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Shoot-tip abortion is a very common phenomenon in some perennial woody plants and it affects the height, architecture, and branch orientation of trees; however, little is currently known about the underlying mechanisms. In this study, we identified a gene in sweet orange (Citrus sinensis) encoding a KNAT-like protein (CsKN1) and found high expression in the shoot apical meristem (SAM). Overexpression of CsKN1 in transgenic plants prolonged the vegetative growth of SAMs, whilst silencing resulted in either the loss or inhibition of SAMs. Yeast two-hybrid analysis revealed that CsKN1 interacted with another citrus KNAT-like protein (CsKN2), and overexpression of CsKN2 in lemon and tobacco caused an extreme multiple-meristem phenotype. Overexpression of CsKN1 and CsKN2 in transgenic plants resulted in the differential expression of numerous genes related to hormone biosynthesis and signaling. Yeast one-hybrid analysis revealed that the CsKN1-CsKN2 complex can bind to the promoter of citrus floral meristem gene LEAFY (CsLFY) and inhibit its expression. These results indicated that CsKN1 might prolong the vegetative growth period of SAMs by delaying flowering. In addition, an ethylene-responsive factor (CsERF) was found to bind to the CsKN1 promoter and suppresses its transcription. Overexpression of CsERF in Arabidopsis increased the contents of ethylene and reactive oxygen species, which might induce the occurrence of shoot-tip abscission. On the basis of our results, we conclude that CsKN1 and CsKN2 might work cooperatively to regulate the shoot-tip abscission process in spring shoots of sweet orange.

Free-living diazotrophs play a critical role in nitrogen (N) supply to ecosystems. Land-use change and plant rhizosphere are two important factors influencing diazotroph populations, but their relative strength in determining the soil diazotrophic community is still unclear, especially in acidic soils. One natural vegetation (the dominant species is green foxtail) and three agricultural land-uses (maize, peanut and soybean, respectively) widely distributed in the acidic soil region of southern China were selected. Bulk and rhizosphere soils were collected from every land-use, and their properties were determined. Quantitative PCR and high-throughput sequencing were applied to investigate soil diazotrophic abundance, diversity and community composition. Land use conversion from natural vegetation to different agricultural land-uses significantly reduced diazotroph abundances in bulk soils, however, the rhizosphere had a positive effect on the abundances in agricultural land-uses. Statistical analysis showed that the rhizosphere exerted a stronger effect on diazotroph abundance than land-use change. Converting natural vegetation to agricultural land-uses also decreased diazotroph richness and land-use types differed significantly in community composition, but plant rhizosphere did not cause these effects. In particular, the community variations in leguminous plants were more distinct than maize. Land-use change also influenced some topological properties of the community network. In acidic soil, land-use change has noticeable effects on the richness and composition of diazotrophic community than the rhizosphere. The rhizosphere, however, has a more obvious effect in increasing the abundance of the diazotrophs. These results highlight the critical role of land-use change in manipulating soil diazotrophic community composition.

Due to rapid urbanization and industrialization, many soils for crop production are contaminated by cadmium (Cd), a heavy metal highly toxic to many organisms. Cereal crops such as rice, wheat, maize, and barley are the primary dietary source of Cd for humans, and reducing Cd transfer from soil to their grains is therefore an important issue for food safety. During the last decade, great progress has been made in elucidating the molecular mechanisms of Cd transport, particularly in rice. Inter- and intraspecific variations in Cd accumulation have been observed in cereal crops. Transporters for Cd have been identified in rice and other cereal crops using genotypic differences in Cd accumulation and mutant approaches. These transporters belong to different transporter families and are involved in the uptake, vacuolar sequestration, root-to-shoot translocation, and distribution of Cd. Attempts have been made to reduce Cd accumulation in grains by manipulating these transporters through overexpression or knockout of the transporter genes, as well as through marker-assisted selection breeding based on genotypic differences in Cd accumulation in the grains. In this review, we describe recent progress on molecular mechanisms of Cd accumulation in cereal crops and compare different molecular strategies for minimizing Cd accumulation in grains.

Although phosphorus (P) availability and plant cultivation affect diazotrophic populations, studies often consider individual factors rather than their combined effects. Their relative importance to diazotrophs remains poorly understood, especially in acidic soils with P deficiency. It is hypothesized that the influences of P fertilization and plant cultivation on diazotrophic communities differ in acidic soils. The objectives were to investigate these influences and identify the key determining factors. Maize was grown in an acidic soil that was supplemented with 0, 20, and 50 mg P kg− 1 for 42 days. Maize biomasses, plant nutrient contents, and soil physicochemical properties were determined. Based on the nifH gene, the abundances and community compositions of diazotrophs in the different plant/soil compartments (bulk soils, rhizosphere soils, and roots) were respectively investigated using quantitative PCR and high-throughput sequencing. P fertilization significantly improved the diazotrophic abundances in the bulk and rhizosphere soils, but not in the roots. The plant/soil compartments had stronger effects on the abundance and diversity of diazotrophs than did P fertilization. Furthermore, the plant/soil compartments influenced diazotrophic community composition, but P fertilization did not. However, in the same sampling site, P fertilization caused community variations in the bulk and rhizosphere soils, rather than in the roots. Although P fertilization affected the abundances and compositions of diazotrophic communities in the bulk and rhizosphere soils, the plant/soil compartments resulting from maize cultivation had more noticeable effects than did P fertilization. These findings improved the understanding of biological nitrogen fixation in acidic soils.

About 60–85% of total phosphorus (P) in cereal crops is finally allocated to seeds, where it is required for seed development, germination and early growth. However, little is known about the molecular mechanisms underlying P allocation to seeds. Here, we found that two members (OsPHO1;1 and OsPHO1;2) of the PHO1 gene family are involved in the distribution of P to seeds in rice. Both OsPHO1;1 and OsPHO1;2 were localized to the plasma membrane and showed influx transport activities for inorganic phosphate. At the reproductive stage, both OsPHO1;1 and OsPHO1;2 showed higher expression in node I, the uppermost node connecting to the panicle. OsPHO1;1 was mainly localized at the phloem region of diffuse vascular bundles (DVBs) of node I, while OsPHO1;2 was expressed in the xylem parenchyma cells of the enlarged vascular bundles (EVBs). In addition, they were also expressed in the ovular vascular trace, the outer layer of the inner integument (OsPHO1;1) and in the nucellar epidermis (OsPHO1;2) of caryopses. Knockout of OsPHO1;2, as well as OsPHO1;1 to a lesser extent, decreased the distribution of P to the seed, resulting in decreased seed size and delayed germination. Taken together, OsPHO1;2 expressed in node I is responsible for the unloading of P from the xylem of EVBs, while OsPHO1;1 is involved in reloading P into the phloem of DVBs for subsequent allocation of P to seeds. Furthermore, OsPHO1;1 and OsPHO1;2 expression in the caryopsis is important for delivering P from the maternal tissues to the filial tissues for seed development.

The accumulation of NH4+ in response to Fe deficiency plays a role not only in the remobilization of Fe from the root cell wall, but also in the transportation of Fe from root to shoot. Ammonium (NH4+) plays an important role in phosphorus-deficiency responses in rice, but its role in responses to Fe deficiency remains unknown. Here, we demonstrate that the accumulation of NH4+ plays a pivotal role when Arabidopsis thaliana plants are subject to Fe deficiency. The Arabidopsis amt1-3 mutant, which is defective in endogenous NH4+ sensing, exhibited increased sensitivity to Fe deficiency compared to WT (wild type; Col-0). In addition, exogenous application of NH4+ significantly alleviated Fe deficiency symptoms in plants. NH4+ triggers the production of nitric oxide (NO), which then induces ferric-chelate reductase (FCR) activity and accelerates the release of Fe from the cell wall, especially hemicellulose, thereby increasing the availability of soluble Fe in roots. NH4+ also increases soluble Fe levels in shoots by upregulating genes involved in Fe translocation, such as FRD3 (FERRIC REDUCTASE DEFECTIVE3) and NAS1 (NICOTIANAMINE SYNTHASE1), hence, alleviating leaf chlorosis. Overall, NH4+ plays an important role in the reutilization of Fe from the cell wall and the redistribution of Fe from root to shoot in Fe-deficient Arabidopsis, a process dependent on NO accumulation.

