Characterization of the complete chloroplast genome of orchid family species Paphiopedilum bellatulum.

The genus Paphiopedilum is well known as the lady's slipper orchid in Orchidaceae family. Paphiopedilum bellatulum (Rchb.f.) Stein 1892, has important medicinal and ornamental value, which occurs in the tropical Asia. However, in recent decades, it was threatened with extinction by significantly reduced small population size. In this study, we sequenced and characterized the complete chloroplast genome of P. bellatulum based on the Illumina Hiseq platform. The size of P. bellatulum chloroplast genome was 156,567 bp, including a large single-copy (LSC) region of 88,243 bp, a small single-copy (SSC) region of 3652 bp, and two inverted repeat regions (IRs) of 32,336 bp. The overall GC contents of the chloroplast genome were 35.71%. A total of 122 genes were annotated, including 76 protein-coding genes, 38 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). The phylogenetic analysis indicated that P. bellatulum formed a close relationship with another Paphiopedilum species P. wenshanense. The results will provide helpful genetic resource for further phylogenetic studies of the genus Paphiopedilum.

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities

Abstract Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6 mL of 0.5 M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing + Ca2+ flocculation) and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP + Triton X-100 + skim milk (100 mM Tris, 100 mM Na4P2O7, 1% polyvinylpyrrolidone, 100 mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0) removed most soil humic contaminants. When the pretreatment was combined with Ca2+ flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB) had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGB revealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities.

Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high purity DNA from soil microbiota, five prewashing agents were compared in terms of their efficiency and effectiveness in removing soil contaminants. Residual contaminants were precipitated by adding 0.6mL of 0.5M CaCl2. Four cell lysis methods were applied to test their compatibility with the pretreatment (prewashing+Ca2+ flocculation) and to ultimately identify the optimal cell lysis method for analyzing fungal communities in forest soils. The results showed that pretreatment with TNP+Triton X-100+skim milk (100mM Tris, 100mM Na4P2O7, 1% polyvinylpyrrolidone, 100mM NaCl, 0.05% Triton X-100, 4% skim milk, pH 10.0) removed most soil humic contaminants. When the pretreatment was combined with Ca2+ flocculation, the purity of all soil DNA samples was further improved. DNA samples obtained by the fast glass bead-beating method (MethodFGB) had the highest purity. The resulting DNA was successfully used, without further purification steps, as a template for polymerase chain reaction targeting fungal internal transcribed spacer regions. The results obtained by terminal restriction fragment length polymorphism analysis indicated that the MethodFGB revealed greater fungal diversity and more distinctive community structure compared with the other methods tested. Our study provides a protocol for fungal cell lysis in soil, which is fast, convenient, and effective for analyzing fungal communities in forest soils.

Photosynthetic Response of Soybean to Microclimate in 26-Year-Old Tree-Based Intercropping Systems in Southern Ontario, Canada.

In order to study the effect of light competition and microclimatic modifications on the net assimilation (NA), growth and yield of soybean (Glycine max L.) as an understory crop, three 26-year-old soybean-tree (Acer saccharinum Marsh., Populus deltoides X nigra, Juglans nigra L.) intercropping systems were examined. Tree competition reduced photosynthetically active radiation (PAR) incident on soybeans and reduced net assimilation, growth and yield of soybean. Soil moisture of 20 cm depth close (< 3 m) to the tree rows was also reduced. Correlation analysis showed that NA and soil water content were highly correlated with growth and yield of soybean. When compared with the monoculture soybean system, the relative humidity (RH) of the poplar-soybean, silver maple-soybean, and black walnut-soybean intercropped systems was increased by 7.1%, 8.0% and 5.9%, soil water content was reduced by 37.8%, 26.3% and 30.9%, ambient temperature was reduced by 1.3°C, 1.4°C and 1.0°C, PAR was reduced by 53.6%, 57.9% and 39.9%, and air CO2 concentration was reduced by 3.7µmol·mol(-1), 4.2µmol·mol(-1) and 2.8µmol·mol(-1), respectively. Compared to the monoculture, the average NA of soybean in poplar, maple and walnut treatments was also reduced by 53.1%, 67.5% and 46.5%, respectively. Multivariate stepwise regression analysis showed that PAR, ambient temperature and CO2 concentration were the dominant factors influencing net photosynthetic rate.

Soil fungal communities of montane natural secondary forest types in China.

