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Wen-jun Li - One of the best experts on this subject based on the ideXlab platform.
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microbacterium Suaedae sp nov isolated from Suaeda aralocaspica
International Journal of Systematic and Evolutionary Microbiology, 2019Co-Authors: Yanru Li, Mohammed A M Wadaan, Dengdi An, Yuqian Li, Wael N Hozzein, Min Xiao, Wen-jun LiAbstract:: Two bacterial strains, YZYP 306T and YZGP 509, were isolated from the halophyte Suaeda aralocaspica collected from the southern edge of the Gurbantunggut desert, north-west China. Cells were Gram-stain-positive, aerobic, non-motile, short rods. Strain YZYP 306T grew at 4-40 °C, while strain YZGP 509 grew at 4-42 °C, with optimum growth at 28 °C, and they both grew at pH 6.0-12.0 and 0-15 % (w/v) NaCl. Phylogenetic analyses of the 16S rRNA gene sequences placed the two strains within the genus Microbacterium with the highest similarities to Microbacterium indicum BBH6T (97.8 %) and Microbacterium sorbitolivorans SZDIS-1-1T (97.2 %). The average nucleotide identity value between YZYP 306T and M. indicum BBH6T was 78.3 %. The genomic DNA G+C contents of strains YZYP 306T and YZGP 509 were 68.49 and 68.53 mol%, respectively. The characteristic cell-wall amino acid was ornithine. Whole-cell sugars were galactose, mannose and ribose. The acyl type of the peptidoglycan was glycolyl. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major menaquinones were MK-10 and MK-11. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. These results are consistent with the classification of the two strains into the genus Microbacterium. On the basis of the evidence presented in this study, strains YZYP 306T and YZGP 509 are representatives of a novel species in the genus Microbacterium, for which the name Microbacterium Suaedae sp. nov. is proposed. The type strain is YZYP 306T (=CGMCC 1.16261T=KCTC 49101T).
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actinotalea Suaedae sp nov isolated from the halophyte Suaeda physophora in xinjiang northwest china
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2015Co-Authors: Shuai Zhao, Mohammed A M Wadaan, Wael N Hozzein, Wen-jun Li, Li Li, Shanhui Li, Hongfei Wang, Yongguang ZhangAbstract:A Gram-stain-positive, aerobic, non-motile, coryneform bacterium, designated strain EGI 60002T, was isolated from the halophyte Suaeda physophora. Cells were coryneform shaped and polymorphic. Phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate was closely related to Actinotalea ferrariae CF5-4T (95.8 % gene sequence similarity). The peptidoglycan type of strain EGI 60002T was A4β, containing l-Orn-d-Ser-d-Asp. The cell-wall sugars were mannose, ribose, rhamnose and glucose. The major fatty acids (>5 %) of strain EGI 60002T were iso-C14:0, iso-C15:0, anteiso-C15:1 A and anteiso-C15:0. The predominant respiratory quinone was MK-10(H4). The major polar lipids were diphosphatidylglycerol (DPG), one unidentified phosphoglycolipid (PGL) and one unidentified phospholipid (PL1). The genomic DNA G+C content was 72.3 mol%. On the basis of morphological, physiological, chemotaxonomic data, and phylogenetic analysis, strain EGI 60002T should be classified as a novel species within the genus Actinotalea, for which the name Actinotalea Suaedae sp. nov. is proposed. The type strain is EGI 60002T (=JCM 19624T = KACC 17839T = KCTC 29256T).
Wael N Hozzein - One of the best experts on this subject based on the ideXlab platform.
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microbacterium Suaedae sp nov isolated from Suaeda aralocaspica
International Journal of Systematic and Evolutionary Microbiology, 2019Co-Authors: Yanru Li, Mohammed A M Wadaan, Dengdi An, Yuqian Li, Wael N Hozzein, Min Xiao, Wen-jun LiAbstract:: Two bacterial strains, YZYP 306T and YZGP 509, were isolated from the halophyte Suaeda aralocaspica collected from the southern edge of the Gurbantunggut desert, north-west China. Cells were Gram-stain-positive, aerobic, non-motile, short rods. Strain YZYP 306T grew at 4-40 °C, while strain YZGP 509 grew at 4-42 °C, with optimum growth at 28 °C, and they both grew at pH 6.0-12.0 and 0-15 % (w/v) NaCl. Phylogenetic analyses of the 16S rRNA gene sequences placed the two strains within the genus Microbacterium with the highest similarities to Microbacterium indicum BBH6T (97.8 %) and Microbacterium sorbitolivorans SZDIS-1-1T (97.2 %). The average nucleotide identity value between YZYP 306T and M. indicum BBH6T was 78.3 %. The genomic DNA G+C contents of strains YZYP 306T and YZGP 509 were 68.49 and 68.53 mol%, respectively. The characteristic cell-wall amino acid was ornithine. Whole-cell sugars were galactose, mannose and ribose. The acyl type of the peptidoglycan was glycolyl. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major menaquinones were MK-10 and MK-11. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. These results are consistent with the classification of the two strains into the genus Microbacterium. On the basis of the evidence presented in this study, strains YZYP 306T and YZGP 509 are representatives of a novel species in the genus Microbacterium, for which the name Microbacterium Suaedae sp. nov. is proposed. The type strain is YZYP 306T (=CGMCC 1.16261T=KCTC 49101T).