Matching a crop’s nitrogen (N) preference with the specific form of N is critical to enhance N recovery efficiency (NRE). Many studies show that maize (Zea mays L.) has a preference for NH4+ uptake over NO3−, but the contribution of this preference to NRE is unclear. This study evaluated the utilization of ammonium (NH4+) and nitrate (NO3−) by maize and its relationship with NRE. Maize (cv. ‘Zhengdan 958’) seedlings were grown in a soil culture experiment with 15NH4+ or 15NO3− applied to sterilized or non-sterilized soils, and in a hydroponic experiment supplied with NH4+ or NO3−. We recorded maize root and shoot growth and N uptake, and the distribution of 15N-labeled N in the soil–plant system. Ammonium application enhanced maize root and shoot growth and N uptake compared with those of NO3−-treated plants in both culture systems. This enhancement by NH4+ was further promoted in sterilized soil. More applied N remained in soil supplied with NO3− than with NH4+ after seedling harvest. The NRE of NH4+ in maize was significantly higher than that of NO3−, while a similar proportion of applied N was lost with NH4+ or NO3−supply. Ammonium supply enhances maize growth and NRE compared with NO3− under the present experimental condition, which may be attributable to the superior capability of maize to utilize NH4+.

Aims The bacteria phoC and phoD genes encode acid and alkaline phosphatase (ACP and ALP), respectively, which mineralize organic phosphorus (P) to inorganic P. The relative importance of P fertilization and the plant rhizosphere on soil phosphatase activities and associated bacterial communities in acidic soils are poorly understood; whether phoC- and phoD-harboring bacterial communities display different responses remains undetermined. Methods Maize was grown in acidic soil supplemented with 0 (P0), 20 (P20), and 200 (P200) mg P2O5 kg− 1 for 42 days. Maize biomasses, plant nutrients, soil properties, phosphatase activities, and associated bacterial abundance and community composition were determined. Results Relative to bulk soils, rhizosphere showed increased ACP and ALP activities, phoC and phoD gene abundance, but these effects were reduced in strength with P200 treatment, except for phoC gene abundance. The rhizosphere effect increased α-diversity of phoC-harboring bacteria under P fertilization but reduced α-diversity of phoD-harboring bacteria under P0 and P20 treatments. The rhizosphere significantly influenced both phoC- and phoD-harboring bacterial community compositions, with stronger effect on phoD-harboring bacteria; while P fertilization affected phoD-harboring bacteria but not phoC-harboring bacteria. Immigrated and extinct species play important roles in reshaping phoC- and phoD-harboring bacterial communities, respectively, in response to the rhizosphere effect. Conclusions Compared with P fertilization, the maize rhizosphere more strongly influenced soil phosphatase activities and phoC- and phoD-harboring bacterial communities in acidic soils, with phoD-harboring bacteria responding more strongly to the rhizosphere effect and P fertilization. Notably, the strength of the rhizosphere effect heavily relied on P fertilization level.

Background Phosphate (Pi) deficiency severely affects crop growth and productivity, including wheat, therefore it is necessary to develop cultivars with enhanced Pi-deficiency tolerance. However, the underlying mechanism of Pi-deficiency tolerance in wheat is still elusive. Two contrasting wheat cultivars, low-Pi tolerant Kenong199 (KN199) and low-Pi sensitive Chinese Spring (CS) were used to reveal adaptations in response to Pi deficiency at the morphological, physiological, metabolic, and molecular levels. Results KN199 was more tolerant to Pi deficiency than CS with significantly increased root biomass and R/S ratio. Root traits, the total root length, total root surface area, and total root volume, were remarkably enhanced by Pi deficiency in KN199. The shoot total P and soluble Pi concentrations of KN199 were significantly higher than those of CS, but not in roots. In KN199, high Pi level in shoots is a higher priority than that in roots under Pi deficiency. It was probably due to differentially regulation in the miR399-mediated signaling network between the shoots of the two cultivars. The Pi deficiency-induced root architecture adaptation in KN199 was attributed to the regulation of the hormone-mediated signaling (ethylene, gibberellin, and jasmonates). The expression of genes associated with root development and Pi uptake was enhanced in KN199. Some primary metabolites (amino acids and organic acids) were significantly accumulated in roots of KN199 under Pi deficiency. Conclusions The low-Pi tolerant wheat cultivar KN199 possessed greater morphological and primary metabolic adaptations in roots than CS under Pi deficiency. The adaption and the underlying molecular mechanisms in wheat provide a better understanding of the Pi-deficiency tolerance and the strategies for improving Pi efficiency in wheat.

Phosphate starvation (-Pi)-induced root hair is crucial for enhancing plants' Pi absorption. Proline-rich extensin-like receptor kinase 13 (PERK13) is transcriptionally induced by -Pi and co-expressed with genes associated with root hair growth. However, how PERK13 participates in -Pi-induced root hair growth remains unclear. Here, we found that PERK13 was transcriptionally responsive to Pi, nitrogen, and iron deficiencies. Loss of PERK13 function (perk13) enhanced root hair growth under Pi/nitrogen limitation. Similar phenotype was also observed in transgenic lines overexpressing PERK13 (PERK13ox). Under -Pi, both perk13 and PERK13ox showed prolonged root hair elongation and increased reactive oxygen species (ROS). Deletion analysis showed, in PERK13ox, the extracellular domain was indispensable for PERK13 in -Pi-induced root hair growth. Different transcription profiles were observed under -Pi between perk13 and PERK13ox with the jasmonate zim-domain genes being repressed in perk13 and genes involved in cell wall remodeling being increased in PERK13ox. Taken together, we demonstrated that PERK13 participates in -Pi-induced root hair growth probably via regulating root hair elongation and the generation of ROS. Our study also suggested PERK13 probably being a vital hub coupling the environmental cues and root hair growth, and might play dual roles in -Pi-induced root hair growth via different processes.

The influence of long-term fertilization on soil microbial communities is critical for revealing the association between belowground microbial flora and aboveground crop productivity—a relationship of great importance to food security, environmental protection, and ecosystem functions. Here, we examined shifts in soil chemical properties, microbial communities, and the nutrient uptake and yield of rice subjected to different chemical and organic fertilization treatments over a 40-year period in red paddy soil. Ten different treatments were used: a control without fertilizer, and applications of nitrogen (N), phosphorus (P), potassium (K), NP, NK, PK, NPK, double NPK, or NPK plus manure. Compared with the effects of withholding one or two nutrients (N, P, or K), the balanced application of chemical NPK and organic fertilizers markedly improved soil nutrient status and rice yield. This improvement of soil fertility and rice yield was not associated with bacterial, archaeal, or fungal alpha diversities. The bacterial abundance and community structure and archaeal abundance effectively explained the variation in rice yield, whereas those of fungi did not. The community structure of bacteria and archaea, but not that of fungi, was correlated with soil properties. Among various soil properties, P was the key factor influencing rice yield and soil microbial communities because of the extremely low content of soil available P. Seven keystones at the operational taxonomic unit level were identified: four archaea (belonging to Thermoplasmata, Methanosaeta, Bathyarchaeia, and Nitrososphaeraceae) and three bacteria (in Desulfobacteraceae and Acidobacteriales). These keystones, which were mainly related to soil C and N transformation and pH, may work cooperatively to influence rice yield by regulating soil fertility. Our results collectively suggest that four decades of balanced fertilization has sustained the bacterial and archaeal abundances, bacterial community structure, and keystones, which potentially contribute to soil fertility and rice yield in red paddy soil.

