Green manure incorporation enhanced soil labile phosphorus and fruit tree growth.

Introduction: The incorporation of green manures substantially enhances the conversion of external phosphorus (P) fertilizers and soil-reserved P into forms readily available to plants. The study aims to evaluate the influence of green manure additions on soil phosphorus dynamics and citrus growth, considering different green manure species and initial soil phosphorus levels. Additionally, the research seeks to elucidate the microbiological mechanisms underlying the observed effects. Methods: A citrus pot experiment was conducted under both P-surplus (1.50 g·P·kg-1) and P-deficient (0.17 g·P·kg-1) soils with incorporating legume (Leg), non-legume (Non-Leg) or no green manure residues (CK), and 18O-P labeled KH2PO4 (0.5 g, containing 80‰ δ18Op) was additionally introduced to trace the turnover characteristics of chemical P fertilizer mediated by soil microorganisms. Results and discussion: In P-surplus soil, compared with the CK treatment, the Leg treatment significantly increased soil H2O-Pi (13.6%), NaHCO3-Po (8.9%), NaOH-Pi (9.5%) and NaOH-Po (30.0%) content. It also promoted rapid turnover of P sources into H2O-Pi and NaHCO3-Pi pools by enhancing the phoC (576.6%) gene abundance. In contrast, the Non-Leg treatment significantly augmented soil H2O-Pi (9.2%) and NaHCO3-Po (8.5%) content, facilitating the turnover of P sources into NaHCO3-Pi pools. Under P-deficient soil conditions, compared with the CK treatment, the Leg treatment notably raised soil H2O-Pi (150.0%), NaHCO3-Pi (66.3%), NaHCO3-Po (34.8%) and NaOH-Pi (59.0%) content, contributing to the transfer of P sources into NaHCO3-Pi and NaOH-Pi pools. This effect was achieved through elevated ALP (33.8%) and ACP (12.9%) activities and increased pqqC (48.1%), phoC (42.9%), phoD (21.7%), and bpp (27.4%) gene abundances. The Non-Leg treatment, on the other hand, led to significant increases in soil NaHCO3-Pi (299.0%) and NaHCO3-Po (132.6%) content, thereby facilitating the turnover of P sources into NaHCO3-Pi and NaOH-Pi pools, except for the phoC gene abundance. Both Leg and Non-Leg treatments significantly improved citrus growth (7.3-20.0%) and P uptake (15.4-42.1%) in P-deficient soil but yielded no substantial effects in P-surplus soil. In summary, introducing green manure crops, particularly legume green manure, emerges as a valuable approach to enhance soil P availability and foster fruit tree growth in orchard production.

Long-term field application of manure induces deep selection of antibiotic resistomes in leaf endophytes of Chinese cabbage.

Antibiotic resistomes in leaf endophytes of vegetables threaten human health through the food chain. However, little is known about the ability of long-term manure fertilization to impact the deep selection of antibiotic resistance genes (ARGs) in leaf endophytes of vegetables planted in different types of soils. Here, by high-throughput quantitative PCR, we characterized the ARGs of leaf endophytes of Chinese cabbage (Brassica pekinensis (Lour.) Rupr.) grown in long-term (14 year) manure-amended acidic, neutral and calcareous soils. In total, 87 ARGs and 4 mobile genetic elements (MGEs) were detected in all the samples. Manure fertilization significantly increased the ARG numbers and normalized abundance in leaf endophytes, especially in acidic soil. Moreover, in acidic soil, manure application also led to a higher increase in the normalized abundance of opportunist and specialist ARGs, and more opportunist and specialist ARGs posed a high risk according to their risk ranks. Random forest analysis revealed that Proteobacteria and MGEs were the major drivers affecting the normalized abundance of opportunist and specialist ARGs in both acidic and neutral soils, respectively. In calcareous soil, Cyanobacteria and Actinobacteria were the most important contributors. Collectively, this study expands our knowledge about the deep selection of plant resistomes under long-term manure application.

Alternate wetting and drying irrigation and phosphorus rates affect grain yield and quality and heavy metal accumulation in rice.

