Morphological and phylogenetic analyses reveal two new Penicillium species isolated from the ancient Great Wall loess in Beijing, China.

Introduction: Penicillium species exhibit a broad distribution in nature and play a crucial role in human and ecological environments. Methods: Two Penicillium species isolated from the ancient Great Wall loess in the Mentougou District of Beijing, China, were identified and described as new species, namely, Penicillium acidogenicum and P. floccosum, based on morphological characteristics and phylogenetic analyses of multiple genes including ITS, BenA, CaM, and RPB2 genes. Results: Phylogenetic analyses showed that both novel species formed a distinctive lineage and that they were most closely related to P. chrzaszczii and P. osmophilum, respectively. Discussion: Penicillium acidogenicum is characterized by biverticillate conidiophores that produce globose conidia and is distinguished from similar species by its capacity to grow on CYA at 30°C. Penicillium floccosum is typically recognized by its restricted growth and floccose colony texture. The description of these two new species provided additional knowledge and new insights into the ecology and distribution of Penicillium.

Thiopseudomonas acetoxidans sp. nov., an aerobic acetic and butyric acids oxidizer isolated from anaerobic fermentation liquid of food waste.

A Gram-stain-negative, oxidase-negative, rod-shaped, motile, facultatively anaerobic bacterial strain, designated as CY1220T, was isolated from an anaerobic fermentation liquid of food waste treatment plant. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain CY1220T belongs to the genus Thiopseudomonas, with the highest sequence similarity to Thiopseudomonas alkaliphila B4199T (95.91%), followed by Thiopseudomonas denitrificans X2T (95.56%). The genomic DNA G + C content of strain CY1220T was 48.6 mol%. The average nucleotide identity values and digital DNA-DNA hybridization values between strain CY1220T and the type species of T. alkaliphila and T. denitrificans were in the range of 70.8-71.6% and 19.2-20.0%, respectively, below the thresholds for species delineation. The strain was able to grow utilizing acetic acid and butyric acid (AABA) as the sole carbon source in aerobic conditions. Genomic analysis predicted that the strain could synthesize vitamin B12 and ectoine. The predominant cellular fatty acids were C18:1 ω7c and/or C18:1 ω6c, C16:0, C16:1 ω7c and/or C16:1 ω6c and C12:0. The polar lipids comprised diphosphatidylglycerol, unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol, and phospholipid. Q-8 (2.1%) and Q-9 (97.9%) were detected as the respiratory quinones. Based on its phenotypic, genotypic and genomic characteristics, strain CY1220T represents a novel species in the genus Thiopseudomonas, for which the name Thiopseudomonas acetoxidans sp. nov. is proposed. The type strain is CY1220T (= GDMCC 1.3503 T = JCM 35747 T).

Enhancing Salt Tolerance in Poplar Seedlings through Arbuscular Mycorrhizal Fungi Symbiosis.

Poplar (Populus spp.) is a valuable tree species with multiple applications in afforestation. However, its growth in saline areas, including coastal regions, is limited. This study aimed to investigate the physiological mechanisms of arbuscular mycorrhizal fungi (AMF) symbiosis with 84K (P. alba × P. tremula var. glandulosa) poplar under salt stress. We conducted pot experiments using NaCl solutions of 0 mM (control), 100 mM (moderate stress), and 200 mM (severe stress) and evaluated the colonization of AMF and various physiological parameters of plants, including photosynthesis, biomass, antioxidant enzyme activity, nutrients, and ion concentration. Partial least squares path modeling (PLS-PM) was employed to elucidate how AMF can improve salt tolerance in poplar. The results demonstrated that AMF successfully colonized the roots of plants under salt stress, effectively alleviated water loss by increasing the transpiration rate, and significantly enhanced the biomass of poplar seedlings. Mycorrhiza reduced proline and malondialdehyde accumulation while enhancing the activity of antioxidant enzymes, thus improving plasma membrane stability. Additionally, AMF mitigated Na+ accumulation in plants, contributing to the maintenance of a favorable ion balance. These findings highlight the effectiveness of using suitable AMF to improve conditions for economically significant tree species in salt-affected areas, thereby promoting their utilization.