Rice is the most aluminum (Al)-tolerant species among the small grain cereals, but there are great variations in the Al tolerance between subspecies, with higher tolerance in japonica subspecies than indica subspecies. Here, we performed a screening of Al tolerance using 65 indica cultivars and found that there was also a large genotypic difference in Al tolerance among indica subspecies. Further characterization of two cultivars contrasting in Al tolerance showed that the expression level of ART1 (ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1) encoding a C2H2-type Zn-finger transcription factor, was higher in an Al-tolerant indica cultivar, Jinguoyin, than in an Al-sensitive indica cultivar, Kasalath. Furthermore, a dose-response experiment showed that ART1 expression was not induced by Al in both cultivars, but Jinguoyin always showed 5.9 to 11.4-fold higher expression compared with Kasalath, irrespectively of Al concentrations. Among genes regulated by ART1, 19 genes showed higher expression in Jinguoyin than in Kasalath. This is associated with less Al accumulation in the root tip cell wall in Jinguoyin. Sequence comparison of the 2-kb promoter region of ART1 revealed the extensive sequence polymorphism between two cultivars. Whole transcriptome analysis with RNA-seq revealed that more genes were up- and downregulated by Al in Kasalath than in Jinguoyin. Taken together, our results suggest that there is a large genotypic variation in Al tolerance in indica rice and that the different expression level of ART1 is responsible for the genotypic difference in the Al tolerance.

This study aimed to explore the interactions between cadmium (Cd) and copper (Cu) during uptake and translocation in plants growing in soil polluted with heavy metals derived from electronic waste (E-waste). We collected the roots, stems, leaves, and root-surrounding soils of ten dominant plant species growing in farmland near an E-waste dismantling site, and analyzed their Cd and Cu concentrations. Among the ten plant species, Echinochloa crus-galli (L.) P. Beauv., Cucurbita moschata (Duch. ex Lam.) Duch. ex Poiret, Phragmites australis (Cav.) Trin. ex Steud., and Benincasa hispida (Thunb.) Cogn. accumulated Cd (2.40–4.56 mg kg−1) and Cu (19.60–35.21 mg kg−1) in the roots. In Polygonum hydropiper L. and Sesbania cannabina (Retz.) Poir., the Cd (0.50–0.81 mg kg−1) and Cu (11.04–15.55 mg kg−1) concentrations were similar among the three organs. Glycine max (L.) Merr. accumulated more Cu in the roots (16.42 mg kg−1) than in the stems (5.61 mg kg−1) and leaves (7.75 mg kg−1), and accumulated Cd at similar levels in the three organs (0.65–0.99 mg kg−1). Sesamum indicum L., Bidens pilosa L., and Solidago decurrens Lour. accumulated Cd at similar levels among the three organs (0.16–3.34 mg kg−1) and accumulated less Cu in the stems (6.89–8.28 mg kg−1) than in the roots (12.61–21.63 mg kg−1) and leaves (12.93–22.38 mg kg−1). S. indicum had a stronger capacity to accumulate and translocate Cd and Cu according to transfer coefficient and translocation factor. The concentrations of Cd and Cu in soils were significantly positively correlated with those in the roots (p

Beyond the role of a nutrient reservoir during germination, the endosperm of wheat seeds also responds to different abiotic stresses via modification of the protein profiles. The endosperm is the main component of wheat seeds. During seed germination, it provides nutrients to support the embryo development, and its constituents vary under environmental stresses such as drought, salinity and submergence that are associated with disordered water supply. However, the molecular mechanism of these stress responses remains unclear. In this study, a comparative label-free proteomic analysis was performed on endosperm from the germinating wheat seeds subjected to PEG, NaCl and submergence treatments. In total, 2273 high confidence proteins were detected, and 234, 207 and 209 of them were identified as differentially expressed proteins (DEPs) under the three stresses, respectively. Functional classification revealed that the DEPs were mainly involved in protein, amino acid and organic acid metabolic process in all stress treatments. While some other metabolic processes were highlighted in one or two of the stresses specifically, such as oxidative phosphorylation in PEG and submergence, and β-alanine metabolism in PEG and NaCl treatments. The identification of a series of stress-related proteins and their biased expression in different stresses indicates the active stress-responding role of endosperm beyond a simple nutrient reservoir during germination, while the overall stress responses of the endosperm were found to be moderate and lag behind the embryo. Besides, some fundamental processes and DEPs shared by the three stresses could be selected priorly for future molecular breeding researches. Our results provide new insights into the mechanism of endosperm responses to abiotic stresses during seed germination.

Iron (Fe) deficient plants employ multiple strategies to increase root uptake and root-to-shoot translocation of Fe. The identification of genes that are responsible for these processes, and a comprehensive understanding of the regulatory effects of transcriptional networks on their expression, including transcription factors (TFs), is underway in Arabidopsis thaliana. Here, we show that a Histone- or heme-associated proteins (HAP) transcription factor (TF), HAP5A, is necessary for the response to Fe deficiency in Arabidopsis. Its expression was induced under Fe deficiency, and the lack of HAP5A significantly decreased Fe translocation from the root to the shoot, resulting in substantial chlorosis of the newly expanded leaves, compared with the wild-type (WT, Col-0). Further analysis found that the expression of a gene encoding nicotianamine (NA) synthase (NAS1) was dramatically decreased in the hap5a mutant, regardless of the Fe status. Yeast-one-hybrid and ChIP analyses suggested that HAP5A directly binds to the promoter region of NAS1. Moreover, overexpression of NAS1 could rescue the chlorosis phenotype of hap5a in Fe deficient conditions. In summary, a novel pathway was elucidated, showing that NAS1-dependent translocation of Fe from the root to the shoot is controlled by HAP5A in Fe-deficient Arabidopsis thaliana.

Nitrogen deficiency usually occurs along with aluminum toxicity in acidic soil, which is one of the major constraints for wheat production worldwide. In order to compare adaptive processes to N deficiency with different Al-tolerant wheat cultivars, we chose Atlas 66 and Scout 66 to comprehensively analyze the physiological responses to N deficiency, coupled with label-free mass spectrometry-based proteomics analysis. Results showed that both cultivars were comparable in most physiological indexes under N deficient conditions. However, the chlorophyll content in Scout 66 was higher than that of Atlas 66 under N deficiency. Further proteomic analysis identified 5592 and 5496 proteins in the leaves of Atlas 66 and Scout 66, respectively, of which 658 and 734 proteins were shown to significantly change in abundance upon N deficiency, respectively. The majority of the differentially expressed proteins were involved in cellular N compound metabolic process, photosynthesis, etc. Moreover, tetrapyrrole synthesis and sulfate assimilation were particularly enriched in Scout 66. Our findings provide evidence towards a better understanding of genotype-dependent responses under N deficiency which could help us to develop N efficient cultivars to various soil types.

The glutathione synthetase system (GSS) is an important pathway of glutathione synthesis and plays a key role in heavy metal resistance. In this work, the response of Acidithiobacillus ferrooxidans to extracellular Cd2+ was investigated, and the interplay between Cd2+ resistance and the expression of GSS related-genes was analyzed by reverse-transcription quantitative PCR (RT-PCR). During growth in the presence of 5, 15 and 30 mM Cd2+, the transcript levels of eight GSS pathway genes were affected between 0.81- and 7.12-fold. Increased transcription was also reflected in increased enzyme activities: with those of glutathione reductase (GR) increased by 1.10-, 2.26- and 1.54-fold in the presence of 5, 15 and 30 mM Cd2+, respectively. In contrast, the activities of catalase (CAT) and superoxide dismutase (SOD) were decreased in the presence of Cd2+. At the metabolite level, intracellular methane dicarboxylic aldehyde (MDA) content was increased 1.97-, 3.31- and 1.92-fold in the presence of 5, 15 and 30 mM Cd2+, respectively. These results suggest that Cd2+ directly inhibits the activities of CAT and SOD, breaks the redox balance of the cells, which leads to the activation of the other antioxidant pathway of GSS. Resistance of A. ferrooxidans to Cd2+ may involve modulation of expression levels of glutathione S-transferase (GST), GR, and glutathione synthetase, which may protect against oxidative damage.

