Expression and promoter analysis of MEP pathway enzyme-encoding genes in Pinus massoniana Lamb.

The methylerythritol phosphate (MEP) pathway provides the universal basic blocks for the biosynthesis of terpenoids and plays a critical role in the growth and development of higher plants. Pinus massoniana is the most valuable oleoresin producer tree with an extensive terrestrial range. It has the potential to produce more oleoresin with commercial value, while being resistant to pine wood nematode (PWN) disease. For this study, eleven MEP pathway associated enzyme-encoding genes and ten promoters were isolated from P. massoniana. Three PmDXS and two PmHDR existed as multi-copy genes, whereas the other six genes existed as single copies. All eleven of these MEP enzymes exhibited chloroplast localization with transient expression. Most of the MEP genes showed higher expression in the needles, while PmDXS2, PmDXS3, and PmHDR1 had high expression in the roots. The expressions of a few MEP genes could be induced under exogenous elicitor conditions. The functional complementation in a dxs-mutant Escherichia coli strain showed the DXS enzymatic activities of the three PmDXSs. High throughput TAIL PCR was employed to obtain the upstream sequences of the genes encoding for enzymes in the MEP pathway, whereby abundant light responsive cis-elements and transcription factor (TF) binding sites were identified within the ten promoters. This study provides a theoretical basis for research on the functionality and transcriptional regulation of MEP enzymes, as well as a potential strategy for high-resin generation and improved genetic resistance in P. massoniana.

Genome and transcriptome analysis of rock-dissolving Pseudomonas sp. NLX-4 strain.

Microbial weathering processes can significantly promote soil properties and reduce rock-to-soil ratio. Some soil-inhabiting bacteria exhibit efficient rock-dissolution abilities by releasing organic acids and other chemical elements from the silicate rocks. However, our understanding of the molecular mechanisms involved during bacterial rock-dissolution is still limited. In this study, we performed silicate rock-dissolution experiments on a Pseudomonas sp. NLX-4 strain isolated from an over-exploited mining site. The results revealed that Pseudomonas sp. NLX-4 strain efficiently accelerates the dissolution of silicate rocks by secreting amino acids, exopolysaccharides, and organic acids. Through employing genome and transcriptome sequencing (RNA-seq), we identified the major regulatory genes. Specifically, 15 differentially expressed genes (DEGs) encoding for siderophore transport, EPS and amino acids synthesis, organic acids metabolism, and bacterial resistance to adverse environmental conditions were highly up-regulated in silicate rock cultures of NLX-4 strain. Our study reports a potential bacterial based approach for improving the ecological restoration of over-exploited rock mining sites.

Comparative effects of the recovery from sulfuric and nitric acid rain on the soil enzyme activities and metabolic functions of soil microbial communities.

Acid rain (AR) is a serious issue in China, particularly in the Yangtze River Delta region where the economy has undergone rapid development. Over the last few years, the composition of acid rain in the Yangtze River Delta region has gradually changed from sulfuric acid rain (SAR) to nitric acid rain (NAR) due to controls on SO2 emissions, but increased NOx emissions. These changes have made ecosystems more complex. For this study, we halted AR treatments in Quercus acutissima forest plots that had received simulated AR for one year and monitored them from the following February to November. We investigated their soil resident enzyme and microbial metabolic activities, as well as community functional diversity. The results revealed that AR treatments negatively affected both the soil microbial activity and soil microbial community functional diversity; however, both managed to recover over time, once the AR treatments were stopped. During the AR treatment and recovery periods, four main categories (carbohydrates, carboxylic acids, amino acids, and polymers) were dominantly utilized. The utilization of pyruvic acid, which was affected by the AR treatments, as well as d-mannitol and tween 80, accounted for changes in the peak values of the C substrate groups during the AR treatment recovery period. Finally, changes in the activities of soil enzymes recorded following AR recovery, were closely related to the utilization of six C substrate groups. Our results suggested that the recovery of soils following the cessation of NAR stress was more rapid than from SAR. Further, that short-term NAR could be easily treated during the transformation from SAR to NAR in the Yangtze River Delta region. These results might also enrich the basic data relating to post-AR treatments on the soil environment, while having significance toward guiding further studies on the recovery of ecosystems from AR.

Tissue-specific transcriptome for Dendrobium officinale reveals genes involved in flavonoid biosynthesis.

