Release of biogenic volatile organic compounds and physiological responses of two sub-tropical tree species to smoke derived from forest fire

Forests emit a large amount of biogenic volatile organic compounds (BVOCs) in response to biotic and abiotic stress. Despite frequent occurrence of large forest fires in recent years, the impact of smoke stress derived from these forest fires on the emission of BVOCs is largely unexplored. Thus, the aims of the study were to quantify the amount and composition of BVOCs released by two sub-tropical tree species, Cunninghamia lanceolata and Schima superba, in response to exposure to smoke. Physiological responses and their relationship with BVOCs were also investigated. The results showed that smoke treatments significantly (p < 0.001) promoted short-term release of BVOCs by C. lanceolata leaves than S. superba; and alkanes, olefins and benzene homologs were identified as major classes of BVOCs. Both C. lanceolata and S. superba seedlings showed significant (p < 0.005) physiological responses after being smoke-stressed where photosynthetic rate remained unaffected, chlorophyll content greatly reduced and Activities of anti-oxidant enzymes and the malondialdehyde content generally increased with the increase in smoke concentration. Activities of anti-oxidant enzymes showed mainly positive correlations with the major BVOCs. In conclusion, the release of BVOCs following smoke stress is species-specific and there exists a link between activities of antioxidant enzymes and BVOCs released. The findings provide insight about management of forest fires in order to control excessive emission of smoke that would trigger increased release of BVOCs.

The Construction of lncRNA/circRNA-miRNA-mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba

Schima superba is a precious timber and fire-resistant tree species widely distributed in southern China. Currently, there is little knowledge related to its growth traits, especially with respect to molecular breeding. The lack of relevant information has delayed the development of modern breeding. The purpose is to identify probable functional genes involved in S. superba growth through whole transcriptome sequencing. In this study, a total of 32,711 mRNAs, 525 miRNAs, 54,312 lncRNAs, and 1522 circRNAs were identified from 10 S. superba individuals containing different volumes of wood. Four possible regulators, comprising three lncRNAs, one circRNA, and eleven key miRNAs, were identified from the regulatory networks of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA to supply information on ncRNAs. Several candidate genes involved in phenylpropane and cellulose biosynthesis pathways, including Ss4CL2, SsCSL1, and SsCSL2, and transcription factors, including SsDELLA2 (SsSLR), SsDELLA3 (SsSLN), SsDELLA5 (SsGAI-like2), and SsNAM1, were identified to reveal the molecular regulatory mechanisms regulating the growth traits of S. superba. The results not merely provide candidate functional genes related to S. superba growth trait and will be useful to carry out molecular breeding, but the strategy and method also provide scientists with an effective approach to revealing mechanisms behind important economic traits in other species.

Effects of nitrogen stress and nitrogen form ratios on the bacterial community and diversity in the root surface and rhizosphere of Cunninghamia lanceolata and Schima superba

Background

The bacterial communities of the root surface and rhizosphere play a crucial role in the decomposition and transformation of soil nitrogen (N) and are also affected by soil N levels and distribution, especially the composition and diversity, which are sensitive to changes in the environment with high spatial and temporal heterogeneity of ammonium N (NH4 +-N) and nitrate N (NO3 --N).

Methods

One-year-old seedlings of Cunninghamia lanceolata and Schima superba were subjected to N stress (0.5 mmol L-1) and normal N supply (2 mmol L-1), and five different N form ratios (NH4 +-N to NO3 --N ratio of 10:0, 0:10, 8:2, 2:8, and 5:5) were created. We analyze the changes in composition and diversity of bacteria in the root surface and rhizosphere of two tree species by high-throughput sequencing.

Results

Differences in the composition of the major bacteria in the root surface and rhizosphere of C.lanceolata and S. superba under N stress and N form ratios were not significant. The dominant bacterial phyla shared by two tree species included Proteobacteria and Bacteroidota. Compared to normal N supply, the patterns of diversity in the root surface and rhizosphere of two tree species under N stress were distinct for each at five N form ratios. Under N stress, the bacterial diversity in the root surface was highest at NH4 +-N to NO3 --N ratio of 10:0 of C. lanceolata, whereas in the root surface, it was highest at the NH4 +-N to NO3 --N ratio of 0:10 of S. superba. The NH4 +-N to NO3 --N ratio of 5:5 reduced the bacterial diversity in the rhizosphere of two tree species, and the stability of the bacterial community in the rhizosphere was decreased in C. lanceolata. In addition, the bacterial diversity in the root surface was higher than in the rhizosphere under the N stress of two tree species.

