102 results on '"Bao-Zhu Fang"'
Search Results
2. Response of microbial diversity and function to the degradation of Barkol Saline Lake
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Yong-Hong Liu, Lei Gao, Hong-Chen Jiang, Bao-Zhu Fang, Yin Huang, Li Li, Shuai Li, Rashidin Abdugheni, Wen-Hui Lian, Jing-Yi Zhang, Zhen-Dong Yang, Osama Abdalla Abdelshafy Mohamad, and Wen-Jun Li
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saline lake ,degradation ,microbial community ,diversity ,ecological function ,Microbiology ,QR1-502 - Abstract
Barkol Lake, a shrinking hypersaline lake situated in the northeast of Xinjiang, China, has experienced the exposure of its riverbed and the gradual drying up of its original sediment due to climate change and human activities, resulting in the formation of alkaline soils. These changes have correspondingly altered the physicochemical characteristics of the surrounding environment. Microorganisms play a crucial role, with special functioning involved in various nutrient cycling and energy transfer in saline lake environments. However, little is known about how the microbial community dynamics and metabolic functions in this shrinking saline lake relate to the degradation process. To address this knowledge gap, a cultivation-independent method of amplicon sequencing was used to identify and analyze the microbial community and its potential ecological functions in the sediment and degraded area. The microbial community diversity was found to be significantly lower in the degraded areas than in the sediment samples. The Pseudomonadota was dominant in Barkol Saline Lake. The abundance of Desulfobacterota and Bacillota in the degraded areas was lower than in the lake sediment, while Pseudomonadota, Acidobacteriota, and Actinobacteriota showed an opposite trend. The βNTI showed that microbial community assembly was primarily associated with deterministic processes in Barkol Saline Lake ecosystems and stochastic processes at the boundary between sediment and degraded areas. Functional predictions showed that sulfur metabolism, particularly sulfate respiration, was much higher in sediment samples than in the degraded areas. Overall, these findings provided a possible perspective for us to understand how microorganisms adapt to extreme environments and their role in saline lakes under environmental change.
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- 2024
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3. Two Novel Alkaliphilic Species Isolated from Saline-Alkali Soil in China: Halalkalibacter flavus sp. nov., and Halalkalibacter lacteus sp. nov
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Pin-Jiao Jin, Lei Sun, Yong-Hong Liu, Kang-Kang Wang, Manik Prabhu Narsing Rao, Osama Abdalla Abdelshafy Mohamad, Bao-Zhu Fang, Li Li, Lei Gao, Wen-Jun Li, and Shuang Wang
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Halalkalibacter ,polyphasic taxonomy ,saline-alkaline soil ,two novel species ,Biology (General) ,QH301-705.5 - Abstract
The degradation of farmland in China underscores the need for developing and utilizing saline-alkali soil. Soil health relies on microbial activity, which aids in the restoration of the land’s ecosystem, and hence it is important to understand microbial diversity. In the present study, two Gram-stain-positive strains HR 1-10T and J-A-003T were isolated from saline-alkali soil. Preliminary analysis suggested that these strains could be a novel species. Therefore, the taxonomic positions of these strains were evaluated using polyphasic analysis. Phylogenetic and 16S rRNA gene sequence analysis indicated that these strains should be assigned to the genus Halalkalibacter. Cell wall contained meso-2,6-diaminopimelic acid. The polar lipids present in both strains were diphosphatidyl-glycerol, phosphatidylglycerol, and an unidentified phospholipid. The major fatty acids (>10%) were anteiso-C15:0, C16:0 and iso-C15:0. Average nucleotide identity and digital DNA#x2013;DNA hybridization values were below the threshold values (95% and 70%, respectively) for species delineation. Based on the above results, the strains represent two novel species of the genus Halalkalibacter, for which the names Halalkalibacter flavus sp. nov., and Halalkalibacter lacteus sp. nov., are proposed. The type strains are HR 1-10T (=GDMCC 1.2946T = MCCC 1K08312T = JCM 36285T), and J-A-003T (=GDMCC 1.2949T = MCCC 1K08417T = JCM 36286T).
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- 2024
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4. Unraveling the genomic diversity and ecological potential of the genus Demequina: insights from comparative analysis of different saline niche strains
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Lei Gao, Bao-Zhu Fang, Chun-Yan Lu, Kun-Hui Hong, Xin-Yu Huang, Ting-Ting She, Min Xiao, and Wen-Jun Li
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Demequina ,comparative genomic analysis ,diversity and identification ,tidal flat ,saline lake ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
During an investigation of the culturable microbial diversity of sediments with salinity from tidal flats and saline lake, seven strains of the genus Demequina were harvested. The genomic analysis and physiological characteristics of strains of this genus have unveiled their significant potential in degrading complex carbon source such as lignin, hemicellulose, chitin, and oligosaccharides. In addition, these strains show potential abilities in nitrite ammonification and sulfide oxidation. These findings not only improved our understanding of their metabolic model, but also provided valuable insights into their ecological roles. Four new species of the genus Demequina are described: Demequina litoralis sp. nov., with SYSU T00192T designated as the type species; Demequina zhanjiangensis sp. nov., with SYSU T00b26T as the type species; Demequina lignilytica sp. nov., with SYSU T00068T as the type species; and Demequina muriae sp. nov., with EGI L300058T as the type species. Additionally, strains SYSU T0a273, SYSU T00039-1, and SYSU T00039 are identified as different strains of Demequina lignilytica. Our study thus sheds light on the diversity, biological significance, and ecological contribution of the Demequina genus in different habitats.
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- 2023
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5. Cultivation strategies for prokaryotes from extreme environments
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Zi‐Wen Yang, Zheng‐Han Lian, Lan Liu, Bao‐Zhu Fang, Wen‐Jun Li, and Jian‐Yu Jiao
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cultivation strategy ,extreme environment ,extremophiles ,multi‐omics ,pure culture ,Computer applications to medicine. Medical informatics ,R858-859.7 - Abstract
Abstract The great majority of microorganisms are as‐yet‐uncultivated, mostly found in extreme environments. High‐throughput sequencing provides data‐rich genomes from single‐cell and metagenomic techniques, which has enabled researchers to obtain a glimpse of the unexpected genetic diversity of “microbial dark matter.” However, cultivating microorganisms from extreme environments remains essential for dissecting and utilizing the functions of extremophiles. Here, we provide a straightforward protocol for efficiently isolating prokaryotic microorganisms from different extreme habitats (thermal, xeric, saline, alkaline, acidic, and cryogenic environments), which was established through previous successful work and our long‐term experience in extremophile resource mining. We propose common processes for extremophile isolation at first and then summarize multiple cultivation strategies for recovering prokaryotic microorganisms from extreme environments and meanwhile provide specific isolation tips that are always overlooked but important. Furthermore, we propose the use of multi‐omics‐guided microbial cultivation approaches for culturing these as‐yet‐uncultivated microorganisms and two examples are provided to introduce how these approaches work. In summary, the protocol allows researchers to significantly improve the isolation efficiency of pure cultures and novel taxa, which therefore paves the way for the protection and utilization of microbial resources from extreme environments.
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- 2023
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6. Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems
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Wen-Hui Lian, Osama Abdalla Abdelshafy Mohamad, Lei Dong, Ling-Yu Zhang, Dong Wang, Lan Liu, Ming-Xian Han, Shuai Li, Shuang Wang, André Antunes, Bao-Zhu Fang, Jian-Yu Jiao, and Wen-Jun Li
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Culturomics ,Metagenomics ,Desert farming systems ,Rhizosphere microbiome ,Environmental sciences ,GE1-350 ,Microbiology ,QR1-502 - Abstract
Abstract Background The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants. Results The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different. Conclusion Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.
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- 2023
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7. Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts
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Xiao-Qing Luo, Pandeng Wang, Jia-Ling Li, Manzoor Ahmad, Li Duan, Ling-Zi Yin, Qi-Qi Deng, Bao-Zhu Fang, Shan-Hui Li, and Wen-Jun Li
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Auxiliary metabolic genes (AMGs) ,Viral lifestyles ,Metagenomes and metatranscriptomes ,Biogeochemical cycles ,Microbial ecology ,QR100-130 - Abstract
Abstract Background Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts’ metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments. Results Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders. Conclusions Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract
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- 2022
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8. Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota
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Yuan-Guo Xie, Zhen-Hao Luo, Bao-Zhu Fang, Jian-Yu Jiao, Qi-Jun Xie, Xing-Ru Cao, Yan-Ni Qu, Yan-Lin Qi, Yang-Zhi Rao, Yu-Xian Li, Yong-Hong Liu, Andrew Li, Cale Seymour, Marike Palmer, Brian P. Hedlund, Wen-Jun Li, and Zheng-Shuang Hua
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Cadidatus Nanohaloarchaeota ,Metabolism ,Environmental adaptations ,Functional differentiation ,Microbial ecology ,QR100-130 - Abstract
Abstract Background Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria. Aside from hypersaline environments, Ca. Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments. Results Three metagenome-assembled genomes (MAGs) representing a new order within the Ca. Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order, Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a “salt-in” strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously described Ca. Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification within Ca. Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages. Conclusions This study provides deeper insight into the ecological functions and evolution of the expanded phylum Ca. Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts. Video Abstract
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- 2022
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9. Microbial Risks Caused by Livestock Excrement: Current Research Status and Prospects
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Rashidin Abdugheni, Li Li, Zhen-Ni Yang, Yin Huang, Bao-Zhu Fang, Vyacheslav Shurigin, Osama Abdalla Abdelshafy Mohamad, Yong-Hong Liu, and Wen-Jun Li
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livestock excrement ,zoonotic pathogens ,ARGs ,virulence genes ,Biology (General) ,QH301-705.5 - Abstract
Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes.