Roseomonas populi sp. nov., an acetate-degrading bacteria isolated from the stem of Populus tomentosa.

Strain CN29T, isolated from the stem of 5- to 6-year-old Populus tomentosa in Shandong, China, was characterized using a polyphasic taxonomic approach. Cells of CN29T were Gram-stain negative, aerobic, nonspore-forming, and nonmotile coccoid. Growth occurred at 20-37 °C, pH 4.0-9.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CN29T was closely related to members of the genus Roseomonas and closest to Roseomonas pecuniae N75T (96.6%). This classification was further supported by phylogenetic analysis using additional core genes. The average nucleotide identity and digital DNA‒DNA hybridization values between strain CN29T and Roseomonas populi CN29T were 82.7% and 27.8%, respectively. The genome size of strain CN29T was 5.87 Mb, with a G + C content of 70.9%. The major cellular fatty acids included summed feature 8 (C18:1 ω7c/C18:1 ω6c), C19:0 cyclo ω8c and C16:0. The major respiratory quinone was Q-10. The polar lipids were phosphatidylcholine, aminolipid, phosphatidylglycerol, and diphosphatidylglycerol. Strain CN29T can utilize acetate as a carbon source for growth and metabolism. Additionally, it contains acid phosphatase (2-naphthyl phosphate), which catalyzes the hydrolysis of phosphoric monoesters. The CN29T strain contains several genes, including maeB, gdhB, and cysJ, involved in carbon, nitrogen, and sulfur cycling. These findings suggest that the strain may actively participate in ecosystem cycling, leading to soil improvement and promoting the growth of poplar trees. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain CN29T is concluded to represent a novel species of the genus Roseomonas, for which the name Roseomonas populi sp. nov. is proposed. The type strain is CN29T (= JCM 35579T = GDMCC 1.3267T).

Modulation of the catalytic activity and thermostability of a thermostable GH7 endoglucanase by engineering the key loop B3.

The loop B3 of glycoside hydrolase family 7 (GH7) endoglucanases is confined into long and short types. TtCel7 is a thermophilic GH7 endoglucanase from Thermothelomyces thermophilus ATCC 42464 with a long loop B3. TtCel7 was distinct for the excellent thermostability (>30 % residual activity after 1-h incubation at 90 °C). The catalytic efficiency was reduced by removing the disulfide bond in loop B3 (C220A) and truncated the loop B3 (B3cut). However, B3cut exhibited improved thermostability, the remaining enzyme activity increased by 39 %-171 % compared toTtCel7 when treated at 70-90 °C for 1-h. Based on the analysis of molecular dynamics simulation, both loops B1 and A3 of B3cut swing toward the catalytic center, which contributed to the reduced cleft-space and increased structure-rigidity. Conversely, the deletion of disulfide bond resulted in a reduction of structural rigidity in C220A. Through structure-directed enzyme modulation, this study has identified two structural elements that are related to the catalysis and thermostability of TtCel7. The loop B3 of TtCel7 possibly stretches the catalytic pocket, thereby increases the openness of the catalytic tunnel and enhancing flexibility for efficient catalysis. Additionally, the disulfide bond within loop B3 serves to enhance structural stability and maintain a heightened level of activity.

Polyphase taxonomy and genome analysis reveal the adaptability of Luteolibacter rhizosphaerae sp. nov. to the rhizosphere soil of Ulmus pumila L.