Alternate wetting and drying (AWD) irrigation was reported to increase rice root activity and element bioavailability, which results in enhanced heavy metal (HM) absorption and this HM ends up in rice grains. HM uptake was also affected by the levels of phosphorus (P) fertilizer application. HMs enter food chain via consumption of rice grains and cause health problems. In this study, we compared the differences in grain yield, grain quality, water use efficiency (WUE), partial factor productivity of applied P (PFPp), HM contents in different tissues and transfer coefficient (TC) of HMs under a combination of treatments involving two irrigation regimes (continuous flooding (CF) and AWD irrigation) and three P fertilizer application levels (0.4 g P2O5/kg soil, HP; 0.2 g P2O5/kg soil, MP; 0 g P2O5/kg soil, LP). Compared to CF, AWD irrigation increased grain yield (without reducing grain quality), decreased irrigation water use and the number of irrigation events needed and improved WUE and PFPp at all three P fertilizer application levels, while the accumulation of HMs in grains increased when more P was applied. This accumulation of HMs in grains thus requires immediate attention to the level of P fertilizer application and its optimization in water-saving AWD irrigation to minimize grain HM content.

Comprehensive transcriptome and proteome analyses reveal a novel sodium chloride responsive gene network in maize seed tissues during germination.

Germination is a plant developmental process by which radicle of mature seeds start to penetrate surrounding barriers for seedling establishment and multiple environmental factors have been shown to affect it. Little is known how high salinity affects seed germination of C4 plant, Zea mays. Preliminary germination assay suggested that isolated embryo alone was able to germinate under 200 mM NaCl treatment, whereas the intact seeds were highly repressed. We hypothesized that maize endosperm may function in perception and transduction of salt signal to surrounding tissues such as embryo, showing a completely different response to that in Arabidopsis. Since salt response involves ABA, we analysed in vivo ABA distribution and quantity and the result demonstrated that ABA level in isolated embryo under NaCl treatment failed to increase in comparison with the water control, suggesting that the elevation of ABA level is an endosperm dependent process. Subsequently, by using advanced profiling techniques such as RNA sequencing and SWATH-MS-based quantitative proteomics, we found substantial differences in post-transcriptional and translational changes between salt-treated embryo and endosperm. In summary, our results indicate that these regulatory mechanisms, such as alternative splicing, are likely to mediate early responses to salt stress during maize seed germination.

Spermidine Enhanced Free Polyamine Levels and Expression of Polyamine Biosynthesis Enzyme Gene in Rice Spikelets under Heat Tolerance before Heading.

High temperatures (HT) before heading strongly inhibit the development of spikelets in rice. Spermidine (Spd) can improve rice's resistance to HT stress; however, the mechanism underlying this effect has not been elucidated. This study investigated several parameters, including yield, superoxide anion (O2.-), protective enzyme activities, and polyamine content, in a heat-sensitive genotype, Shuanggui 1. The yield and yield components decreased dramatically when subjected to HT stress, while this reduction could be partially recovered by exogenous Spd. Spd also slowed the generation rate of O2.- and increased protective enzyme, superoxide dismutase (SOD) and catalase (CAT) activities both under normal and high temperatures, which suggested that Spd may participate in the antioxidant system. Furthermore, genes involved in polyamine synthesis were analyzed. The results show that HT before heading significantly increased the expression of arginine decarboxylase OsADC1, Spd synthase OsSPDS1 and OsSPDS3 and had little effect on the expression of the S-adenosylmethionine decarboxylase OsSAMDC2 and ornithine decarboxylase OsODC1. In addition, exogenous Spd considerably reduced the expression of OsSAMDC2, OsSPDS1 and OsSPDS3 under HT but not the expression of OsADC1. The above mentioned results indicate that the exogenous Spd could help young rice spikelets to resist HT stress by reducing the expression of OsSAMDC2, OsSPDS1 and OsSPDS3, resulting in higher levels of endogenous Spd and Spm, which were also positively correlated with yield. In conclusion, the adverse effect of HT stress on young spikelets seems to be alleviated by increasing the amounts of Spd and Spm, which provides guidance for adaptation to heat stress during rice production.