Cd accumulation in rice grain was effectively reduced by expressing OsHMA3, which encodes a transporter responsible for vacuolar Cd sequestration, under the control of the OsHMA2 promoter., Reducing cadmium (Cd) accumulation in rice grain is an important issue for human health. The aim of this study was to manipulate both expression and tissue localization of OsHMA3, a tonoplast-localized Cd transporter, in the roots by expressing it under the control of the OsHMA2 promoter, which shows high expression in different organs including roots, nodes, and shoots. In two independent transgenic lines, the expression of OsHMA3 was significantly enhanced in all organs compared with non-transgenic rice. Furthermore, OsHMA3 protein was detected in the root pericycle cells and phloem region of both the diffuse vascular bundle and the enlarged vascular bundle of the nodes. At the vegetative stage, the Cd concentration in the shoots and xylem sap of the transgenic rice was significantly decreased, but that of the whole roots and root cell sap was increased. At the reproductive stage, the concentration of Cd, but not other essential metals, in the brown rice of transgenic lines was decreased to less than one-tenth that of the non-transgenic rice. These results indicate that expression of OsHMA3 under the control of the OsHMA2 promoter can effectively reduce Cd accumulation in rice grain through sequestering more Cd into the vacuoles of various tissues.

Increasing cadmium (Cd) pollution severely affects plant growth and development, posing risks to human health via food chains. The Cd toxicity could be mitigated by improving Fe nutrient in plants. IMA1 and IMA3, two novel small peptides functionally epistatic to the key transcription factor bHLH39 but independent of bHLH104, were recently identified as the newest additions to the Fe regulatory cascade, but their roles in Cd uptake and toxicity remain not addressed. Here, the functions of two IMAs and two transcription factors related to Cd tolerance were verified. Overexpression of either bHLH39 or bHLH104 in Arabidopsis showed weak roles in Cd tolerance, but overexpression of IMAs, which activates the Fe-deficient response, significantly enhanced Cd tolerance, showing greater root elongation, biomass and chlorophyll contents. The Cd contents did not show significant difference among the overexpression lines. Further investigations revealed that the tolerance of transgenic plants to Cd mainly depended on higher Fe accumulation, which decreased the MDA contents and enhanced root elongation under Cd exposure, finally contributing to attenuating Cd toxicity. Taken together, the results suggest that increasing Fe accumulation is promising for improving plant tolerance to Cd toxicity and that IMAs are potential candidates for solving Cd toxicity problem.

Although diazotrophs are important in the nitrogen (N)-cycle and contribute to the pool of plant available N, the population response to long-term inorganic fertilization is largely unknown. Here, we investigated the diazotrophic populations in both the bulk and rhizosphere soils of maize grown in an acidic farmland soil that experienced 25 years of inorganic fertilization. The fertilization regimes included unfertilized control, N fertilizer alone, N fertilizer with quicklime, phosphorus (P) and potassium (K) fertilizers, N + P + K fertilizers, and N + P + K fertilizers with quicklime. Quantitative PCR and high-throughput pyrosequencing of the nifH gene were used to analyze diazotrophic abundance and community composition. All of the fertilizer treatments improved soil nutrient availability, but those without quicklime caused soil acidification. Maize biomasses and nifH copy numbers were significantly lower under N and N + P + K treatments but increased under P + K fertilization. Quicklime applications effectively alleviated the inhibitory effect of N input. Fertilization led to decreases in operational taxonomic unit richness and shifts in diazotrophic community composition. Soil pH and nutrient availability had a cooperative effect on diazotrophic abundance, while soil nutrient availability appeared to be the main factor shaping diazotrophic community structure. Rhizosphere effects increased the nifH gene copy number but did not obviously change the diazotrophic community composition on the current research scale. Overall, the long-term inorganic fertilization affected both diazotrophic abundance and community composition, and the fertilizer treatment had a greater influence than quicklime remediation or crop cultivation on community composition.

Glucuronoxylan (GX), an important component of hemicellulose in the cell wall, appears to affect aluminium (Al) sensitivity in plants. To investigate the role of GX in cell-wall-localized xylan, we examined the Arabidopsis thaliana parvus mutant in detail. This mutant lacks α-D-glucuronic acid (GlcA) side chains in GX and has greater resistance to Al stress than wild-type (WT) plants. The parvus mutant accumulated lower levels of Al in its roots and cell walls than WT despite having cell wall pectin content and pectin methylesterase (PME) activity similar to those of WT. Our results suggest that the altered properties of hemicellulose in the mutant contribute to its decreased Al accumulation. Although we observed almost no differences in hemicellulose content between parvus and WT under control conditions, less Al was retained in parvus hemicellulose than in WT. This observation is consistent with the finding that GlcA substitutions in WT GX, but not mutant GX, were increased under Al stress. Taken together, these results suggest that the modulation of GlcA levels in GX affects Al resistance by influencing the Al binding capacity of the root cell wall in Arabidopsis.

The present study was undertaken to investigate the mechanism underlying NaCl-alleviated Fe (iron) deficiency in Arabidopsis thaliana Col-0 (Columbia ecotype). Six-week-old Col-0 with rosettes of similar diameters was grown in full-strength nutrient solution lacking Fe (Fe-deficient) or full-strength nutrient solution (Fe-sufficient) with or without 10 mM NaCl for 7 days. Roots were then harvested for analysis of total Fe content, soluble Fe concentration, and abscisic acid (ABA) content as well as for cell wall and RNA extraction, while shoots were harvested for total Fe content and soluble Fe concentration measurements. The total Fe content and the soluble Fe concentration were higher in roots and shoots of −Fe + NaCl-treated plants than −Fe-treated plants, whereas Fe retention in the cell wall was reduced, suggesting the presence of a cell wall Fe-reutilization mechanism. This conclusion was confirmed by the observation that less hemicelluloses Fe was found in plants under −Fe + NaCl treatment. In addition, associated to the upregulation of genes related to the long-distance transport of Fe, such as FRD3 (FERRIC REDUCTASE DEFECTIVE3), YSL2 (YELLOW STRIPE-LIKE), and NAS1 (NICOTIANAMINE SYNTHASE1) under −Fe + NaCl treatment, more Fe was available in shoots. Furthermore, endogenous ABA is involved in NaCl-alleviated Fe deficiency, as the addition of Flu (fluridone), an inhibitor of ABA biosynthesis, abolished the positive effect of NaCl on Fe deficiency. Under −Fe condition, NaCl not only is involved in the reutilization of cell wall Fe but also participates in the translocation of Fe from root to shoot in Arabidopsis, partially through its effect on ABA contents.

Phosphorus (P) deficiency is an important factor that limits the agricultural production potential in acidic soils. The bacterial phoC gene encodes non-specific acid phosphatase (ACP), which participates in the mineralization of soil organic P and is therefore important for the improvement of soil P availability. However, the function and community population of phoC-harboring bacteria and their driving factors in acidic soil remain largely unknown. For this study, 51 soil samples and 207 plant samples were collected from four locations in the acidic soil region of southern China. Quantitative PCR and high-throughput sequencing were employed to analyze abundance and community composition of phoC-harboring bacteria. The results showed that soil P availability was the important nutrient element limiting the growth of both plants and soil bacteria. Soil ACP activity was clearly higher than alkaline phosphatase, indicating the important effect of phoC-harboring bacteria in acidic soils. ACP activity and phoC gene abundance showed a significant positive correlation, and both were closely related to soil available P, total carbon, and total nitrogen. The dominant genera of phoC-harboring bacteria involved Cupriavidus, Stenotrophomonas, and Xanthomonas. Compared to land-use pattern, sampling location, and soil parent material, soil property played a more important role in affecting phoC-harboring bacterial community structure, where N-related variables including soil NO 3 - -N, NH 4 + -N, and C/N ratio appeared to be the main factors. These findings suggest that phoC-harboring bacteria should provide an important contribution to soil P availability in acidic soil, and its function and community composition were strongly associated with soil nutrients.