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- 2023
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10. The Metabolic Potential of Endophytic Actinobacteria Associated with Medicinal Plant Thymus roseus as a Plant-Growth Stimulator
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Osama Abdalla Abdelshafy Mohamad, Yong-Hong Liu, Yin Huang, Li Li, Jin-Biao Ma, Dilfuza Egamberdieva, Lei Gao, Bao-Zhu Fang, Shaimaa Hatab, Hong-Chen Jiang, and Wen-Jun Li
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agriculture sustainability ,environmental microbiology ,medicinal plants ,endophytes ,biofertilizer ,biocontrol ,Biology (General) ,QH301-705.5 - Abstract
Bio-fertilizer practice considers not only economical but also environmentally friendly, sustainable agriculture. Endophytes can play important beneficiary roles in plant development, directly, indirectly, or synergistically. In this study, the majority of our endophytic actinobacteria were able to possess direct plant growth-promoting (PGP) traits, including auxin (88%), ammonia (96%), siderophore production (94%), and phosphate solubilization (24%), along with cell-wall degrading enzymes such as protease (75%), cellulase (81%), lipase (81%), and chitinase (18%). About 45% of tested strains have an inhibitory effect on the phytopathogen Fusarium oxysporum, followed by 26% for Verticillium dahlia. Overall, our results showed that strains XIEG63 and XIEG55 were the potent strains with various PGP traits that caused a higher significant increase (p ≤ 0.05) in length and biomass in the aerial part and roots of tomato and cotton, compared to the uninoculated plants. Our data showed that the greatest inhibition percentages of two phytopathogens were achieved due to treatment with strains XIEG05, XIEG07, XIEG45, and XIEG51. The GC-MS analysis showed that most of the compounds were mainly alkanes, fatty acid esters, phenols, alkenes, and aromatic chemicals and have been reported to have antifungal activity. Our investigation emphasizes that endophytic actinobacteria associated with medicinal plants might help reduce the use of chemical fertilization and potentially lead to increased agricultural productivity and sustainability.
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- 2022
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11. Synergistic Plant-Microbe Interactions between Endophytic Actinobacteria and Their Role in Plant Growth Promotion and Biological Control of Cotton under Salt Stress
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Osama Abdalla Abdelshafy Mohamad, Yong-Hong Liu, Li Li, Jin-Biao Ma, Yin Huang, Lei Gao, Bao-Zhu Fang, Shuang Wang, Ashraf F. El-Baz, Hong-Chen Jiang, and Wen-Jun Li
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environmental microbiology ,medicinal plants ,endophytes ,biofertilizer ,biocontrol ,Verticillium dahliae ,Biology (General) ,QH301-705.5 - Abstract
Bacterial endophytes are well-acknowledged inoculants to promote plant growth and enhance their resistance toward various pathogens and environmental stresses. In the present study, 71 endophytic strains associated with the medicinal plant Thymus roseus were screened for their plant growth promotion (PGP), and the applicability of potent strains as bioinoculant has been evaluated. Regarding PGP traits, the percentage of strains were positive for the siderophore production (84%), auxin synthesis (69%), diazotrophs (76%), phosphate solubilization (79%), and production of lytic enzymes (i.e., cellulase (64%), lipase (62%), protease (61%), chitinase (34%), and displayed antagonistic activity against Verticillium dahliae (74%) in vitro. The inoculation of strain XIEG05 and XIEG12 enhanced plant tolerance to salt stress significantly (p < 0.05) through the promotion of shoot, root development, and reduced the activities of antioxidant enzymes (SOD, POD, and CAT), compared with uninoculated controls in vivo. Furthermore, inoculation of strain XIEG57 was capable of reducing cotton disease incidence (DI) symptoms caused by V. dahliae at all tested salt concentrations. The GC-MS analysis showed that many compounds are known to have antimicrobial and antifungal activity. Our findings provide valuable information for applying strains XIEG05 and XIEG12 as bioinoculant fertilizers and biological control agent of cotton under saline soil conditions.
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- 2022
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12. Insights on the Effects of Heat Pretreatment, pH, and Calcium Salts on Isolation of Rare Actinobacteria from Karstic Caves
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Bao-Zhu Fang, Nimaichand Salam, Ming-Xian Han, Jian-Yu Jiao, Juan Cheng, Da-Qiao Wei, Min Xiao, and Wen-Jun Li
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Sigangli Cave ,rare Actinobacteria ,heat pretreatment ,pH ,calcium salts ,Microbiology ,QR1-502 - Abstract
The phylum Actinobacteria is one of the most ubiquitously present bacterial lineages on Earth. In the present study, we try to explore the diversity of cultivable rare Actinobacteria in Sigangli Cave, Yunnan, China by utilizing a combination of different sample pretreatments and under different culture conditions. Pretreating the samples under different conditions of heat, setting the isolation condition at different pHs, and supplementation of media with different calcium salts were found to be effective for isolation of diverse rare Actinobacteria. During our study, a total of 204 isolates affiliated to 30 genera of phylum Actinobacteria were cultured. Besides the dominant Streptomyces, rare Actinobacteria of the genera Actinocorallia, Actinomadura, Agromyces, Alloactinosynnema, Amycolatopsis, Beutenbergia, Cellulosimicrobium, Gordonia, Isoptericola, Jiangella, Knoellia, Kocuria, Krasilnikoviella, Kribbella, Microbacterium, Micromonospora, Mumia, Mycobacterium, Nocardia, Nocardioides, Nocardiopsis, Nonomuraea, Oerskovia, Pseudokineococcus, Pseudonocardia, Rhodococcus, Saccharothrix, Streptosporangium, and Tsukamurella were isolated from these cave samples.
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- 2017
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13. Metabonomic analysis to identify exometabolome changes underlying antifungal and growth promotion mechanisms of endophytic Actinobacterium Streptomyces albidoflavus for sustainable agriculture practice.
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Abdelshafy Mohamad, Osama Abdalla, Yong-Hong Liu, Yin Huang, Kuchkarova, Nigora, Lei Dong, Jian-Yu Jiao, Bao-Zhu Fang, Jin-Biao Ma, Hatab, Shaimaa, and Wen-Jun Li
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SUSTAINABILITY ,BOTANY ,SUSTAINABLE agriculture ,CYCLIC peptides ,MICROBIAL ecology - Abstract
In recent years, there has been an increasing focus on microbial ecology and its possible impact on agricultural production, owing to its eco-friendly nature and sustainable use. The current study employs metabolomics technologies and bioinformatics approaches to identify changes in the exometabolome of Streptomyces albidoflavus B24. This research aims to shed light on the mechanisms and metabolites responsible for the antifungal and growth promotion strategies, with potential applications in sustainable agriculture. Metabolomic analysis was conducted using Q Exactive UPLC-MS/MS. Our findings indicate that a total of 3,840 metabolites were identified, with 137 metabolites exhibiting significant differences divided into 61 up and 75 downregulated metabolites based on VIP >1, |FC| >1, and p < 0.01. The interaction of S. albidoflavus B24 monoculture with the co-culture demonstrated a stronger correlation coefficient. The Principal Component Analysis (PCA) demonstrates that PCA1 accounted for 23.36%, while PCA2 accounted for 20.28% distinction. OPLS-DA score plots indicate significant separation among different groups representing (t1) 24% as the predicted component (to1) depicts 14% as the orthogonal component. According to the findings of this comprehensive study, crude extracts from S. albidoflavus demonstrated varying abilities to impede phytopathogen growth and enhance root and shoot length in tested plants. Through untargeted metabolomics, we discovered numerous potential molecules with antagonistic activity against fungal phytopathogens among the top 10 significant metabolites with the highest absolute log2FC values. These include Tetrangulol, 4-Hydroxybenzaldehyde, and Cyclohexane. Additionally, we identified plant growth-regulating metabolites such as N-Succinyl-L-glutamate, Nicotinic acid, L-Aspartate, and Indole-3-acetamide. The KEGG pathway analysis has highlighted these compounds as potential sources of antimicrobial properties The inhibitory effect of S. albidoflavus crude extracts on pathogen growth is primarily attributed to the presence of specific gene clusters responsible for producing cyclic peptides such as ansamycins, porphyrin, alkaloid derivatives, and neomycin. Overall, it is apparent that crude extracts from S. albidoflavus exhibited varying abilities to inhibit the growth of three phytopathogens and enhancement in both root and shoot length of tested plants. This research enhances our understanding of how secondary metabolites contribute to growth promotion and biocontrol, supporting ecosystem sustainability and resilience while boosting productivity in sustainable agriculture. [ABSTRACT FROM AUTHOR]
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- 2024
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14. Comparative Genome Analysis of a Novel Alkaliphilic Actinobacterial Species Nesterenkonia haasae
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Shuang Wang, Lei Sun, Manik Prabhu Narsing Rao, Bao‑zhu Fang, and Wen‑jun Li
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Microbiology (medical) ,General Medicine ,Applied Microbiology and Biotechnology ,Microbiology - Abstract
In the present study, a comparative genome analysis of the novel alkaliphilic actinobacterial Nesterenkonia haasae with other members of the genus Nesterenkonia was performed. The genome size of Nesterenkonia members ranged from 2,188,008 to 3,676,111 bp. N. haasae and Nesterenkonia members of the present study encode the essential glycolysis and pentose phosphate pathway genes. In addition, some Nesterenkonia members encode the crucial genes for Entner-Doudoroff pathways. Some Nesterenkonia members possess the genes responsible for sulfate/thiosulfate transport system permease protein/ ATP-binding protein and conversion of sulfate to sulfite. Nesterenkonia members also encode the genes for assimilatory nitrate reduction, nitrite reductase, and the urea cycle. All Nesterenkonia members have the genes to overcome environmental stress and produce secondary metabolites. The present study helps to understand N. haasae and Nesterenkonia members’ environmental adaptation and niches specificity based on their specific metabolic properties. Further, based on genome analysis, we propose reclassifying Nesterenkonia jeotgali as a later heterotypic synonym of Nesterenkonia sandarakina.
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- 2022
15. Rhodoflexus caldus gen. nov., sp. nov., a new member of the phylum Bacteroidota isolated from a hot spring sediment
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Ze-Tao Liu, Lan Liu, Wen-Dong Xian, Zheng-Han Lian, Jun-Yi Dai, Bao-Zhu Fang, Meng-Meng Li, Ai-Ping Lv, Zhen-Hao Luo, Jian-Yu Jiao, and Wen-Jun Li
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DNA, Bacterial ,China ,RNA, Ribosomal, 16S ,Fatty Acids ,Sequence Analysis, DNA ,General Medicine ,Molecular Biology ,Microbiology ,Hot Springs ,Phospholipids ,Phylogeny ,Bacterial Typing Techniques - Abstract
A thermophilic bacterium, designated strain SYSU G04325
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- 2022
16. Salinibacterium sedimenticola sp. nov., Isolated from Tidal Flat Sediment
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Chun-Yan Lu, Lei Dong, Shuai Li, Wen-Hui Lian, Zhi-Liang Lin, Zhuo-Huan Zheng, Lei Gao, Bao-Zhu Fang, and Wen-Jun Li
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General Medicine ,Applied Microbiology and Biotechnology ,Microbiology - Published
- 2023
17. Aquiflexum gelatinilyticum sp. nov., isolated from river water
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Dan-Dan Zhang, Xiao-Juan Zhang, Danni Wu, Bin-Bin Li, Hong-Can Liu, Yu-Guang Zhou, Bao-Zhu Fang, Wen-Jun Li, and Man Cai
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General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
Two Gram-stain-negative, strictly aerobic, rod-shaped, non-motile and non-gliding bacteria, designated as XJ19-10T and XJ19-11, were isolated from river water in Xinjiang Uygur Autonomous Region, PR China. Cells of these strains were catalase-, oxidase- and gelatinase-positive and contained carotenoids but no flexirubins. Growth occurred at 10–30 °C, pH 7.0–9.0 and with 0–2.5% (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence and genome analyses, the two isolates represented members of the genus Aquiflexum , and the closest relative was Aquiflexum aquatile Z0201T with 16S rRNA gene sequence pairwise similarities of 97.9–98.1%. Furthermore, the average nucleotide identities and digital DNA–DNA hybridization identities between the two isolates and other relatives were all less than 82.9 and 28.2 %, respectively, all below the species delineation thresholds. The results of pan-genomic analysis indicated that the type strain XJ19-10T shared 2813 core gene clusters with other three type strains of members of the genus Aquiflexum , as well as having 623 strain-specific clusters. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid and unidentified lipids. The predominant fatty acids (>10% of the total contents) were iso-C15 : 0, iso-C15 : 1G, iso-C17 : 0 3-OH and summed feature 9, and MK-7 was the respiratory quinone. On the basis of the results of phenotypic, physiological, chemotaxonomic and genotypic characterization, strains XJ19-10T and XJ19-11 are considered to represent a novel species, for which the name Aquiflexum gelatinilyticum sp. nov. is proposed. The type strain is XJ19-10T (=CGMCC 1.19385T =KCTC 92266T).
