De novo transcriptome sequencing and analysis of salt-, alkali-, and drought-responsive genes in Sophora alopecuroides.

BACKGROUND: Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora, is a highly salt-tolerant sand-fixing pioneer species distributed mostly in Western Asia and northwestern China. Few studies have assessed responses to abiotic stress in S. alopecuroides. The transcriptome of the genes that confer stress-tolerance in this species has not previously been sequenced. Our objective was to sequence and analyze this transcriptome. RESULTS: Twelve cDNA libraries were constructed in triplicate from mRNA obtained from Sophora alopecuroides for the control and salt, alkali, and drought treatments. Using de novo assembly, 902,812 assembled unigenes were generated, with an average length of 294 bp. Based on similarity searches, 545,615 (60.43%) had at least one significant match in the Nr, Nt, Pfam, KOG/COG, Swiss-Prot, and GO databases. In addition, 1673 differentially expressed genes (DEGs) were obtained from the salt treatment, 8142 from the alkali treatment, and 17,479 from the drought treatment. A total of 11,936 transcription factor genes from 82 transcription factor families were functionally annotated under salt, alkali, and drought stress, these include MYB, bZIP, NAC and WRKY family members. DEGs were involved in the hormone signal transduction pathway, biosynthesis of secondary metabolites and antioxidant enzymes; this suggests that these pathways or processes may be involved in tolerance towards salt, alkali, and drought stress in S. alopecuroides. CONCLUSION: Our study first reported transcriptome reference sequence data in Sophora alopecuroides, a non-model plant without a reference genome. We determined digital expression profile and discovered a broad survey of unigenes associated with salt, alkali, and drought stress which provide genomic resources available for Sophora alopecuroides.

Estimating the nitrogen source apportionment of Sophora japonica in roadside green spaces using stable isotope.

It is generally accepted that urban vegetation absorbs air pollutants resulting in improved air quality. However, limited work has provided experimental data that can be used to quantify this. In this study, Sophora japonica in the near-road environment was studied, and stable isotopes were used to estimate the proportional contributions of different nitrogen sources to the trees. δ15N and δ18O values were quantified for plant (n = 254) and soil samples (n = 86) collected from 12 sampling sites in Beijing. The elemental composition (total nitrogen (TN) and total carbon (TC)) of both samples types, and the ionic concentration (NO3- and NH4+) of soil samples were also measured. δ15N in S. japonica sampled near the road was significantly lower than in samples collected far from the road. Variation of δ18O, TN, and TC in plant samples could not be explained by the road distance. Using the SIAR Bayesian isotope mixing model and the mixing polygon method, the average proportional contributions of three nitrogen sources for the tree samples among all experiment sites were estimated, with the proportion for each nitrogen source following the order: soil (69.2%) > traffic-related NOx (19.3%) > dry deposition (11.5%). In addition, the results of the Bayesian model revealed that the nitrogen contribution of traffic-related NOx at road-adjacent sites (23.0%) was higher than the contribution of traffic-related NOx at sites far from the road (16.4%). These results indicated that the S. japonica in near-road green spaces was significantly influenced by traffic-related NOx emissions that were characterized by lower δ15N values. We found that using the SIAR Bayesian isotope mixing model and mixing polygon method, the potential nitrogen sources of plants could be estimated and the proportional contributions estimated by the model can reflect the plant's ability to absorb air-borne NOx.

Nonspecific Symbiosis Between Sophora flavescens and Different Rhizobia.

We explored the genetic basis of the promiscuous symbiosis of Sophora flavescens with diverse rhizobia. To determine the impact of Nod factors (NFs) on the symbiosis of S. flavescens, nodulation-related gene mutants of representative rhizobial strains were generated. Strains with mutations in common nodulation genes (nodC, nodM, and nodE) failed to nodulate S. flavescens, indicating that the promiscuous nodulation of this plant is strictly dependent on the basic NF structure. Mutations of the NF decoration genes nodH, nodS, nodZ, and noeI did not affect the nodulation of S. flavescens, but these mutations affected the nitrogen-fixation efficiency of nodules. Wild-type Bradyrhizobium diazoefficiens USDA110 cannot nodulate S. flavescens, but we obtained 14 Tn5 mutants of B. diazoefficiens that nodulated S. flavescens. This suggested that the mutations had disrupted a negative regulator that prevents nodulation of S. flavescens, leading to nonspecific nodulation. For Ensifer fredii CCBAU 45436 mutants, the minimal NF structure was sufficient for nodulation of soybean and S. flavescens. In summary, the mechanism of promiscuous symbiosis of S. flavescens with rhizobia might be related to its nonspecific recognition of NF structures, and the host specificity of rhizobia may also be controlled by currently unknown nodulation-related genes.