Conclusion

The bacterial compositions were relatively conserved, but abundance and diversity changed in the root surface and rhizosphere of C. lanceolata and S. superba under N stress and different N form ratios. The heterogeneity of ammonium and nitrate N addition should be considered for N-stressed environments to improve bacterial diversity in the rhizosphere of two tree species.

A 6-year study on the mortality dynamics of sprouts germinated on Schima superba after a severe ice storm in southern China

Introduction

Natural disturbances modify forest structure by affecting regeneration dynamics and can change main ecosystem functions. An ice storm unusually took place in southern China in early 2008, which caused huge damage to forests. Resprouting of woody plants in a subtropical forest has received little attention. The role of survival time and mortality has been assessed for newsprouts after an ice storm.

Methods

In this study, damage types, in addition to the annual number and mortality rates of sprouts for all tagged and sampled resprouted Chinese gugertree (Schima superba Gardner & Champ.) individuals more than or equal to 4 cm in basal diameter (BD), were monitored. A total of six plots (20 m × 20 m) wererecorded in a subtropical secondary forest dominated by S. superba in Jianglang Mountain, China. This investigation had been conducted for six consecutive years.

Results

The results showed that the survival rates of the sprouts were dependent on the year they sprouted. The earlier the year they boomed, the lower the mortality. The sprouts produced in 2008 were of the highest vitality and survival rates. Sprouts of the decapitated trees exhibited a better survival rate than those of uprooted or leaning trees. Sprouting position also plays a role in regeneration. Sprouts at the basal trunks of uprooted trees and the sprouts at the upper trunksof the decapitated trees exhibited the lowest mortality. The relationship between the accumulative mortality rate and the average diameter of new sprouts isaffected by damage types.

Discussion

We reported the mortality dynamics of sproutsin a subtropical forest after a rare natural disaster. This information could serve asa reference for the construction of a branch sprout dynamic model ormanagement of forest restoration after ice storms.

Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis

One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.

The XTH Gene Family in Schima superba: Genome-Wide Identification, Expression Profiles, and Functional Interaction Network Analysis

Xyloglucan endotransglucosylase/hydrolase (XTH), belonging to glycoside hydrolase family 16, is one of the key enzymes in plant cell wall remodeling. Schima superba is an important timber and fireproof tree species in southern China. However, little is known about XTHs in S. superba. In the present study, a total of 34 SsuXTHs were obtained, which were classified into three subfamilies based on the phylogenetic relationship and unevenly distributed on 18 chromosomes. Furthermore, the intron-exon structure and conserved motif composition of them supported the classification and the members belonging to the same subfamily shared similar gene structures. Segmental and tandem duplication events did not lead to SsuXTH gene family expansion, and strong purifying selection pressures during evolution led to similar structure and function of SsuXTH gene family. The interaction network and cis-acting regulatory elements analysis revealed the SsuXTH expression might be regulated by multiple hormones, abiotic stresses and transcription factors. Finally, expression profiles and GO enrichment analysis showed most of the tandem repeat genes were mainly expressed in the phloem and xylem and they mainly participated in glycoside metabolic processes through the transfer and hydrolysis of xyloglucan in the cell wall and then regulated fiber elongation.

Identification and Validation of Reference Genes for Gene Expression Analysis in Schima superba

Real-time quantitative PCR (RT-qPCR) is a reliable and high-throughput technique for gene expression studies, but its accuracy depends on the expression stability of reference genes. Schima superba is a fast-growing timber species with strong resistance. However, thus far, reliable reference gene identifications have not been reported in S. superba. In this study, 19 candidate reference genes were selected and evaluated for their expression stability in different tissues of S. superba. Three software programs (geNorm, NormFinder, and BestKeeper) were used to evaluate the reference gene transcript stabilities, and comprehensive stability ranking was generated by the geometric mean method. Our results show that SsuACT was the most stable reference gene and that SsuACT + SsuRIB was the best reference gene combination for different tissues. Finally, the stable and less stable reference genes were verified using SsuSND1 expression in different tissues. To our knowledge, this is the first report to verify appropriate reference genes for normalizing gene expression in S. superba for different tissues, which will facilitate the future elucidation of gene regulations in this species and useful references for relative species.

PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings

Schima superba (Theaceae) is a subtropical evergreen tree and is used widely for forest firebreaks and gardening. It is a plant that tolerates salt and typically accumulates elevated amounts of manganese in the leaves. With large ecological amplitude, this tree species grows quickly. Due to its substantial biomass, it has a great potential for soil remediation. To evaluate the thorough framework of the mRNA, we employed PacBio sequencing technology for the first time to generate S. Superba transcriptome. In this analysis, overall, 511,759 full length non-chimeric reads were acquired, and 163,834 high-quality full-length reads were obtained. Overall, 93,362 open reading frames were obtained, of which 78,255 were complete. In gene annotation analyses, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Genes (COG), Gene Ontology (GO), and Non-Redundant (Nr) databases were allocated 91,082, 71,839, 38,914, and 38,376 transcripts, respectively. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT), and Coding Non-Coding Index (CNCI) databases and observed 8,551, 9,174, 20,720, and 18,669 lncRNAs, respectively. Moreover, nine genes were randomly selected for the expression analysis, which showed the highest expression of Gene 6 (Na_Ca_ex gene), and CAX (CAX-interacting protein 4) was higher in manganese (Mn)-treated group. This work provided significant number of full-length transcripts and refined the annotation of the reference genome, which will ease advanced genetic analyses of S. superba.

Biogenic volatile organic compound emissions from Pinus massoniana and Schima superba seedlings: Their responses to foliar and soil application of nitrogen

Increasing nitrogen (N) deposition is one of the main drivers of global change, while the emission of biogenic volatile organic compounds (BVOCs) from plant in response to elevated N deposition is poorly understood, especially with respect to the response to foliar application of N. In this study, BVOC emissions from two tree species (Pinus massoniana Lamb. and Schima superba Gardn. et Champ.) were determined by dynamic chamber coupled with a proton transfer reaction-time of flight-mass spectrometer. Two N application methods, namely soil application of N (SAN) and foliar application of N (FAN), and three N levels (5.6, 15.6 and 20.6 g N m^-2 yr^-1) were employed by applying NH₄NO₃ every week for 1.5 years. The results showed that: (1) oxygenated volatile organic compounds (OVOCs, mainly acetaldehyde, methyl alcohol, ethenone and acetone) and non-methane hydrocarbons (NMHCs, mainly monoterpenes, propyne, 1,3-butadiene and propylene) were the dominant BVOCs for all the treatments, accounting for 32.40-65.72% and 19.21-47.39% of total 100 determined BVOC compounds, respectively; (2) for S. superba seedlings, both SAN and FAN treatments significantly decreased total BVOC emissions (11.83% to 66.23%). However, total BVOCs from P. massoniana significantly increased with N addition for SAN treatment, while no difference were found in the FAN treatment; (3) BVOC emission rates for FAN treatment were significantly lower than those for SAN treatment, indicating that previous studies which simulated N deposition by adding N directly to soil might have imprecisely estimated their effects on plant BVOC emissions. Considering the inconsistent responses of BVOC emissions to different N application methods for different plant species, close attention should be paid on the effects of N deposition or even global change on plant BVOC emissions in the future.

Anticandidal Potential of Stem Bark Extract from Schima superba and the Identification of Its Major Anticandidal Compound

Plant-derived extracts are a promising source of new drugs. Schima superba is traditionally used in China for heat clearing, detoxification, and treatment of furuncles. In this study, the anticandidal properties and mechanism of action of S. superba (SSE) were explored using a stem bark extract. SSE possessed high polyphenol and saponin contents of 256.6 ± 5.1 and 357.8 ± 31.5 µg/mg, respectively. A clear inhibition zone was observed for C. albicans growth through the disc diffusion method and the 50% inhibition of C. albicans by SSE was 415.2 µg/mL. Transcriptomic analysis in C. albicans treated with different doses of SSE was conducted through RNA-seq. Average values of 6068 genes and 20,842,500 clean reads were identified from each sample. Among these samples, 1680 and 1956 genes were differentially expressed genes (DEGs) from the SSE treatments of 0.2 and 0.4 mg/mL, respectively. C. albicans growth was inhibited by the changes in gene expression associated with the cell wall and membrane composition including the regulation of chitin degradation and ergosterol biosynthesis. This result could be reflected in the irregularly wrinkled morphology of the ruptured cell as revealed through SEM analysis. ESI-MS and NMR analyses revealed that the major compound purified from SSE was sasanquasaponin III and the 50% inhibition of C. albicans was 93.1 µg/mL. In summary, the traditional Chinese medicine S. superba can be applied as an anticandidal agent in complementary and alternative medicine.

