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During characterization of rhizobacteria, strain DBTS2T was isolated from the rhizosphere soil samples of healthy tomato plants and characterized using a polyphasic taxonomic approach. Phylogenetic analysis using 16S rRNA gene sequences showed this strain belonged to the genus Rhizobium and was most closely related to Rhizobium subbaraonis JC85T (99.1%) and Rhizobium daejeonense CCBAU 10050T (97%). Cells of strain DBTS2T were Gram-negative, short rod, aerobic and non-motile. This novel strain was found to grow at 20–45 °C (optimum 25–37 °C), pH 5–9 (optimum 8) and in the presence of 4% NaCl. It was positive for catalase and oxidase. The predominant cellular fatty acids were Summed Feature 8 (52.7%) and C19:0 cyclo ω8c (23.3%). The polar lipids of strain DBTS2T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipid, unidentified aminolipid, four unidentified phospholipids, unidentified lipid, phosphatidylcholine, unknown glycolipid and unknown aminophosphoglycolipids. Q-10 was the major quinone. The DNA–DNA hybridization similarity values between the strain DBTS2T and R. subbaraonis JC85T, R. daejeonense CCBAU 10050T and Rhizobium azooxidifex DSM100211T were 46.4%, 20.7% and 25.5%, respectively. The ANI value was 91.96% between strain DBTS2T and R. subbaraonis JC85T and 75.18% between strain DBTS2T and R. daejeonense CCBAU 10050T. The DNA G+C content of the genomic DNA was 63.1 mol%. Based on these results, it was concluded that the isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium rhizolycopersici sp. nov. is proposed, with DBTS2T (= CICC 24887T = ACCC61707 = JCM 34245) as the type strain.
Kyu Kyu Thin; Shan-Wen He; Xing Wang; Yao Wang; Ma Rong; Ji-Gang Han; Xiaoxia Zhang. Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China. Current Microbiology 2021, 78, 830 -836.
AMA StyleKyu Kyu Thin, Shan-Wen He, Xing Wang, Yao Wang, Ma Rong, Ji-Gang Han, Xiaoxia Zhang. Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China. Current Microbiology. 2021; 78 (2):830-836.
Chicago/Turabian StyleKyu Kyu Thin; Shan-Wen He; Xing Wang; Yao Wang; Ma Rong; Ji-Gang Han; Xiaoxia Zhang. 2021. "Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China." Current Microbiology 78, no. 2: 830-836.
Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the “core flora” of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81–99.99%). At the genus level, Pantoea (8.77–87.77%), Pseudomonas (1.15–61.58%), Methylobacterium (0.40–4.64%), Sphingomonas (0.26–3.85%), Microbacterium (0.01–4.67%) and Aurantimonas (0.04–4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.
Zhishan Wang; Yongqiang Zhu; Ruixue Jing; Xianyu Wu; Ni Li; Hai Liu; Xiaoxia Zhang; Weiping Wang; Yang Liu. High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice. Archives of Microbiology 2020, 203, 609 -620.
AMA StyleZhishan Wang, Yongqiang Zhu, Ruixue Jing, Xianyu Wu, Ni Li, Hai Liu, Xiaoxia Zhang, Weiping Wang, Yang Liu. High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice. Archives of Microbiology. 2020; 203 (2):609-620.
Chicago/Turabian StyleZhishan Wang; Yongqiang Zhu; Ruixue Jing; Xianyu Wu; Ni Li; Hai Liu; Xiaoxia Zhang; Weiping Wang; Yang Liu. 2020. "High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice." Archives of Microbiology 203, no. 2: 609-620.