The polysaccharides extracted from the achenes of jelly fig, Ficus awkeotsang Makino, were mainly composed of low methyl pectin and used as a novel shell material for encapsulating lipophilic bioactives in the core of microcapsule. The polysaccharide microcapsules with oil core were prepared using a novel acrylic-based millifluidic device developed in this study. To investigate the physiochemical properties of and find the suitable formula of polysaccharide shells, the films casted with jelly fig polysaccharide were thoroughly characterized. For the preparation of microcapsules, the millifluidic device was optimized by controlling the flow rate to obtain uniform spherical shape with a core diameter of 1.4−1.9 mm and the outer diameter of 2.1–2.8 mm. The encapsulation efficiency was around 90%, and the microcapsules displayed a clear boundary between the polysaccharide shell and oil core. Encapsulation of curcumin in the microcapsules was prepared to test the applicability of the device and processes developed in this study, and the results showed that the microencapsulation could enhance the stability of curcumin against external environment. Overall, the results suggested that the jelly fig polysaccharides and the developed millifluidic device can be useful for the preparation of core-shell microcapsules for encapsulation of lipophilic bioactives.

The present study was carried out to investigate how plant growth-promoting bacteria (PGPB) influence plant growth and uptake of boron (B) and phosphorus (P) in rapeseed (Brassica napus). Rapeseed was subjected to control, B, P and B + P treatments, either with or without B. pumilus (PGPB) inoculation, and grown in pot culture for 6 weeks. In the absence of B. pumilus, the addition of B, P or both elements improved the growth of rapeseed compared with the control. Interestingly, B. pumilus inoculation inhibited plant growth and enhanced B uptake under B and B + P but not under control and P conditions. In addition, B. pumilus inoculation decreased the pH of soil under B and B + P supplies. Bacillus pumilus inoculation thus increased rapeseed B uptake and inhibited growth under B supply, which suggests that the effects of PGPB on rapeseed growth depend on the addition of B to soil. Bacillus pumilus inoculation may therefore be recommended for the enhancement of rapeseed B levels in B-deficient soils but not in B-sufficient ones., The present study indicates that Bacillus pumilus (plant growth-promoting bacteria, PGPB) enhances B uptake by rapeseed, which is consistent with previous reports. However, interestingly, increased B accumulation in rapeseed inhibited the growth of rapeseed under B-sufficient soil conditions. These inhibitory effects of B. pumilus on rapeseed growth were related to soil acidification, which increased the B availability in the soil–plant system. This novel information on the role of PGPB in B nutrition and plant growth improves our understanding of how PGPB influence B uptake and has potential implications for instructing the application of PGPB in agriculture.

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

WUSCHEL-related homeobox (WOX) transcription factors (TFs) are well known for their role in plant development but are rarely studied in citrus. In this study, we identified 11 putative genes from the sweet orange genome and divided the citrus WOX genes into three clades (modern/WUSCHEL(WUS), intermediate, and ancient). Subsequently, we performed syntenic relationship, intron-exon organization, motif composition, and cis-element analysis. Co-expression analysis based on RNA-seq and tissue-specific expression patterns revealed that CsWOX gene expression has multiple intrinsic functions. CsWUS homolog of AtWUS functions as a transcriptional activator and binds to specific DNA. Overexpression of CsWUS in tobacco revealed dramatic phenotypic changes, including malformed leaves and reduced gynoecia with no seed development. Silencing of CsWUS in lemon using the virus-induced gene silencing (VIGS) system implied the involvement of CsWUS in cells of the plant stem. In addition, CsWUS was found to interact with CsCYCD3, an ortholog in Arabidopsis (AtCYCD3,1). Yeast one-hybrid screening and dual luciferase activity revealed that two TFs (CsRAP2.12 and CsHB22) bind to the promoter of CsWUS and regulate its expression. Altogether, these results extend our knowledge of the WOX gene family along with CsWUS function and provide valuable findings for future study on development regulation and comprehensive data of WOX members in citrus.

Acid and alkaline phosphatase (ACP and ALP), encoded separately by the bacterial phoC and phoD genes, participate in the mineralization of organic phosphorus (P) to inorganic P. However, the influence of chemical fertilization on soil phosphatase activities and associated bacterial communities in acidic soils remains unclear. Here, we conducted a 27 year continuous chemical fertilization experiment consisting of the no-fertilizer control (CK), N and P fertilizer (NP), N and K fertilizer (NK), P and K fertilizer (PK), and N, P and K fertilizer (NPK) treatments, in order to investigate phosphatase activities and phoC- and phoD-harboring bacterial communities. Results demonstrated that ACP and ALP activities increased significantly in the NP (198.70 and 35.46 μg pNP g−1 soil h−1, respectively) and NPK treatments (199.62 and 36.51 μg pNP g−1 soil h−1, respectively) compared to CK (143.81 and 22.49 μg pNP g−1 soil h−1, respectively), while ALP activity was reduced for the NK treatment (13.86 μg pNP g−1 soil h−1). The abundance and diversity index of phoC- and phoD-harboring bacteria differed among treatments. The two bacterial community structures exhibited similar trends in terms of the significant differences between N-free (CK and PK) and N-containing (NP, NK and NPK) treatments (Adonis, p

Phosphorus (P) deficiency is a major problem in agriculture, thus identifying mechanisms affecting plant’s ability to reutilize previously assimilated P is a prerequisite for improving the P homeostasis in crops grown with P deficient soil. Here, we reported the involvement of a NAC (No apical meristem [NAM], Arabidopsis transcription activation factor [ATAF] and Cup-shaped cotyledon [CUC]) transcription factor in response to P deficiency. Compared to the wild type (WT, Col-0) and two independent complementary lines, the anac044 mutant displayed P deficiency resistant phenotype, together with the increased root length, root and shoot biomass under P deficiency. In addition, ANAC044 was highly expressed in root and silique. Upon P deficient treatment even within 1 d, ANAC044 transcript accumulation was strongly up-regulated. Further analysis revealed that, under P-deficient condition, the cell wall, particularly the pectin of anac044, released more P than that of WT and complementary lines, accompanied by an increment of ethylene production, as a result, more soluble and total P were available in anac044 root and shoot. Thus, the study here uncovers the role of ANAC044-regulated cell wall P remobilization through ethylene signaling under P deficiency.

Summary Expansins are cell wall loosening proteins, which are encoded by multigene families. However, the physiological role of most expansin genes is still poorly understood. Here, we functionally characterized an Al-inducible expansin gene, OsEXPA10, which is regulated by a C2H2-type zinc-finger transcription factor, ART1 in rice. A detailed expression analysis showed that OsEXPA10 was expressed in both the roots and shoots at a similar level, but only the expression in the roots was rapidly upregulated in response to Al. Furthermore, spatial expression analysis showed that the Al-induced expression was only found in the root tips (0–3 mm), but not in the mature root zones. The expression was neither induced by other metals including Cd and La nor by low pH. Immunostaining showed that OsEXPA10 was localized at all cells of the root tips. Knockout of OsEXPA10 resulted in a significant decrease in the cell elongation of the roots in the absence of Al. In the presence of Al, knockout of OsEXPA10 did not alter the Al sensitivity evaluated by relative root elongation, but the root cell wall of knockout lines accumulated less Al compared to those of the wild-type rice. Collectively, our results indicate that OsEXPA10 expressed in the root tips is required for the root cell elongation, but that the contribution of this gene to high Al tolerance in rice is small.

Rhodotorula taiwanensis RS1 (Rt) is a high-aluminum (Al)-tolerant yeast that can survive Al at concentrations up to 200 mM. In this study, we compared Rt with an Al-sensitive congeneric strain, R. mucilaginosa AKU 4812 (Rm) and Al sensitive mutant 1 (alsm1) of Rt, to explore the Al tolerance mechanisms of Rt. The growth of Rm was completely inhibited by 1 mM Al, but that of Rt was not inhibited until Al concentration was more than 70 mM. The growth of alsm1 was inhibited much more by 70 mM and 100 mM Al than that of Rt. Compared with Rm cells, Rt cells accumulated less Al in the cell wall and cytoplasm. A time-course analysis showed that Al was absorbed by Rm cells much more rapidly than by Rt cells when exposed to the same Al concentration. Meanwhile, the Al content of alsm1 was higher than that of Rt. Although the cell wall of Rt was thicker than that of alsm1 and Rm under control and 0.1 mM Al, that of Rt was thinner than that of alsm1 under 70 mM Al despite that their cell walls were thickened. The alcian blue adsorption was lower and cell wall zeta-potential was higher in Rt and alsm1 than in Rm, indicating a less negative charge of cell wall of Rt and alsm1 than that of Rm. Taken together, the less negatively charged cell wall of Rt may restrict the adsorption of cationic Al in cells, potentially contributing to its high Al tolerance. Copyright © 2016 John Wiley & Sons, Ltd.