Tripartite symbiosis of Sophora tomentosa, rhizobia and arbuscular mycorhizal fungi

ABSTRACT Sophora tomentosa is a pantropical legume species with potential for recovery of areas degraded by salinization, and for stabilization of sand dunes. However, few studies on this species have been carried out, and none regarding its symbiotic relationship with beneficial soil microorganisms. Therefore, this study aimed to evaluate the diversity of nitrogen-fixing bacteria isolated from nodules of Sophora tomentosa, and to analyze the occurrence of colonization of arbuscular mycorrhizal fungi on the roots of this legume in seafront soil. Thus, seeds, root nodules, and soil from the rhizosphere of Sophora tomentosa were collected. From the soil samples, trap cultures with this species were established to extract spores and to evaluate arbuscular mycorhizal fungi colonization in legume roots, as well as to capture rhizobia. Rhizobia strains were isolated from nodules collected in the field or from the trap cultures. Representative isolates of the groups obtained in the similarity dendrogram, based on phenotypic characteristics, had their 16S rRNA genes sequenced. The legume species showed nodules with indeterminate growth, and reddish color, distributed throughout the root. Fifty-one strains of these nodules were isolated, of which 21 were classified in the genus Bacillus, Brevibacillus, Paenibacillus, Rhizobium and especially Sinorhizobium. Strains closely related to Sinorhizobium adhaerens were the predominant bacteria in nodules. The other genera found, with the exception of Rhizobium, are probably endophytic bacteria in the nodules. Arbuscular mycorrhizal fungi was observed colonizing the roots, but arbuscular mycorhizal fungi spores were not found in the trap cultures. Therefore Sophora tomentosa is associated with both arbuscular mycorhizal fungi and nodulating nitrogen-fixing bacteria.

Tripartite symbiosis of Sophora tomentosa, rhizobia and arbuscular mycorhizal fungi.

Sophora tomentosa is a pantropical legume species with potential for recovery of areas degraded by salinization, and for stabilization of sand dunes. However, few studies on this species have been carried out, and none regarding its symbiotic relationship with beneficial soil microorganisms. Therefore, this study aimed to evaluate the diversity of nitrogen-fixing bacteria isolated from nodules of Sophora tomentosa, and to analyze the occurrence of colonization of arbuscular mycorrhizal fungi on the roots of this legume in seafront soil. Thus, seeds, root nodules, and soil from the rhizosphere of Sophora tomentosa were collected. From the soil samples, trap cultures with this species were established to extract spores and to evaluate arbuscular mycorhizal fungi colonization in legume roots, as well as to capture rhizobia. Rhizobia strains were isolated from nodules collected in the field or from the trap cultures. Representative isolates of the groups obtained in the similarity dendrogram, based on phenotypic characteristics, had their 16S rRNA genes sequenced. The legume species showed nodules with indeterminate growth, and reddish color, distributed throughout the root. Fifty-one strains of these nodules were isolated, of which 21 were classified in the genus Bacillus, Brevibacillus, Paenibacillus, Rhizobium and especially Sinorhizobium. Strains closely related to Sinorhizobium adhaerens were the predominant bacteria in nodules. The other genera found, with the exception of Rhizobium, are probably endophytic bacteria in the nodules. Arbuscular mycorrhizal fungi was observed colonizing the roots, but arbuscular mycorhizal fungi spores were not found in the trap cultures. Therefore Sophora tomentosa is associated with both arbuscular mycorhizal fungi and nodulating nitrogen-fixing bacteria.

Effects of road dust on the growth characteristics of Sophora japonica L. seedlings.

