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Pastor-Lopez EJ, Casas ME, Hellman D, Müller JA, Matamoros V. Nature-based solutions for antibiotics and antimicrobial resistance removal in tertiary wastewater treatment: Microbiological composition and risk assessment. WATER RESEARCH 2024; 261:122038. [PMID: 38996727 DOI: 10.1016/j.watres.2024.122038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/15/2024] [Accepted: 07/02/2024] [Indexed: 07/14/2024]
Abstract
This field-scale study evaluates the seasonal effectiveness of employing nature-based solutions (NBSs), particularly surface flow and horizontal subsurface flow constructed wetland configurations, as tertiary treatment technologies for the removal of antibiotics (ABs) and antibiotic resistance genes (ARGs) compared to a conventional treatment involving UV and chlorination. Out of the 21 monitored ABs, 13 were detected in the influent of three tertiary wastewater treatments, with concentrations ranging from 2 to 1218 ng·L-1. The ARGs sul1 and dfrA1 exhibited concentrations ranging from 1 × 105 to 9 × 106 copies/100 mL. NBSs were better at reducing ABs (average 69 to 88 %) and ARGs (2-3 log units) compared to the conventional tertiary system (average 36 to 39 % and no removal to 2 log units) in both seasons. Taxonomic compositions in influent water samples shifted from wastewater-impacted communities (Actinomycetota and Firmicutes) to a combination of plant rhizosphere-associated and river communities in NBS effluents (Alphaproteobacteria). In contrast, the conventional technology showed no substantial differences in community composition. Moreover, NBSs substantially reduced the ecotoxicological risk assessment (cumulative RQs). Furthermore, NBSs reduced the ecotoxicological risk (cumulative RQs) by an average of over 70 % across seasons, whereas the benchmark technology only achieved a 6 % reduction. In conclusion, NBSs present a robust alternative for minimizing the discharge of ABs and ARGs into surface water bodies.
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Affiliation(s)
- Edward J Pastor-Lopez
- Department of Environmental Chemistry. IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
| | - Mònica Escola Casas
- Department of Environmental Chemistry. IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain
| | - Dominik Hellman
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Jochen A Müller
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, 76344, Eggenstein-Leopoldshafen, Germany
| | - Víctor Matamoros
- Department of Environmental Chemistry. IDAEA-CSIC, Jordi Girona, 18-26, 08034, Barcelona, Spain.
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Liu WJ, Zhang Y, Cao K, Li JX, Wen YQ, Sun C, Xu L. Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov., two novel Erythrobacteraceae species isolated from tidal flat sediments. Int J Syst Evol Microbiol 2024; 74. [PMID: 39052323 DOI: 10.1099/ijsem.0.006469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024] Open
Abstract
Two Gram-stain-negative, rod-shaped, non-motile, aerobic and carotenoid-producing strains, belonging to the family Erythrobacteraceae, designated as H149T and Z2T, were isolated from tidal flat sediment samples collected in Hainan and Zhejiang, PR China, respectively. Growth of strain H149T occurred at 15-42 °C, 0-10.0 % (w/v) NaCl, and pH 6.0-8.5, with the optima at 35-37 °C, 3.0-3.5 % (w/v) NaCl and pH 7.0. Strain Z2T grew at 15-37 °C, 0-6.0 % (w/v) NaCl, and pH 6.0-9.5, with the optima at 25-30 °C, 0.5-1.0 % (w/v) NaCl and pH 6.0-6.5. Ubiquinone-10 was the sole ubiquinone in two strains. The predominant cellular fatty acids of strain H149T were C16 : 0, summed feature 3 and summed feature 8, while those of strain Z2T were C17 : 1 ω6c, summed feature 3 and summed feature 8. Strains H149T and Z2T shared diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid as major polar lipids. The 16S rRNA gene sequence identity analysis indicated that strain H149T had the highest sequence identity of 98.4 % with Aurantiacibacter odishensis KCTC 23981T, and strain Z2T had that of 98.2 % with Qipengyuania pacifica NZ-96T. Phylogenetic trees based on 16S rRNA gene and core-genome sequences revealed that strains H149T and Z2T formed two independent clades in the genera Aurantiacibacter and Qipengyuania, respectively. Strain H149T had average nucleotide identity values of 74.0-81.3 % and in silico DNA-DNA hybridization values of 18.5-23.1 % with Aurantiacibacter type strains, while strain Z2T had values of 73.3-78.7 % and 14.5-33.3 % with Qipengyuania type strains. The genomic DNA G+C contents of strains H149T and Z2T were 64.3 and 61.8 %, respectively. Based on the genetic, genomic, phylogenetic, physiological and chemotaxonomic results, strains H149T (=KCTC 8397T=MCCC 1K08920T) and Z2T (=KCTC 8396T=MCCC 1K08946T) are concluded to represent two novel Erythrobacteraceae species for which the names Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov. are proposed, respectively.