A Gram-stain-negative, rod-shaped, non-flagellated, pale-yellow bacterium, designated GHJ8T, was isolated from the rhizosphere soil of Ulmus pumila L., Shanxi Province, China. Growth occurred at 20-37 °C (optimum, 28 °C), pH 6.0-11.0 (optimum, pH 8.0), and 0-1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain GHJ8T was related to members of the genus Luteolibacter, and close to Luteolibacter flavescens GKXT (98.5%), Luteolibacter luteus G-1-1-1T (97.3%), Luteolibacter arcticus MC 3726T (97.2%), and Luteolibacter marinus NBU1238T (96.0%). The genome size of strain GHJ8T was 6.2 Mbp, with a G + C content of 62.5%. Genomic mining revealed that the strain contained antibiotic resistance genes and secondary metabolic gene clusters, indicating that it had adaptation mechanisms to environmental stress. Comparative genomic analyses clearly separated strain GHJ8T from the recognized species of the genus Luteolibacter based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. The major cellular fatty acids were iso-C14:0 (30.8%), C16:1 ω9c (23.0%), C16:0 (17.3%), and C14:0 (13.4%). The quinone system was composed of the major menaquinones MK-8, MK-9, and MK-10, and the principal polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified glycolipid, two unidentified phospholipids, and three unidentified lipids. Based on its phenotypic and genotypic properties and phylogenetic inference, strain GHJ8T is a novel species of the genus Luteolibacter, for which the name Luteolibacter rhizosphaerae sp. nov. is proposed. The type strain is GHJ8T (= GDMCC 1.2160T = KCTC 82452T = JCM 34400T).

Alcanivorax quisquiliarum sp. nov., isolated from anaerobic fermentation liquid of food waste by high-throughput cultivation.

Strain CY1518T was isolated from an anaerobic fermentation liquid of food waste treatment plant in Beijing, PR China, and characterized to assess its taxonomy. Cells of CY1518T were Gram-stain-negative, oxidase-negative, catalase-positive and ellipsoidal. Growth occurred at 20-42 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8) and with 0-6.0 % (w/v) NaCl (optimum, 1.5%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CY1518T belongs to the genus Alcanivorax, with the highest sequence similarity to Alcanivorax pacificus W11-5T (95.97 %), followed by Alcanivorax indicus SW127T (95.08%). The similarity between strain CY1518T and other strains of Alcanivorax was less than 95 %. The genomic DNA G+C content of strain CY1518T was 60.88 mol%. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CY1518T and the closely related taxa A. pacificus W11-5T and A. indicus SW127T were 77.61, 78.03 and 21.2 % and 74.15, 70.02 and 19.3%, respectively. The strain was able to use d-serine, Tween 40 and some organic acid compounds for growth. The polar lipids comprised aminophospholipid, diphosphatidylglycerol, glycolipid, an unknown polar lipid, phosphatidylethanolamine, phosphatidylglycerol and phospholipid. The principal fatty acids (>5 %) were C19 : 0 cyclo ω8c (36.3%), C16 : 0 (32.3%), C12 : 0 3-OH (8.3%) and C12 : 0 (7.6%). Based on its phenotypic, genotypic and genomic characteristics, strain CY1518T represents a novel species in the genus Alcanivorax, for which the name Alcanivorax quisquiliarum sp. nov. is proposed. The type strain is CY1518T (=GDMCC 1.2918T=JCM 35120T).

Development of an efficient method for separation and purification of cordycepin from liquid fermentation of Cordyceps militaris and analysis of cordycepin antitumor activity.

Cordycepin (3 '-deoxyadenosine) is the main active component of Cordyceps militaris, which is a chemical marker for quality detection of Cordyceps militaris and has important medicinal development value. Existing methods for obtaining cordycepin are complex and costly. In this study, an economical and simple method for separation and purification of cordycepin from Cordyceps militaris fermentation liquid through physical crystallization was explored. First, lyophilized powdered fermentation liquid (LPFL) and pure methanol (1 g/100 mL, w/v) were mixed, and then repeatedly dissolved and crystallized until the precipitation was white. Purified product was obtained by freeze-drying the precipitate. The substance was determined to be cordycepin by high performance liquid chromatography, mass spectrometry and infrared spectroscopy, and the purity was 94.26%. Compared with the existing methods, this method is simple and low cost. In addition, the functional activity of cordycepin was determined by in vitro test. The results exhibited that cordycepin caused death and morphological changes in human colon cancer Caco-2 cells, and significantly inhibited the proliferation of Caco-2 cells, with a half-maximal inhibitory concentration (IC50) of 107.2 µg/mL. Cordycepin could induce early apoptosis of Caco-2 and caused cell cycle arrest in the G2 phase. Caco-2 cell apoptosis and cell cycle arrest showed dose dependence to cordycepin over a certain range. These results improved cordycepin purification method, provided insights into the mechanism of cordycepin in cancer inhibition, and would provide important reference for further development and clinical application of cordycepin.