Road dust is one of the most common pollutants and causes a series of negative effects on plant physiology. Dust's impacts on plants can be regarded as a combination of load, composition and grain size impacts on plants; however, there is a lack of integrated dust effect studies involving these three aspects. In our study, Sophora japonica seedlings were artificially dusted with road dust collected from the road surface of Beijing so that we could study the impacts of this dust on nitrogen/carbon allocation, biomass allocation and photosynthetic pigments from the three aspects of composition, load and grain size. The results showed that the growth characteristics of S. japonica seedlings were mostly influenced by dust composition and load. Leaf N, root-shoot ratio and chlorophyll a/b were significantly affected by dust composition and load; leaf C/N, shoot biomass, total chlorophyll and carotenoid were significantly affected by dust load; stem N and stem C/N were significantly affected by dust composition; while the dust grain size alone did not affect any of the growth characteristics. Road dust did influence the growth characteristics more extensively than loam. Therefore, a higher dust load could increase the differences between road dust and loam treatments. The elements in dust are well correlated to the shoot N, shoot C/N, and root-shoot ratio of S. japonica seedlings. This knowledge could benefit the management of urban green spaces.

Functional traits contributed to the superior performance of the exotic species Robinia pseudoacacia: a comparison with the native tree Sophora japonica.

Functional traits determine the ecological strategies of plants and therefore are widely considered to feature in the success of invasive species. By comparing a widespread exotic invasive species Robinia pseudoacacia L. with a related native one Sophora japonica L., this research aimed to study strategies of R. pseudoacacia for superior performance from the perspective of functional traits. We conducted a greenhouse experiment in which seedlings of R. pseudoacacia and S. japonica were grown separately under a factorial combination of two light regimes and three levels of nitrogen (N) fertilization, including a control and two levels intended to represent ambient and future levels of N deposition in Chinese forests. After 90 days of treatment, performance and functional traits were determined for the two species, the former referred to as the total biomass (TB) that directly affected fitness. Trait plasticity and integration (the pattern and extent of functional covariance among different plant traits) were analyzed and compared. We found that the two species showed significantly different plastic responses to light increase: in the low-light regime, they were similar in performance and functional traits, while in the high-light regime, R. pseudoacacia achieved a significantly higher TB and a suite of divergent but advantageous functional traits versus S. japonica, such as significantly greater photosynthetic capacity and leaf N concentration, and lower carbon-to-N ratio and root-to-shoot ratio, which conferred it the greater performance. Moreover, across the light gradient, R. pseudoacacia showed higher correlations between photosynthetic capacity and other functional traits than S. japonica. In contrast, N deposition showed little impact on our experiment. Our results suggested that across light regimes, three aspects of functional traits contributed to the superior performance of R. pseudoacacia: functional trait divergence, significantly different plasticity of these traits, as well as greater overall trait coordination.

The compounding effects of high pollen limitation, selfing rates and inbreeding depression leave a New Zealand tree with few viable offspring.

BACKGROUND AND AIMS: Interactions between species are especially sensitive to environmental changes. The interaction between plants and pollinators is of particular interest given the potential current global decline in pollinators. Reduced pollinator services can be compensated for in some plant species by self-pollination. However, if inbreeding depression is high, selfed progeny could die prior to reaching adulthood, leading to cryptic recruitment failure. METHODS: To examine this scenario, pollinator abundance, pollen limitation, selfing rates and inbreeding depression were examined in 12 populations of varying disturbance levels in Sophora microphylla (Fabaceae), an endemic New Zealand tree species. KEY RESULTS: High pollen limitation was found in all populations (average of 58 % reduction in seed production, nine populations), together with high selfing rates (61 % of offspring selfed, six populations) and high inbreeding depression (selfed offspring 86 % less fit, six populations). Pollen limitation was associated with lower visitation rates by the two endemic bird pollinators. CONCLUSIONS: The results suggest that for these populations, over half of the seeds produced are genetically doomed. This reduction in the fitness of progeny due to reduced pollinator service is probably important to population dynamics of other New Zealand species. More broadly, the results suggest that measures of seed production or seedling densities may be a gross overestimate of the effective offspring production. This could lead to cryptic recruitment failure, i.e. a decline in successful reproduction despite high progeny production. Given the global extent of pollinator declines, cryptic recruitment failure may be widespread.