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Affiliation(s)
- Wen-Jia Liu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd., Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
| | - Yu Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd., Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
| | - Ke Cao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Jia-Xi Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Yu-Qiao Wen
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd., Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
- Shaoxing Biomedical Research Institute of Zhejiang Sci-Tech University Co., Ltd., Zhejiang Engineering Research Center for the Development Technology of Medicinal and Edible Homologous Health Food, Shaoxing 312075, PR China
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Sugiyama A, Nakata K, Hirano SI, Hasegawa T. Identification of groundwater microbes that decrease the concentration of the conservative tracer uranine. Heliyon 2024; 10:e27397. [PMID: 38496874 PMCID: PMC10944235 DOI: 10.1016/j.heliyon.2024.e27397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/20/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Fluorescent dyes are commonly used as conservative groundwater tracers to track the migration of water. Over- or underestimation of important parameters such as the water flow rate can occur if the concentration of a dye is changed by unexpected reactions. Because such errors may seriously affect the results of experiments, the reactions and processes that change fluorescent dye concentrations need to be understood. In this study, we focused on the widely used fluorescent dye uranine (UR) and aimed to identify microbes contributing to decreases in UR concentrations in groundwater. First, we identified the conditions (water temperature, pH, and salinity) under which significant decreases in UR concentrations occurred to show that the decrease in UR concentrations were caused by the effects of microbes in the groundwater. Next, we obtained information about the metabolism of organic matter by potential contributing microbes. These results were used to narrow down possible microbes that could decrease the UR concentration. Analysis of the microbial community in groundwater using 16S rRNA gene sequencing was then used to further identify contributing microbes. Finally, a verification experiment was conducted using a strain of one of the identified microbes (Parapontixanthobacter aurantiacus). Our results showed that conservation of the concentration of fluorescent dye solutions prepared with on-site groundwater was affected by several microbes with different metabolic characteristics, including P. aurantiacus. When fluorescent dye solutions prepared with on-site groundwater are used in field investigations or tracer tests, the pros and cons of using fluorescent dyes should be carefully evaluated because of the potential effects of microbes in the groundwater.
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Affiliation(s)
- Ayumi Sugiyama
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Kotaro Nakata
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Shin-Ichi Hirano
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
| | - Takuma Hasegawa
- Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry (CRIEPI), 1646 Abiko, Abiko-shi, Chiba 270-1194, Japan
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Nguyen KU, Zhang Y, Liu Q, Zhang R, Jin X, Taniguchi M, Miller ES, Lindsey JS. Tolyporphins-Exotic Tetrapyrrole Pigments in a Cyanobacterium-A Review. Molecules 2023; 28:6132. [PMID: 37630384 PMCID: PMC10459692 DOI: 10.3390/molecules28166132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Tolyporphins were discovered some 30 years ago as part of a global search for antineoplastic compounds from cyanobacteria. To date, the culture HT-58-2, comprised of a cyanobacterium-microbial consortium, is the sole known producer of tolyporphins. Eighteen tolyporphins are now known-each is a free base tetrapyrrole macrocycle with a dioxobacteriochlorin (14), oxochlorin (3), or porphyrin (1) chromophore. Each compound displays two, three, or four open β-pyrrole positions and two, one, or zero appended C-glycoside (or -OH or -OAc) groups, respectively; the appended groups form part of a geminal disubstitution motif flanking the oxo moiety in the pyrroline ring. The distinct structures and repertoire of tolyporphins stand alone in the large pigments-of-life family. Efforts to understand the cyanobacterial origin, biosynthetic pathways, structural diversity, physiological roles, and potential pharmacological properties of tolyporphins have attracted a broad spectrum of researchers from diverse scientific areas. The identification of putative biosynthetic gene clusters in the HT-58-2 cyanobacterial genome and accompanying studies suggest a new biosynthetic paradigm in the tetrapyrrole arena. The present review provides a comprehensive treatment of the rich science concerning tolyporphins.
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Affiliation(s)
- Kathy-Uyen Nguyen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Yunlong Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Qihui Liu
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Ran Zhang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Xiaohe Jin
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Masahiko Taniguchi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
| | - Eric S. Miller
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695-7612, USA;
| | - Jonathan S. Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, USA; (K.-U.N.); (Y.Z.); (Q.L.); (R.Z.); (X.J.); (M.T.)