Distinctive plant communities may provide specific physical and chemical properties with soils by specific litters and root exudates to exert effects on soil microorganisms. Past logging activities in the Qinling Mountains induced diverse natural secondary forest types (NSFTs). How these recovered NSFTs regulate patterns of soil microbial communities remain limited. In the study, we used terminal-restriction fragment length polymorphism (T-RFLP) to precisely determine forest type-specific soil fungal diversity and composition in five NSFTs. Our results indicated that NSFTs had significant impacts on the soil fungal communities. The most diverse fungal species were found in the Armand pine (Pinus armandi) and Chinese pine (Pinus tabulaeformis) forest soils, followed by sharptooth oak (Quercus aliena var. acuteserrata) and Chinese pine-sharptooth oak forest soils, the wilson spruce (Picea wilsonii) forests had the lowest soil fungal diversity. The analyses of community composition suggested that the fungal communities of Armand pine forest soils were similar to those of Chinese pine forest soils, while other communities prominently differed from each other. Stepwise multiple regression analysis revealed that soil silt, clay, pH, and ammonium nitrogen had intimate linkages with soil fungal diversity. Furthermore, the patterns of soil fungal communities were strongly governed by the specific soil environments of the tested NSFTs, as described by canonical correspondence analysis (CCA). Finally, our study showed that soil fungal communities may be mediated by NSFTs via specific soil edaphic status. Hence, such a comparable study may provide fundamental information for fungal diversity and community structure of natural forests and assist with better prediction and understanding how soil fungal composition and function alter with forest type transformation.

Soil microbial biomass, basal respiration and enzyme activity of main forest types in the Qinling Mountains.

Different forest types exert essential impacts on soil physical-chemical characteristics by dominant tree species producing diverse litters and root exudates, thereby further regulating size and activity of soil microbial communities. However, the study accuracy is usually restricted by differences in climate, soil type and forest age. Our objective is to precisely quantify soil microbial biomass, basal respiration and enzyme activity of five natural secondary forest (NSF) types with the same stand age and soil type in a small climate region and to evaluate relationship between soil microbial and physical-chemical characters. We determined soil physical-chemical indices and used the chloroform fumigation-extraction method, alkali absorption method and titration or colorimetry to obtain the microbial data. Our results showed that soil physical-chemical characters remarkably differed among the NSFs. Microbial biomass carbon (Cmic) was the highest in wilson spruce soils, while microbial biomass nitrogen (Nmic) was the highest in sharptooth oak soils. Moreover, the highest basal respiration was found in the spruce soils, but mixed, Chinese pine and spruce stands exhibited a higher soil qCO2. The spruce soils had the highest Cmic/Nmic ratio, the greatest Nmic/TN and Cmic/Corg ratios were found in the oak soils. Additionally, the spruce soils had the maximum invertase activity and the minimum urease and catalase activities, but the maximum urease and catalase activities were found in the mixed stand. The Pearson correlation and principle component analyses revealed that the soils of spruce and oak stands obviously discriminated from other NSFs, whereas the others were similar. This suggested that the forest types affected soil microbial properties significantly due to differences in soil physical-chemical features.

[Effects of NaCl stress on leaf photosynthesis characteristics and free amino acid metabolism of Heyedysarum scoparium].

This paper studied the variations of leaf photosynthesis gas exchange, chlorophyll fluorescence, and free amino acid contents of Heyedysarum scoparium under the stress of different concentration NaCl, aimed to understand the effects of salt stress on the leaf physiological characteristics and free amino acid metabolism of the plant. Under mild salt stress, the photo-damage of the leaf photosystem II was avoided via the dissipation of excess excitation energy, and stomatal limitation was the main factor reducing the photosynthesis rate. With the increase of salt stress, the leaf photoprotection was not sufficient to avoid oxidative damage, and thus, the damage to photosystem II happened. Under the stress of 200 mmol NaCl x L(-1), non-stomatal limitation was the main factor responsible for the inhibition of photosynthesis. The accumulation and metabolism of major free amino acids in H. scoparium leaves varied under salt stress. Under mild salt stress, the major free amino acids such as proline, glutamate, aspartate, and alanine had a significant accumulation, but with the further increase of salt stress, the aspartate and alanine contents in H. scoparium leaves decreased, while the synthesis and accumulation of praline increased.

[Light competition and productivity of agroforestry system in loess area of Weibei in Shaanxi].

Agroforestry is the most effective way for the restoration of disturbed land on Loess Plateau and the development of poorly local economy. Taking the tree-based intercropping systems of walnut or plum with soybean or pepper in the loess area of Weibei as test objects, the photosynthesis, growth, and yield of soybean (Qindou 8) and pepper (Shanjiao 981) in the systems were studied. The results showed that the photosynthetic active radiation (PAR), net photosynthetic rate (Pn), growth, and yield of individual soybean or pepper plants were significantly decreased, with the effects increased with decreasing distance from tree rows. Leaf water potential was not significantly or poorly correlated with the Pn, growth, and yield of the two crops. However, there were significant positive correlations between the soil moisture content in 10-20 cm layer and the biomass and yield of soybean, and the above-ground biomass of pepper. PAR was highly correlated with the yield of both crops, which indicated that light competition was one of the key factors leading to the decrease of crop yield.