The phenotypic and genotypic characterization of eight rhizobial isolates obtained from Arachis hypogaea nodules grown under stress environment was performed. Isolates were screened for their ability to tolerate different abiotic stresses (high temperature (60° C), salinity (1–5% (w/v) NaCl), and pH (1–12). The genomic analysis of 16S rRNA and housekeeping genes (atpD, recA, and glnII) demonstrated that native groundnut rhizobia from these stress soils are representatives of fast growers and phylogenetically related to Rhizobium sp. The phenotypic characterization (generation time, carbon source utilization) also revealed the isolates as fast-growing rhizobia. All the isolates can tolerate NaCl up to 3% and were able to grow between 20 and 37 °C with a pH between 5 to 10, indicating that the isolates were alkali and salt-tolerant. The tested isolates effectively utilize mono and disaccharides as carbon source. Out of eight, three rhizobial isolates (BN-20, BN-23, and BN-50) were able to nodulate their host plant, exhibiting their potential to be used as native groundnut rhizobial inoculum. The plant growth promoting characterization of all isolates revealed their effectiveness to solubilize inorganic phosphate (56–290 µg mL−1), synthesize indole acetic acid (IAA) (24–71 µg mL−1), and amplification of nitrogen fixing nifH gene, exploring their ability to be used as groundnut biofertilizer to enhance yield and N2-fixation for the resource poor farmers of rainfed Pothwar region. `
Rabia Khalid; Xiao Zhang; Rifat Hayat; Mukhtar Ahmed. Molecular Characteristics of Rhizobia Isolated from Arachis Hypogaea Grown under Stress Environment. Sustainability 2020, 12, 6259 .
AMA StyleRabia Khalid, Xiao Zhang, Rifat Hayat, Mukhtar Ahmed. Molecular Characteristics of Rhizobia Isolated from Arachis Hypogaea Grown under Stress Environment. Sustainability. 2020; 12 (15):6259.
Chicago/Turabian StyleRabia Khalid; Xiao Zhang; Rifat Hayat; Mukhtar Ahmed. 2020. "Molecular Characteristics of Rhizobia Isolated from Arachis Hypogaea Grown under Stress Environment." Sustainability 12, no. 15: 6259.
Mu Us Sandy Land in China is a very fragile ecological environment due to serious desertification. While attempting to gain insights into the biodiversity of biological soil crusts of Mu Us Sandy Land, a novel bacterial strain, SLN-3T, was isolated. It was phylogenetically placed into the genus Arthrobacter within the family Micrococcaceae based on its 16S rRNA gene sequence. The most closely related species were Arthrobacter ruber MDB1-42T (98.6%) and Arthrobacter agilis DSM 20550T (98.3%). Cells of the novel species were Gram-stain-positive, aerobic, and non-endospore-forming. The values of average nucleotide identity and the digital DNA-DNA hybridization between SLN-3T and MDB1-42T were 84.9% and 21.3%, respectively. The draft genome size of strain SLN-3T was 3.67 Mb, and its genomic G+C content was 68.1%. The predominant cellular fatty acids were anteiso-C15:0 and C17:0 anteiso. Glucose, galactose, and ribose were the whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipid, and phospholipid. The peptidoglycan contained lysine, glutamic acid, and alanine. The predominant menaquinone was MK-9(H2). Based on the data from the chemotaxonomic, phylogenetic, and phenotypic evidence, a novel species named Arthrobacter crusticola sp. nov is proposed, whose type strain is SLN-3T (= ACCC 61595T = JCM 33723T).
Lei Liu; Lixiong Liang; Shanwen He; Lijun Xu; Miao Chi; Shaowen Shi; Xiaoxia Zhang; Lubin Li. Arthrobacter crusticola sp. nov., Isolated from Biological Soil Crusts in the Mu Us Sandy Land, China. Current Microbiology 2020, 77, 2042 -2048.
AMA StyleLei Liu, Lixiong Liang, Shanwen He, Lijun Xu, Miao Chi, Shaowen Shi, Xiaoxia Zhang, Lubin Li. Arthrobacter crusticola sp. nov., Isolated from Biological Soil Crusts in the Mu Us Sandy Land, China. Current Microbiology. 2020; 77 (9):2042-2048.
Chicago/Turabian StyleLei Liu; Lixiong Liang; Shanwen He; Lijun Xu; Miao Chi; Shaowen Shi; Xiaoxia Zhang; Lubin Li. 2020. "Arthrobacter crusticola sp. nov., Isolated from Biological Soil Crusts in the Mu Us Sandy Land, China." Current Microbiology 77, no. 9: 2042-2048.