Diverse novel mesorhizobia nodulate New Zealand native Sophora species.

Forty eight rhizobial isolates from New Zealand (NZ) native Sophora spp. growing in natural ecosystems were characterised. Thirty eight isolates across five groups showed greatest similarity to Mesorhizobium ciceri LMG 14989(T) with respect to their 16S rRNA and concatenated recA, glnll and rpoB sequences. Seven isolates had a 16S rRNA sequence identical to M. amorphae ATCC 19665(T) but showed greatest similarity to M. septentrionale LMG 23930(T) on their concatenated recA, glnll and rpoB sequences. All isolates grouped closely together for their nifH, nodA and nodC sequences, clearly separate from all other rhizobia in the GenBank database. None of the type strains closest to the Sophora isolates based on 16S rRNA sequence similarity nodulated Sophora microphylla but they all nodulated their original host. Twenty one Sophora isolates selected from the different 16S rRNA groupings produced N2-fixing nodules on three Sophora spp. but none nodulated any host of the type strains for the related species. DNA hybridisations indicated that these isolates belong to novel Mesorhizobium spp. that nodulate NZ native Sophora species.

Arbuscular mycorrhizal fungi play a role in protecting roots of Sophora viciifolia Hance. from Pb damage associated with increased phytochelatin synthase gene expression.

Understanding the influence of arbuscular mycorrhizal (AM) fungi on the expressions of the dominant plant-related genes under heavy metal (HM) stress is important for developing strategies to reclaim polluted sites. In this study, we cloned full-length cDNAs of phytochelatin synthase gene (PCS1) and Actin of Sophora viciifolia Hance., a predominant plant in Qiandongshan lead and zinc mine, by rapid amplification of cDNA ends. Consequently, we studied the response of SvPCS1 to Funneliformis mosseae inoculation under lead stress (0, 50, and 200 µM Pb(NO3)2) at different durations (1, 3, and 7 days) using quantitative reverse-transcription polymerase chain-reaction (qRT-PCR) technique. The Pb concentrations and chlorophyll fluorescence parameters were also measured to assay Pb toxicity to Sophora viciifolia. We found that Pb concentrations in roots increased with increasing Pb application and the durations; the F v /F m , F v /F o , qP, and Y(II) decreased; NPQ rose with increasing Pb concentrations; mycorrhizal symbiosis alleviated the Pb toxicity to plants; and SvPCS1 was constitutively expressed in the roots. It was also found that F. mosseae inoculation could promote the expression of SvPCS1 with the concentration ≤ 200 µM at the exposure time shorter than 7 days.

A tolerance gene for prenylated flavonoid encodes a 26S proteasome regulatory subunit in Sophora flavescens.

Yeast functional screening with a Sophora flavescens cDNA library was performed to identify the genes involved in the tolerant mechanism to the self-producing prenylated flavonoid sophoraflavanone G (SFG). One cDNA, which conferred SFG tolerance, encoded a regulatory particle triple-A ATPase 2 (SfRPT2), a member of the 26S proteasome subunit. The yeast transformant of SfRPT2 showed reduced SFG accumulation in the cells.

[Distribution and morphological variation of germplasm resource of Sophora alopecuroides].

OBJECTIVE: To analyze the genetic difference of biological characters on germplasm resources of Sophora alopecuroides. METHOD: Twenty-three populations of S. alopecuroides from Ningxia, Gansu, Qinghai, Xinjiang and Inner Mongolian were used to analyze the seed size, 1 000-grain weight, and germination characteristics and so on. RESULT: It showed that there were significant differences in seed size, 1 000-grain weight and the vitality of seeds. The biggest seed of S. alopecuroides was 4.7 mm x 3.5 mm, and the smallest was 3.8 mm x 2.9 mm, and the 1 000-grain weight was 15-26 g. Results of seeds vitality in 8 populations indicated that the highest vitality of seeds were No. 103 and No. 122. The germination index was 36.51 and 36.24 respectively, and the vitality index was 1 323.49 and 1 274.56. The coefficient of variation in seed traits exceeded 10% except the seed size. CONCLUSION: There are some differences and different heredity background in various S. alopecuroides germplasm resources.