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Gu YY, Liang XY, Zhang HY, Fu R, Li M, Chen CJ. Effect of biochar and bioorganic fertilizer on the microbial diversity in the rhizosphere soil of Sesbania cannabina in saline-alkaline soil. Front Microbiol 2023; 14:1190716. [PMID: 37455751 PMCID: PMC10339320 DOI: 10.3389/fmicb.2023.1190716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Biochar and bioorganic fertilizer (BOF) application in agriculture has garnered increasing interest recently. However, the effects of biochar and BOF on rhizosphere soil microecology, especially in a region with saline-alkaline soil, remain largely unexplored. Methods In this study, we performed Illumina-based 16S rRNA sequencing to investigate the effects of biochar with or without BOF addition, as well as at different addition rates and particles sizes, on the microecology of saline-alkaline rhizosphere soil. Results In the field experiment, biochar and BOF application altered the rhizosphere soil microecology. Actinobacteriota, Proteobacteria, and Chloroflexi accounted for >60% of the total bacterial population in each treatment. In the different treatments, Actinobacteria and Alphaproteobacteria were the predominant classes; Micromonosporales and Vicinamibacterales were the dominant orders; norank_f__Geminicoccaceae and Micromonosporaceae were the most abundant families; and Micromonospora and norank_f_Geminicoccaceae were the predominant genera. Application of biochar with or without BOF decreased soil electrical conductivity (EC) by 7% -11.58% only at the depth of 10 cm below the surface, again, soil EC can be significantly reduced by an average of 4% at 10 cm depth soil after planting Sesbania cannabina. Soil organic carbon, organic matter, available potassium, and available phosphorus contents had significant effects on the soil bacterial community structure. Conclusion Co-application of biochar and BOF resulted in the greatest improvement of rhizosphere soil microecology, either by promoting plant growth or improving the nutrition and physicochemical properties of soil, followed by BOF alone and biochar alone. Additionally, higher application rate of biochar was better than lower application rate, and fine biochar had a stronger effect than coarse biochar. These results provide guidance for the development of new saline-alkaline soil remediation strategies.
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Yang R, Zhou S, Zhang L, Qin C. Pronounced temporal changes in soil microbial community and nitrogen transformation caused by benzalkonium chloride. J Environ Sci (China) 2023; 126:827-835. [PMID: 36503808 PMCID: PMC9553405 DOI: 10.1016/j.jes.2022.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 05/16/2023]
Abstract
As one typical cationic disinfectant, quaternary ammonium compounds (QACs) were approved for surface disinfection in the coronavirus disease 2019 pandemic and then unintentionally or intentionally released into the surrounding environment. Concerningly, it is still unclear how the soil microbial community succession happens and the nitrogen (N) cycling processes alter when exposed to QACs. In this study, one common QAC (benzalkonium chloride (BAC) was selected as the target contaminant, and its effects on the temporal changes in soil microbial community structure and nitrogen transformation processes were determined by qPCR and 16S rRNA sequencing-based methods. The results showed that the aerobic microbial degradation of BAC in the two different soils followed first-order kinetics with a half-life (4.92 vs. 17.33 days) highly dependent on the properties of the soil. BAC activated the abundance of N fixation gene (nifH) and nitrification genes (AOA and AOB) in the soil and inhibited that of denitrification gene (narG). BAC exposure resulted in the decrease of the alpha diversity of soil microbial community and the enrichment of Crenarchaeota and Proteobacteria. This study demonstrates that BAC degradation is accompanied by changes in soil microbial community structure and N transformation capacity.
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Affiliation(s)
- Rui Yang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Shaohong Zhou
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
| | - Lilan Zhang
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China.
| | - Cunli Qin
- State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing 400044, China; Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China
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Göker M. Filling the gaps: missing taxon names at the ranks of class, order and family. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748602 DOI: 10.1099/ijsem.0.005638] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) recently underwent some major modifications regarding the higher taxonomic ranks. On the one hand, the phylum category was introduced into the ICNP, which rapidly led to the valid publication of more than forty names of phyla. On the other hand, a decision on the retroactivity of Rule 8 regarding the names of classes was made, which removed most of the nomenclatural uncertainty that had affected those names during the last decade. However, it turned out that a number of names at the ranks of class, order and family are either not validly published or are validly published but illegitimate, although these names occur in the literature and are based on the type genus of a phylum with a validly published name. A closer examination of the literature for these and similar cases indicates that the names are unavailable under the ICNP either because of minor formal errors in the original descriptions, because another name should have been adopted for the taxon when the name was proposed, because of taxonomic uncertainties that were settled in the meantime, or because the names were placed on the list of rejected names. The purpose of this article is to fill the gaps by providing the missing formal descriptions and to ensure that the resulting taxon names are attributed to the original authors who did the taxonomic work.