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- 2023
18. Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov., two novel resistant bacteria isolated from pearl river estuary
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Li Duan, Bao-Zhu Fang, Pandeng Wang, Xiao-Qing Luo, Lei Dong, Ze-Tao Liu, Wen-Jun Li, Ling-Zi Yin, Shan-Hui Li, and Jia-Ling Li
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DNA, Bacterial ,Diamino acid ,Microbiology ,Cell wall ,chemistry.chemical_compound ,Rivers ,RNA, Ribosomal, 16S ,Deinococcus ,Molecular Biology ,Phospholipids ,Phylogeny ,geography ,geography.geographical_feature_category ,biology ,Phylogenetic tree ,Estuary ,Sequence Analysis, DNA ,General Medicine ,Polar lipids ,biology.organism_classification ,16S ribosomal RNA ,Bacterial Typing Techniques ,Resistant bacteria ,chemistry ,Estuaries - Abstract
Two novel species of the genus Deinococcus, designated SYSU M49105T and SYSU M42101T, were isolated from freshwater samples of the Pearl River estuary in Guangdong, China. Phylogenetic analysis using 16S rRNA gene sequence indicated that strains SYSU M49105T and SYSU M42101T showed the highest sequence similarities to Deinococcus aetherius JCM 11751 T (93.6%) and Deinococcus multiflagellatus NBRC 112888 T (97.3%), respectively. Cells of both strains were Gram-staining positive, aerobic, coccus-shaped, oxidase-negative and non-motile. The cell wall contained meso-diaminopimelic acid as their diagnostic diamino acid. MK-8 was the predominant respiratory quinone for both strains. The polar lipid profile of SYSU M49105T contained two unidentified phosphoglycolipids, nine unidentified glycolipids, and five unidentified polar lipids. SYSU M42101T had one unidentified phosphoglycolipid, nine unidentified glycolipids, one unidentified aminophospholipid and four unidentified polar lipids. The major fatty acids of strains SYSU M49105T and SYSU M42101T were summed feature 3 (C16:1 ω7c and/ or C16:1 ω6c) and C16:0. The G + C contents of the novel isolates based on genomic DNAs were 69.6% and 67.4%, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU M49105T and SYSU M42101T should be considered to represent two novel species in the genus Deinococcus, for which the names Deinococcus aestuarii sp. nov. and Deinococcus aquaedulcis sp. nov. were proposed with the type strains SYSU M49105T (= KCTC 43258 T = CGMCC 1.18609 T) and SYSU M42101T (= KCTC 43257 T = CGMCC 1.18614 T), respectively.
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- 2021
19. Devosia ureilytica sp. nov., isolated from Kuche River in China
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Bin-Bin Li, Xiao-Juan Zhang, Danni Wu, Dan-Dan Zhang, Bao-Zhu Fang, Hong-Can Liu, Yu-Guang Zhou, Man Cai, Wen-Jun Li, and Guo-Xing Nie
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General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
Two novel strains, designated XJ19-45T and XJ19-1, were isolated from water of Kuche River in Xinjiang Uygur Autonomous Region, China. Their cells were Gram-stain-negative, aerobic and motile rods. The phylogenetic analyses based on 16S rRNA genes and genomes showed that the two isolates belonged to the genus Devosia and the closest relative was Devosia subaequoris HST3-14T. The 16S rRNA genes sequences pairwise similarities, average nucleotide identities, digital DNA–DNA hybridizations and average amino acid identities between type strain XJ19-45T and other relatives were all less than 98.3, 80.3, 23.6 and 85.7 %, respectively, all below the species delineation thresholds. Pan-genomic analysis indicated that the novel isolate XJ19-45T shared 1594 core gene clusters with the 11 closely related type strains in Devosia , and the number of strain-specific clusters was 390. The major cellular fatty acids (>10 %) of the two isolates were summed feature 8, C18 : 1 ω7c 11-methyl and C16 : 0. Diphosphatidylglycerol, phosphatidylglycerol and glycolipids were the major polar lipids, and Q10 was the detected respiratory quinone. Based on the results of phenotypic, physiological, chemotaxonomic and genotypic characterizations, we propose that the isolates represent a novel species, for which the name Devosia ureilytica sp. nov. is proposed. The type strain is XJ19-45T (=CGMCC 1.19388T=KCTC 92263T).
- Published
- 2022
20. Biogeographical distributions of nitrogen‐cycling functional genes in a subtropical estuary
- Author
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Lin Jiang, Bao-Zhu Fang, Xiao-Qing Luo, Manzoor Ahmad, Ling-Zi Yin, Pandeng Wang, Shan-Hui Li, Li Duan, Wen-Jun Li, Jia-Ling Li, and Yuchun Yang
- Subjects
geography ,geography.geographical_feature_category ,Ecology ,Estuary ,Functional genes ,Subtropics ,Biology ,Nitrogen cycle ,Ecology, Evolution, Behavior and Systematics - Published
- 2021
21. Complete genome sequencing and comparative genome analysis of the extremely halophilic archaea, Haloterrigena daqingensis
- Author
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Shuang Wang, Wen-Jun Li, Dan Wei, Manik Prabhu Narsing Rao, Bao-Zhu Fang, Lei Sun, Li-Hong Yu, and Wei-Qun Li
- Subjects
Genetics ,Whole genome sequencing ,Halobacteriaceae ,Whole Genome Sequencing ,Process Chemistry and Technology ,Circular bacterial chromosome ,Biomedical Engineering ,Bioengineering ,Sequence Analysis, DNA ,General Medicine ,Biology ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Genome ,DNA sequencing ,Haloterrigena ,DNA, Archaeal ,Plasmid ,RNA, Ribosomal, 16S ,Drug Discovery ,Molecular Medicine ,Gene ,Genome size ,Phylogeny ,Biotechnology - Abstract
In the present study, we report the complete genome sequencing of Haloterrigena daqingensis species. The genome of H. daqingensis JX313T consisted of a circular chromosome with three plasmids. The genome size and G+C content were estimated to be 3835796 bp and 61.7%, respectively. A total of 4158 genes were predicted with six rRNAs and 45 tRNAs. Metabolic pathway analysis suggests that H. daqingensis JX313T codes for all the necessary genes responsible to sustain its life at saline environment. The pan-genome analysis suggests that the number of singleton-gene between H. daqingensis and other Haloterrigena species varied. The study not only helps us understand H. daqingensis strategy for dealing with high stress, but it also provides an overview of its genomic makeup.
- Published
- 2021
22. Pseudalkalibacillus salsuginis sp. nov., a novel salt-tolerant bacterium isolated from a saline lake sediment
- Author
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Lei Gao, Bao-Zhu Fang, Yong-Hong Liu, Yin Huang, Dan-Dan Zhang, Shuang Wang, Hong-Chen Jiang, and Wen-Jun Li
- Subjects
General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
A salt-tolerant bacterium, designated strain EGI L200015T, was isolated from saline lake sediment in Xinjiang Uygur Autonomous Region, PR China. The taxonomic position of the isolate was determined using polyphasic taxonomic analysis and phylogenomic analysis. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that EGI L200015T formed a distinct clade with Pseudalkalibacillus berkeleyi KCTC 12718T with sequence identity of 98.3%. The novel isolate could be distinguished from species of the genus Pseudalkalibacillus by its distinct phenotypic, physiological and genotypic characteristics. Cells of EGI L200015T were aerobic, Gram-stain-positive, non-motile and rod-shaped. Optimal growth conditions for EGI L200015T occurred on marine agar 2216 at pH 8.0 at 30 °C. The major respiratory quinone was MK-7, while the major fatty acids (> 10 %) were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The detected polar lipids of included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. On the basis of the genome sequence data, the DNA G+C content of EGI L200015T was 41.6 %. On the basis of the phenotypic, physiological, genotypic and phylogenetic data, strain EGI L200015T represents a novel species of the genus Pseudalkalibacillus , for which the name Pseudalkalibacillus salsuginis sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L200015T (= KCTC 43363T = CGMCC 1.19260T).
- Published
- 2022
23. Dongia deserti sp. nov., Isolated from the Gurbantunggut Desert Soil
- Author
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Chun-Yan Lu, Lei Dong, Dong Wang, Shuai Li, Bao-Zhu Fang, Ming-Xian Han, Feng Liu, Hong-Chen Jiang, Iftikhar Ahmed, and Wen-Jun Li
- Subjects
DNA, Bacterial ,Phosphatidylethanolamines ,Fatty Acids ,Quinones ,Sequence Analysis, DNA ,General Medicine ,Sodium Chloride ,Applied Microbiology and Biotechnology ,Microbiology ,Bacterial Typing Techniques ,Agar ,Soil ,RNA, Ribosomal, 16S ,Phospholipids ,Phylogeny ,Soil Microbiology - Abstract
A Gram-stain-negative, aerobic, short rod-shaped strain, designated as SYSU D60009
- Published
- 2022
24. Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan
- Author
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Bao-Zhu Fang, Lei Gao, Jian-Yu Jiao, Zi-Tong Zhang, Meng-Meng Li, Osama Abdalla Abdelshafy Mohamad, Iftikhar Ahmed, Li Li, Yong-Hong Liu, and Wen-Jun Li
- Subjects
General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
A novel actinobacterial strain, designated SYSU K20354T, was isolated from a soil sample collected from a karst cave in Shaoguan city, Guangdong province, southern China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU K20354T was most closely related to Agromyces humatus JCM 14319T, and shared the highest sequence identity of 98.3 % based on NCBI database. In addition, 2,4-diaminobutyric acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were galactose, glucose, mannose and ribose. The major isoprenoid quinone was MK-12, while the major fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, three unknown glycolipids, three unknown phospholipids and two unknown lipids. The draft genome size of strain SYSU K20354T was 3.96 Mbp with G+C content of 69.7 mol%. Furthermore, the average nucleotide identity and digital DNA–DNA hybridization values between strain SYSU K20354T and A. humatus JCM 14319T were 90.3 and 55.6 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K20354T represents a novel species of the genus Agromyces , for which the name Agromyces cavernae sp. nov. is proposed. The type strain is SYSU K20354T (=KCTC 49499T= CGMCC 4.7691T).