[Effects of land use change on soil organic carbon and its components in karst rocky desertification of southwest China]. / è¥¿å—å–€æ–¯ç‰¹çŸ³æ¼ åŒ–çŽ¯å¢ƒä¸‹åœŸåœ°åˆ©ç”¨å˜åŒ–å¯¹åœŸå£¤æœ‰æœºç¢³åŠå ¶ç»„åˆ†çš„å½±å“.

Soil organic carbon (SOC) is the dynamic medium of carbon transfer and the main pathway of carbon transfer in the karst ecosystem. SOC and its components are the important parts in soil carbon cycling of karst ecosystem. However, few studies have focused on SOC and its components in the karst ecosystem. We analyzed the effects of land use change on the SOC content, SOC reserve (SOCS), water-soluble organic carbon (WSOC), easily oxidizable organic carbon (EOC), particu-late organic carbon (POC), and light fraction organic carbon (LFOC), and heavy fraction organic carbon (HFOC) and their distribution ratio, with six different land-use patterns [Zanthoxylum bungeanum forest (HJ), Hylocereus undulates forest (HL), mixed forest of Z. bungeanum and H. undulates (HHL), Sabina chinensis forest (YB), mixed forest of S. chinensis and Ligustrum luci-dum (YBN), and slope cropland (PD)] in Huajiang Canyon of Guanling County, Guizhou Pro-vince. Results showed that SOC and SOCS in YB, YBN and HJ were significantly higher than those in HL, HHL and PD. In the 0-20 cm soil layer, the concentrations of SOCS followed the order of HJ＞YB＞YBN＞PD＞HHL＞HL. Contents of WSOC, EOC, POC, LFOC and HFOC in YB, YBN, and HJ were all higher than those in the other three patterns. Significant positive correlations existed between SOC and each of its components (WSOC, EOC, POC, LFOC and HFOC), also between any two of those components. Z. bungeanum could be used as a priority economic species for the ecological rehabilitation of karst rocky desertification and mountain agriculture development in Southwest China. WSOC, EOC, POC, LFOC and HFOC could be used as indicators of soil organic carbon pool.

Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species.

MAIN CONCLUSION: This study systematically identifies plant SYF2/NTC31/p29 genes from 62 plant species by a combinatory bioinformatics approach, revealing the importance of this gene family in phylogenetics, duplication, transcriptional, and post-transcriptional regulation. Alternative splicing is a post-transcriptional regulatory mechanism, which is critical for plant development and stress responses. The entire process is strictly attenuated by a complex of splicing-related proteins, designated splicing factors. Human p29, also referred to as synthetic lethal with cdc forty 2 (SYF2) or the NineTeen complex 31 (NTC31), is a core protein found in the NTC complex of humans and yeast. This splicing factor participates in a variety of biological processes, including DNA damage repair, control of the cell cycle, splicing, and tumorigenesis. However, its function in plants has been seldom reported. Thus, we have systematically identified 89 putative plant SYF2s from 62 plant species among the deposited entries in the Phytozome database. The phylogenetic relationships and evolutionary history among these plant SYF2s were carefully examined. The results revealed that plant SYF2s exhibited distinct patterns regarding their gene structure, promoter sequences, and expression levels, suggesting their functional diversity in response to developmental cues or stress treatments. Although local duplication events, such as tandem duplication and retrotransposition, were found among several plant species, most of the plant species contained only one copy of SYF2, suggesting the existence of additional mechanisms to confer duplication resistance. Further investigation using the model dicot and monocot representatives Arabidopsis and rice SYF2s indicated that the splicing pattern and resulting protein isoforms might play an alternative role in the functional diversity.

Alternative splicing and translation play important roles in hypoxic germination in rice.

Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia. In total, 10 253 intron-containing genes were identified. Of these, ~1741 differentially expressed AS (DAS) events from 811 genes were identified in hypoxia-treated seeds compared with controls. Over 95% of these were not present in the list of differentially expressed genes. In particular, regulatory pathways such as the spliceosome, ribosome, endoplasmic reticulum protein processing and export, proteasome, phagosome, oxidative phosphorylation, and mRNA surveillance showed substantial AS changes under hypoxia, suggesting that AS responses are largely independent of transcriptional regulation. Considerable AS changes were identified, including the preferential usage of some non-conventional splice sites and enrichment of splicing factors in the DAS data sets. Taken together, these results not only demonstrate that AS and ATI function during hypoxic germination but they have also allowed the identification of numerous novel proteins/peptides produced via ATI.

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants.

BACKGROUND: The next-generation sequencing (NGS) technology has greatly facilitated genomic and transcriptomic studies, contributing significantly in expanding the current knowledge on genome and transcriptome. However, the continually evolving variety of sequencing platforms, protocols and analytical pipelines has led the research community to focus on cross-platform evaluation and standardization. As a NGS pioneer in China, the Beijing Genomics Institute (BGI) has announced its own NGS platform designated as BGISEQ-500, since 2016. The capability of this platform in large-scale DNA sequencing and small RNA analysis has been already evaluated. However, the comparative performance of BGISEQ-500 platform in transcriptome analysis remains yet to be elucidated. The Illumina series, a leading sequencing platform in China's sequencing market, would be a preferable reference to evaluate new platforms. METHODS: To this end, we describe a cross-platform comparative study between BGISEQ-500 and Illumina HiSeq4000 for analysis of Arabidopsis thaliana WT (Col 0) transcriptome. The key parameters in RNA sequencing and transcriptomic data processing were assessed in biological replicate experiments, using aforesaid platforms. RESULTS: The results from the two platforms BGISEQ-500 and Illumina HiSeq4000 shared high concordance in both inter- (correlation, 0.88-0.93) and intra-platform (correlation, 0.95-0.98) comparison for gene quantification, identification of differentially expressed genes and alternative splicing events. However, the two platforms yielded highly variable interpretation results for single nucleotide polymorphism and insertion-deletion analysis. CONCLUSION: The present case study provides a comprehensive reference dataset to validate the capability of BGISEQ-500 enabling it to be established as a competitive and reliable platform in plant transcriptome analysis.

Natural variation in the promoter of rice calcineurin B-like protein10 (OsCBL10) affects flooding tolerance during seed germination among rice subspecies.

Rice (Oryza sativa L.) has two ecotypes, upland and lowland rice, that have been observed to show different tolerance levels under flooding stress. In this study, two rice cultivars, upland (Up221, flooding-intolerant) and lowland (Low88, flooding-tolerant), were initially used to study their molecular mechanisms in response to flooding germination. We observed that variations in the OsCBL10 promoter sequences in these two cultivars might contribute to this divergence in flooding tolerance. Further analysis using another eight rice cultivars revealed that the OsCBL10 promoter could be classified as either a flooding-tolerant type (T-type) or a flooding-intolerant type (I-type). The OsCBL10 T-type promoter only existed in japonica lowland cultivars, whereas the OsCBL10 I-type promoter existed in japonica upland, indica upland and indica lowland cultivars. Flooding-tolerant rice cultivars containing the OsCBL10 T-type promoter have shown lower Ca2+ flow and higher α-amylase activities in comparison to those in flooding-intolerant cultivars. Furthermore, the OsCBL10 overexpression lines were sensitive to both flooding and hypoxic treatments during rice germination with enhanced Ca2+ flow in comparison to wild-type. Subsequent findings also indicate that OsCBL10 may affect OsCIPK15 protein abundance and its downstream pathways. In summary, our results suggest that the adaptation to flooding stress during rice germination is associated with two different OsCBL10 promoters, which in turn affect OsCBL10 expression in different cultivars and negatively affect OsCIPK15 protein accumulation and its downstream cascade.

Inhibitory effect of eugenol on seed germination and pre-harvest sprouting of hybrid rice (Oryza sativa L.).