Dendrobium officinale is a kind of crop and precious herbal that is widely distributed in China. We applied transcriptomics to investigate the flavonoids and their biosynthesis-related genes from different tissues. Total flavonoid was determined in three different tissues. In this study, nine cDNA libraries were generated from Dendrobium officinale. A total of 530 million (70.73%) of the high-quality reads were successfully mapped to the reference genome of Dendrobium officinale and nine libraries were combined and assembled into 24,927 non-redundant genes. We mapped all of these genes to reference pathways in the KEGG database to identify polysaccharide and secondary metabolites pathways in which the genes may be involved. We outlined the biosynthetic pathway of flavonoids and identified putative genes, which provide understanding of the biosynthesis and regulation of Dendrobium officinale flavonoids at the molecular level. We identified five CHS genes from Dendrobium officinale and characterized the CHS gene family. The flavonoid-related key enzyme genes were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR. These data on flavonoid genes obtained in this work will be useful in understanding the molecular mechanisms of different tissues in Dendrobium officinale.

Converting evergreen broad-leaved forests into tea and Moso bamboo plantations affects labile carbon pools and the chemical composition of soil organic carbon.

This study aimed to explore the effects of conversion from evergreen broad-leaved forests (EBFs) to tea plantations (TPs) and Moso bamboo (Phyllostachys heterocycla var. pubescens) plantations (MBPs) and the subsequent long-term intensive management on the soil carbon pool and the chemical composition of soil organic carbon (SOC). Soil samples from three layers (0-10, 10-30 and 30-60 cm, respectively) were collected from adjacent EBFs, TPs and MBPs in An'ji County, Zhejiang Province, China. The physico-chemical properties of soils, including bulk density, SOC and its different fractions were determined. The chemical composition of SOC was also measured using 13C-nuclear magnetic resonance spectroscopy (NMR). The results showed that conversion from EBFs to TPs and MBPs decreased the concentrations of water soluble organic carbon (WSOC), light and heavy fraction organic carbon (LFOC, HFOC) and humus carbon (HC) (P < 0.05), reduced the O-alkyl C and carbonl C content, but increased the alkyl C, Aromatic C, aromaticity and the ratio of alkyl C/O-alkyl C (A/O-A) (P < 0.05). These results suggested that intensive management markedly altered the chemical structure of SOC and labile carbon pools. Our results demonstrated that converting EBFs to TPs and MBPs had a negative effect on SOC content and a positive effect on SOC stability. Therefore, management practices such as rational fertilization and sod cultivation are recommended after land-use conversion.

Polysaccharide biosynthetic pathway profiling and putative gene mining of Dendrobium moniliforme using RNA-Seq in different tissues.

BACKGROUND: Dendrobium moniliforme (Linnaeus) Swartz is a well-known plant used in traditional Chinese medicine due to bioactive constituents. Polysaccharides are the main medicinal ingredients, yet no studies have been published on polysaccharide biosynthesis in D. moniliforme. To comprehensively investigate the polysaccharide at the transcription level, we performed de novo transcriptome sequencing for the first time to produce a comprehensive transcriptome of D. moniliforme. RESULTS: In our study, a database of 562,580 unigenes (average length = 1115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, we identified 1204 carbohydrate-active related unigenes against CAZy database, including 417 glycosyltransferase genes (GTs), 780 glycoside hydrolases (GHs), 19 carbohydrate esterases (CEs), 75 carbohydrate-binding modules (CBMs), and 44 polysaccharide lyases (PLs). In the cellulose synthase family, 21 differential expression genes (DEGs) related to polysaccharide were identified. Subsequently, the tissue-specific expression patterns of the genes involved in polysaccharide pathway were investigated, which provide understanding of the biosynthesis and regulation of DMP at the molecular level. The two key enzyme genes (Susy and SPS) involved in the polysaccharide pathway were identified, and their expression patterns in different tissues were further analyzed using quantitative real-time PCR. CONCLUSIONS: We determined the content of polysaccharides from Dendrobium moniliforme under different tissues, and we obtained a large number of differential genes by transcriptome sequencing. This database provides a pool of candidate genes involved in biosynthesis of polysaccharides in D. moniliforme. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb.

Impacts of changes in vegetation on saturated hydraulic conductivity of soil in subtropical forests.

Saturated hydraulic conductivity (Ks) is one of the most important soil properties that determines water flow behavior in terrestrial ecosystems. However, the Ks of forest soils is difficult to predict due to multiple interactions, such as anthropological and geomorphic processes. In this study, we examined the impacts of vegetation type on Ks and associated mechanisms. We found that Ks differed with vegetation type and soil depth, and the impact of vegetation type on Ks was dependent on soil depth. Ks did not differ among vegetation types at soil depths of 0-10 and 20-30 cm, but was significantly lower in managed forest types (mixed evergreen broad-leaved and coniferous forests, bamboo forests, and tea gardens) than native evergreen broadleaf forests at a depth of 10-20 cm. Boosted regression tree analysis indicated that total porosity, non-capillary porosity, and macro water-stable aggregates were the primary factors that influenced Ks. Our results suggested that vegetation type was a key factor that influences hydraulic properties in subtropical forest soils through the alteration of soil properties, such as porosity and macro water-stable aggregates.