A novel Gram-stain-positive, rod-shaped, endospore-forming bacterium, which we designated as strain 03113T, was isolated from greenhouse soil in Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 03113T is in the genus Bacillus and had the highest similarity to Bacillus solani CCTCC AB 2014277T (98.14%). The strain grew at 4 °C–50 °C (optimum 37 °C), with 0–10% (w/v) NaCl (optimum 5%), and in the range of pH 3.0–12.0 (optimum pH 8.0). Menaquinone was identified as MK-7, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The main major cellular fatty acids detected were anteiso-C15:0 (51.35%) and iso-C15:0 (11.06%), which are the predominant cellular fatty acids found in all recognized members of the genus Bacillus. The 16S rRNA gene sequence and core-genome analysis, the average nucleotide identity (ANI), and in silico DNA—DNA hybridization (DDH) value between strain 03113T and the most closely related species were 70.5% and 22.6%, respectively, which supported our conclusion that 03113T represented a novel species in the genus Bacillus. We demonstrated that type strain 03113T (=ACCC 03113T=JCM 33017T) was a novel species in the genus Bacillus, and the name Bacillus telluris sp. nov. was proposed. Strain 03113T secreted auxin IAA and carried the nitrogenase iron protein (nifH) gene, which indicated that strain 03113T has the potential to fix nitrogen and promote plant growth. Bacillus telluris sp. nov. 03113T is a potential candidate for the biofertilizers of organic agriculture areas.
He-Bao Guo; Shan-Wen He; Xing Wang; Kyu-Kyu Thin; Hai-Lei Wei; Xiao-Xia Zhang. Bacillus telluris sp. nov. Isolated from Greenhouse Soil in Beijing, China. Microorganisms 2020, 8, 702 .
AMA StyleHe-Bao Guo, Shan-Wen He, Xing Wang, Kyu-Kyu Thin, Hai-Lei Wei, Xiao-Xia Zhang. Bacillus telluris sp. nov. Isolated from Greenhouse Soil in Beijing, China. Microorganisms. 2020; 8 (5):702.
Chicago/Turabian StyleHe-Bao Guo; Shan-Wen He; Xing Wang; Kyu-Kyu Thin; Hai-Lei Wei; Xiao-Xia Zhang. 2020. "Bacillus telluris sp. nov. Isolated from Greenhouse Soil in Beijing, China." Microorganisms 8, no. 5: 702.
A flagellate, rod–shaped bacterium designated strain M15T was isolated from rice roots. Phylogenetic analysis based on the sequences of the 16S rRNA, housekeeping genes and genomes showed that the isolate belonged to the genus Rhizobium, with the highest 16S rRNA similarity to Rhizobium radiobacter LMG140T (99.64%) and Rhizobium pusense NRCPB10T (99.36%), respectively. The complete genome of the strain M15T has a 59.28% G+C content, and the highest average nucleotide identity (ANI) and DNA-DNA relatedness (DDH) values were obtained with R. radiobacter LMG140T (88.11%, 54.80%), R. pusense NRCPB10T (86.00%, 53.00%) and R. nepotum 39/7T (88.80%, 49.80%), respectively. Plant growth-promoting characteristics tests showed that the strain M15T produced siderophore, 1–aminocyclopropane–1–carboxylate (ACC) deaminase and indole-3-acetic acid (IAA) and also produced some secondary metabolites according to the analysis of the comparative genomes. Based on the data mentioned above, we proposed that the strain M15T represented a novel species of the genus Rhizobium, named Rhizobium oryzihabitans sp. nov. The type strain is M15T (=JCM 32903T = ACCC 60121T), and the strain M15T can be a novel biofertilizer Rhizobium to reduce the use of synthetic fertilizers for plant growth promotion.
Juanjuan Zhao; Xia Zhao; Junru Wang; Qi Gong; Xiaoxia Zhang; Guishan Zhang. Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture. Microorganisms 2020, 8, 608 .
