ion sulfur subunit and PsbP domain-containing protein 6. Furthermore, we identified five proteins with an increase in relative abundance after Cd treatment, they were involved in the functional groups active in response to stress and transport. The present study provided novel insights into Se-mediated tolerance of cucumber seedlings against Cd toxicity at the proteome level.

Differences in physiological features associated with aluminum tolerance in Tibetan wild and cultivated barleys.

Aluminum (Al) toxicity is a major limiting factor for plant production in acid soils. Wild barley germplasm is a treasure trove of useful genes and offers rich sources of genetic variation for crop improvement. Al-stress-hydroponic-experiments were performed, and the physiochemical characteristic of two contrasting Tibetan wild barley genotypes (Al-resistant XZ16 and Al-sensitive XZ61) and Al-resistant cv. Dayton were compared. Ultrastructure of chloroplasts and root cells in XZ16 was less injured than that in Dayton and XZ61. Moreover, XZ16 secreted significantly more malate besides citrate and exhibited less Al uptake and distribution than both of XZ61 and Dayton in response to Al stress, simultaneously maintained higher H⁺-, Ca²âºMg²âº- and total-ATPase activities over XZ61. The protein synthesis inhibitor cycloheximide reduced citrate secretion from XZ16, but not from Dayton. In Tibetan wild barley, our findings highlight the significant correlations between Al tolerance, ATPase activity and citrate secretion, providing some insights into the physiological basis for Al-detoxification.

Comparative proteomic analysis of aluminum tolerance in tibetan wild and cultivated barleys.

Aluminum (Al) toxicity is a major limiting factor for plant production in acid soils. Wild barley germplasm is rich in genetic diversity and may provide elite genes for crop Al tolerance improvement. The hydroponic-experiments were performed to compare proteomic and transcriptional characteristics of two contrasting Tibetan wild barley genotypes Al- resistant/tolerant XZ16 and Al-sensitive XZ61 as well as Al-resistant cv. Dayton. Results showed that XZ16 had less Al uptake and translocation than XZ61 and Dayton under Al stress. Thirty-five Al-tolerance/resistance-associated proteins were identified and categorized mainly in metabolism, energy, cell growth/division, protein biosynthesis, protein destination/storage, transporter, signal transduction, disease/defense, etc. Among them, 30 were mapped on barley genome, with 16 proteins being exclusively up-regulated by Al stress in XZ16, including 4 proteins (S-adenosylmethionine-synthase 3, ATP synthase beta subunit, triosephosphate isomerase, Bp2A) specifically expressed in XZ16 but not Dayton. The findings highlighted the significance of specific-proteins associated with Al tolerance, and verified Tibetan wild barley as a novel genetic resource for Al tolerance.

Comparative study of alleviating effects of GSH, Se and Zn under combined contamination of cadmium and chromium in rice (Oryza sativa).

A hydroponic experiment was conducted to study the ameliorative effects of separate or combined application of exogenous glutathione (GSH), selenium (Se) and zinc (Zn) upon 20 µM cadmium (Cd) plus 20 µM chromium (Cr) heavy metal stress (HM) in rice seedlings. The results showed that HM caused a marked reduction in seedling height, chlorophyll content (SPAD) and biomass, and activities of catalase (CAT) and ascorbate peroxidase (APX) in leaves and H(+)-ATPase in roots/leaves, but elevated superoxide dismutase (SOD) and guaiacol peroxidase (POD) activities in leaves with elevated malondialdehyde (MDA) accumulation both in leaves and roots over the control. The best mitigation effect was recorded in HM+GSH+Zn and HM+GSH (addition of GSH+Zn and GSH to HM solution), which greatly alleviated HM-induced growth inhibition and oxidative stress. Compared with HM alone, HM+GSH and HM+GSH+Zn markedly reduced Cr uptake and translocation but not affected Cd concentration; improved H(+)-ATPase activity and Fe, Zn, Mn uptake and translocation, and repressed MDA accumulation. Meanwhile exogenous GSH and GSH+Zn counteracted HM-induced response of antioxidant enzymes, via suppressing HM-induced dramatic increase of root/leaf SOD and leaf POD activities, and elevating stress-depressed leaf APX and leaf/root CAT activities.

Genotypic differences in physiological characteristics in the tolerance to drought and salinity combined stress between Tibetan wild and cultivated barley.