To reduce cadmium (Cd) intake, remediation of Cd-contaminated soil and breeding crops with low Cd accumulation are important. This study aims to isolate rice mutants with altered accumulation of Cd. We used rice seeds mutated by N-methyl-N-nitrosourea for screening. The mutant was physiologically, genetically, and molecularly characterized. Cd accumulation was compared among five rice varieties cultivated in a Cd-contaminated soil. From 1000 lines screened, we isolated a line (TCM213) with high Cd accumulation. There was no difference in the root Cd uptake, but a higher root-to-shoot translocation of Cd was found in TCM213 compared with a common rice cultivar, T-65. The expression and sequence of OsNramp5 and OsHMA2 did not differ between TCM213 and T-65. However, several SNPs and deletion were found in the sequence of OsHMA3, although its expression and tissue localization were similar to those of T-65. Genetic analysis of an F2 population derived from T-65 and TCM213 showed that the variation of OsHMA3 explained 72 % of variation in total Cd accumulation. TCM213 accumulated the largest Cd amount in the shoots among five Cd-accumulating varieties. High Cd accumulation in TCM213 results from loss of function of OsHMA3, and its high Cd accumulation has potential for efficient phytoremediation of Cd-contaminated soil.

Background and aims Plants are able to grow under phosphorus (P)-deficient conditions by coordinating Pi acquisition, translocation from roots to shoots and remobilization within the plant. Previous reports have demonstrated that cell-wall pectin contributes greatly to rice cell-wall Pi re-utilization under P-deficient conditions, but whether other factors such as ethylene also affect the pectin-remobilizing capacity remains unclear. Methods Two rice cultivars, 'Nipponbare' (Nip) and 'Kasalath' (Kas) were cultured in the +P (complete nutrient solution), -P (withdrawing P from the complete nutrient solution), +P+ACC (1-amino-cyclopropane-1-carboxylic acid, an ethylene precursor, adding 1 μm ACC to the complete nutrient solution) and -P+ACC (adding 1 μm ACC to -P nutrient solution) nutrient solutions for 7 d. Key Results After 7 d -P treatment, there was clearly more soluble P in Nip root and shoot, accompanied by additional production of ethylene in Nip root compared with Kas. Under P-deficient conditions, addition of ACC significantly increased the cell-wall pectin content and decreased cell-wall retained P, and thus more soluble P was released to the root and translocated to the shoot, which was mediated by the expression of the P deficiency-responsive gene OsPT2, which also strongly induced by ACC treatment under both P-sufficient and P-deficient conditions. Conclusions Ethylene positively regulates pectin content and expression of OsPT2, which ultimately makes more P available by facilitating the solubilization of P fixed in the cell wall and its translocation to the shoot.

Plant growth promoting rhizobacteria (PGPR) confer plant tolerance to abiotic stresses like salinity and high boron (B) due to limited uptake of toxic ions as well as increased production of antioxidants. The current study was aimed to investigate whether particular PGPR strain is responsible either for the decreased uptake of B together with salt toxic ions or to promote rice growth through an efficient antioxidative system under combined stresses of salinity and high B. Rice seedlings were maintained in pots according to completely randomized design (CRD) and stressed with high B (0.92 mmol L −1 or 10 ppm) and NaCl (150 mmol L −1 or ECw of 14.7 dS m −1 ) for 8 weeks. Half of the pots received Bacillus pumilus -inoculated rice seedlings, whereas the other half received un-inoculated ones. Subsequently, plants were harvested and analyzed for mineral composition and antioxidation activity either using atomic absorption spectrometer (AAS) or spectrophotometer. In the absence of PGPR, NaCl salinity significantly enhanced the leaf B and salt toxic ions concentrations, thereby resulting in the shoot growth reduction when compared with the control. Similarly, combined treatment increased the leaf and xylem sap B as compared to NaCl alone, however, remained insignificant for salt toxic ions. Contrary, NaCl + high B decreased the leaf B concentrations as compared to high B alone. Application of PGPR enhanced the plant growth under individual stresses due to enhanced activity of certain of antioxidative enzymes. In combined treatment, B. pumilus showed a positive potential for limiting the Na + accumulation in rice leaves, but not for leaf B. Moreover, limited uptake of Na + resulted in the decreased plant antioxidation activity irrespective of increasing leaf B concentrations which in turn enhanced the rice tolerance.

Plants and other multicellular organisms consist of many types of specialized cells. Systems-wide exploration of large-scale information from singe cell level is essential to understand how cell works. Root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, in the interaction with microbe, and in plant anchorage, and represent an ideal model to study the biology of a single cell type. Single cell sampling combined with omics approaches has been applied to study plant root hairs. This review emphasizes the integration of omics approaches towards understanding the systems biology of root hairs, unraveling the common and plant species-specific properties of root hairs, as well as the concordance of protein and transcript abundance. Understanding plant root hair biology by mining the integrated omics data will provide a way to know how a single cell differentiates, elongates, and functions, which might help molecularly modify crops for developing sustainable agriculture practices.

Low soil nutrient availability severely constrains plant growth and productivity in acidic soil ecosystems. Diazotrophs and arbuscular mycorrhizal fungi (AMF) are the important microbial groups that improve the bioavailability of soil nitrogen (N) and phosphorus (P), respectively. Therefore, the objective was to investigate the biogeographic patterns and co-occurrence networks of the diazotrophic and AMF communities in the acidic soil ecosystem. We collected 52 soil samples from four long-term field observation stations with spatial distances of 961.3 km in the acidic soil region of southern China, and analyzed the community composition and biogeographic distributions of the diazotrophs and AMF using high-throughput sequencing of the functional gene amplicons. The variation partition analysis indicated that soil physicochemical factors provided more contributions than geographic distance, sampling stations and land-use types in the assembly of the diazotrophic and AMF community communities. Distance-decay relationships and Mantel tests showed that soil physicochemical factors had remarkable effects on both microbial community structures, whereas geographic distance only significantly affected the diazotrophic community variations. Co-occurrence network analysis revealed that AMF network was more complex and stable than the diazotrophic network. Furthermore, the dominant genera Bradyrhizbium and Glomus might be the more important keystone taxa in the diazotrophic and AMF networks, respectively. These findings suggest that the diazotrophic and AMF communities exhibit different assembly mechanisms and co-occurrence ecological networks in the acidic soil region of southern China, and both community assemblies were mainly driven by soil physicochemical factors.

The nitrogen (N) cycle process in agricultural soil is affected by fertilization. However, there is limited information on the abundance of N-cycling microbial community and its response to the different fertilization strategies in acidic soil. Using quantitative PCR, we investigated the microbial abundance involving 11 functional genes of the N cycle (nifH, chiA, aprA, archaeal and bacterial amoA, napA, narG, nirS, nirK, norB and nosZ) in an acidic agricultural soil. The soils were subjected to no fertilizer (Control), chemical NPK fertilizer (NPK), NPK combined with quicklime (NPKCa), NPK combined with crop residues (NPKS), NPK combined with quicklime and crop residues (NPKSCa), NPK combined with manure (NPKM) and only manure (M) fertilization for 27 years. Results showed that fertilization improved crop yield and soil nutrient availability, changed soil pH levels and affected the abundance of N-cycling functional genes. Manure application markedly increased the abundance of all genes and was associated with the largest shift in community structure. The variation of microbial community in the fertilization treatments (NPK, NPKCa, NPKS, NPKSCa, M and NPKM) resulted from the distinct contribution of functional genes, in which the nifH, napA and archaeal amoA genes highly contributed to the community variations between manure fertilization and Control. Soil variables, particularly pH, NO3−-N and AP, significantly affected the N-cycling microbial community structure. Overall, the different fertilization strategies demonstrated varying influential patterns on the N-cycling microbial abundance and community by altering soil properties and affecting specific functional gene abundance; in particular, manure treatments had a greater influence compared to chemical fertilizers.