Pre-harvest sprouting (PHS) is a constrain problem in hybrid rice production. The present study was conducted to investigate the inhibitory effect of eugenol on seed germination and PHS of hybrid rice variety (Qian You 1). The results showed that seed germination speed and the activities of α-amylase were inhibited by eugenol pre-soaking and these effects enhanced with the increasing of eugenol concentrations; while seedling growth was not negatively affected. In field trials, eugenol application caused a significant decline in PHS as compared with control, whereas no sustained inhibition in post-harvested seed germination was observed. The HPLC analysis indicated that eugenol raised the internal ABA content by 1-4 times more than control, and seeds treated with eugenol had relatively lower OsABA8OH2 and higher transcript levels of OsNCED2 expression during early stages of seed imbibitions. In addition, seed germinated faster after GA3 application than eugenol alone, and seed endogenous ABA content decreased obviously. It suggested that eugenol strongly delayed seed germination and the PHS in the field, which might be mainly due to the increased ABA contents caused by eugenol. However, the phenomenon of delayed germination and high ABA content caused by eugenol could be effectively recovered by exogenous GA3.

Exogenous spermidine improves seed germination of sweet corn via involvement in phytohormone interactions, H2O2 and relevant gene expression.

BACKGROUND: The low seed vigor and poor field emergence are main factors that restricting the extension of sweet corn in China. Spermidine (Spd) plays an important role in plant growth and development, but little is known about the effect of Spd on sweet corn seed germination. Therefore the effect of exogenous Spd on seed germination and physiological and biochemical changes during seed imbibition of Xiantian No.5 were investigated in this study. RESULTS: Spd soaking treatment not only improved seed germination percentage but also significantly enhanced seed vigor which was indicated by higher germination index, vigor index, shoot heights and dry weights of shoot and root compared with the control; while exogenous CHA, the biosynthesis inhibitor of Spd, significantly inhibited seed germination and declined seed vigor. Spd application significantly increased endogenous Spd, gibberellins and ethylene contents and simultaneously reduced ABA concentration in embryos during seed imbibition. In addition, the effects of exogenous Spd on H2O2 and MDA productions were also analyzed. Enhanced H2O2 concentration was observed in Spd-treated seed embryo, while no significant difference of MDA level in seed embryo was observed between Spd treatment and control. However, the lower H2O2 and significantly higher MDA contents than control were detected in CHA-treated seed embryos. CONCLUSIONS: The results suggested that Spd contributing to fast seed germination and high seed vigor of sweet corn might be closely related with the metabolism of hormones including gibberellins, ABA and ethylene, and with the increase of H2O2 in the radical produced partly from Spd oxidation. In addition, Spd might play an important role in cell membrane integrity maintaining.

Seed priming with polyethylene glycol induces antioxidative defense and metabolic regulation of rice under nano-ZnO stress.

The present study was carried out to investigate the beneficial impact of seed priming with polyethylene glycol (PEG) under different concentrations of zinc oxide nanoparticles (nano-ZnO), i.e., 0, 250, 500, and 750 mg L(-1) in two cultivars of Oryza sativa (Zhu Liang You 06 and Qian You No. 1). Physiological parameters were improved by priming with 30 % PEG in both cultivars under stress treatments. Seed priming with 30 % PEG improved α-amylase activities and total soluble sugar contents of both cultivars under nano-ZnO stress. In addition, glutathione reductase (GR) activity, reactive oxygen species (ROS) accumulation, and proline contents decreased after the priming treatment in both cultivars under different nano-ZnO concentrations. Expression of GR1, GR2, Amy2A, and Amy3A genes in shoots and roots of both cultivars increased and had higher transcription levels under the nano-ZnO stress condition. Fourier transform infrared spectroscopy (FTIR) analysis did not show any significant effects of the priming treatment on the band observed at 3400, 900, 1600, and 1000 cm(-1) corresponding to alkenyl stretch (C = C), carboxyl acid (O-H), nitrile (C = N), and aromatic (C-H), respectively, in both cultivars under nano-ZnO stress.

Physiological changes and sHSPs genes relative transcription in relation to the acquisition of seed germination during maturation of hybrid rice seed.