AMA StyleJuanjuan Zhao, Xia Zhao, Junru Wang, Qi Gong, Xiaoxia Zhang, Guishan Zhang. Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture. Microorganisms. 2020; 8 (4):608.
Chicago/Turabian StyleJuanjuan Zhao; Xia Zhao; Junru Wang; Qi Gong; Xiaoxia Zhang; Guishan Zhang. 2020. "Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture." Microorganisms 8, no. 4: 608.
A novel gram-negative, aerobic, non-spore-forming, rod-shaped, and non-nitrogen-fixing bacterium, named SPY-1T, was isolated from biological soil crusts collected at Mu Us Sandy Land, China. Based on 16S rRNA sequence similarity, strain SPY-1T was most closely related to Neorhizobium alkalisoli CCTCC AB 2014138T (98.7%), Neorhizobium huautlense CGMCC 1.2538T (98.6%), Neorhizobium galegae DSM 11542T (98.4%), Rhizobium wenxiniae 166T (97.9%), and Rhizobium smilacinae CCTCC AB 2013016T (97.5%). Phylogenetic analysis based on 16S rRNA sequencing and multilocus sequence analysis of partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain SPY-1T was a member of the genus Rhizobium. The draft genome of strain SPY-1T was 4.75 Mb in size, and the G + C content was 60.0%. The average nucleotide identity (ANI) values to N. alkalisoli CCTCC AB 2014138T and R. smilacinae CCTCC AB 2013016T were both 84.0%. The digital DNA–DNA hybridization (dDDH) values to N. alkalisoli CCTCC AB 2014138T and R. smilacinae CCTCC AB 2013016T were 20.9% and 20.2%, respectively. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C16:0. Based on the data from chemotaxonomic, phylogenetic, and phenotypic evidence, strain SPY-1T represents a novel species in the genus Rhizobium, for which the name Rhizobium deserti sp. nov. is proposed. The type strain is SPY-1T (= ACCC 61627T = JCM 33732T).
Lei Liu; Lixiong Liang; Lijun Xu; Miao Chi; Xiaoxia Zhang; Lubin Li. Rhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China. Current Microbiology 2019, 77, 327 -333.
AMA StyleLei Liu, Lixiong Liang, Lijun Xu, Miao Chi, Xiaoxia Zhang, Lubin Li. Rhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China. Current Microbiology. 2019; 77 (2):327-333.
Chicago/Turabian StyleLei Liu; Lixiong Liang; Lijun Xu; Miao Chi; Xiaoxia Zhang; Lubin Li. 2019. "Rhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China." Current Microbiology 77, no. 2: 327-333.
A novel gram-negative, aerobic, non-spore-forming, rod-shaped and non-nitrogen fixing bacterium named strain 24NRT was isolated from wild Lilium pumilum bulbs in Fuping, Baoding City, Hebei province, PR China. The 16S rRNA gene sequences of strains 24NRT showed the highest similarity to Neorhizobium alkalisoli DSM 21826T (98.5%) and N. galegae HAMBI 540T (98.1%). Phylogenetic analysis based on 16S rRNA genes and multilocus sequence analysis (MLSA) based on the partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain 24NRT is a member of the genus Neorhizobium. The average nucleotide identity between the genome sequence of strain 24NRT and that of the isolate N. alkalisoli DSM 21826T was 83.1%, and the digital DNA–DNA hybridization was 20.1%. The G+C content of strain 24NRT was 60.3 mol %. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. Based on phenotypic, phylogenetic, and genotypic data, strain 24NRT is considered to represent a novel species of the genus Neorhizobium, for which the name Neorhizobium lilium sp. nov. is proposed. The type strain is 24NRT (= ACCC 61588T = JCM 33731T).
Lei Liu; Shaowen Shi; Lixiong Liang; Lijun Xu; Miao Chi; Xiaoxia Zhang; Lubin Li. Neorhizobium lilium sp. nov., an endophytic bacterium isolated from Lilium pumilum bulbs in Hebei province. Archives of Microbiology 2019, 202, 609 -616.