Potassium (K) plays an important role in plant development and in plant responses to various environmental stresses; however, its involvement in the mitigation of heavy metal stress by altering the binding capacity of the cell wall in Arabidopsis thaliana remains elusive. Here, we examined the effect of K (0–12 mM) in the regulation of cadmium (Cd) resistance in Arabidopsis thaliana. Toxic levels of Cd (50 μM) cause chlorosis in young leaves; however, the application of 3 mM K significantly alleviated this symptom in Arabidopsis thaliana, while other K concentrations did not rescue this phenotype. Moreover, 3 mM K significantly increased cell wall polysaccharide (hemicellulose) content and Cd adsorption in the root cell walls, suggesting that the modification of the cell wall composition is responsible for the Cd retention in the root under 3 mM K application. The 3 mM K treatment significantly reduced the expression of genes related to Cd uptake when plants were exposed to Cd, implying a decrease in Cd entering the cells. Furthermore, endogenous Nitric oxide (NO) was demonstrated to be involved in 3 mM K ameliorated-Cd toxicity as nia1nia2 and noa1 mutants, which are defective in NO biosynthesis, this positive effect of 3 mM K on Cd toxicity was abolished. Taken together, our results indicated that the 3 mM K alleviated deleterious effects of Cd by modifying the cell wall Cd binding capacity, particularly through the regulation of the NO accumulation in Arabidopsis thaliana.

Some plant growth-promoting bacteria (PGPB) are capable of fixing atmospheric N2 and can be used to reduce nitrogen (N) fertilizer application in agriculture. Large amounts of N fertilizers are applied in tomato (Solanum lycopersicum L.). However, less attention has been given to the role of PGPB in the N nutrition of tomato. The present study was carried out under greenhouse conditions to investigate the principal mechanisms underlying PGPB-improved N nutrition in tomato. Tomato plants were grown in pots under –N (native soil N without N fertilization) or + N (supply 150 mg N kg–1 dry soil in the form of urea), with or without Bacillus pumilus (PGPB) inoculation. Nitrogen supply improved the growth of tomato, soil NH4+ concentration, and plant N uptake. Nitrogen increased the rhizobacterial population, bacterial nifH gene expression, and soil nitrogenase activity only with the inoculation of B. pumilus. B. pumilus inoculation improved the tomato growth, N uptake, soil NH4+ concentrations, rhizobacterial population levels, soil bacterial gene expression, and soil nitrogenase activity only under + N condition. These results suggest that the inoculation of B. pumilus improves the growth of tomato under the condition of additional fertilizer N supply due to an increase in N uptake by roots from B. pumilus-assisted fixed N in soil.

SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron&ndash, exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis.

Wheat (Triticum aestivum L.) is one of the major crops worldwide and its production is inevitably subjected to various biotic/abiotic stresses during the life cycle. Drought, salinity and flooding are among the most severe abiotic stresses restricting wheat yields and could occur at very early stages such as seed germination. How wheat seed germination responds to these different stresses remains incomplete. To fill the information gap, a label-free proteomic analysis was applied to decipher the proteomic profiling of the germinating wheat seeds subjected to PEG, NaCl and submergence treatments. In total, 4295 proteins were detected, of which 465, 397 and 732 showed significant alterations in abundance under those stresses when compared with control. A common denominator found in the response observed to all three stresses are changes related to small molecule metabolic processes, and particularly in pathways associated with phenylpropanoid biosynthesis and fatty acid degradation. It was also noticeable that pathways like cysteine and methionine metabolism in the PEG or submergence treatment and starch and sucrose metabolism in the submergence treatment are specifically pronounced. Functional analysis of putative proteins participating in these pathways revealed distinct responsive patterns across different stresses. SIGNIFICANCE: Wheat (Triticum aestivum L.) is one of the most important staple crops in the world, but its growth and productivity are frequently restrained by stresses such as drought, salinity and flooding. To date, many resources have been documented to investigate how wheat responds and adapts to these individual stresses during plant development and yield formation, but little attention was paid to the understandings of the internal link between different conditions, especially during the germination process, a critical stage that determines the optimal growth of wheat. In this study, we carried out the proteome profiling of the germinating seeds of a common wheat cultivar, Chinese Spring, subjected to PEG, NaCl and submergence stresses. We found that the phenylpropanoid biosynthesis and fatty acid degradation pathways were enriched as the ubiquitous stress responses, while some pathways were stress-specific, for instance, starch and sucrose metabolism against submergence. The changes in some of the altered processes were further validated by physiological and molecular approaches. Our results suggest that the overall pathway profiles concerned with the three stresses were similar, but the specific procedures and components in each process varied greatly. The altered proteins and processes can be taken as effective candidates in future breeding and agronomic modification researches.

Low availability of inorganic phosphate (Pi), together with aluminum (Al), is a major constraint for plant growth and development in acidic soils. To investigate whether or not Al-resistant cultivars can perform better under Pi deficiency, we chose two wheat cultivars with different Al-responses&mdash, Atlas 66, being Al-tolerant, and Scout 66, which is Al-sensitive&mdash, and analyzed their responses to Pi deficiency. Results showed that, unexpectedly, the Al-sensitive cultivar Scout 66 contained comparatively higher amount of soluble phosphate (Pi) and total phosphorus (P) both in the roots and in the shoots than Atlas 66 under P deficiency. In addition, Scout 66 exhibited higher root biomass, root volume, and root tip numbers, compared with Atlas 66. The expression of Pi-responsive marker genes, TaIPS1, TaSPX3, and TaSQD2 was strongly induced in both cultivars, but the extents of induction were higher in Scout 66 than in Atlas 66 under long-term Pi starvation. Taken together, our results suggest that the Al-sensitive cultivar Scout 66 performed much better under sole Pi starvation, which sets the following experimental stage to uncover the underlying mechanisms of why Scout 66 can display better under Pi deficiency. Our study also raises an open question whether Al-resistant plants are more sensitive to Pi deficiency.

Plants challenged with abiotic stress show enhanced polyamines levels. Here, we show that the polyamine putrescine (Put) plays an important role to alleviate Fe deficiency. The adc2-1 mutant, which is defective in Put biosynthesis, was hypersensitive to Fe deficiency compared with wild type (Col-1 of Arabidopsis [Arabidopsis thaliana]). Exogenous Put decreased the Fe bound to root cell wall, especially to hemicellulose, and increased root and shoot soluble Fe content, thus alleviating the Fe deficiency-induced chlorosis. Intriguingly, exogenous Put induced the accumulation of nitric oxide (NO) under both Fe-sufficient (+Fe) and Fe-deficient (-Fe) conditions, although the ferric-chelate reductase (FCR) activity and the expression of genes related to Fe uptake were induced only under -Fe treatment. The alleviation of Fe deficiency by Put was diminished in the hemicellulose-level decreased mutant-xth31 and in the noa1 and nia1nia2 mutants, in which the endogenous NO levels are reduced, indicating that both NO and hemicellulose are involved in Put-mediated alleviation of Fe deficiency. However, the FCR activity and the expression of genes related to Fe uptake were still up-regulated under -Fe+Put treatment compared with -Fe treatment in xth31, and Put-induced cell wall Fe remobilization was abolished in noa1 and nia1nia2, indicating that Put-regulated cell wall Fe reutilization is dependent on NO. From our results, we conclude that Put is involved in the remobilization of Fe from root cell wall hemicellulose in a process dependent on NO accumulation under Fe-deficient condition in Arabidopsis.