Luteimonas galliterrae sp. nov., isolated from poultry farm soil.

Strain SX5T was isolated from the soil of a poultry farm in Shanxi Province, PR China. The isolate was a Gram-stain-negative, rod-shaped, non-flagellated, and yellow bacterium. Growth occurred at 20-37 °C (optimum, 28 °C), pH 6.0-10.0 (optimum, pH 8.0) and 0-1 % NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SX5T was related to members of the genus Luteimonas, and close to Luteimonas gilva H23T (97.9 %), Luteimonas cucumeris Y4T (97.9 %), Luteimonas aquatica RIB1-20T (96.8 %), Luteimonas notoginsengisoli SYP-B804T (96.4 %) and Luteimonas panaciterrae Gsoil 068T (96.1 %). The major cellular fatty acids of strain SX5T were iso-C16 : 0, iso-C17 : 1 ω9c, iso-C15 : 0 and iso-C11 : 0 3OH. The sole isoprenoid quinone was ubiquinone Q-8, and the major polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Genome analyses revealed that strain SX5T had a genome size of 3.6 Mbp with a G+C content of 65.7 mol% and contained abundant carbohydrate-active enzyme genes and three putative distinct biosynthetic gene clusters, suggesting that it may have great potential to degrade and utilize complex biological organic matter and produce special secondary metabolites. Comparative genomic analyses clearly separated strain SX5T from the known species of the genus Luteimonas based on average nucleotide identity and digital DNA-DNA hybridization values below the thresholds for species delineation. Based on its phenotypic, genotypic properties and phylogenetic inference, strain SX5T represents a novel species in the genus Luteimonas, for which the name Luteimonas galliterrae sp. nov. is proposed. The type strain is SX5T (=GDMCC 1.2162T=KCTC 82443T=JCM 34401T).

Model construction and validation of airflow velocity attenuation through pear tree canopies.

To investigate the airflow velocity attenuation inside pear tree canopies and the factors that influence its effect on air-assisted spraying, the relationship between the resistance of the canopies to airflow and airflow velocity inside the canopies was determined. At the same time, the theoretical model of airflow velocity attenuation in the canopy was constructed, in which the velocity attenuation factor k and the incoming velocity were the model input values, and the airflow velocity in the canopy was the model output value. Then, experimental verification of the theoretical model was completed. The determination test of airflow velocity inside canopies with three leaf area densities revealed that the error range between the established theoretical model and the experimental airflow velocity inside the pear tree canopy was 0.11-1.25 m/s, and the mean size of the model accuracy was 83.4% under various working conditions. The results revealed that the region from a depth of 0 m to 0.3 m inside the canopy was the rapid attenuation area of the airflow and that from 0.3 m to 0.9 m was the low attenuation area. Furthermore, they revealed that high-speed airflow could strongly disturb the outer branches and leaves, greatly changing the windward area of the canopy blades and thus affecting the accuracy of the model. By introducing a dynamic parameter of the canopy leaf windward area for model correction, the R2 of the model was above 0.9. Finally, validation of the model was performed in an air-assisted spraying operation in an orchard. This study can provide a theoretical basis for the regulation of airflow parameters of air-assisted spraying of pear trees.

Enhancing control of multidrug-resistant plasmid and its host community with a prolonged thermophilic phase during composting.

The plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) among bacteria facilitates the evolution and dissemination of antibiotic resistance. Broad-host-range plasmids can be transferred to different bacterial hosts in soil, plant rhizospheres, and wastewater treatment plants. Although composting is an effective way to convert organic waste into fertilizer and reduce some ARGs, few studies have focused on its effects on the spread of ARG-carrying plasmids and their bacterial host communities during composting. In this study, a fluorescently labeled Pseudomonas putida (P. putida) harboring a broad-host-range plasmid RP4 carrying three ARGs was inoculated into a raw material microcosm and composted with different durations of the thermophilic phase. The fate of the donor and RP4 in composting was investigated. The prolonged thermophilic composting removed 95.1% of dsRed and 98.0% of gfp, and it inhibited the rebound of P. putida and RP4 during the maturation phase. The spread potential of RP4 decreased from 10-4 to 10-6 transconjugants per recipient after composting. In addition, we sorted and analyzed the composition of RP4 recipient bacteria using fluorescence-activated cell sorting combined with 16S rRNA gene amplicon sequencing. The recipient bacteria of RP4 belonged to eight phyla, and Firmicutes, accounting for 75.3%-90.1%, was the dominant phylum in the transconjugants. The diversity and richness of the RP4 recipient community were significantly reduced by prolonged thermophilic periods. Overall, these findings provide new insights for assessing the contribution of composting in mitigating the dissemination of plasmid-mediated ARGs, and the prolonged thermophilic phase of composting can limit the transfer of multidrug-resistant plasmids.

Roseococcus pinisoli sp. nov., lacking pufL and pufM bacteriochlorophyll a: synthesizing genes.

A Gram-stain-negative, cocci-to-oval-shaped bacterial strain, designated XZZS9T, was isolated from the rhizosphere soil of Pinus sylvestris var. mongolica and characterized taxonomically using a polyphasic approach. Growth occurred at 20-35 °C (optimum, 28 °C), pH 6.0-11.0 (optimum, pH 7.0), and in 0-1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain XZZS9T was related to members of the genus Roseococcus, with the highest sequence identity to Roseococcus microcysteis NIBR12T (96.9%). The major cellular fatty acids (> 5% of the total) were C18:1 ω7c and C19:0 cyclo ω8c. The major isoprenoid quinone was Q-9 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified glycophospholipid, and an unidentified phospholipid. Genome sequencing revealed that had a genome size of 4.79 Mbp with a G + C content of 69.5%. Comparative genomic analyses clearly separated strain XZZS9T from the known species of the genus Roseococcus based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below the thresholds for species delineation. Genome annotations did not find pufL and pufM genes in strain XZZS9T, suggesting a possible lack of photosynthetic reaction. Based on genotypic and phenotypic characteristics, strain XZZS9T represents a novel species of the genus Roseococcus, for which we propose the name Roseococcus pinisoli sp. nov. The type strain is XZZS9T (= KCTC 82435T = JCM 34402T = GDMCC 1.2158T).

Sphingomonas quercus sp. nov., Isolated from Rhizosphere Soil of Quercus mongolica.

Strain XMGL2T, isolated from rhizosphere soil of Quercus mongolica in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and rod-shaped. Growth occurred at 20-37 °C (optimum, 28 °C), pH 5.0-10.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XMGL2T was related to members of the genus Sphingomonas and had the highest 16S rRNA gene sequence identity to Sphingomonas oleivorans FW-11 T (96.4%). The average nucleotide identity and digital DNA-DNA hybridization values between strain XMGL2T and the closely related taxa Sphingomonas oleivorans FW-11 T and Sphingomonas fennica K101T were 75.3/19.8% and 75.8/20.2%, respectively. The major cellular fatty acids were C18:1 ω7c, C14:0 2-OH, and C16:0. The major isoprenoid quinone was Q-10 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid and an unidentified phospholipid. The genomic DNA G + C content was 67.9%. Based on the phenotypic and genotypic properties and phylogenetic inference, strain XMGL2T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas quercus sp. nov. is proposed. The type strain is XMGL2T (= JCM 34441 T = GDMCC 1.2153 T).