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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Vasilyeva L, Grouzdev D, Koziaeva V, Berestovskaya Y, Novikov A, Pimenov N. Prosthecodimorpha staleyi gen. nov., sp. nov., Novel Prosthecate Bacteria within the Family Ancalomicrobiaceae and Reclassification of the Polyphyletic Genus Prosthecomicrobium. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722601105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Winogradskyella luteola sp.nov., Erythrobacter ani sp. nov., and Erythrobacter crassostrea sp.nov., isolated from the hemolymph of the Pacific Oyster Crassostrea gigas. Arch Microbiol 2022; 204:488. [PMID: 35835967 PMCID: PMC9283347 DOI: 10.1007/s00203-022-03099-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/24/2022] [Indexed: 11/09/2022]
Abstract
Three new bacterial strains, WHY3T, WH131T, and WH158T, were isolated and described from the hemolymph of the Pacific oyster Crassostrea gigas utilizing polyphasic taxonomic techniques. The 16S rRNA gene sequence analysis revealed that strain WHY3T was a member of the genus Winogradskyella, whereas strains WHI31T and WH158T were members of the genus Erythrobacter. According to the polygenomic study the three strains formed individual lineages with strong bootstrap support. The comparison of dDDH-and ANI values, percentage of conserved proteins (POCP), and average amino acid identity (AAl) between the three strains and their relatives established that the three strains represented two separate genera. Menaquinone-6 was reported as the major respiratory quinone in strain WHY3T and Ubiquinone-10 for strains WH131T and WH158T, respectively. The major cellular fatty acids for strain WHY3T were C15:0, anteiso-C15:1 ω7c, iso-C15:0, C16:1ω7c. The major cellular fatty acids for strains WH131T and WH158T were C14:02-OH and t18:1ω12 for WH131T and C17:0, and C18:1ω7c for strain WH158T. Positive Sudan Black B staining Indicated the presence of polyhydroxyalkanoic acid granules for strains WH131T and WH158T but not for strain WHY3T. The DNA G + C contents of strains WHY3T, WH131T and WH158T were 34.4, 59.7 and 56.6%, respectively. Gene clusters predicted some important genes involved in the bioremediation process. Due to the accomplishment of polyphasic taxonomy, we propose three novel species Winogradskyella luteola sp.nov. (type strain WHY3T = DSM 111804T = NCCB 100833T), Erythrobacter ani sp.nov. (WH131T = DSM 112099T = NCCB 100824T) and Erythrobacter crassostrea sp.nov. (WH158T = DSM 112102T = NCCB 100877T).
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Kuzyk SB, Jafri M, Humphrey E, Maltman C, Kyndt JA, Yurkov V. Prosthecate aerobic anoxygenic phototrophs Photocaulis sulfatitolerans gen. nov. sp. nov. and Photocaulis rubescens sp. nov. isolated from alpine meromictic lakes in British Columbia, Canada. Arch Microbiol 2022; 204:444. [PMID: 35776224 DOI: 10.1007/s00203-022-03007-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/27/2022]
Abstract
Seven Gram-negative flagellated and subsequent prosthecate bacteria were isolated from meromictic Mahoney Lake and Blue Lake in British Columbia, Canada. Each became pink-red after 1-2 weeks of incubation, containing bacteriochlorophyll a incorporated into light harvesting and reaction center pigment-protein complexes. They did not grow anaerobically under illuminated conditions, supporting their identification as obligate aerobic anoxygenic phototrophs (AAP). All isolates preferred high salinity and BL14T tolerated up to 6.5% NaCl or 16.0% Na2SO4. In addition to phenotypic differences, analysis of 16S rRNA gene sequences found both strains BL14T and ML37T were related to Alkalicaulis satelles, G-192T by 98.41 and 98.84%, respectively, and distantly associated to members of the non-phototrophic genus Glycocaulis profundi, ZYF765T (95.59 and 95.36%, respectively) within the newly recognized Maricaulales order of α-Proteobacteria. BL14T and ML37T contained photosynthetic operons of 46,143 and 46,315 bp, where genes of BL14T were uniquely split into two distal operons. Furthermore, A. satelles was not originally published as an AAP, but was also found in this work to contain a similar 45,131 bp fragment. The distinct morphological features, physiological traits and genomic analysis including average nucleotide identity and digital DNA:DNA hybridization of circularized genomes supported the proposal of new genus and species Photocaulis sulfatitolerans gen. nov. sp. nov., type strain BL14T and Photocaulis rubescens sp. nov. type strain ML37T.
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Affiliation(s)
- Steven B Kuzyk
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Murtaza Jafri
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Elaine Humphrey
- Department of Mechanical Engineering, University of Victoria, Victoria, BC, Canada
| | - Chris Maltman
- Department of Biology, Slippery Rock University, Slippery Rock, PA, USA
| | - John A Kyndt
- College of Science and Technology, Bellevue University, Bellevue, NE, USA
| | - Vladimir Yurkov
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.