A high-density genetic map of Schima superba based on its chromosomal characteristics

BACKGROUND

Schima superba (Theaceae) is a popular woody tree in China. The obscure chromosomal characters of this species are a limitation in the development of high-density genetic linkage maps, which are valuable resources for molecular breeding and functional genomics.

RESULTS

We determined the chromosome number and the karyotype of S. superba as 2n = 36 = 36 m, which is consistent with the tribe Schimeae (n = 18). A high-density genetic map was constructed using genotyping by sequencing (GBS). A F1 full-sib with 116 individuals and their parents (LC31 × JO32) were sequenced on the Illumina HiSeq™ platform. Overall, 343.3 Gb of raw data containing 1,191,933,474 paired-end reads were generated. Based on this, 99,966 polymorphic SNP markers were developed from the parents, and 2209 markers were mapped onto the integrated genetic linkage map after data filtering and SNP genotyping. The map spanned 2076.24 cM and was distributed among 18 linkage groups. The average marker interval was 0.94 cM. A total of 168 quantitative trait loci (QTLs) for 14 growth traits were identified.

CONCLUSIONS

The chromosome number and karyotype of S. superba was 2n = 36 = 36 m and a linkage map with 2209 SNP markers was constructed to identify QTLs for growth traits. Our study provides a basis for molecular-assisted breeding and genomic studies, which will contribute towards the future research and genetic improvement of S. superba.

Effects of cadmium on photosynthesis of Schima superba young plant detected by chlorophyll fluorescence

Contamination by heavy metals has become a serious environmental pollution issue today due to its potential threat to plant, wildlife, and human health. Photosynthesis, a process in which light energy is used to produce sugar and other organic compounds, is sensitive to heavy metals. In the present study, the response of photosynthetic process and carbon assimilation of Schima superba was investigated under cadmium (Cd) stress. Three Cd concentrations (0, 300, and 600 mg kg^-1) were used designated as control (CK), low Cd (L₁), and high Cd treatment (L₂) of plants. Results showed that photosystem II (PSII) acceptor and donor side electron transport were more easily blocked in treatment compared to control, and L₂ have more significant changes than L₁. A substantial decrease of 820 nm reflection curve absorption was observed both in L₁ and L₂ treatments. Special energy fluxes showed significant difference between the control group and the treated group, which indicated that low concentration Cd stress can cause decrease in quantum yield of PSII in plants studied. Non-stomatal factors resulted in a decrease in net photosynthetic rate and a decrease in photosystem activity. Our results suggested that Cd can damage structure and function of the photosynthesis of S. superba young plants.

[Effects of neighbor competition on growth, fine root morphology and distribution of Schima superba and Cunninghamia lanceolata in different nutrient environments]

Taking Schima superba and Cunninghamia lanceolata as test materials, a pot experiment was conducted to simulate the heterogeneous and homogeneous forest soil nutrient environments, and design three planting modes including single plant, two-strain pure plant and two-strain mixed ones to reason the promotion in mixed S. superba and C. lanceolata plantation and the competitive advantage of S. superba. Results showed that compared with the homogeneous nutrient environment, both S. superba and C. lanceolata had the higher seedling height and dry matter accumulation, when mixed in the heterogeneous nutrient environment, S. superba displayed the obviously competitive advantage, which related to its root plasticity. The fine root of S. superba mixed in each diameter class showed a lot of hyperplasia, and the root total length, surface area and volume of which were 80%-180% higher than that of C. lanceolata. S. superba took the advantage of the compensatory growth strategy of vertical direction in fine roots, namely, they still multiplied to gain greater competitive advantage in low nutrient patches, besides occupying eutrophic surface. The different soil colonization and niche differentiation in fine root of S. superba and C. lanceolata alleviated the strong competition for nutrients of the roots of the two species, and improved the mixed-plantation production. Pure plantation of S. superba harvested the lower yield, which due to the root self-recognition inhibited the growth of root system. Fine roots staggered and evenly distributed on the space might be a reason for stable structure of pure S. superba plantation. So, it was recommended that block surface layer soil preparation and fertilization are used to improve the soil nutrient distribution, and the mixed plantation is constructed to promote the growth of S. superba and C. lanceolata, at the same time, the stand density is regulated to promote tree growth for the pure artificial S. superba plantation which had already been built.