AMA StyleLei Liu, Shaowen Shi, Lixiong Liang, Lijun Xu, Miao Chi, Xiaoxia Zhang, Lubin Li. Neorhizobium lilium sp. nov., an endophytic bacterium isolated from Lilium pumilum bulbs in Hebei province. Archives of Microbiology. 2019; 202 (3):609-616.
Chicago/Turabian StyleLei Liu; Shaowen Shi; Lixiong Liang; Lijun Xu; Miao Chi; Xiaoxia Zhang; Lubin Li. 2019. "Neorhizobium lilium sp. nov., an endophytic bacterium isolated from Lilium pumilum bulbs in Hebei province." Archives of Microbiology 202, no. 3: 609-616.
Super hybrid rice is one of the important research achievements in the field of rice super-high yield breeding in China. Compared with general high-yield rice, the yield potential of super hybrid rice is relatively high, and the average yields per hectare can exceed 10.5 t. This study aimed to study the endophytic bacterial community among a super hybrid rice combination and its parental lines and to reveal the potential relationship and association of endophytic bacteria between rice genotypes and their genetic relevance. In this research, through high-throughput sequencing based on Illumina Hiseq 2500 platform, the seeds of super hybrid rice variety ‘Shenliangyou 5814’ (sample C) and its parental lines ‘Y58S’ (sample M) and ‘C4114’ (sample F) independently cultivated by China were used as plant materials to study their endophytic bacterial structure and diversity. The number of OTUs for sample M, F and C was 327, 288 and 283 respectively, and among them 218 endophytic OTUs coexisted in the 3 samples. Pantoea (18.6–31.1%) was the first dominant groups shared in all three samples, and other dominant shared groups belonged to Methylobacterium (4.48%~17.65%), Sphingomonas (4.0%~11.4%), Rhizobium (5.69–8.78%), Microbacterium (3.85%~9.41%) and Pseudomonas (4.13%~5.68%). Although Principal Coordinates Analysis (PCoA) and Non-metric Multidimensional Scaling (NMDS) analysis showed that there were obvious differences in endophytic bacterial community composition and structure among the 3 samples, the dominant endophytic bacterial genus sample C and its parental lines remained consistency. This study would provide scientific clues for the future research on the vertical transmission of endophytes between rice generations.
Yang Liu; Pengpeng Xu; Fuzhen Yang; Miao Li; Hai Yan; Ni Li; Xiaoxia Zhang; Weiping Wang. Composition and diversity of endophytic bacterial community in seeds of super hybrid rice ‘Shenliangyou 5814’ (Oryza sativa L.) and its parental lines. Plant Growth Regulation 2018, 87, 257 -266.
AMA StyleYang Liu, Pengpeng Xu, Fuzhen Yang, Miao Li, Hai Yan, Ni Li, Xiaoxia Zhang, Weiping Wang. Composition and diversity of endophytic bacterial community in seeds of super hybrid rice ‘Shenliangyou 5814’ (Oryza sativa L.) and its parental lines. Plant Growth Regulation. 2018; 87 (2):257-266.
Chicago/Turabian StyleYang Liu; Pengpeng Xu; Fuzhen Yang; Miao Li; Hai Yan; Ni Li; Xiaoxia Zhang; Weiping Wang. 2018. "Composition and diversity of endophytic bacterial community in seeds of super hybrid rice ‘Shenliangyou 5814’ (Oryza sativa L.) and its parental lines." Plant Growth Regulation 87, no. 2: 257-266.
Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geographic origins as well as in ecological preferences. Based on phylogenomic analysis, we clustered the six A. caldus strains isolated from various ecological niches into two groups: group 1 strains with smaller genomes and group 2 strains with larger genomes. We found no obvious intraspecific divergence with respect to predicted genes that are related to central metabolism and stress management strategies between these two groups. Although numerous highly homogeneous genes were observed, high genetic diversity was also detected. Preliminary inspection provided a first glimpse of the potential correlation between intraspecific diversity at the genome level and environmental variation, especially geochemical conditions. Evolutionary genetic analyses further showed evidence that the difference in environmental conditions might be a crucial factor to drive the divergent evolution of A. caldus species. We identified a diverse pool of mobile genetic elements including insertion sequences and genomic islands, which suggests a high frequency of genetic exchange in these harsh habitats. Comprehensive analysis revealed that gene gains and losses were both dominant evolutionary forces that directed the genomic diversification of A. caldus species. For instance, horizontal gene transfer and gene duplication events in group 2 strains might contribute to an increase in microbial DNA content and novel functions. Moreover, genomes undergo extensive changes in group 1 strains such as removal of potential non-functional DNA, which results in the formation of compact and streamlined genomes. Taken together, the findings presented herein show highly frequent gene turnover of A. caldus species that inhabit extremely acidic environments, and shed new light on the contribution of gene turnover to the evolutionary adaptation of acidophiles.
Xian Zhang; Xueduan Liu; Qiang He; Weiling Dong; Xiaoxia Zhang; Fenliang Fan; Deliang Peng; Wenkun Huang; Huaqun Yin. Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics. Frontiers in Microbiology 2016, 7, 1960 .
AMA StyleXian Zhang, Xueduan Liu, Qiang He, Weiling Dong, Xiaoxia Zhang, Fenliang Fan, Deliang Peng, Wenkun Huang, Huaqun Yin. Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics. Frontiers in Microbiology. 2016; 7 ():1960.
Chicago/Turabian StyleXian Zhang; Xueduan Liu; Qiang He; Weiling Dong; Xiaoxia Zhang; Fenliang Fan; Deliang Peng; Wenkun Huang; Huaqun Yin. 2016. "Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics." Frontiers in Microbiology 7, no. : 1960.
Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.
Xian Zhang; Siyuan She; Weiling Dong; Jiaojiao Niu; Yunhua Xiao; Yili Liang; Xueduan Liu; Xiaoxia Zhang; Fenliang Fan; Huaqun Yin. Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus. Systematic and Applied Microbiology 2016, 39, 493 -502.
AMA StyleXian Zhang, Siyuan She, Weiling Dong, Jiaojiao Niu, Yunhua Xiao, Yili Liang, Xueduan Liu, Xiaoxia Zhang, Fenliang Fan, Huaqun Yin. Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus. Systematic and Applied Microbiology. 2016; 39 (8):493-502.
Chicago/Turabian StyleXian Zhang; Siyuan She; Weiling Dong; Jiaojiao Niu; Yunhua Xiao; Yili Liang; Xueduan Liu; Xiaoxia Zhang; Fenliang Fan; Huaqun Yin. 2016. "Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus." Systematic and Applied Microbiology 39, no. 8: 493-502.
This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2 %, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function.
Yunhua Xiao; Yongdong Xu; Weiling Dong; Yili Liang; Fenliang Fan; Xiaoxia Zhang; Xian Zhang; Jiaojiao Niu; Liyuan Ma; Siyuan She; Zhili He; Xueduan Liu; Huaqun Yin. The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system. Applied Microbiology and Biotechnology 2015, 99, 10311 -10322.
AMA StyleYunhua Xiao, Yongdong Xu, Weiling Dong, Yili Liang, Fenliang Fan, Xiaoxia Zhang, Xian Zhang, Jiaojiao Niu, Liyuan Ma, Siyuan She, Zhili He, Xueduan Liu, Huaqun Yin. The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system. Applied Microbiology and Biotechnology. 2015; 99 (23):10311-10322.
Chicago/Turabian StyleYunhua Xiao; Yongdong Xu; Weiling Dong; Yili Liang; Fenliang Fan; Xiaoxia Zhang; Xian Zhang; Jiaojiao Niu; Liyuan Ma; Siyuan She; Zhili He; Xueduan Liu; Huaqun Yin. 2015. "The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system." Applied Microbiology and Biotechnology 99, no. 23: 10311-10322.