Combined transcriptome and metabolome analyses reveal the effects of selenium on the growth and quality of Lilium lancifolium.

Lilium lancifolium Thunb (L. lancifolium) is an important medicinal and edible plant with outstanding functionality for selenium (Se) biofortification. However, the molecular response of L. lancifolium to exogenous Se has not been fully elucidated. In this study, the effects of different levels of Se on L. lancifolium growth and quality were explored by transcriptome, metabolome and biochemical analyses. The results showed that the total Se and organic Se content in L. lancifolium bulbs increased with increasing Se dosage (0-8.0 mmol/L). Moreover, Se stimulated the growth of L. lancifolium at low level (2.0 mmol/L) but showed an inhibitory effect at high levels (≥4.0 mmol/L). Metabolomic and biochemical analyses revealed that the bulb weight and the content of amino acid, soluble sugar, and soluble protein were significantly increased in the 2.0 mmol/L Se treatment compared with those in the control (0 mmol/L Se). Transcriptome and metabolome analyses revealed that the significant upregulation of the GPD1, GPAT and ADPRM genes promoted glycerophospholipid accumulation. Additionally, the significantly upregulated glyA and downregulated asnB, nadB, thrA and SAT genes coordinate to the regulation of amino acid biosynthesis. The significantly upregulated SUS, bgl B, BAM, and SGA1 genes were involved in soluble sugar accumulation under Se treatment. In summary, this study identified the optimal Se concentration (2.0 mmol/L), which significantly improved the growth and nutritional quality of L. lancifolium and contributed to understanding the combined effects of Se treatment on the expression of genes and the accumulation of metabolites in L. lancifolium bulbs.

TMT-Based Proteomic Analysis of Continuous Cropping Response in Codonopsis tangshen Oliv.

The growth and development of Codonopsis tangshen, an important herb used in Chinese traditional medicine, have been seriously affected by continuous cropping obstacles. Therefore, understanding the molecular responses of C. tangshen to continuous cropping is imperative to improve its resistance to continuous cropping obstacles. Here, physiological and biochemical results showed that the levels of chlorophyll and malonaldehyde (MDA) were higher in the continuous cropping (LZ) group compared with those of the non-continuous cropping (FLZ) group, while superoxide dismutase (SOD) content was lower in the LZ group than in the FLZ group. Tandem mass tag (TMT)-based proteomic analysis was performed to investigate the response mechanism to continuous cropping obstacles in C. tangshen. A total of 70 differentially expressed proteins (DEPs) were significantly involved in relevant pathways, including photosynthesis, oxidative phosphorylation, ribosome activity, and secondary metabolites. The results suggest that these DEPs in C. tangshen might play a critical role in response to continuous cropping. These findings could provide scientific basis for improving C. tangshen's resistance to continuous cropping obstacles.

Transcriptomic Analysis Provides Novel Insights into the Heat Stress-Induced Response in Codonopsis tangshen.

Codonopsis tangshen Oliv (C. tangshen) is a valuable traditional Chinese medicinal herb with tremendous health benefits. However, the growth and development of C. tangshen are seriously affected by high temperatures. Therefore, understanding the molecular responses of C. tangshen to high-temperature stress is imperative to improve its thermotolerance. Here, RNA-Seq analysis was performed to investigate the genome-wide transcriptional changes in C. tangshen in response to short-term heat stress. Heat stress significantly damages membrane stability and chlorophyll biosynthesis in C. tangshen, as evidenced by pronounced malonaldehyde (MDA), electrolyte leakage (EL), and reduced chlorophyll content. Transcriptome analysis showed that 2691 differentially expressed genes (DEGs) were identified, including 1809 upregulated and 882 downregulated. Functional annotations revealed that the DEGs were mainly related to heat shock proteins (HSPs), ROS-scavenging enzymes, calcium-dependent protein kinases (CDPK), HSP-HSP network, hormone signaling transduction pathway, and transcription factors such as bHLHs, bZIPs, MYBs, WRKYs, and NACs. These heat-responsive candidate genes and TFs could significantly regulate heat stress tolerance in C. tangshen. Overall, this study could provide new insights for understanding the underlying molecular mechanisms of thermotolerance in C. tangshen.

Transcriptome and metabolome analyses reveal novel insights into the seed germination of Michelia chapensis, an endangered species in China.