- Published
- 2022
25. Paracoccus salsus sp. nov., a novel slightly halophilic bacterium isolated from saline lake sediment
- Author
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Lei Gao, Bao-Zhu Fang, Yong-Hong Liu, Yin Huang, Shuang Wang, Hong-Chen Jiang, and Wen-Jun Li
- Subjects
General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
A Gram-stain-negative, non-motile, slightly halophilic and non-endospore-forming alphaproteobacterium, designated strain EGI L200073T, was isolated from saline lake sediment sampled in Xinjiang Uygur Autonomous Region, China. The taxonomic position of the isolate was determined using the polyphasic taxonomic analysis and phylogenomic analysis. Phylogenetic analysis based on 16S rRNA gene sequence similarities indicated that strain EGI L200073T formed a distinct clade with Paracoccus seriniphilus DSM 14827T and shared sequence identity of 98.56 %. The novel isolate could be distinguished from other species of the genus Paracoccus by its distinct phenotypic, physiological and genotypic characteristics. Optimal growth of strain EGI L200073T occurred on marine agar 2216 at pH 8.0 and 30 °C. The major respiratory quinone was Q-10, while the major fatty acids (>10%) were summed feature 8 (C17 : 1 ω6c and/or C17 : 1 ω7c) and C18 : 0. The detected polar lipids included diphosphatidylglycerol, phosphatidylcholine and phosphatidylglycerol. Based on the genome sequence of strain EGI L200073T, the G+C content of the novel isolate was 65.7 mol%. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of strain EGI L200073T against related members in the genus Paracoccus were below the cut-off points proposed for delineation of a novel species. According our polyphasic taxonomic data, strain EGI L200073T represents a new species of the genus Paracoccus , for which the name Paracoccus salsus sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L200073T (=KCTC 92045T=CGMCC 1.19242T).
- Published
- 2022
26. Sediment prokaryotic microbial community and potential biogeochemical cycle from saline lakes shaped by habitat
- Author
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Yong-Hong Liu, Osama Abdalla Abdelshafy Mohamad, Lei Gao, Yuan-Guo Xie, Rashidin Abdugheni, Yin Huang, Li Li, Bao-Zhu Fang, and Wen-Jun Li
- Subjects
Microbiology - Published
- 2023
27. Insight into the function and evolution of the Wood–Ljungdahl pathway in Actinobacteria
- Author
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Jian-Yu Jiao, Nimaichand Salam, Bao Zhu Fang, Rob Knight, Aharon Oren, Zheng-Shuang Hua, Brian P. Hedlund, Qiyun Zhu, Lan Liu, En-Min Zhou, Geng Wu, Pengfei Liu, Wen Dong Xian, Ai Ping Lv, Li Fu, Lei Cheng, Wen-Jun Li, and Hongchen Jiang
- Subjects
Genetics ,Carbon Monoxide ,0303 health sciences ,biology ,030306 microbiology ,Thermodesulfobacteria ,biology.organism_classification ,Deltaproteobacteria ,Aldehyde Oxidoreductases ,Microbiology ,Article ,Nitrospirae ,Actinobacteria ,03 medical and health sciences ,Multienzyme Complexes ,Acetogenesis ,Horizontal gene transfer ,Wood–Ljungdahl pathway ,biology.protein ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Carbon monoxide dehydrogenase - Abstract
Carbon fixation by chemoautotrophic microbes such as homoacetogens had a major impact on the transition from the inorganic to the organic world. Recent reports have shown the presence of genes for key enzymes associated with the Wood–Ljungdahl pathway (WLP) in the phylum Actinobacteria, which adds to the diversity of potential autotrophs. Here, we compiled 42 actinobacterial metagenome-assembled genomes (MAGs) from new and existing metagenomic datasets and propose three novel classes, Ca. Aquicultoria, Ca. Geothermincolia and Ca. Humimicrobiia. Most members of these classes contain genes coding for acetogenesis through the WLP, as well as a variety of hydrogenases (NiFe groups 1a and 3b–3d; FeFe group C; NiFe group 4-related hydrogenases). We show that the three classes acquired the hydrogenases independently, yet the carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS) was apparently present in their last common ancestor and was inherited vertically. Furthermore, the Actinobacteria likely donated genes for CODH/ACS to multiple lineages within Nitrospirae, Deltaproteobacteria (Desulfobacterota), and Thermodesulfobacteria through multiple horizontal gene transfer events. Finally, we show the apparent growth of Ca. Geothermincolia and H(2)-dependent acetate production in hot spring enrichment cultures with or without the methanogenesis inhibitor 2-bromoethanesulfonate, which is consistent with the proposed homoacetogenic metabolism.
- Published
- 2021
28. Thermomonas flagellata sp. nov. and Thermomonas alba sp. nov., two novel members of the phylum Pseudomonadota isolated from hot spring sediments
- Author
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Ze-Tao Liu, Jun-Yi Dai, Zheng-Han Lian, Lan Liu, Wen-Dong Xian, Meng-Meng Li, Bao-Zhu Fang, Jian-Yu Jiao, and Wen-Jun Li
- Subjects
General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
Two novel species, designated strains SYSU G04041T and SYSU G04536T, were isolated from hot spring sediments collected in Yunnan, PR China. Phenotypic and chemotaxonomic analyses, and whole-genome sequencing were used to determine the taxonomic positions of the candidate strains. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain SYSU G04041T showed the highest sequence similarity to Thermomonas haemolytica A50-7-3T (97.5 %), and SYSU G04536T showed the highest sequence similarity to Thermomonas hydrothermalis SGM-6T (98.2 %). The strains could be differentiated from other species of the genus Thermomonas by their distinct phenotypic and genotypic characteristics. Cells of strains SYSU G04041T and SYSU G04536T were aerobic, motile and Gram-stain-negative. Growth both occurred optimally at 45 °C and pH 7.0 for SYSU G04041T and SYSU G04536T. In addition, the predominant respiratory quinone in both isolates was ubiquinone Q-8. The major fatty acids (>10 %) of strain SYSU G04041T were C16 : 0, iso-C15 : 0 and iso-C16 : 0, while the major fatty acids (>10 %) of strain SYSU G04536T were iso-C15 : 0 and iso-C16 : 0. The main detected polar lipids in strains SYSU G04041T and SYSU G04536T included phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The G+C contents of the genomic DNA of strains SYSU G04041T and SYSU G04536T based on draft genomic sequences were 72.5 and 68.3 %, respectively. On the basis of phenotypic, genotypic and phylogenetic data, strains SYSU G04041T and SYSU G04536T represent two novel species of the genus Thermomonas , for which the names Thermomonas flagellata sp. nov. and Thermomonas alba sp. nov. are proposed, with the type strains SYSU G04041T (=CGMCC 1.19366T=KCTC 92228T) and SYSU G04536T (=CGMCC 1.19367T=KCTC 82839T), respectively.
- Published
- 2022
29. Rhabdothermincola salaria sp. nov., a novel actinobacterium isolated from a saline lake sediment
- Author
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Lei Gao, Bao-Zhu Fang, Yong-Hong Liu, Jian-Yu Jiao, Meng-Meng Li, André Antunes, and Wen-Jun Li
- Subjects
General Medicine ,Microbiology ,Ecology, Evolution, Behavior and Systematics - Abstract
An actinobacterium, designated strain EGI L10124T, was isolated from saline lake sediment collected in Xinjiang province, PR China. The taxonomic position of the isolate was determined based on polyphasic taxonomic and phylogenomic analyses. Phylogenetic analysis and 16S rRNA gene sequence similarities indicated that strain EGI L10124T formed a distinct clade with Rhabdothermincola sediminis SYSU G02662T, with a shared sequence identity of 95.2 %. The novel isolate could be distinguished from species in the genus Rhabdothermincola by its distinct phenotypic, physiological and genotypic characteristics. The cells of strain EGI L10124T were aerobic, Gram-stain-positive and short rod-shaped. Optimal growth conditions of strain EGI L10124T on marine agar 2216 were registered at pH 8.0 at 37 °C. In addition, meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major respiratory quinone was MK-9 (H8), while the major fatty acids were iso-C16 : 0, C17 : 0 and C16 : 0. The polar lipids included diphosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. Based on the genome sequence of strain EGI L10124T, it appears that the G+C content of the novel isolate was 71.8 mol%. According to our data, strain EGI L10124T represents a new species of the genus Rhabdothermincola , for which the name Rhabdothermincola salaria sp. nov. is proposed. The type strain of the proposed novel isolate is EGI L10124T (=CGMCC 1.19113T=KCTC 49679T).
- Published
- 2022
30. Aquiflexum lacus sp. nov., isolated from a lake sediment sample
- Author
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Jian Yang, Hongchen Jiang, Dongmei Yu, Ming-Xian Han, Jianrong Huang, Xiying Zhang, Jibin Han, Haiyi Xiao, Bao-Zhu Fang, and Wen-Jun Li
- Subjects
0303 health sciences ,Strain (chemistry) ,Phylogenetic tree ,biology ,030306 microbiology ,Chemistry ,Sediment ,General Medicine ,16S ribosomal RNA ,medicine.disease_cause ,biology.organism_classification ,Biochemistry ,Microbiology ,03 medical and health sciences ,Monophyly ,Botany ,Genetics ,medicine ,Aquiflexum ,Molecular Biology ,Aquiflexum balticum ,Bacteria ,030304 developmental biology - Abstract
A novel Gram-staining negative, crescent-like or rod-shaped, non-motile bacterium, designated strain CUG 91378 T, was isolated from a sediment sample of Qinghai Lake, Qinghai Province, China. The strain was red-colored, and catalase- and oxidase-positive. Strain CUG 91378 T was able to grow at 15–37 °C (optimum, 28 °C), pH 7–9 (pH 7.0) and in the presence of up to 3.0% (w/v) NaCl (0–2%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CUG 91378 T formed a well-supported monophyletic clade with Aquiflexum balticum DSM 16537 T (95.4%) and Aquiflexum aquatile Z0201T (93.2%). The DNA G + C content of CUG 91378 T was 39.0%. Low ( 5.0%) were iso-C15:0 (19.1%), iso-C16:0 (12.0%), iso-C16:1 H (10.9%), iso-C16:0 3OH (9.2%), iso-C17:0 3OH (7.7%), C17:1ω6c (6.1%) and anteiso-C15:0 (5.8%). Strain CUG 91378 T contained as phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and four unidentified lipids (L1, L2, L3 and L4). Based on the data from the current polyphasic study, the isolate represents a novel species of the genus Aquiflexum for which the name Aquiflexum lacus is proposed. The type strain of the proposed new taxon is CUG 91378 T (= KCTC 62637 T = CGMCC 1.13988 T).