[Different responses of growth and root development of Schima superba provenance to the adjacent plant competition in different nutrient conditions]

Growth and root development of three Schima superba seedling provenances were influenced by adjacent plant competition in the homogeneous and heterogeneous nutrient environment, which revealed the reasons of S. superba competition differences in the different genotypes. The results indicated that, compared with homogeneous nutrient environment, all three S. superba provenances showed higher seedling height, more dry matter accumulation, and significant root proliferation in heterogeneous nutrient environment. Under heterogeneous nutrient environment, the seedlings of S. superba from Jian'ou of Fujian exhibited higher competitive advantage in growth than that of S. superba from Longquan of Zhejiang and Xinfeng of Jiangxi, especially standing out under mixed cultivation with seedlings of Cunninghamia lanceolata. Under mixed cultivation, the root growth parameters of S. superba such as root length, root surface area and volume increased by 20.4%-69.0% compared with the single plant, which enhanced the foraging ability and growth advantage. To some extent, however, the root development in Longquan of Zhejiang and Xinfeng of Jiangxi was suppressed when subjected to the pattern of mixed cultivation. Besides, the root growth and development of all three S. superba provenances were suppressed, which might be due to their root self-recognition in the pattern of mono cultivation. Therefore, the seedling growth in Jian'ou of Fujian decreased significantly, but seedling growth in Longquan of Zhejiang and Xinfeng of Jiangxi was not suppressed, even increased evidently, as their root physiological plasticity might play the crucial role in seedling growth. Hence the S. superba from Jian'ou of Fujian with high foraging efficiency and competition ability was suggested with the method of mixed forestation to improve the S. superba forest plantation productivity.

Stomatal uptake of O3 in a Schima superba plantation in subtropical China derived from sap flow measurements

Canopy stomatal ozone (O3) flux (Fst,O3) in a plantation of Schima superba, an ecologically and economically important evergreen pioneer tree species in subtropical China, was quantified based on sap flow measurements during a 2-year period. Mean Fst,O3 and accumulated Fst,O3 (AFst0) were significantly higher in wet seasons from April to September (4.62 nmol m(-2) s(-1) and 35.37 mmol m(-2), respectively) than in dry seasons from October to March (3.90 nmol m(-2) s(-1) and 24.15 mmol m(-1), respectively), yet comparable between the 2 years of the experiment, being 4.23 nmol m(-2) s(-1) and 58.23 mmol m(-2) in April 2013-March 2014 and 4.29 nmol m(-2) s(-1) and 60.80 mmol m(-2) in April 2014-March 2015, respectively. At the diurnal scale, Fst,O3 generally peaked in the early to middle afternoon hours (13:00-15:00), while the maximum stomatal conductance (Gst,O3) typically occurred in the middle to late morning hours (09:00-11:00). Monthly integrated AFst0 reached the maximum in July, although accumulated O3 exposure (SUM0) was highest in October. Seasonally or yearly, the accumulated O3 doses, either exposure-based or flux-based, notably exceeded the currently adopted critical thresholds for the protection of forest trees. These results, on the one hand, demonstrated the decoupling between the stomatal uptake of O3 and its environmental exposure level; on the other hand, indicated the potential O3 risk for S. superba in the experimental site. Therefore, the present study endorses the use of sap flow measurements as a feasible tool for estimating Fst,O3, and the transition from the exposure-based toward flux-based metrics for assessing O3 risk for forest trees. Further studies are urgently needed to relate stomatal O3 uptake doses with tree growth reductions for an improved understanding of O3 effects on trees under natural conditions.