Michelia chapensis Dandy, a well-known medicinal woody plant endemic to China, is endangered and seriously constricted by seed dormancy-induced low-regeneration in natural conditions. Cold stratification can effectively reduce seed dormancy and promote the seed germination of M. chapensis. However, the molecular events and systematic changes that occurred during seed germination in M. chapensis remain largely unknown. In this study, we carried out transcriptomic and metabolomic analyses to elucidate the potential molecular mechanisms underlying seed germination in M. chapensis under cold stratification. The results showed that the embryo cells became bigger and looser with increasing stratification time. Moreover, the endosperm appeared reduced due to the consumption of nutrients. Seventeen phytohormones were examined by the metabolome targeted for hormones. Compared with the ES (no stratification), the levels of indole-3-acetic acid (IAA) and gibberellin A3 (GA3) were increased in the MS (stratification for 45 days), while the abscisic acid (ABA) was downregulated in both MS and LS (stratification for 90 days). The transcriptome profiling identified 24975 differentially expressed genes (DEGs) in the seeds during germination. The seed germination of M. chapensis was mainly regulated by the biological pathways of plant hormone signal transduction, energy supply, secondary metabolite biosynthesis, photosynthesis-related metabolism, and transcriptional regulation. This study reveals the biological evidence of seed germination at the transcriptional level and provides a foundation for unraveling molecular mechanisms regulating the seed germination of M. chapensis.

Transcriptome analysis provides novel insights into the soil amendments induced response in continuously cropped Codonopsis tangshen.

Codonopsis tangshen Oliv (C. tangshen) is an important Chinese traditional medicinal plant with various health benefits. However, the growth of C. tangshen are seriously affected by continuous cropping, which led to the decrease of the yield and quality. A field experiment was conducted to learn the effects of soil amendments on the growth of C. tangshen under continuous cropping condition, and the biological events which occurred at molecular level were investigated. The results indicated that the content of chlorophyll a (Chl a), chlorophyll b (Chl b), and carotenoid (Car) was significantly higher in SCPM (silicon-calcium-potassium-magnesium fertilizer), SCPMA (SCPM combined with azoxystrobin) and SCPMAOM (SCPM combined with azoxystrobin and organic manure) treatments. Moreover, the yield and the levels of alkaloid, polysaccharide, flavone and total protein in the treatments of SCPM, SCPMA and SCPMAOM were significantly higher than those in the control, and these indexes were all highest in the SCPMAOM treatment. RNA-sequencing (RNA-Seq) is an economical and efficient method to obtain genetic information for species with or without available genome data. In this study, RNA-Seq was performed to understand how continuously cropped C. tangshen responded to the soil amendments at the transcriptome level. The number of differentially expressed genes (DEGs) were as follows: CK vs. SCPM (719 up- and 1456 down-), CK vs. SCPMA (1302 up- and 1748 down-), CK vs. SCPMAOM (1274 up- and 1678 down-). The soil amendments affected the growth of C. tangshen mainly by regulating the genes involved in pathways of 'photosynthesis,' 'plant hormone signal transduction,' 'biosynthesis of unsaturated fatty acids,' 'phenylpropanoid biosynthesis,' and 'starch and sucrose metabolism,' etc. qRT-PCR was performed to validate the expressions of 10 target genes such as CP26, PsaF, and POX, etc., which verified the reliability of RNA-Seq results. Overall, this study revealed the roles and underlying mechanisms of the soil amendments in regulating the growth of continuously cropped C. tangshen at transcriptome level. These findings are beneficial for improving the continuous cropping tolerance and may be valuable for future genetic improvement of C. tangshen.

Effects of foliar selenium application on growth and rhizospheric soil micro-ecological environment of Atractylodes macrocephala Koidz.