Effects of sulfuric, nitric, and mixed acid rain on Chinese fir sapling growth in Southern China.

The influence of acid rain on plant growth includes direct effects on foliage as well as indirect soil-mediated effects that cause a reduction in root growth. In addition, the concentration of NO3- in acid rain increases along with the rapid growth of nitrogen deposition. In this study, we investigated the impact of simulated acid rain with different SO42-/NO3- (S/N) ratios, which were 1:0, 5:1, 1:1, 1:5 and 0:1, on Chinese fir sapling growth from March 2015 to April 2016. Results showed that Chinese fir sapling height growth rate (HGR) and basal diameter growth rate (DGR) decreased as acid rain pH decreased, and also decreased as the percentage of NO3- increased in acid rain. Acid rain pH significantly decreased the Chlorophyll a (Chla) and Chlorophyll b (Chlb) content, and Chla and Chlb contents with acid rain S/N 1:5 were significantly lower than those with S/N 1:0 at pH 2.5. The chlorophyll fluorescence parameters, maximal efficiency of Photosystem II photochemistry (Fv/Fm) and non-photochemical quenching coefficient (NPQ), with most acid rain treatments were significantly lower than those with CK treatments. Root activities first increased and then decreased as acid rain pH decreased, when acid rain S/N ratios were 1:1, 1:5 and 0:1. Redundancy discriminant analysis (RDA) showed that the Chinese fir DGR and HGR had positive correlations with Chla, Chlb, Fv/Fm ratio, root activity, catalase and superoxide dismutase activities in roots under the stress of acid rain with different pH and S/N ratios. The structural equation modelling (SEM) results showed that acid rain NO3- concentration and pH had stronger direct effects on Chinese fir sapling HGR and DGR, and the direct effects of acid rain NO3- concentration and pH on HGR were lower than those on DGR. Our results suggest that the ratio of SO42- to NO3- in acid rain is an important factor which could affect the sustainable development of monoculture Chinese fir plantations in southern China.

Comparative effects of simulated acid rain of different ratios of SO42- to NO3- on fine root in subtropical plantation of China.

The influence of acid rain on forest trees includes direct effects on foliage as well as indirect soil-mediated effects that cause a reduction in fine-root growth. In addition, the concentration of NO3- in acid rain increases with the rapidly growing of nitrogen deposition. In this study, we investigated the impact of simulated acid rain with different SO42-/NO3- (S/N) ratios, which were 5:1 (S), 1:1 (SN) and 1:5 (N), on fine-root growth from March 2015 to February 2016. Results showed that fine roots were more sensitive to the effects of acid rain than soils in the short-term. Both soil pH and fine root biomass (FRB) significantly decreased as acid rain pH decreased, and also decreased with the percentage of NO3- increased in acid rain. Acid rain pH significantly influenced soil total carbon and available potassium in summer. Higher acidity level (pH=2.5), especially of the N treatments, had the strongest inhibitory impact on soil microbial activity after summer. The structural equation modelling results showed that acid rain S/N ratio and pH had stronger direct effects on FRB than indirect effects via changed soil and fine root properties. Fine-root element contents and antioxidant enzymes activities were significantly affected by acid rain S/N ratio and pH during most seasons. Fine-root Al ion content, Ca/Al, Mg/Al ratios and catalase activity were used as better indicators than soil parameters for evaluating the effects of different acid rain S/N ratios and pH on forests. Our results suggest that the ratio of SO42- to NO3- in acid rain is an important factor which could affect fine-root growth in subtropical forests of China.

Vegetation change impacts on soil organic carbon chemical composition in subtropical forests.

Changes in the chemical composition of soil organic carbon (SOC) might strongly affect the global carbon cycle as it controls the SOC decomposition rate. Vegetation change associated with long-term land use changes is known to strongly impact the chemical composition of SOC; however, data on the impacts of vegetation change following disturbance events of short durations and succession that occur frequently in forest ecosystems via diverse management objectives on SOC chemical composition are negligible. Here we examined the impacts of vegetation changes on the chemical composition of SOC by sampling soils of native broad-leaved forests, planted mixed broad-leaved and coniferous forests, and tea gardens in eastern China. We used nuclear magnetic resonance spectroscopy to quantify SOC chemical composition. We found that among all components of SOC chemical composition, alkyl carbon (C) and aryl C were more liable to change with vegetation than other SOC components. Soil pH was negatively correlated to the relative abundances of alkyl C and N-alkyl C, and Shannon's index of overstory plant species was positively correlated to the relative abundances of phenolic C and aromaticity. Our results suggest that vegetation changes following short disturbance events and succession may strongly alter SOC chemical composition in forest ecosystems.