- Published
- 2021
31. Revealing the salinity adaptation mechanism in halotolerant bacterium Egicoccus halophilus EGI 80432T by physiological analysis and comparative transcriptomics
- Author
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Li Li, Yonghong Liu, Wen-Sheng Shu, Osama Abdalla Mohamad, Bao-Zhu Fang, Ahmad Manzoor, Wen-Jun Li, and Dai-Di Chen
- Subjects
0303 health sciences ,030306 microbiology ,Chemistry ,General Medicine ,Ectoine ,Applied Microbiology and Biotechnology ,Trehalose ,Salinity ,03 medical and health sciences ,chemistry.chemical_compound ,Biochemistry ,Halotolerance ,Osmoprotectant ,Proline ,Threonine ,Histidine ,030304 developmental biology ,Biotechnology - Abstract
Egicoccus halophilus EGI 80432T, a halotolerant bacterium isolated from a saline-alkaline soil, belongs to a member of the class Nitriliruptoria, which exhibits high adaptability to salt environments. At present, the detailed knowledge of the salinity adaptation strategies of Nitriliruptoria was limited except for one research by using comparative genomics analysis. Here, we investigated the salinity adaptation mechanism of E. halophilus EGI 80432T by comparative physiological and transcriptomic analyses. The results of physiological analyses showed that trehalose and glutamate were accumulated by salt stress and showed the maximum at moderate salinity condition. Furthermore, the contents of histidine, threonine, proline, and ectoine were increased with increasing salt concentration. We found that both 0% and 9% NaCl conditions resulted in increased expressions of genes involved in carbohydrate and energy metabolisms, but negatively affected the Na+ efflux, iron, and molybdate transport. Moreover, the high salt condition led to enhancement of transcription of genes required for the synthesis of compatible solutes, e.g., glutamate, histidine, threonine, proline, and ectoine, which agree with the results of physiological analyses. The above results revealed that E. halophilus EGI 80432T increased inorganic ions uptake and accumulated trehalose and glutamate in response to moderate salinity condition, while the salinity adaptation strategy was changed from a "salt-in-cytoplasm" strategy to a "compatible solute" strategy under high salinity condition. The findings in this study would promote further studies in salt tolerance molecular mechanism of Nitriliruptoria and provide a theoretical support for E. halophilus EGI 80432T's application in ecological restoration.Key Points• Salt stress affected gene expressions responsible for carbohydrate and energy metabolisms of E. halophilus EGI 8042T.• E. halophilus EGI 80432T significantly accumulated compatible solutes under salt stress.• E. halophilus EGI 80432T adopted a "compatible solute" strategy to withstand high salt stress.
- Published
- 2021
32. Thermaurantiacus tibetensis gen. nov., sp. nov., a novel moderately thermophilic bacterium isolated from hot spring microbial mat in Tibet
- Author
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Wen-Dong Xian, Bao-Zhu Fang, Meng-Meng Li, Ai-Ping Lv, Lan Liu, Jian-Yu Jiao, Ze-Tao Liu, Yu-Zhen Ming, and Wen-Jun Li
- Subjects
0106 biological sciences ,0301 basic medicine ,chemistry.chemical_classification ,Oxidase test ,biology ,Strain (chemistry) ,Thermophile ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,Amino acid ,03 medical and health sciences ,Pigment ,030104 developmental biology ,Glycolipid ,chemistry ,visual_art ,visual_art.visual_art_medium ,Molecular Biology ,Bacteria - Abstract
Two bacterial strains SYSU G02173T and SYSU G03142 were isolated from hot springs in Tibet, China. Based on the results of nearly full-length 16S rRNA gene sequences and phylogenetic analyses, strains SYSU G02173T and SYSU G03142 were assigned to the family Sphingosinicellaceae, and were closest to Sandaracinobacter sibiricus RB16-17 T (96.04% and 96.12% similarity, respectively). Cells of the both new strains were observed to be motile rod-shape, Gram-staining negative. Growth occurred at pH 6–8 (optimal: pH 7.0) and 37–55 °C (optimal: 45 °C) with 0–1.0% (w/v) NaCl in T4 broth. The cells were found to be positive for oxidase and catalase activities. The major respiratory ubiquinone was Q-8. The major fatty acids were identified as summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, C14:0 2-OH. The major polar lipids were found to consist of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified phospholipid, one unidentified glycolipid, three unidentified aminolipids and two unidentified polar lipids. The DNA G + C contents of strains SYSU G02173T and SYSU G03142 were 71.8%. The average nucleotide identity (ANI) value between strain SYSU G02173T and SYSU G03142 was 99.98%. The amino acid identity (AAI) values between them and their closely related species were below 66.14%. The isolates are characterized by aerobic growth, a yellow endocellular pigment and a higher optimum growth temperature. The results showed that strains SYSU G02173T and SYSU G03142 represent a novel species of a novel genus in the family Sphingomonadaceae, and thus the name Thermaurantiacus tibetensis (type strain SYSU G02173T = KCTC 72052 T = CGMCC 1.16680 T) is proposed.
- Published
- 2021
33. Seramator thermalis gen. nov., sp. nov., a novel cellulose- and xylan-degrading member of the family Dysgonamonadaceae isolated from a hot spring
- Author
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Bao-Zhu Fang, Min Xiao, Jian-Yu Jiao, Ai-Ping Lv, Meng-Meng Li, Lan Liu, Nimaichand Salam, Yu-Zhen Ming, and Wen-Jun Li
- Subjects
Hot spring ,Phylogenetic tree ,Strain (chemistry) ,General Medicine ,Biology ,16S ribosomal RNA ,Microbiology ,Xylan ,Molecular biology ,chemistry.chemical_compound ,genomic DNA ,chemistry ,Anaerobic bacteria ,Cellulose ,Ecology, Evolution, Behavior and Systematics - Abstract
Two anaerobic bacteria, designated strains SYSU GA16112T and SYSU GA16107, were isolated from a hot spring in Tengchong County, Yunnan Province, south-west PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SYSU GA16112T and SYSU GA16107 belong to the family Dysgonamonadaceae. Cells of strains SYSU GA16112T and SYSU GA16107 were Gram-stain-negative, rod-shaped and non-motile. The major fatty acids (>10 %) of strains SYSU GA16112T and SYSU GA16107 were identified as anteiso-C15 : 0 and anteiso-C17 : 0 3OH. The polar lipid profile of strain SYSU GA16112T was found to consist of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phosphoglycolipids, two unidentified aminolipids and one unidentified polar lipid, while that of strain SYSU GA16107 consisted of phosphatidylethanolamine, two unidentified polar lipids, three unidentified aminophospholipids, two unidentified phosphoglycolipids and one unidentified aminolipid. The genomic DNA G+C contents of strains SYSU GA16112T and SYSU GA16107 were determined to be 41.90 and 41.89 %, respectively, and the average nucleotide identity value between them was 99.99 %. Based on their morphological and physiological properties, and results of phylogenetic analyses, strains SYSU GA16112T and SYSU GA16107 are considered to represent a novel species of a novel genus, for which the name Seramator thermalis gen. nov., sp. nov. (type strain SYSU GA16112T=CGMCC 1.5281T=KCTC 15753T) is proposed.
- Published
- 2020
34. Ornithinimicrobium sediminis sp. nov., a novel actinobacterium isolated from a saline lake sediment
- Author
-
Lei Gao, Bao-Zhu Fang, Yong-Hong Liu, Yin Huang, Jian-Yu Jiao, Li Li, André Antunes, and Wen-Jun Li
- Subjects
DNA, Bacterial ,China ,Fatty Acids ,Sequence Analysis, DNA ,General Medicine ,Biochemistry ,Microbiology ,Bacterial Typing Techniques ,Lakes ,RNA, Ribosomal, 16S ,Actinomycetales ,Genetics ,Molecular Biology ,Phospholipids ,Phylogeny - Abstract
An actinobacterium, designated strain EGI L100131
- Published
- 2022
35. Nesterenkonia haasae sp. nov., an alkaliphilic actinobacterium isolated from a degraded pasture in Songnen Plain
- Author
-
Zhou-Yan Dong, Dan Wei, Lei Sun, Bao-Zhu Fang, Nimaichand Salam, Xiao-Yu Hao, Mingyi Zhang, Shuang Wang, Zhe Zhang, and Wen-Jun Li
- Subjects
China ,Peptidoglycan ,Diamino acid ,Biochemistry ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,Glycolipid ,Species Specificity ,RNA, Ribosomal, 16S ,Genetics ,Molecular Biology ,Gene ,Phospholipids ,Phylogeny ,Soil Microbiology ,030304 developmental biology ,Phosphatidylglycerol ,Base Composition ,0303 health sciences ,Halophila ,Phylogenetic tree ,Strain (chemistry) ,biology ,030306 microbiology ,Chemistry ,Fatty Acids ,General Medicine ,16S ribosomal RNA ,biology.organism_classification ,Glycolipids ,Micrococcaceae - Abstract
An alkaliphilic actinobacterial strain, designated Hz 6-5T, was isolated from saline-alkaline soil from Songnen Plain in north-eastern China. The isolate formed light yellow-colored colonies and its cells were Gram-staining positive, non-motile, and non-spore-forming short rods. The strain was aerobic with optimal growth at 33 °C, pH 9.0, and in the presence of 0.5% (w/v) NaCl or 3% (w/v) KCl. It was catalase-positive and oxidase-negative. The isolate had highest 16S rRNA gene sequence similarities to the type strains of the species Nesternkonia natronophila M8T (98.2%), N. salmonea GY074T (98.1%), and N. sphaerica GY239T (97.4%), and the isolate formed a subclade with the type strains of these species in the neighbor-joining tree based on the 16S rRNA gene sequences. The phylogenetic tree based on the phylogenomic analysis also showed the same results. The DNA‒DNA relatedness (DDH) values of isolate Hz 6-5T with N. natronophila M8T, N. halophila DSM 16378T, and N. halobia CGMCC 1.2323T were 21.2%, 36.5%, and 32.0%, respectively. The characteristic diamino acid of strain Hz 6-5T was found to be lysine. The respiratory quinones were MK-9, MK-8, MK-7(H4), MK-7(H2) and MK-7 and the major cellular fatty acids (> 10%) were anteiso-C15:0, anteiso-C17:0 and iso-C16:0. The polar lipids detected for strain Hz 6-5T were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid, and two unidentified phospholipids. The DNA G + C content of isolate Hz 6-5T was 60.8%. Based on the results of phylogenetic analysis supported by morphological, physiological, chemotaxonomic, and other differentiating phenotypic evidence, strain Hz 6-5T is considered to represent a novel species of the genus Nesterenkonia, for which the name Nesterenkonia haasae sp. nov. is proposed. The type strain is Hz 6-5T (=CPCC 205100T=NBRC 113521T).