High rates of phosphorus (P) are generally applied to vegetable crops, but this carries a risk of polluting the environment. There has been little research to define optimum soil P levels and strategies to reduce P requirements in the field. We hypothesized that high rates of P fertilization at the seedling stage followed by lower rates later could reduce total P fertilizer use in cucumber ( Cucumis sativus L.). In this study, we explored the optimum P application via pot experiments in which three P levels at the seedling stage (0, 80, and 240 mg P kg −1 soil) were used in factorial combination with three P levels after transplanting (0, 80, and 160 mg P kg −1 soil). Results showed that P applied in the seedling stage was much more effective at maintaining optimal growth than in the field after transplanting. For example, 72 mg P pot −1 applied in the mode 240/0 (P application rates at the seedling vs transplant stages) produced a biomass dry weight (DW) of 17.7 g pot −1 , whereas 360 mg P pot −1 applied in the mode 0/80 produced only 13.8 g pot −1 . An ancillary study measured the depletion of P from solution by cucumber seedlings between 13 and 21 days after sowing. Over this period V max (the maximum uptake velocity) decreased from 1.18 to 0.50 nmol g −1 root dry weight s −1 , while K m (the half-saturation constant where uptake is 50% of V max ) increased from 5.60 to 8.14 μM. That indicates that since cucumber plants have a high capacity to absorb P as seedlings, it would be expected to reduce the P requirement in field soils. There are therefore efficiencies in applying higher P at the seedling stage and lower levels later.

Background and aims Manganese (Mn) and aluminium (Al) phytotoxicities occur mainly in acid soils. In some plant species, Al alleviates Mn toxicity, but the mechanisms underlying this effect are obscure. Methods Rice (Oryza sativa) seedlings (11 d old) were grown in nutrient solution containing different concentrations of Mn(2+) and Al(3+) in short-term (24 h) and long-term (3 weeks) treatments. Measurements were taken of root symplastic sap, root Mn plaques, cell membrane electrical surface potential and Mn activity, root morphology and plant growth. Key results In the 3-week treatment, addition of Al resulted in increased root and shoot dry weight for plants under toxic levels of Mn. This was associated with decreased Mn concentration in the shoots and increased Mn concentration in the roots. In the 24-h treatment, addition of Al resulted in decreased Mn accumulation in the root symplasts and in the shoots. This was attributed to higher cell membrane surface electrical potential and lower Mn(2+) activity at the cell membrane surface. The increased Mn accumulation in roots from the 3-week treatment was attributed to the formation of Mn plaques, which were probably related to the Al-induced increase in root aerenchyma. Conclusions The results show that Al alleviated Mn toxicity in rice, and this could be attributed to decreased shoot Mn accumulation resulting from an Al-induced decrease in root symplastic Mn uptake. The decrease in root symplastic Mn uptake resulted from an Al-induced change in cell membrane potential. In addition, Al increased Mn plaques in the roots and changed the binding properties of the cell wall, resulting in accumulation of non-available Mn in roots.

Boron (B) alleviates aluminum (Al) toxicity in higher plants; however, the underlying mechanisms behind this phenomenon remain unknown. Here, we used bromocresol green pH indicator, noninvasive microtest, and microelectrode ion flux estimation techniques to demonstrate that B promotes root surface pH gradients in pea (Pisum sativum) roots, leading to alkalization in the root transition zone and acidification in the elongation zone, while Al inhibits these pH gradients. B significantly decreased Al accumulation in the transition zone (∼1.0–2.5 mm from the apex) of lateral roots, thereby alleviating Al-induced inhibition of root elongation. Net indole acetic acid (IAA) efflux detected by an IAA-sensitive platinum microelectrode showed that polar auxin transport, which peaked in the root transition zone, was inhibited by Al toxicity, while it was partially recovered by B. Electrophysiological experiments using the Arabidopsis (Arabidopsis thaliana) auxin transporter mutants (auxin resistant1-7; pin-formed2 [pin2]) and the specific polar auxin transporter inhibitor1-naphthylphthalamic acid showed that PIN2-based polar auxin transport is involved in root surface alkalization in the transition zone. Our results suggest that B promotes polar auxin transport driven by the auxin efflux transporter PIN2 and leads to the downstream regulation of the plasma membrane-H+-ATPase, resulting in elevated root surface pH, which is essential to decrease Al accumulation in this Al-targeted apical root zone. These findings provide a mechanistic explanation for the role of exogenous B in alleviation of Al accumulation and toxicity in plants.

Two Melaleuca species, M. cajuputi and M. bracteata, were compared to identify the factors determining their distinct aluminum (Al) resistance levels. The presence of Al in a liquid culture medium (maximum tested concentration, 2 mM) did not affect the growth of M. cajuputi, but severely inhibited the growth of M. bracteata. The Al content in the roots was 50% higher in Al-sensitive M. bracteata than in Al-resistant M. cajuputi. Al penetration and tissue damage were obvious in the roots of M. bracteata, but only mild in the roots of M. cajuputi. Relatively high levels of fumarate were released by the roots of M. cajuputi, but not by those of M. bracteata. Supplementation of Al-containing liquid media with fumarate resulted in a reduction of Al toxicity on M. bracteata. These results suggest that Al-resistant M. cajuputi releases fumarate from its roots, thereby detoxifying Al.

The integrated effects of environmental factors on soil nitrification are largely unknown. Here, we performed a microcosm experiment to investigate the interactive effects of pH and NH 4 + on nitrification activity in two acidic soils with different land use patterns (Anhui soil, a forest soil; Jiangxi soil, a brush land soil). Both soils were incubated under native pH and CaCO 3 -manipulated pH in the presence or absence of added ammonium for 60 days. The addition of CaCO 3 alone did not change the nitrification activity of either soil. Ammonium addition stimulated nitrification in Anhui soil, but not in Jiangxi soil, and this stimulation was more pronounced with increased CaCO 3 . The ammonia monooxygenase ( amoA ) gene copy number of both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) was much higher in Anhui soil than in Jiangxi soil. The amoA gene copy number of AOB in Anhui soil was more highly upregulated under CaCO 3 + NH 4 + than NH 4 + during incubation. In Anhui soil, changes in the denaturing gradient gel electrophoresis (DGGE) fingerprint patterns of bacterial amoA genes were parallel to changes in the amoA gene copy number of AOB. In Jiangxi soil, DGGE could not be performed because the PCR for bacterial DGGE did not yield any products, while quantitative PCR revealed that the amoA gene copy number of AOB changed during incubation. These results suggest that AOB plays an important role in CaCO 3 -enhanced nitrification of Anhui soil with ammonium addition. The low nitrification rates of Jiangxi soil regardless of CaCO 3 with or without NH 4 + supply may be ascribed to the lower activity of both AOB and AOA, especially AOA.

A total of 558 potential circular RNAs (circRNAs) were identified in citrus, and these were analyzed and compared. One hundred seventy-six differentially expressed circRNAs were identified in two genotypes of trifoliate orange. Circular RNAs (circRNAs) play diverse roles in transcriptional control and microRNA (miRNA) function. However, little information is known about circRNAs in citrus. To identify citrus circRNAs and investigate their functional roles, high-throughput sequencing of precocious trifoliate orange (an early-flowering trifoliate orange mutant, Poncirus trifoliata L. Raf.) and its wild type was performed. A total of 558 potential circRNAs were identified by bioinformatic analysis, and 86.02% of these were sense-overlapping circRNAs. Their sequence features, alternative circularization, and other characteristics were investigated in this study. Compared with the wild type, 176 circRNAs were identified as differentially expressed circRNAs, 61 were significantly up-regulated and 115 were down-regulated in precocious trifoliate orange, indicating that they may play an important role in the early flowering process. Alternative circularization and differential expression of some circRNAs were verified by Sanger sequencing and real-time polymerase chain reaction. The functions of differentially expressed circRNAs and their host genes were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. We found that many differentially expressed circRNAs had abundant miRNA binding sites: 29 circRNAs were found to act as the 16 miRNA targets. Overall, these results will help to reveal the biological functions of circRNAs in growth and development of citrus.