BACKGROUND: During the production of early hybrid rice seed, the seeds dehydrated slowly and retained high moisture levels when rainy weather lasted for a couple of days, and the rice seeds easily occurred pre-harvest sprouting (PHS) along with high temperature. Therefore it is necessary to harvest the seeds before the PHS occurred. RESULTS: The seeds of hybrid rice (Oryza sativa L. subsp. indica) cv. Qianyou No1 that harvests from 19 to 28 days after pollination (DAP) all had high seed vigour. The seed moisture content at 10 DAP was 36.1%, and declined to 28.6% at 19 DAP; the contents of soluble sugar and total starch increased significantly with the development of seeds. The soluble protein content, the level of abscisic acid (ABA) and gibberellin (GA3 ), and ascorbate peroxidase (APX) activity continued to decrease from 10 DAP to 19 DAP. The seeds at 19 DAP had the highest peroxidase (POD) activity and lowest catalase (CAT) activity while the superoxide dismutase (SOD) activity had no significant difference among the different developing periods. The relative expressions of genes 64S Hsp18.0 and Os03g0267200 transcripts increased significantly from 10 to 19 DAP, and then decreased. However, no significant change was recorded in soluble protein, sugar and GA3 after 16 DAP, and they all significantly correlated with seed viability and vigour during the process of seed maturity. CONCLUSION: The seeds of hybrid rice Qianyou No1 had a higher viability and vigour when harvested from 19 DAP to 28 DAP, the transcription levels of 64S Hsp18.0 and Os03g0267200 increased significantly from 10 DAP to 19 DAP and the highest value was recorded at 19 DAP. The seeds could be harvested as early as 19 DAP without negative influence on seed vigour and viability.

A strategy for finding the optimal scale of plant core collection based on Monte Carlo simulation.

Core collection is an ideal resource for genome-wide association studies (GWAS). A subcore collection is a subset of a core collection. A strategy was proposed for finding the optimal sampling percentage on plant subcore collection based on Monte Carlo simulation. A cotton germplasm group of 168 accessions with 20 quantitative traits was used to construct subcore collections. Mixed linear model approach was used to eliminate environment effect and GE (genotype × environment) effect. Least distance stepwise sampling (LDSS) method combining 6 commonly used genetic distances and unweighted pair-group average (UPGMA) cluster method was adopted to construct subcore collections. Homogeneous population assessing method was adopted to assess the validity of 7 evaluating parameters of subcore collection. Monte Carlo simulation was conducted on the sampling percentage, the number of traits, and the evaluating parameters. A new method for "distilling free-form natural laws from experimental data" was adopted to find the best formula to determine the optimal sampling percentages. The results showed that coincidence rate of range (CR) was the most valid evaluating parameter and was suitable to serve as a threshold to find the optimal sampling percentage. The principal component analysis showed that subcore collections constructed by the optimal sampling percentages calculated by present strategy were well representative.

Establishing an efficient way to utilize the drought resistance germplasm population in wheat.

Drought resistance breeding provides a hopeful way to improve yield and quality of wheat in arid and semiarid regions. Constructing core collection is an efficient way to evaluate and utilize drought-resistant germplasm resources in wheat. In the present research, 1,683 wheat varieties were divided into five germplasm groups (high resistant, HR; resistant, R; moderate resistant, MR; susceptible, S; and high susceptible, HS). The least distance stepwise sampling (LDSS) method was adopted to select core accessions. Six commonly used genetic distances (Euclidean distance, Euclid; Standardized Euclidean distance, Seuclid; Mahalanobis distance, Mahal; Manhattan distance, Manhat; Cosine distance, Cosine; and Correlation distance, Correlation) were used to assess genetic distances among accessions. Unweighted pair-group average (UPGMA) method was used to perform hierarchical cluster analysis. Coincidence rate of range (CR) and variable rate of coefficient of variation (VR) were adopted to evaluate the representativeness of the core collection. A method for selecting the ideal constructing strategy was suggested in the present research. A wheat core collection for the drought resistance breeding programs was constructed by the strategy selected in the present research. The principal component analysis showed that the genetic diversity was well preserved in that core collection.