- Published
- 2020
36. Cyclobacterium salsum sp. nov. and Cyclobacterium roseum sp. nov., isolated from a saline lake
- Author
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Wael N. Hozzein, Osama Abdalla Mohamad, Wen-Jun Li, Yuan-Guo Xie, Yonghong Liu, Bao-Zhu Fang, Li Li, and Hongchen Jiang
- Subjects
Genetics ,food.ingredient ,Phylogenetic tree ,Lineage (evolution) ,Cyclobacterium ,Genus Cyclobacterium ,General Medicine ,Biology ,16S ribosomal RNA ,medicine.disease_cause ,Microbiology ,Marker gene ,food ,medicine ,Cyclobacterium jeungdonense ,Ecology, Evolution, Behavior and Systematics - Abstract
Two novel strains, designated SYSU L10167T and SYSU L10180T, were isolated from sediment sampled at Dabancheng saline lake in Xinjiang, PR China. A polyphasic approach was used to clarify the taxonomic positions of the two strains. Cells of the isolates were curved ring-like, horseshoe-shaped or rod-shaped, non-motile and non-spore-forming. Cells were Gram-stain-negative, aerobic, heterotrophic and rose-pigmented. The phylogenetic trees based on 16S rRNA gene sequences showed that strains SYSU L10167T and SYSU L10180T formed a distinct lineage within the genus Cyclobacterium . Strains SYSU L10167T and SYSU L10180T showed highest similarities to Cyclobacterium jeungdonense KCTC 23150T (98.0 and 97.4%, respectively). Results of genomic analyses (including average nucleotide identity, digital DNA–DNA hybridization and the marker gene tree) and pan-genome analysis further confirmed that strains SYSU L10167T and SYSU L10180T were separate from each other and other species of the genus Cyclobacterium . The draft genomes of the isolates had sizes of 5.5–5.7 Mb and reflected their major physiological capabilities. Based on phenotypic, physiological, chemotaxonomic and genotypic characterization, we propose that the isolates represent two novel species, for which the names Cyclobacterium salsum sp. nov. and Cyclobacterium roseum sp. nov. are proposed. The type strains of the species are SYSU L10167T (=KCTC 72390T=CGMCC 1.17521T) and SYSU L10180T (=KCTC 72391T=CGMCC 1.17278T).
- Published
- 2020
37. Marinactinospora
- Author
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Bao‐Zhu Fang and Wen‐Jun Li
- Published
- 2020
38. Microvirga arsenatis sp. nov., an arsenate reduction bacterium isolated from Tibet hot spring sediments
- Author
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Wen-Dong Xian, Wen-Jun Li, Lan Liu, Bao-Zhu Fang, Ze-Tao Liu, Yu-Zhen Ming, Meng-Meng Li, Min Xiao, and Jian-Yu Jiao
- Subjects
DNA, Bacterial ,0106 biological sciences ,0301 basic medicine ,Geologic Sediments ,food.ingredient ,Microvirga ,Tibet ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,Genome ,Hot Springs ,03 medical and health sciences ,food ,RNA, Ribosomal, 16S ,Molecular Biology ,Phylogeny ,Base Composition ,biology ,Phylogenetic tree ,Thermophile ,Fatty Acids ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,Bacterial Typing Techniques ,genomic DNA ,Phenotype ,030104 developmental biology ,Arsenates ,lipids (amino acids, peptides, and proteins) ,Taxonomy (biology) ,Methylobacteriaceae ,Bacteria - Abstract
Two novel Gram-stain negative, moderately thermophilic, aerobic, rod-shaped strains, designated 3D203T and 3D207, were isolated from hot spring sediment samples collected from Tibet, western China. Phylogenetic analyses based on 16S rRNA gene sequence similarities showed that two isolates belonged to the genus Microvirga and were most closely related to Microvirga makkahensis SV1470T (98.5% and 98.4%, respectively) and two strains had 99.8% similarity to each other. The average nucleotide identity (ANI) based on whole genome sequences of two strains and M. makkahensis SV1470T was 80.8% and 80.78%, respectively. Optimum growth was observed at 45 °C, pH 7.0 and 0.5% NaCl. They both could tolerate to high concentration arsenic. Ubiquinone 10 (Q10) was their predominant quinone. The differences of strains 3D203T and 3D207 were phosphatidyl dimethyl ethanolamine, phosphatidyl-N-methylethanolamine, phosphatidylglycerol, unidentified glycolipids and unidentified lipids. The major fatty acids (> 5%) were identified C18:1ω7c and/or C18:1ω6c, C18:0 and C16:0. The genomic DNA G + C contents of strain 3D203T and 3D207 based on whole genome sequences were 64.8% and 64.7%, respectively. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that two strains represent a novel species of the genus Microvirga, for which the name Microvirga arsenatis sp. nov. is proposed. The type strain is 3D203T (= CGMCC 1.17691T = KCTC 72653T).
- Published
- 2020
39. Roseibium aestuarii sp. nov., isolated from Pearl River Estuary
- Author
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Lei Dong, Jia-Ling Li, Xiaozhen Mou, Bao-Zhu Fang, Wen-Jun Li, Li Duan, Xin Li, and Min Xiao
- Subjects
geography ,geography.geographical_feature_category ,Strain (chemistry) ,biology ,Sequence analysis ,Estuary ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,Microbiology ,Roseibium ,Water sample ,Genus Roseibium ,Food science ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
A novel bacterium, designated strain SYSU M00256-3T, was isolated from a water sample collected from Pearl River Estuary at Guangzhou, PR China. Its taxonomic position was determined by using a polyphasic approach. Cells of the strain were Gram-staining-negative, motile, aerobic and rod-shaped with peritrichous flagella. It could grow at 15–45 °C, pH 4.0–10.0 and in the presence of 0–7.5 % (w/v) NaCl. The chemotaxonomic features of strain SYSU M00256-3T included ubiquinone-10 (Q-10) as the sole respiratory quinone; phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as major polar lipids; summed feature 8 (C18 : 1 ω7c and C18 : 1 ω6c) as the predominant fatty acids (>70 %). On the basis of 16S rRNA gene sequence analysis, strain SYSU M00256-3T was most closely related to the type strains of Roseibium hamelinense CGMCC 1.12584T (97.7 %) and R. aquae CGMCC 1.12426T (97.2 %), R. sediminis KCTC 52373T (96.7 %), R. denhamense CGMCC 1.12583T (96.4 %). The average nucleotide identity (ANI) values between R. aestuarii SYSU M00256-3T and R. hamelinense CGMCC 1.12584T, R. aquae CGMCC 1.12426T, R. denhamense CGMCC 1.12583T and R. sediminis KCTC 52373T were 78.0, 78.2, 77.7 and 78.8, and the dDDH value is 20.0, 20.8, 20.1 and 20.6 correspondingly. Based on the analyses of the phenotypic, genotypic and phylogenetic characteristics, strain SYSU M00256-3T is characterized to represent a novel species of the genus Roseibium , for which the name Roseibium aestuarii sp. nov. is proposed. The type strain is SYSU M00256-3T (=NBRC 112946T=CGMCC 1.16156T).
- Published
- 2020
40. Pseudorivibacter rhizosphaerae gen. nov., sp. nov., isolated from rhizosphere soil of Camellia sinensis (L.) O. Ktze and emended description of the genus Rivibacter
- Author
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Yan-Qing Duan, Che Ok Jeon, Bao-Zhu Fang, Lan Liu, Li-Min Dong, Wen-Jun Li, Qing-Qing Li, Deng-Qiang Yang, and Xing-Kui Zhou
- Subjects
0106 biological sciences ,0301 basic medicine ,Rhizosphere ,Strain (chemistry) ,Phylogenetic tree ,General Medicine ,Biology ,biology.organism_classification ,16S ribosomal RNA ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,03 medical and health sciences ,genomic DNA ,030104 developmental biology ,Genus ,Botany ,Camellia sinensis ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
A Gram-stain-negative, facultative anaerobic, motile and straight rod-shaped bacterium, designated strain C1-9T, was isolated from rhizosphere soil of Camellia sinensis (L.) O. Ktze collected from a tea garden in Huize, south-western PR China. Cells were oxidase-positive and catalase-negative. Growth occurred at 20–40 °C and pH 6.0–10.0, with an optimal growth at 30 °C and pH 7.0. The respiratory quinone was detected as ubiquinone-8 (Q-8). The major fatty acids were identified as summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c or C18 : 1ω6c). The cellular polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, two unidentified lipids, one unidentified aminophospholipid and one unidentified aminolipid. The polyamine types were detected as 1,8-diaminooctane and 2-hydroxyputrescine. The genomic DNA G+C content was 68.6 mol%. Based on the results of 16S rRNA gene sequence analysis, strain C1-9T (MF687442) showed highest sequence similarity to Rivibacter subsaxonicus DSM 19570T (97.1 %). The phylogenetic tree based on 16S rRNA gene sequences showed that strain C1-9T clustered close to R. subsaxonicus DSM 19570T, Methylibium petroleiphilum CCTCC AB 2014193T and species belonging to the genera Rhizobacter and Piscinibacter . The phylogenomic tree indicated that strain C1-9T formed a clade with R. subsaxonicus . The average nucleotide identity value was 76.0 % between strain C1-9T and R. subsaxonicus DSM 19570T, which is lower than the prokaryotic species delineation threshold of 95.0–96.0 %. The polyphasic taxonomic characteristics indicated that strain C1-9T represents a novel species of a new genus within the order Burkholderiales , for which the name Pseudorivibacter rhizosphaerae gen. nov., sp. nov. (type strain C1-9T = KCTC 62325T=CGMCC 1.13864T) is proposed.