[Effects of sand-burying on seed germination and seedling emergence of six psammophytes species].

This paper studied the effects of sand-burying on the seed germination and seedling emergence of six dominance plants in Keerqin Sandy Land. Six treatments of artificially sand-burying to depths 0, 2, 4, 6, 8, 10 and 12 cm were designed. The results showed that the seed germination of Agriophyllum squarrosum was significantly different (P < 0.05) between different treatments, but that of Artemesia halodendron was only significantly different (P< 0.05) between 2 cm and other burial depths. For other four plants, their seed germination was significantly different (P < 0.05) only between 0 cm and other burial depths. Sand-burying significantly affected the seedling emergence of all plant species. The emergence rate decreased with increasing burial depth. Higher emergence percentages were obtained at 2 and 4 cm burial depths. The species with larger seeds emerged from deeper depth, and the maximum burial depth of seedling emergence was Sophora flavescdens > Atraphaxis manshurica > or = Agriophyllum squarrosum > Hedysarum fruticosum > Bassia dasyphylla > Artemesia halodendron.

Changes in pit membrane porosity due to deflection and stretching: the role of vestured pits.

The effect of increasing pressure difference (DeltaP) on intervessel pit membrane porosity was studied in two angiosperm tree species with differing pit architecture. Fraxinus americana L. possesses typical angiosperm bordered pit structure while Sophora japonica L. exhibits well-developed vestures in intervessel pit chambers. It was hypothesized (a) that large DeltaP across intervessel pits would cause the deflection of pit membranes in the stems of F. americana resulting in significant increases in porosity and thus lower cavitation thresholds, and (b) that the presence of vestures would prevent the deflection of pit membranes in S. japonica. To determine if the porosity of pit membranes increased under mechanical stress, suspensions of colloidal gold, 5 nm and 20 nm in diameter, were perfused across intervessel pit membranes at DeltaP ranging from 0.25 MPa to 6.0 MPa. The effect of increasing DeltaP on membrane porosity was also tested by comparing air seeding thresholds (Pa) in stems perfused with water or a solution with lower surface tension. Air seeding and colloidal gold experiments indicated that pit membrane porosity increased significantly with DeltaP in F. americana. In S. japonica, increases in permeability to colloidal gold with DeltaP were small and maximum pore diameters predicted from Pa were independent of DeltaP, suggesting that vestures limited the degree to which the membrane can be deflected from the centre of the pit cavity. This provides the first experimental evidence that vestures reduce the probability of air seeding through pit membranes.

Seed chemistry of Sophora chrysophylla (mamane) in relation to diet of specialist avian seed predator Loxioides bailleui (palila) in Hawaii.

This study describes the chemical ecology of a tritrophic interaction among species endemic to the island of Hawaii, USA: a tree (Sophora chrysophylla: mamane), an endangered bird (Loxioides bailleui; palila), and moth larvae (Cydia spp.). Palila and Cydia both specialize on the seed embryos of mamane but avoid eating the seed coats. Palila actively seek out and feed mamane embryos and Cydia larvae to their nestlings. Because mamane embryos contain potentially toxic levels of alkaloids, including broadly toxic quinolizidine alkaloids, and because insects often sequester alkaloids from their food plants, we focus on the questions of why palila forage upon mamane embryos and why they supplement their diet with Cydia larvae. Our data show that mamane embryos contain high amounts of potentially toxic alkaloids, but are well balanced nutritionally and contain lipids, carbohydrates, proteins, amino acids, and minerals at levels that are likely to be sufficient for maintenance and breeding. Mamane seed coats contain lower levels of alkaloids and nutrients, somewhat higher levels of phenolics, and much higher levels of nondigestible fiber. Taken together, these results suggest that palila have evolved tolerance to high levels of alkaloids and that they forage upon embryos primarily because of their availability in the habitat and high nutritional reward. Our data also suggest that Cydia are used by palila because they are readily accessible, nontoxic, and nutritious; the larvae apparently do not sequester alkaloids while feeding upon mamane seeds. Our results are interpreted with respect to the likelihood of current and historical coadaptive responses in this ecologically isolated and simplified island setting.