A novel atmospheric-pressure air plasma jet for wound healing.

Current low-temperature plasma (LTP) devices essentially use a rare gas source with a short working distance (8 to 20 mm), low gas flow rate (0.12 to 0.3 m3 /h), and small effective treatment area (1-5 cm2 ), limiting the applications for which LTP can be utilised in clinical therapy. In the present study, a novel type of LTP equipment was developed, having the advantages of a free gas source (surrounding air), long working distance (8 cm), high gas flow rate (10 m3 /h), large effective treatment area (20 cm2 ), and producing an abundance of active substances (NOγ, OH, N2 , and O), effectively addressing the shortcomings of current LTP devices. Furthermore, it has been verified that the novel LTP device displays therapeutic efficacy in terms of acceleration of wound healing in normal and Type I diabetic rats, with enhanced wound kinetics, rate of condensation of wound area, and recovery ratio. Cellular and molecular analysis indicated that LTP treatment significantly reduced inflammation and enhanced re-epithelialization, fibroblast proliferation, deposition of collagen, neovascularization, and expression of TGF-ß, superoxide dismutase, glutathione peroxidase, and catalase in Type I diabetic rats. In conclusion, the novel LTP device provides a convenient and efficient tool for the treatment of clinical wounds.

Multidimensional analysis reveals environmental factors that affect community dynamics of arbuscular mycorrhizal fungi in poplar roots.

Introduction: Poplar is a tree species with important production and application value. The symbiotic relationship between poplar and arbuscular mycorrhizal fungi (AMF) has a key role in ecosystem functioning. However, there remain questions concerning the seasonal dynamics of the AMF community in poplar roots, the relationship between AMF and the soil environment, and its ecological function. Method: Poplar roots and rhizosphere soil were sampled at the end of April and the end of October. The responses of AMF communities to season, host age, and host species were investigated; the soil environmental factors driving community changes were analyzed. Results: The diversity and species composition of the AMF community were higher in autumn than in spring. Season, host age, host species, and soil environmental factors affected the formation of the symbiotic mycorrhizal system and the AMF community. Differences in the communities could be explained by soil pH, total nitrogen, total phosphorus, total potassium, available potassium, and glomalin content. Discussion: The AMF community was sensitive to changes in soil physicochemical properties caused by seasonal dynamics, particularly total potassium. The change in the mycorrhizal symbiotic system was closely related to the growth and development of poplar trees.

A non-symbiotic novel species, Rhizobium populisoli sp. nov., isolated from rhizosphere soil of Populus popularis.

Strain XQZ8T, isolated from the rhizosphere soil of a Populus popularis plant in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XQZ8T was related to members of the genus Rhizobium and had the highest 16S rRNA gene sequence similarity to Rhizobium smilacinae PTYR-5T (96.6%). The average nucleotide identity and digital DNA-DNA hybridization value between strain XQZ8T and R. smilacinae PTYR-5T were 77.5% and 21.4%, respectively. TYGS whole-genome-based taxonomic and multi-locus sequence analyses of three concatenated housekeeping genes (atpD-recA-glnII) further indicated that strain XQZ8T was a new member of the genus Rhizobium. The major cellular fatty acids included summed feature 8 (C18:1 ω7c/C18:1 ω6c), summed feature 2 (C12:0 aldehyde/unknown 10.928), C16:0, and C19:0 cyclo ω8c. The major respiratory quinones were Q-9 and Q-10. The polar lipids were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid, and three unidentified lipids. The genomic DNA G + C content of the strain was 60.1 mol%. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XQZ8T represents a novel species of the genus Rhizobium, for which the name Rhizobium populisoli sp. nov. is proposed. The type strain is XQZ8T (= JCM 34442T = GDMCC 1.2201T).

Transcriptional differentiation driving Cucumis sativus-Botrytis cinerea interactions based on the Skellam model and Bayesian networks.