- Published
- 2020
41. Description of Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov., isolated from cave soil
- Author
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Min Xiao, Zhou-Yan Dong, Yu Kan, Ying-Qian Kang, Bao-Zhu Fang, Wen-Jun Li, Manik Prabhu Narsing Rao, and Kun Zhang
- Subjects
0106 biological sciences ,0301 basic medicine ,Strain (chemistry) ,General Medicine ,Biology ,16S ribosomal RNA ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,Terpenoid ,03 medical and health sciences ,chemistry.chemical_compound ,Paenibacillus ,030104 developmental biology ,Glycolipid ,chemistry ,Optimum growth ,Peptidoglycan ,Paenibacillus thermoaerophilus ,Ecology, Evolution, Behavior and Systematics - Abstract
Two Gram-positive, rod-shaped, motile, endospore-forming strains, SYSU K30003T and SYSU K30004T, were isolated from cave soil sampled in Xingyi County, Guizhou Province, south-west PR China. The 16S rRNA gene sequence results indicated that strains SYSU K30003T and SYSU K30004T had highest sequence similarities to Paenibacillus thermoaerophilus DSM 26310T (93.2 %) and Paenibacillus haemerocallicola KCTC 33185T (97.8 %), respectively. Optimum growth for both strains occurred at pH 7.0 and 37 °C. Both strains contained meso-2,6-diaminopimelic acid in their cell-wall peptidoglycan and MK-7 was the only isoprenoid quinone detected. The polar lipid profile of strain SYSU K30004T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, an unidentified glycolipid, unidentified phospholipids and two unidentified polar lipids. The polar lipid profile of strain SYSU K30003T contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified glycolipid. The major fatty acids (>5 %) of strain SYSU K30003T were anteiso-C15:0, C16 : 0, anteiso-C17 : 0 and iso-C16 : 0, while those of strain SYSU K30004T were anteiso-C15:0, C16:0, anteiso-C17 : 0, iso-C15 : 0, iso-C16:0 and iso-C17 : 0. The genome G+C contents of strains SYSU K30003T and SYSU K30004T were 59.0 and 53.6 mol%, respectively. The average nucleotide identity values between strains SYSU K30003T and SYSU K30004T and other closely related Paenibacillus members were below the cut-off level (95–96 %) for species identification. Based on the results of phenotypic, chemotaxonomic and genome analyses, strains SYSU K30003T and SYSU K30004T represent two novel species of the genus Paenibacillus , for which the names Paenibacillus antri sp. nov. and Paenibacillus mesophilus sp. nov. are proposed. The type strains are SYSU K30003T (=KCTC 33956T=CGMCC 1.13505T) and SYSU K30004T (=KCTC 33957T=CGMCC 1.13872T).
- Published
- 2020
42. Lysobacter prati sp. nov., isolated from a plateau meadow sample
- Author
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Wen-Jun Li, Jian-Yu Jiao, Min Xiao, Xiao-Tong Zhang, Xing-Kui Zhou, Yuan-Guo Xie, Lan Liu, and Bao-Zhu Fang
- Subjects
0106 biological sciences ,0301 basic medicine ,China ,Secondary Metabolism ,Lysobacter ,Biology ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,Genome ,03 medical and health sciences ,Bacteriocins ,Bacteriocin ,RNA, Ribosomal, 16S ,Polyketide synthase ,Molecular Biology ,Phylogeny ,Genetics ,Phylogenetic tree ,Strain (chemistry) ,Fatty Acids ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,Grassland ,Anti-Bacterial Agents ,genomic DNA ,030104 developmental biology ,Genes, Bacterial ,biology.protein ,Genome, Bacterial - Abstract
A novel proteobacterial strain designated SYSU H10001T was isolated from a soil sample collected from plateau meadow in Hongyuan county, Sichuan province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU H10001T was most closely related to Lysobacter soli KCTC 22011T (98.6%, sequence similarity) and Lysobacter panacisoli JCM 19212T (98.2%). The prediction result of secondary metabolites based on genome shown that the strain SYSU H10001T contained 3 clusters of bacteriocins, 1 cluster of non-ribosomal peptide synthetase, 1 cluster of type 1 polyketide synthase and 1 cluster of arylpolyene. In addition, the major isoprenoid quinone was Q-8 and the major fatty acids were identified as iso-C15:0, iso-C17:0 and Summed feature 9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and three unidentified phospholipids. The genomic DNA G + C content of strain SYSU H10001T was 66.5% (genome). On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU H10001T represents a novel species of the genus Lysobacter, for which the name Lysobacter prati sp. nov. is proposed. The type strain is SYSU H10001T (= KCTC 72062T = CGMCC 1.16662T).
- Published
- 2020
43. Streptomyces cavernae sp. nov., a novel actinobacterium isolated from a karst cave sediment sample
- Author
-
Wen-Jun Li, Lan Liu, Xiao-Tong Zhang, Ming-Xian Han, Zi-Tong Zhang, Jian-Yu Jiao, Yuan-Guo Xie, Min Xiao, and Bao-Zhu Fang
- Subjects
0106 biological sciences ,0301 basic medicine ,Strain (chemistry) ,biology ,Phylogenetic tree ,Stereochemistry ,Rhamnose ,General Medicine ,Diamino acid ,biology.organism_classification ,16S ribosomal RNA ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,Streptomyces ,03 medical and health sciences ,genomic DNA ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Peptidoglycan ,Ecology, Evolution, Behavior and Systematics - Abstract
A novel actinobacterial strain, designated SYSU K10008T, was isolated from a soil sample collected from a karst cave in Xingyi County, Guizhou Province, south-western PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive and non-motile. On the basis of 16S rRNA gene sequence similarities and the results of phylogenetic analysis, strain SYSU K10008T was most closely related to Streptomyces cyaneus CGMCC 4.1671T, and shared the highest sequence identity of 98.3 % based on the NCBI database. In addition, ll-diaminopimelic acid was the diagnostic diamino acid in cell-wall peptidoglycan. The whole-cell sugars were glucose and rhamnose. The major isoprenoid quinone was MK-9(H6), while the major fatty acids (>10 %) were C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c). The polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unidentified lipid. The genomic DNA G+C content of strain SYSU K10008T was 70.5 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU K10008T represents a novel species of the genus Streptomyces , for which the name Streptomyces cavernae sp. nov. is proposed. The type strain is SYSU K10008T (=KCTC 39850T=DSM 104115T).
- Published
- 2020
44. Insights into the effects of drying treatments on cultivable microbial diversity of marine sediments
- Author
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Jing-Yi, Zhang, Zheng-Han, Lian, Manik Prabhu, Narsing Rao, Pandeng, Wang, Lan, Liu, Bao-Zhu, Fang, Meng-Meng, Li, Ze-Tao, Liu, Ai-Ping, Lv, Sha, Tan, Lei, Dong, Jia-Ling, Li, Jian-Yu, Jiao, and Wen-Jun, Li
- Subjects
Geologic Sediments ,Bacteria ,Microbiota ,RNA, Ribosomal, 16S ,Humans ,Seawater ,Biodiversity ,Microbiology - Abstract
Microbes are widespread in the sea that covers more than two-thirds of the earth's surface and most microorganisms living in the marine environment have yet to be cultured. Previous studies showed that drying treatment, a strategy of sample pre-treatment widely applied in microbial isolation and incubation, may alter the cultivable microbial diversity, such as Actinomycetota, essential for exploring novel secondary metabolites from the marine environment, isolated from drying-treated samples. However, whether drying treatments actually can change microbial community diversity and how the drying treatments of samples influence the cultivable microbial diversity of marine samples have not yet adequately been evaluated. Here, three marine sediment samples were dried and incubated at 28 ºC, 37 ºC, and 45 ºC, and the microbial diversity was assessed with high-throughput sequencing. Our results suggested that drying treatments had different effects on different genera and some potential novel species could be cultured only from drying-treated samples, including the novel members from the families Paenibacillaceae and Thermoactinomycetaceae. Non-metric multidimensional scaling analysis showed that the treated samples were clustered according to the cultivation temperatures rather than the drying conditions at high cultivation temperatures. However, at the cultivation temperatures of 28 ºC, drying treatments were the larger separation between cultivable microbial communities in the process of microbial isolation. These results showed that the drying treatments influenced the cultivated microbes in a taxon-specific pattern and extended potential novel taxa. Combining high-throughput sequencing to various drying conditions and incubation temperatures, this study provides new insight into the effects of drying treatment on the cultivable microbial diversity of marine sediments.
- Published
- 2023
45. Antribacter gilvus gen. nov., sp. nov., a new member of the family Promicromonosporaceae from a karstic cavern
- Author
-
Ling-Yu Zhang, Xiaolin Meng, Hong Ming, Lan Liu, Guoxing Nie, Wen-Jun Li, Bao-Zhu Fang, Jian-Yu Jiao, and Xiao-Tong Zhang
- Subjects
0106 biological sciences ,0301 basic medicine ,Strain (chemistry) ,Phylogenetic tree ,Rhamnose ,Mannose ,General Medicine ,Biology ,16S ribosomal RNA ,medicine.disease_cause ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Promicromonospora xylanilytica ,Genus ,medicine ,Promicromonosporaceae ,Ecology, Evolution, Behavior and Systematics - Abstract
A novel actinobacterium, designated strain CFH 30434T, was isolated from a soil sample collected from a karst cave in Luoyang, Henan Province, PR China. The taxonomic position of the strain was investigated by using a polyphasic approach. Cells of the strain were aerobic, Gram-stain-positive, non-motile and coccoid or short rods. The strain was found to be oxidase-positive and weakly catalase-positive. Strain CFH 30434T grew optimally at 28 °C, pH 7.0–9.0 and in the presence of up to 0–1.5 % NaCl (w/v). The whole-cell sugars were glucose, mannose and rhamnose. The major isoprenoid quinone was MK-9(H8) and the major fatty acids (>10 % of the total fatty acids compositions) were anteiso-C15 : 0, iso-C15:0 and iso-C14 : 0. The polar lipids detected were diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified phosphoglycolipid, an unidentified phospholipid and an unidentified glycolipid. The genomic DNA G+C content was determined to be 72.3 mol%. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that CFH 30434T clustered within the family Promicromonosporaceae , and closely with the type strains of Xylanimicrobium pachnodae DSM 12657T, Myceligenerans crystallogenes DSM 17134T and Promicromonospora xylanilytica CCTCC AA 208046T (97.3 %, 96.2 and 95.9 % sequence similarities, respectively). Phylogenetic analysis showed that strain CFH 30434T formed a separate evolutionary branch, and was parallel to other related genera of Promicromonosporaceae . Its phylogenetic distinctiveness and distinguishing phenotypic characteristics supported that strain CFH 30434T represents a novel genus of the family Promicromonosporaceae , for which the name Antribacter gilvus gen. nov., sp. nov. is proposed. The type strain is CFH 30434T (=CGMCC 1.13856T=KCTC 49093T).