Atractylodes macrocephala (A. macrocephala), a famous medicinal herb in China, is widely cultivated and consumed in China with various beneficial effects. Numerous studies have shown that selenium (Se) plays an important role in promoting plant growth, although Se has not been considered an essential element for higher plants. The objectives of this research were to determine the effects of foliar Se application (0, 2.5, 5.0, 10.0 and 20.0 mg m-2 Se in sodium selenite, sprayed monthly from May to August) on the growth and rhizospheric soil micro-ecological environment of A. macrocephala, and explore the possible mechanisms underlying plant response to foliar Se application through a field experiment. The results were: The foliar application of 5.0 mg m-2 Se significantly increased the survival rate of A. macrocephala compared to the control. The yield of A. macrocephala was increased when the Se level maintained belowed 10.0 mg m-2 but decreased when Se level reached 20.0 mg m-2. The Se content in the rhizome of A. macrocephala showed a significant positive correlation with the Se level, while the insect attack rate was significantly negatively correlated with the Se level. However, foliar Se application hardly affected the concentration of bioactive compound atractylenolide in the rhizome of A. macrocephala. Notably, the application of foliar Se changed the content of partial soil nutrients, microbial diversity and composition in the rhizosphere soil of A. macrocephala. Bacterial diversity was positively correlated with A. macrocephala growth whereas fungal diversity was negatively correlated, suggesting that microbial diversity in the rhizosphere soils is closely related to plant growth. Moreover, correlation analysis showed that available potassium, Burkholderia and Cupriavidus in rhizospheric soil might be critical factors for promoting the growth of A. macrocephala. Overall, the foliar application of Se at moderate concentration was beneficial for the growth of A. macrocephala, and 5.0-10.0 mg m-2 Se level was the optimum. Our findings revealed novel insights into the response of A. macrocephala to foliar Se application from plant growth, rhizospheric soil nutrient and microbial community composition .

Transcriptomic analysis of short-term heat stress response in Pinellia ternata provided novel insights into the improved thermotolerance by spermidine and melatonin.

Heat stress has been a major environmental factor limiting the growth and development of Pinellia ternata which is an important Chinese traditional medicine. It has been reported that spermidine (SPD) and melatonin (MLT) play pivotal roles in modulating heat stress response (HSR). However, the roles of SPD and MLT in HSR of P. ternata, and the potential mechanism is still unknown. Here, exogenous SPD and MLT treatments alleviated heat-induced damages in P. ternata, which was supported by the increased chlorophyll content, OJIP curve, and relative water content, and the decreased malondialdehyde and electrolyte leakage. Then, RNA sequencing between CK (control) and Heat (1 h of heat treatment) was conducted to analyze how genes were in response to short-term heat stress in P. ternata. A total of 14,243 (7870 up- and 6373 down-regulated) unigenes were differentially expressed after 1 h of heat treatment. Bioinformatics analysis revealed heat-responsive genes mainly included heat shock proteins (HSPs), ribosomal proteins, ROS-scavenging enzymes, genes involved in calcium signaling, hormone signaling transduction, photosynthesis, pathogen resistance, and transcription factors such as heat stress transcription factors (HSFs), NACs, WRKYs, and bZIPs. Among them, PtABI5, PtNAC042, PtZIP17, PtSOD1, PtHSF30, PtHSFB2b, PtERF095, PtWRKY75, PtGST1, PtHSP23.2, PtHSP70, and PtLHC1 were significantly regulated by SPD or MLT treatment with same or different trends under heat stress condition, indicating that exogenous application of MLT and SPD might enhance heat tolerance in P. ternata through regulating these genes but may with different regulatory patterns. These findings contributed to the identification of potential genes involved in short-term HSR and the improved thermotolerance by MLT and SPD in P. ternata, which provided important clues for improving thermotolerance of P. ternata.

Transcriptome analysis reveals novel insights into the continuous cropping induced response in Codonopsis tangshen, a medicinal herb.

Codonopsis tangshen Oliv. (C. tangshen Oliv.), a famous medicinal herb in China, is seriously affected by continuous cropping (C-cro). The physiological and biochemical results indicated that C-cro significantly affected the malonaldehyde (MDA) and chlorophyll content, as well as activities of catalase (CAT) and superoxide dismutase (SOD) when compared with the non-continuous cropping (NC-cro) group. Transcriptome profiling found 762 differentially expressed genes, including 430 up-regulated and 332 down-regulated genes by C-cro. In addition, pathway enrichment analysis revealed that genes related to 'Tyrosine degradation I', 'Glycogen synthesis' and 'Phenylalanine and tyrosine catabolism' were up-regulated, and genes associated with 'Signal transduction', 'Immune system', etc. were down-regulated by C-cro. The expression of target genes was further validated by Q-PCR. In this study, we demonstrated the effects of C-cro on C. tangshen at the transcriptome level, and found possible C-cro responsive candidate genes. These findings could be further beneficial for improving the continuous cropping tolerance.

Water management impacts the soil microbial communities and total arsenic and methylated arsenicals in rice grains.