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Guo Z, Lv L, Liu D, He X, Wang W, Feng Y, Islam MS, Wang Q, Chen W, Liu Z, Wu S, Abied A. A global meta-analysis of animal manure application and soil microbial ecology based on random control treatments. PLoS One 2022; 17:e0262139. [PMID: 35061792 PMCID: PMC8782357 DOI: 10.1371/journal.pone.0262139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: -1.15 and M-I: -1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.
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Affiliation(s)
- Zhenhua Guo
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- * E-mail: , (ZG); (DL)
| | - Lei Lv
- Wood Science Research Institute of Heilongjiang Academy of Forestry, Harbin, P. R. China
| | - Di Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- * E-mail: , (ZG); (DL)
| | - Xinmiao He
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Wentao Wang
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Yanzhong Feng
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Md. Saiful Islam
- Department of Animal Production & Management, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, Bangladesh
| | - Qiuju Wang
- Key laboratory of Heilongjiang Soil Environment and Plant Nutrient, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin, P. R. China
| | - Wengui Chen
- Animal Science and Technology College, Northeast Agricultural University, Harbin, P. R. China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Saihui Wu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
| | - Adam Abied
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Harbin, P. R. China
- Dry Land Research Center (DLRC) and Animal Production, Agricultural Research Corporation (ARC), Khartoum, Sudan
- Projects and Programs Secretary of the Sudan Youth Organization on Climate Change, Khartoum, Sudan
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12
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Yoon J, Lee EY, Nam SJ. Erythrobacter rubeus sp. nov., a carotenoid-producing alphaproteobacterium isolated from coastal seawater. Arch Microbiol 2022; 204:125. [PMID: 34997854 DOI: 10.1007/s00203-021-02736-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/02/2021] [Accepted: 12/17/2021] [Indexed: 11/26/2022]
Abstract
A study based on a polyphasic taxonomic approach was carried out to identify and classify a novel marine alphaproteobacterium, designated as KMU-140T, isolated from coastal seawater collected at Jeju Island, Republic of Korea. Cells of strain KMU-140T were spherical, Gram-stain-negative, reddish-orange colored, strictly aerobic, catalase- and oxidase-positive, non-motile, and chemoorganoheterotrophic. The novel isolate was able to grow at NaCl concentrations of 0-5%, pH 6.0-9.5, and 10-45 °C. A phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KMU-140T belongs to the family Erythrobacteraceae and was most closely related to Erythrobacter longus OCh101T (98.7%). Strain KMU-140T contained ubiquinone-10 (Q-10) as the only respiratory quinone and C18:1 ω7c, iso-C18:0, and C16:0 as the main (> 10%) cellular fatty acids. Strain KMU-140T produced carotenoid compounds that rendered the cell biomass a reddish-orange color. The assembled draft genome size of strain KMU-140T was 3.04 Mbp with G + C content of 60.6 mol%. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values of KMU-140T and the species of the genus Erythrobacter were found to be 76.6-78.4%, 14.0-18.7%, and 69.6-77.8%, respectively. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, and two unidentified lipids were identified as major polar lipids. On the basis of the polyphasic taxonomic features presented, the strain is considered to represent a novel species of the genus Erythrobacter for which the name Erythrobacter rubeus sp. nov. is proposed. The type strain of E. rubeus sp. nov. is KMU-140T (= KCCM 90479T = NBRC 115159T).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-gu, Daegu, 42601, Republic of Korea.
| | - Eun-Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 03760, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul, 03760, Republic of Korea.
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13
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Caragata EP, Otero LM, Tikhe CV, Barrera R, Dimopoulos G. Microbial Diversity of Adult Aedes aegypti and Water Collected from Different Mosquito Aquatic Habitats in Puerto Rico. MICROBIAL ECOLOGY 2022; 83:182-201. [PMID: 33860847 PMCID: PMC11328149 DOI: 10.1007/s00248-021-01743-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 03/19/2021] [Indexed: 05/06/2023]
Abstract
Mosquitoes, the major vectors of viruses like dengue, are naturally host to diverse microorganisms, which play an important role in their development, fecundity, immunity, and vector competence. The composition of their microbiota is strongly influenced by the environment, particularly their aquatic larval habitat. In this study, we used 2×300 bp 16s Illumina sequencing to compare the microbial profiles of emerging adult Aedes aegypti mosquitoes and the water collected from common types of aquatic habitat containers in Puerto Rico, which has endemic dengue transmission. We sequenced 141 mosquito and 46 water samples collected from plastic containers, septic tanks, discarded tires, underground trash cans, tree holes, or water meters. We identified 9 bacterial genera that were highly prevalent in the mosquito microbiome, and 77 for the microbiome of the aquatic habitat. The most abundant mosquito-associated bacterial OTUs were from the families Burkholderiaceae, Pseudomonadaceae, Comamonadaceae, and Xanthomonadaceae. Microbial profiles varied greatly between mosquitoes, and there were few major differences explained by container type; however, the microbiome of mosquitoes from plastic containers was more diverse and contained more unique taxa than the other groups. Container water was significantly more diverse than mosquitoes, and our data suggest that mosquitoes filter out many bacteria, with Alphaproteobacteria in particular being far more abundant in water. These findings provide novel insight into the microbiome of mosquitoes in the region and provide a platform to improve our understanding of the fundamental mosquito-microbe interactions.