- Published
- 2019
46. Dyella tabacisoli sp. nov., a bacterium isolated from an arable soil sample of Nicotiana tabacum L
- Author
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Yan-Qing Duan, Bao-Zhu Fang, Min Xiao, Li-Min Dong, Qing-Qing Li, Xing-Kui Zhou, Xing Chen, and Wen-Jun Li
- Subjects
0106 biological sciences ,0301 basic medicine ,Phosphatidylglycerol ,Phylogenetic tree ,Strain (chemistry) ,Nicotiana tabacum ,General Medicine ,Biology ,16S ribosomal RNA ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,03 medical and health sciences ,chemistry.chemical_compound ,genomic DNA ,030104 developmental biology ,chemistry ,Botany ,Gene ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated strain L4-6T, was isolated from an arable soil sample of tobacco in Huize, south-western China and subjected to polyphasic taxonomic characterization. The cells showed oxidase-positive and catalase-positive reactions. Growth occurred at 20–35 °C, at pH 5.0–8.0 and with 0–2 % (w/v) NaCl, optimally at 30 °C, pH 6.0–7.0 and 0–1 % (w/v) NaCl. The major respiratory lipoquinone was ubiquinone-8. The predominant cellular fatty acids (>10.0 %) were identified as summed feature 9 (iso-C17 : 1ω9c or C16 : 0 10-methyl), iso-C15 : 0 and iso-C17 : 0. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, two unidentified aminophospholipids and five unidentified aminolipids. The genomic DNA G+C content was 60.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain L4-6T should be affiliated to the genus Dyella and formed a clade with the most closely related organism Dyella soli JS12-10T. 16S rRNA gene sequences similarity analysis showed that strain L4-6T was mostly closely related to D. soli JS12-10T (98.73 %) and Dyella lipolytica DHOB07T (98.02 %). DNA–DNA hybridization data indicated that strain L4-6T represented a novel genomic species belonging to the genus Dyella . The polyphasic taxonomic characteristics indicated that the strain L4-6T represents a novel species of the genus Dyella , for which the name Dyella tabacisoli sp. nov. (type strain L4-6T=CGMCC 1.16273T=KCTC 62035T) is proposed.
- Published
- 2019
47. Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary
- Author
-
Li Duan, Jia-Ling Li, Ling-Zi Yin, Xiao-Qing Luo, Manzoor Ahmad, Bao-Zhu Fang, Shan-Hui Li, Qi-Qi Deng, Pandeng Wang, and Wen-Jun Li
- Subjects
Microbiota ,Water ,Cyanobacteria ,Estuaries ,Biochemistry ,Archaea ,General Environmental Science - Abstract
Microbes (e.g., bacteria and archaea) are indispensable components for the key biological processes of estuarine ecosystems and three main habitats (sediment, particle, and water) are harboring diverse estuarine microbes. However, we still know little about how the microbial community structures, potential keystone species, and network properties change among these three habitats in estuarine ecosystems. In this study, we collected size-fractioned water and sediment samples from the Pearl River Estuary to reveal their microbial diversity, community structures, network properties, and potential keystone taxa. We found that the sediment microbial community was remarkably more diverse than particle-attached (PA) and free-living (FL) communities, whereas its ecological network was less complex in terms of node distance and connectivity. TOC was determined as the main driver of sediment community, while the PA and FL communities were predominantly shaped by NO
- Published
- 2021
48. Roseomonas ponticola sp. nov., a novel bacterium isolated from Pearl River estuary
- Author
-
Xiao-Qing Luo, Ling-Zi Yin, Bao-Zhu Fang, Li Duan, Lei Dong, Ze-Tao Liu, Wen-Jun Li, Shan-Hui Li, Jia-Ling Li, and Pandeng Wang
- Subjects
New Taxa ,biology ,Phylogenetic tree ,Strain (chemistry) ,Roseomonas ponticola sp. nov ,General Medicine ,Ponticola ,biology.organism_classification ,16S ribosomal RNA ,Microbiology ,Pearl River estuary ,Roseomonas ,genomic DNA ,Proteobacteria ,Botany ,lipids (amino acids, peptides, and proteins) ,Taxonomy (biology) ,Ecology, Evolution, Behavior and Systematics ,Bacteria - Abstract
A novel species of the genus Roseomonas , designated SYSU M41301T, was isolated from water sample of the Pearl River estuary in Guangdong, China. Polyphasic, taxonomic and phylogenomic analyses were used to determine the taxonomy position of the strain. Phylogenetic analysis using 16S rRNA gene sequence indicated that strain SYSU M41301T showed the highest sequence similarity to Roseomonas stagni KCTC 22213T (97.9 %) and Roseomonas riguiloci KCTC 23339T (96.4 %). The novel species could be differentiated from other species of the genus Roseomonas by its distinct phenotypic and genotypic characteristics. The isolate was Gram-staining-negative, aerobic, short rod-shape, oxidase-positive and non-motile. The predominant respiratory quinone was ubiquinone 8 (Q-8). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and one unidentified polar lipid. The major fatty acids (>10 % of total) were 11-methyl C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/ or C16 : 1 ω6c) and summed feature 8 (C18: :1 ω7c and/or C18 : 1 ω6c). The G+C content of the novel isolate based on genomic DNA was 72.0 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU M41301T should be considered to represent a novel species in the genus Roseomonas, for which the name Roseomonas ponticola sp. nov. is proposed with the type strain SYSU M41301T (=KCTC 72726T=CGMCC 1.18613T).
- Published
- 2021
49. Agilicoccus flavus gen. nov., sp. nov., a novel member of the family Dermatophilaceae isolated from the Pearl River
- Author
-
Lei Dong, Wen-Jun Li, Li Duan, Jia-Ling Li, Ling-Zi Yin, Xiao-Qing Luo, Bao-Zhu Fang, Pandeng Wang, and Ze-Tao Liu
- Subjects
Strain (chemistry) ,Phylogenetic tree ,General Medicine ,Diamino acid ,Biology ,engineering.material ,Microbiology ,Cell wall ,chemistry.chemical_compound ,genomic DNA ,chemistry ,Genus ,Botany ,engineering ,Family Dermatophilaceae ,Pearl ,Ecology, Evolution, Behavior and Systematics - Abstract
A novel actinobacterium, designated strain SYSU M44304T, was isolated from freshwater samples in the Pearl River Estuary. The isolate was Gram-stain-positive, aerobic, coccus-shaped, oxidase-positive and motile. The cell wall contained meso-diaminopimelic acid as its diagnostic diamino acid. The predominant menaquinone was MK-8. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine and seven unidentified phospholipids. The major fatty acids were C16 : 0 and C16 : 1. The G+C content based on genomic DNA was 73.2 mol %. The nearest phylogenetic neighbours to the novel strain were Mobilicoccus pelagius NBRC 104925T and Mobilicoccus caccae YIM 101593T. On the basis of chemotaxonomic and physiological characteristics and phylogenetic analysis, strain SYSU M44304T should be considered to represent a novel species of a new genus in the family Dermatophilaceae , for which we propose the name Agilicoccus flavus gen. nov., sp. nov. The type strain of Agilicoccus flavus is SYSU M44304T (=NBRC 114808T=CGMCC 1.18608T).
- Published
- 2021
50. Transcriptomic analysis of two endophytes involved in enhancing salt stress ability of Arabidopsis thaliana
- Author
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Yonghong Liu, Zhou-Yan Dong, Bao-Zhu Fang, Min Xiao, Wen-Jun Li, Manik Prabhu Narsing Rao, Li Li, and Hong-Fei Wang
- Subjects
Environmental Engineering ,010504 meteorology & atmospheric sciences ,Arabidopsis ,Plant Development ,010501 environmental sciences ,Reductase ,Plant Roots ,Salt Stress ,01 natural sciences ,Actinobacteria ,chemistry.chemical_compound ,Halophyte ,Endophytes ,Environmental Chemistry ,Arabidopsis thaliana ,Waste Management and Disposal ,Soil Microbiology ,0105 earth and related environmental sciences ,biology ,Strain (chemistry) ,Phenylpropanoid ,Salt-Tolerant Plants ,biology.organism_classification ,Pollution ,Biochemistry ,chemistry ,Chlorophyll ,Rhizosphere ,Transcriptome ,Bacteria - Abstract
Soil salinity is one of the serious environmental issues worldwide. In the present study, we made an attempt to isolate endophytic actinobacteria from halophyte and evaluate their growth promoting ability in Arabidopsis thaliana under salt stress through transcriptomic analysis. Two endophytic strains SYSU 333322 and SYSU 333140 were isolated and 16S rRNA gene sequence analysis suggests that these strains belong to Arthrobacter endophyticus and Nocardiopsis alba, respectively. To evaluate the growth promoting ability of two strains in Arabidopsis thaliana four experimental set up were designed. Set up designated s322 and s140 includes strains SYSU 333322 and SYSU 333140, respectively inoculated with A. thaliana under salt stress; set up designated MS322 and MS140 includes strains SYSU 333322 and SYSU 333140, respectively inoculated with A. thaliana without salt stress; MS includes seedlings without bacterial strains and salt stress; C150 includes seedlings grown in 150 mmol L−1NaCl. A. endophyticus strain SYSU 333322 and N. alba strain SYSU 333140 were efficient to promote A. thaliana growth under salt stress A. endophyticus strain SYSU 333322 was more efficient than N. alba strain SYSU 333140 for growth promotion. Although A. endophyticus strain SYSU 333322 and N. alba strain SYSU 333140 were isolated from the same host, their mechanism of growth promotion in A. thaliana under salt stress was different. Gene encoding for chlorophyll a reductase, peptide-methionine (R)-S-oxide reductase, and potassium ion uptake were up-regulated when A. thaliana inoculated with strain SYSU 333322 and SYSU 333140 under salt stress. Pathways such as carotenoid biosynthesis, phenylalanine metabolism, phenylpropanoid biosynthesis, glycerolipid metabolism, and nitrogen metabolism played a crucial role in enhancing the salt stress tolerance of A. thaliana. Our results suggest that different bacteria have a different mechanism to promote plant growth under salt stress and hence it is necessary to understand the mechanism to overcome soil salinity problem.
- Published
- 2019
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