The bioavailability of the metalloid arsenic (As) in paddy soil is controlled by microbial cycling of As and other elements such as iron (Fe) and sulfur (S), which are strongly influenced by water management in paddy fields. In this study, we evaluated how water management affects As bioavailability by growing rice plants in a geogenic As-contaminated soil. We determined As speciation in soil porewater and the diversity of the associated microbial community. Continuous flooding enhanced the release of Fe and As and increased arsenite (As(III)) and methylated As species concentrations in the rice grain compared with aerobic treatment. Total inorganic and organic As in the grain was 84% and 81% lower, respectively, in the aerobic treatment compared with the continuous flooding treatment. The amounts of Fe(III)-reducing bacteria (FeRB) increased in the flooded rhizosphere soil. The abundance of FeRB in the soil correlated with the dissolution of Fe and As. Among the As-transformation genes quantified, the aioA gene for As(III) oxidation and arsM gene for As(III) methylation were most abundant. The arsM copy number correlated positively with the levels of dsrB (dissimilatory (bi) sulfite reductase ß-subunit), suggesting that dissimilatory sulfate-reducing bacteria (SRB) may play an important role in dimethylarsenate (DMAs(V)) production in soil. Our results show that decreased populations of rhizosphere FeRB and SRB contributed to a lower bioavailability of As, and decreased production of methylated arsenicals under oxic conditions.

Nitrate Stimulates Anaerobic Microbial Arsenite Oxidation in Paddy Soils.

Arsenic (As) bioavailability to rice plants is elevated in flooded paddy soils due to reductive mobilization of arsenite [As(III)]. However, some microorganisms are able to mediate anaerobic As(III) oxidation by coupling to nitrate reduction, thus attenuating As mobility. In this study, we investigated the impact of nitrate additions on As species dynamics in the porewater of four As-contaminated paddy soils. The effects of nitrate on microbial community structure and the abundance and diversity of the As(III) oxidase (aioA) genes were quantified using 16S rRNA sequencing, quantitative PCR, and aioA gene clone libraries. Nitrate additions greatly stimulated anaerobic oxidation of As(III) to As(V) and decreased total soluble As in the porewater in flooded paddy soils. Nitrate additions significantly enhanced the abundance of aioA genes and changed the microbial community structure by increasing the relative abundance of the operational taxonomic units (OTUs) from the genera Acidovorax and Azoarcus. The aioA gene sequences from the Acidovorax related OTU were also stimulated by nitrate. A bacterial strain (ST3) belonging to Acidovorax was isolated from nitrate-amended paddy soil. The strain was able to oxidize As(III) and Fe(II) under anoxic conditions using nitrate as the electron acceptor. Abiotic experiments showed that Fe(II), but not As(III), could be oxidized by nitrite. These results show that nitrate additions can stimulate As(III) oxidation in flooded paddy soils by enhancing the population of anaerobic As(III) oxidizers, offering a potential strategy to decrease As mobility in As-contaminated paddy soils.

Anaerobic arsenite oxidation by an autotrophic arsenite-oxidizing bacterium from an arsenic-contaminated paddy soil.

Microbe-mediated arsenic (As) redox reactions play an important role in the biogeochemical cycling of As. Reduction of arsenate [As(V)] generally leads to As mobilization in paddy soils and increased As availability to rice plants, whereas oxidation of arsenite [As(III)] results in As immobilization. A novel chemoautotrophic As(III)-oxidizing bacterium, designated strain SY, was isolated from an As-contaminated paddy soil. The isolate was able to derive energy from the oxidation of As(III) to As(V) under both aerobic and anaerobic conditions using O2 or NO3(-) as the respective electron acceptor. Inoculation of the washed SY cells into a flooded soil greatly enhanced As(III) oxidation to As(V) both in the solution and adsorbed phases of the soil. Strain SY is phylogenetically closely related to Paracoccus niistensis with a 16S rRNA gene similarity of 96.79%. The isolate contains both the denitrification and ribulose 1,5-bisphosphate carboxylase/oxygenase gene clusters, underscoring its ability to denitrify and to fix CO2 while coupled to As(III) oxidation. Deletion of the aioA gene encoding the As(III) oxidase subunit A abolished the As(III) oxidation ability of strain SY and led to increased sensitivity to As(III), suggesting that As(III) oxidation is a detoxification mechanism in this bacterium under aerobic and heterotrophic growth conditions. Analysis of the aioA gene clone library revealed that the majority of the As(III)-oxidizing bacteria in the soil were closely related to the genera Paracoccus of α-Proteobacteria. Our results provide direct evidence for As(III) oxidation by Paracoccus species and suggest that these species may play an important role in As(III) oxidation in paddy soils under both aerobic and denitrifying conditions.