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Affiliation(s)
- E P Caragata
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - L M Otero
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
- Entomology and Ecology Team, Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - C V Tikhe
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - R Barrera
- Entomology and Ecology Team, Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - G Dimopoulos
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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14
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Yi M, Zhang L, Qin C, Lu P, Bai H, Han X, Yuan S. Temporal changes of microbial community structure and nitrogen cycling processes during the aerobic degradation of phenanthrene. CHEMOSPHERE 2022; 286:131709. [PMID: 34340117 DOI: 10.1016/j.chemosphere.2021.131709] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Phenanthrene (PHE) is frequently detected in worldwide soils. But it is still not clear that how the microbial community succession happens and the nitrogen-cycling processes alter during PHE degradation. In this study, the temporal changes of soil microbial community composition and nitrogen-cycling processes during the biodegradation of PHE (12 μg g-1) were explored. The results showed that the biodegradation of PHE followed the second-order kinetics with a half-life of 7 days. QPCR results demonstrated that the bacteria numbers increased by 67.1%-194.7% with PHE degradation, whereas, no significant change was observed in fungi numbers. Thus, high-throughput sequencing based on 16 S rRNA was conducted and showed that the abundances of Methylotenera, Comamonadaceae, and Nocardioides involved in PHE degradation and denitrification were significantly increased, while those of nitrogen-metabolism-related genera such as Nitrososphaeraceae, Nitrospira, Gemmatimonadacea were decreased in PHE-treated soil. Co-occurrence network analysis suggested that more complex interrelations were constructed, and Proteobacteria instead of Acidobacteriota formed intimate associations with other microbes in responding to PHE exposure. Additionally, the abundances of nifH and narG were significantly up-regulated in PHE-treated soil, while that of amoA especially AOAamoA was down-regulated. Finally, correlation analysis found several potential microbes (Methylotenera, Comamonadaceae, and Agromyces) that could couple PHE degradation and nitrogen transformation. This study confirmed that PHE could alter microbial community structure, change the native bacterial network, and disturb nitrogen-cycling processes.
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Affiliation(s)
- Meiling Yi
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Lilan Zhang
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China.
| | - Cunli Qin
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Peili Lu
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Hongcheng Bai
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
| | - Xinkuan Han
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Shupei Yuan
- Key Laboratory of Three Gorges Reservoir Region's Eco-environment, Ministry of Education, Chongqing University, Chongqing, 400045, China; State Key Laboratory of Coal Mine Disaster Dynamics and Control, Chongqing University, Chongqing, 400044, People's Republic of China
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15
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Kim D, Yoo Y, Khim JS, Yang D, Pathiraja D, Park B, Choi IG, Kim JJ. Altererythrobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat and reclassification of Altererythrobacter deserti, Altererythrobacter estronivorus and Altererythrobacter muriae as Tsuneonella deserti comb. nov., Croceicoccus estronivorus comb. nov. and Alteripontixanthobacter muriae comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34874248 DOI: 10.1099/ijsem.0.005134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yellow-coloured bacterium, designated strain JGD-16T, was isolated from a tidal flat in Janggu-do, Garorim Bay, Taean-gun, Chungcheongbuk-do, Republic of Korea. Cells were Gram-stain-negative, aerobic, non-flagellated and short ovoid to coccoid-shaped. Growth was observed at 10-37 °C (optimum, 30 °C), pH 6.0-9.0 (pH 8.0) and with 1-5% (w/v) NaCl (2%). Results of 16S rRNA gene sequence analysis indicated that strain JGD-16T was closely related to Altererythrobacter xiamenensis LY02T (97.1 %), Altererythrobacter aurantiacus O30T (96.3 %), Altererythrobacter ishigakiensis JPCCMB0017T (95.8 %), Altererythrobacter epoxidivorans JCS350T (95.7 %) and Altererythrobacter insulae BPTF-M16T (95.3%). Phylogenomic analysis using the maximum-likelihood algorithm showed that strain JGD-16T formed a clade with the genus Altererythrobacter. The genomic DNA G+C content was 57.8 mol%. The predominant respiratory quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, a sphingoglycolipid, an unidentified glycolipid and an unidentified lipid. The major fatty acids were C18:1 ω7c (31.5 %) and C18:3 ω6c (19.6 %). On the basis of its phylogenomic, physiological and chemotaxonomical characteristics, strain JGD-16T represents a novel species within the genus Altererythrobacter, for which the name Altererythrobacter lutimaris JGD-16Tsp. nov. is proposed. The type strain is JGD-16T (=KCTC 72632T=KACC 21405T=JCM 33750T). We also propose the reclassification of Altererythrobacter deserti as Tsuneonella deserti comb. nov., Altererythrobacter estronivorus as Croceicoccus estronivorus comb. nov. and Altererythrobacter muriae as Alteripontixanthobacter muriae comb. nov.