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actinotalea Suaedae sp nov isolated from the halophyte Suaeda physophora in xinjiang northwest china
Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 2015Co-Authors: Shuai Zhao, Mohammed A M Wadaan, Wael N Hozzein, Wen-jun Li, Li Li, Shanhui Li, Hongfei Wang, Yongguang ZhangAbstract:A Gram-stain-positive, aerobic, non-motile, coryneform bacterium, designated strain EGI 60002T, was isolated from the halophyte Suaeda physophora. Cells were coryneform shaped and polymorphic. Phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate was closely related to Actinotalea ferrariae CF5-4T (95.8 % gene sequence similarity). The peptidoglycan type of strain EGI 60002T was A4β, containing l-Orn-d-Ser-d-Asp. The cell-wall sugars were mannose, ribose, rhamnose and glucose. The major fatty acids (>5 %) of strain EGI 60002T were iso-C14:0, iso-C15:0, anteiso-C15:1 A and anteiso-C15:0. The predominant respiratory quinone was MK-10(H4). The major polar lipids were diphosphatidylglycerol (DPG), one unidentified phosphoglycolipid (PGL) and one unidentified phospholipid (PL1). The genomic DNA G+C content was 72.3 mol%. On the basis of morphological, physiological, chemotaxonomic data, and phylogenetic analysis, strain EGI 60002T should be classified as a novel species within the genus Actinotalea, for which the name Actinotalea Suaedae sp. nov. is proposed. The type strain is EGI 60002T (=JCM 19624T = KACC 17839T = KCTC 29256T).
Xiaolei Wu - One of the best experts on this subject based on the ideXlab platform.
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sphingobacterium Suaedae sp nov isolated from the rhizosphere soil of Suaeda corniculata
International Journal of Systematic and Evolutionary Microbiology, 2015Co-Authors: Xinying Wang, Lian Xu, Xiaolei WuAbstract:A Gram-stain-negative, non-motile, non-spore-forming bacterium, designated T47T, was isolated from saline soil of the Suaeda corniculata rhizosphere, located on the bank of Wuliangsuhai Lake, Inner Mongolia, northern China. Strain T47T could grow at 10–40 °C (with 30 °C the optimal temperature), pH 6.0–8.0 (optimal pH 6.0) and in the presence of 0–6.0 % (w/v) NaCl [optimal 0–1.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain T47T formed a stable clade with Sphingobacterium composti 4M24T, Sphingobacterium bambusae IBFC2009T, Sphingobacterium paludis S37T and Sphingobacterium wenxiniae LQY-18T, with the 16S rRNA gene sequence similarities ranging from 91.9–95.4 %. Its major cellular fatty acids contained iso-C15 : 0 (39.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c, 23.0 %), C16 : 0 (12.8 %) and iso-C17 : 0 3-OH (9.9 %). MK7 was the major menaquinone. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain T47T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium Suaedae sp. nov. is proposed. The type strain is T47T ( = CGMCC 1.15277T = KCTC 42662T).
Changyan Tian - One of the best experts on this subject based on the ideXlab platform.
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transcriptome assembly in Suaeda aralocaspica to reveal the distinct temporal gene mirna alterations between the dimorphic seeds during germination
BMC Genomics, 2017Co-Authors: Lei Wang, Hongling Wang, Changyan TianAbstract:Dimorphic seeds from Suaeda aralocaspica exhibit different germination behaviors that are thought to be a bet-hedging strategy advantageous in harsh and unpredictable environments. To understand the molecular mechanisms of Suaeda aralocaspica dimorphic seed germination, we applied RNA sequencing and small RNA sequencing for samples collected at three germination stages. A total of 79,414 transcripts were assembled using Trinity, of which 57.67% were functionally annotated. KEGG enrichment unveiled that photosynthesis and flavonol biosynthesis pathways were activated earlier in brown seed compared with black seed. Gene expression analysis revealed that nine candidate unigenes in gibberellic acid and abscisic acid signal transduction and 23 unigenes in circadian rhythm-plant pathway showed distinct expression profiles to promote dimorphic seed germination. 194 conserved miRNAs comprising 40 families and 21 novel miRNAs belonging to 20 families in Suaeda aralocaspica were identified using miRDeep-P and Mfold. The expression of miRNAs in black seed was suppressed at imbibition stage. Among the identified miRNAs, 59 conserved and 13 novel miRNAs differentially expressed during seed germination. Of which, 43 conserved and nine novel miRNAs showed distinct expression patterns between black and brown seed. Using TAPIR, 208 unigenes were predicted as putative targets of 35 conserved miRNA families and 17 novel miRNA families. Among functionally annotated targets, genes participated in transcription regulation constituted the dominant category, followed by genes involved in signaling and stress response. Seven of the predicted targets were validated using 5′ rapid amplification of cDNA ends or real-time quantitative reverse transcription-PCR. Our results indicate that specific genes and miRNAs are regulated differently between black and brown seed during germination, which may contribute to the different germination behaviors of Suaeda aralocaspica dimorphic seeds in unpredictable variable environments. Our results lay a solid foundation for further studying the roles of candidate genes and miRNAs in Suaeda aralocaspica dimorphic seed germination.