Greenhouse pot experiments were conducted to investigate genotypic differences in response to individual and combined stresses of drought and salinity between Tibetan wild barley genotypes (XZ5, drought-tolerant; XZ16, salinity/aluminum tolerant) and cv. CM72 (salinity-tolerant). Either drought (D) or salinity (S) alone and in combination (D + S) stresses significantly decreased plant growth, chlorophyll content, net photosynthetic rate (Pn), maximal photochemical efficiency of PSII (Fv/Fm), water potential and osmotic potential, with the largest suppression under combined stress, and two wild genotypes showing more tolerance than CM72. Water use efficiency (WUE) increased significantly in XZ5 and XZ16 after D + S, but no significant change in CM72. XZ5 and XZ16 showed 30.9% and 12.1% higher K(+) level and 30.5% and 24.1% lower Na(+)/K(+) ratio in plants, compared with CM72, with increased metal nutrients as Ca, Fe and Mn under D + S. The peak accumulation in proline and glycine-beatine was recorded in combined stress with larger accumulation in two wild genotypes. Moreover, larger increases in the level of ASA and GSH, and the activities of Ca(2+)Mg(2+)-ATPase, and superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX), guaiacol peroxidase (POD) and glutathione reductase (GR) under D + S vs control were observed in XZ5 and XZ16 than CM72, with less accumulation of H(2)O(2) and malondialdehyde. These results suggest that high tolerance to D + S stress of XZ5 and XZ16 is closely related to lower Na(+)/K(+) ratio and enhanced Ca(2+)Mg(2+)-ATPase, proline, glycine-beatine and WUE, and improved capacity of antioxidative performance to scavenge reactive oxygen species and thus suppressed level of lipid peroxidation.

Selenium reduces cadmium uptake and mitigates cadmium toxicity in rice.

Hydroponic experiments were performed to investigate physiological mechanisms of selenium (Se) mitigation of Cd toxicity in rice. Exogenous Se markedly reduced Cd concentration in leaves, roots, and stems. Addition or pretreatment of 3 µM Se in 50 µM Cd solution significantly addressed Cd-induced growth inhibition, recovered root cell viability, and dramatically depressed O(2)(-), H(2)O(2), and malondialdehyde (MDA) accumulation. Supplemental Se counteracted 50 µM Cd-induced alterations of certain antioxidant enzymes, and uptake of nutrients, e.g. depressed Cd-induced increase in leaf and root superoxide dismutase (SOD) and leaf peroxidase (POD) activities, but elevated depressed catalase (CAT) activity; decreased Cd-induced high S and Cu concentrations in both leaves and roots. External Se counteracted the pattern of alterations in ATPase activities induced by Cd, e.g. significantly elevated the depressed root H(+)- and Ca(2+)-ATPase activities, but decreased the ascent root Na(+)K(+)-ATP activity. Results indicate that alleviated Cd toxicity by Se application is related to reduced Cd uptake and ROS accumulation, balanced nutrients, and increased H(+)- and Ca(2+)-ATPase activities in rice.

Effects of cadmium, chromium and lead on growth, metal uptake and antioxidative capacity in Typha angustifolia.

This study investigates the modulation of antioxidant defence system of Typha angustifolia after 30 days exposure of 1 mM chromium (Cr), cadmium (Cd), or lead (Pb). T. angustifolia showed high tolerance to heavy metal toxicity with no visual toxic symptom when exposed to metal stress, and Cd/Pb addition also increased plant height and biomass especially in Pb treatment. Along with increased Cr, Cd, and Pb uptake in metal treatments, there was enhanced uptake of plant nutrients including Ca and Fe, and Zn in Pb treatment. A significant increase in malondialdehyde (MDA) content and superoxide dismutase (SOD) and peroxidase (POD) activities were recorded in plants subjected to Cr, Cd, or Pb stress. Furthermore, Pb stress also improved catalase (CAT), ascorbate peroxidase (APX), and glutathione peroxidase (GPX) activities; whereas Cr stress depressed APX and GPX. The results indicate that enzymatic antioxidants and Ca/Fe uptake were important for heavy metal detoxification in T. angustifolia, stimulated antioxidative enzymes, and Ca, Fe, and Zn uptake could partially explain its hyper-Pb tolerance.

Comparative proteomic analysis of Typha angustifolia leaf under chromium, cadmium and lead stress.

The present study investigated Typha angustifolia leaf proteome in response to Cr, Cd and Pb stress. T. angustifolia of 90 (D90) and 130d (D130) old plants were subjected to 1mM Cr, Cd and Pb and samples were collected 30d after treatment. 2-DE coupled with MS (mass spectrometry) was used to analyze and identify Cr, Cd and Pb-responsive proteins. More than 1600 protein spots were reproducibly detected on each gel, wherein 44, 46, 66 and 33, 26, 62 spots in D90 and D130 samples were differentially expressed by Cr, Cd, Pb over the control, respectively. Of these differentially expressed proteins, 3, 1, 8 overlapped in D90 and D130; while 5, 8, 5 with regulation factors above 3 in one of D90 or D130 samples. Total of 22 and 4 up- and down-regulated proteins were identified using MS and data bank analysis. Cr-induced expression of ATP synthase, RuBisCO small subunit and coproporphyrinogen III oxidase; Cd-induced RuBisCO large subunit; Pb up-regulated carbohydrate metabolic pathway enzymes of fructokinase, and improved RuBisCO activase and large subunit, Mg-protoporphyrin IX chelatase. Contrarily, elF4F was inhibited by Cr/Pb, chloroplast FtsZ-like protein and GF14 omega impeded by Cd and Pb, respectively.