Robust statistical tools such as the Skellam model and Bayesian networks can capture the count properties of transcriptome sequencing data and clusters of genes among treatments, thereby improving our knowledge of gene functions and networks. In this study, we successfully implemented a model to analyze a transcriptome dataset of Cucumis sativus and Botrytis cinerea before and after their interaction. First, 4200 differentially expressed genes (DEGs) from C. sativus were clustered into 17 distinct groups, and 670 DEGs from B. cinerea were clustered into 12 groups. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied on these DEGs to assess the interactions between C. sativus and B. cinerea. In C. sativus, more DEGs were divided into terms in the molecular function and biological process domains than into cellular components, and 277 DEGs were allocated to 19 KEGG pathways. In B. cinerea, more DEGs were divided into terms in the biological process and cellular component domains than into molecular functions, and 150 DEGs were allocated to 26 KEGG pathways. In this study, we constructed networks of genes that interact with each other to screen hub genes based on a directed graphical model known as Bayesian networks. Through a detailed GO analysis, we excavated hub genes which were biologically meaningful. These results verify that availability of Skellam model and Bayesian networks in clustering gene expression data and sorting out hub genes. These models are instrumental in increasing our knowledge of gene functions and networks in plant-pathogen interaction.

Matrix-assisted laser desorption ionization mass spectrometry based quantitative analysis of cordycepin from Cordyceps militaris.

Cordycepin, which has great immunomodulatory activities such as anticancer, antifungal, antivirus, antileukemia and lipid-lowering ones, is the secondary metabolite of Cordyceps militaris (C. militaris). Liquid submerged fermentation is the common cultivation process to produce cordycepin. To optimize the fermentation process and improve production, monitoring the cordycepin secretion in the fermentation is essential. The measurement based on chromatography-mass spectrometry methods is generally involved in the complex sample pretreatments and time-consuming separation, so more rapid and convenient methods are required. Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is more attractive for faster and direct detection. Therefore, MALDI-MS detection combined with isotope-labeled internal standard was applied to the measurement of cordycepin content in the fermentation broth and mycelium. This method made accurate quantification of cordycepin in the range of 5-400 µg/mL with a relative standard deviation of 5.6%. The recovery rates of fermentation samples after the 1, 13, and 25 days were 90.15%, 94.27%, and 95.06%, respectively. The contents of cordycepin in the mycelium and fermentation broth were 136 mg/g and 148.39 mg/mL on the 20th culture day, respectively. The cordycepin secretion curve of the liquid fermentation of C. militaris was real-time traced over 25 days.

Matrix-assisted laser desorption ionization mass spectrometry based quantitative analysis of cordycepin from Cordyceps militaris / 药物分析学报

Cordycepin,which has great immunomodulatory activities such as anticancer,antifungal,antivirus,antileukemia and lipid-lowering ones,is the secondary metabolite of Cordyceps militaris (C.militaris).Liquid submerged fermentation is the common cultivation process to produce cordycepin.To optimize the fermentation process and improve production,monitoring the cordycepin secretion in the fermen-tation is essential.The measurement based on chromatography-mass spectrometry methods is generally involved in the complex sample pretreatments and time-consuming separation,so more rapid and convenient methods are required.Matrix-assisted laser desorption ionization mass spectrometry(MALDI-MS) is more attractive for faster and direct detection.Therefore,MALDI-MS detection combined with isotope-labeled internal standard was applied to the measurement of cordycepin content in the fermentation broth and mycelium.This method made accurate quantification of cordycepin in the range of 5-400 μg/mL with a relative standard deviation of 5.6％.The recovery rates of fermentation samples after the 1,13,and 25 days were 90.15％,94.27％,and 95.06％,respectively.The contents of cordycepin in the mycelium and fermentation broth were 136 mg/g and 148.39 mg/mL on the 20th culture day,respectively.The cordycepin secretion curve of the liquid fermentation of C.militaris was real-time traced over 25 days.