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effects of salinity and nitrate on production and germination of dimorphic seeds applied both through the mother plant and exogenously during germination in Suaeda salsa
Plant Species Biology, 2016Co-Authors: Jie Song, Lei Wang, Jiachao Zhou, Weiwei Zhao, Hualing Xu, Fengxia Wang, Yange Xu, Changyan TianAbstract:Salinity and nitrogen are two important environmental factors that affect the distribution of halophytes in their natural saline habitats. Seeds of the euhalophyte Suaeda salsa L. were harvested from plants that had been treated with 1 or 500 mm NaCl combined with 0.5 or 5 mm NO3−-N (nitrate) for 115 days in a glasshouse. Germination was evaluated under different concentrations of NaCl and nitrate. Plants exposed to high salinity (500 mm) and low nitrate (0.5 mm) tended to produce heavy seeds. Either high salinity (500 mm) or high nitrate (5 mm) increased the brown/black seed ratio. The concentrations of Na+, K+, and Cl− were higher in brown than in black seeds, and NO3− concentrations were higher in black than in brown seeds, regardless of NaCl and nitrate treatments during plant culture. Regardless of NaCl and nitrate concentrations during germination, seeds from plants grown with 0.5 mm nitrate generally germinated more rapidly than seeds from plants grown with 5 mm nitrate, and the difference was greater for black than for brown seeds. Exogenous nitrate during germination enhanced the germination of brown seeds less than that of black seeds. Producing more brown seeds and heavy black or brown seeds appears to be an adaptation of S. Suaeda to saline environments. Producing more black seeds, which tend to remain dormant, should reduce competition for nitrogen and appears to be an adaptation to nitrogen-limited environments. In conclusion, nitrate provided exogenously or by mother plants to black seeds may act as a signal molecule that enhances the germination of black S. Suaeda seeds.
Brent L Nielsen - One of the best experts on this subject based on the ideXlab platform.
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transcriptome assembly profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance
BMC Genomics, 2015Co-Authors: Joann Dirayarce, Mark J Clement, Ajmal M Khan, Brent L NielsenAbstract:Improvement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases. This has stimulated research on salt tolerance in plants. Most crops tolerate a limited amount of salt to survive and produce biomass, while halophytes (salt-tolerant plants) have the ability to grow with saline water utilizing specific biochemical mechanisms. However, little is known about the genes involved in salt tolerance. We have characterized the transcriptome of Suaeda fruticosa, a halophyte that has the ability to sequester salts in its leaves. Suaeda fruticosa is an annual shrub in the family Chenopodiaceae found in coastal and inland regions of Pakistan and Mediterranean shores. This plant is an obligate halophyte that grows optimally from 200–400 mM NaCl and can grow at up to 1000 mM NaCl. High throughput sequencing technology was performed to provide understanding of genes involved in the salt tolerance mechanism. De novo assembly of the transcriptome and analysis has allowed identification of differentially expressed and unique genes present in this non-conventional crop. Twelve sequencing libraries prepared from control (0 mM NaCl treated) and optimum (300 mM NaCl treated) plants were sequenced using Illumina Hiseq 2000 to investigate differential gene expression between shoots and roots of Suaeda fruticosa. The transcriptome was assembled de novo using Velvet and Oases k-45 and clustered using CDHIT-EST. There are 54,526 unigenes; among these 475 genes are downregulated and 44 are upregulated when samples from plants grown under optimal salt are compared with those grown without salt. BLAST analysis identified the differentially expressed genes, which were categorized in gene ontology terms and their pathways. This work has identified potential genes involved in salt tolerance in Suaeda fruticosa, and has provided an outline of tools to use for de novo transcriptome analysis. The assemblies that were used provide coverage of a considerable proportion of the transcriptome, which allows analysis of differential gene expression and identification of genes that may be involved in salt tolerance. The transcriptome may serve as a reference sequence for study of other succulent halophytes.