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Affiliation(s)
- Dongjun Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, Republic of Korea
| | - Yeonjae Yoo
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jong Seong Khim
- School of Earth and Environmental Science and Research Institute of Oceanography, Seoul National University, Seoul, Republic of Korea
| | - Dongmin Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Duleepa Pathiraja
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Byeonghyeok Park
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Science & Biotechnology, Korea University, Seoul, Republic of Korea
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16
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Azpiazu-Muniozguren M, Martinez-Ballesteros I, Gamboa J, Seoane S, Alonso R, Laorden L, Garaizar J, Bikandi J. Altererythrobacter muriae sp. nov., isolated from hypersaline Añana Salt Valley spring water, a continental thalassohaline-type solar saltern. Int J Syst Evol Microbiol 2021; 71. [PMID: 33666546 DOI: 10.1099/ijsem.0.004734] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel salt-tolerant alpha-proteobacterium, designated SALINAS58T, was isolated from Santa Engracia hypersaline spring water in the Añana Salt Valley, Álava, Spain. The isolate was Gram-negative, aerobic, non-motile, catalase-positive, oxidase-negative, rod-shaped and formed orange colonies on marine agar. Optimal growth was observed at pH 6.0-6.5, at 30 °C and in the presence of 1% (w/v) NaCl. The main cellular fatty acids (>20%) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The major respiratory quinone was ubiquinone Q-10 and the major polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidilglycerol, four unidentified glycolipids and one unidentified phospholipid. Strain SALINAS58T had the highest 16S rRNA gene sequence similarity to Altererythrobacter marensis MSW-14T (96.6%), Altererythrobacter aquaemixtae JSSK-8T (96.5%) and Pontixanthobacter luteolus SW-109T (96.5%) followed by Altererythrobacter atlanticus 26DY36T (96.4%). Results of the phylogenetic analysis, based on 16S rRNA gene sequences, and phylogenetic approaches based on whole genome nucleotide differences, showed that strain SALINAS58T could be distinguished from recognized species of the genus Altererythrobacter. The genomic DNA G+C content was 61.4 mol%. Digital DNA-DNA hybridization, average nucleotide identity and average aminoacid identity values between the genome of strain SALINAS58T and A. marensis MSW-14T were 18.4, 73.1 and 68.1%, respectively. Based on data from this polyphasic characterization, strain SALINAS58T (=CECT 30029T=LMG 31726T) is considered to be classified as representing a novel species in the genus Altererythrobacter, for which the name Altererythrobacter muriae sp. nov. is proposed.
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Affiliation(s)
- Maia Azpiazu-Muniozguren
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | - Ilargi Martinez-Ballesteros
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | | | - Sergio Seoane
- Plant Biology and Ecology Department, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Rodrigo Alonso
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | - Lorena Laorden
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | - Javier Garaizar
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
| | - Joseba Bikandi
- MikroIker Research Group. Immunology, Microbiology and Parasitology Department, Farmacy Faculty, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Álava, Spain
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17
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Thin KK, He SW, Wang X, Wang Y, Rong M, Han JG, Zhang X. Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China. Curr Microbiol 2021; 78:830-836. [PMID: 33398443 DOI: 10.1007/s00284-020-02323-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/07/2020] [Indexed: 11/27/2022]
Abstract
During characterization of rhizobacteria, strain DBTS2T was isolated from the rhizosphere soil samples of healthy tomato plants and characterized using a polyphasic taxonomic approach. Phylogenetic analysis using 16S rRNA gene sequences showed this strain belonged to the genus Rhizobium and was most closely related to Rhizobium subbaraonis JC85T (99.1%) and Rhizobium daejeonense CCBAU 10050T (97%). Cells of strain DBTS2T were Gram-negative, short rod, aerobic and non-motile. This novel strain was found to grow at 20-45 °C (optimum 25-37 °C), pH 5-9 (optimum 8) and in the presence of 4% NaCl. It was positive for catalase and oxidase. The predominant cellular fatty acids were Summed Feature 8 (52.7%) and C19:0 cyclo ω8c (23.3%). The polar lipids of strain DBTS2T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipid, unidentified aminolipid, four unidentified phospholipids, unidentified lipid, phosphatidylcholine, unknown glycolipid and unknown aminophosphoglycolipids. Q-10 was the major quinone. The DNA-DNA hybridization similarity values between the strain DBTS2T and R. subbaraonis JC85T, R. daejeonense CCBAU 10050T and Rhizobium azooxidifex DSM100211T were 46.4%, 20.7% and 25.5%, respectively. The ANI value was 91.96% between strain DBTS2T and R. subbaraonis JC85T and 75.18% between strain DBTS2T and R. daejeonense CCBAU 10050T. The DNA G+C content of the genomic DNA was 63.1 mol%. Based on these results, it was concluded that the isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium rhizolycopersici sp. nov. is proposed, with DBTS2T (= CICC 24887T = ACCC61707 = JCM 34245) as the type strain.
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Affiliation(s)
- Kyu Kyu Thin
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12 Hao, Beijing, People's Republic of China.,Department of Zoology, University of Magway, Magway, Myanmar
| | - Shan-Wen He
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, 200232, People's Republic of China
| | - Xing Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12 Hao, Beijing, People's Republic of China
| | - Yao Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12 Hao, Beijing, People's Republic of China
| | - Ma Rong
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12 Hao, Beijing, People's Republic of China
| | - Ji-Gang Han
- Shanghai Academy of Landscape Architecture Science and Planning, Shanghai, 200232, People's Republic of China
| | - Xiaoxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12 Hao, Beijing, People's Republic of China.
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18
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Yang D, Liu Y, Wang Y, Gao F, Zhao J, Li Y, Li X. Effects of Soil Tillage, Management Practices, and Mulching Film Application on Soil Health and Peanut Yield in a Continuous Cropping System. Front Microbiol 2020; 11:570924. [PMID: 33424781 PMCID: PMC7785755 DOI: 10.3389/fmicb.2020.570924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Our objective was to optimize soil management practices to improve soil health to increase peanut (Arachis hypogaea L.) yield. We studied the effects of using rotary tillage with mulching film or without [rotary tillage with no mulching (RTNM)], plow tillage with mulching film or without, and green manure with mulching film (GMMF) or without [green manure with no mulching (GMNM)] over 3 years in Tai'an, China. Results showed that compared with RTNM treatment, GMNM and GMMF treatments significantly (P < 0.05) increased soil organic carbon, enzymatic activity, and the available nitrogen, phosphorus, and potassium content. The dominant bacterial phyla in the soil across all treatments were Proteobacteria, Acidobacteria, and Actinobacteria. Bacterial richness and diversity in the soil were significantly (P < 0.05) enhanced after GMMF and GMNM treatments compared with those after RTNM treatment. The linear discriminant analysis effect size analysis indicated that Chloroflexi abundance in the 0-10 and 10-20 cm soil layers changed significantly (P < 0.05) after rotary tillage with mulching film and RTNM treatments, respectively, whereas that of Bacteroidetes changed significantly (P < 0.05) in the 0-10 layer after GMNM treatment. The abundance of the Xanthobacteraceae family of Proteobacteria in both soil layers changed significantly (P < 0.05) after GMNM and GMMF treatments. Redundancy analysis revealed that soil physical (soil bulk density and water content), chemical (soil organic carbon, available nitrogen, phosphorus, and potassium), and biological (soil enzymatic activity and nutrient content) characteristics affect the soil bacterial community. Changed soil quality indices may be favorable for leaf photo-assimilate accumulation. Compared with RTNM treatment, GMNM and GMMF treatments significantly increased photosynthesis rate in the peanut leaf and decreased intercellular carbon dioxide concentration. Our results showed that compared with that after RTNM treatment, the average pod yield after GMMF and GMNM treatments increased by 27.85 and 21.26%, respectively, due to increases in the pods per plant and plant numbers. The highest yield of all treatments was obtained from the GMMF-treated plot, followed by that from the GMNM-treated plots. Thus, taking into consideration the residual pollution caused by plastic films, we propose GMNM as a suitable strategy to improve soil physicochemical and microbial properties and to increase the peanut pod yield.
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Affiliation(s)
- Dongqing Yang
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Yan Liu
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Ying Wang
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Fang Gao
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Jihao Zhao
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Ying Li
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
| | - Xiangdong Li
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai'an, China
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19
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Kevbrin V, Boltyanskaya Y, Koziaeva V, Uzun M, Grouzdev D. Alkalicaulis satelles gen. nov., sp. nov., a novel haloalkaliphile isolated from a laboratory culture cyanobacterium Geitlerinema species and proposals of Maricaulaceae fam. nov., Robiginitomaculaceae fam. nov., Maricaulales ord. nov. and Hyphomonadales ord. nov. Int J Syst Evol Microbiol 2020; 71. [PMID: 33351741 DOI: 10.1099/ijsem.0.004614] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A prosthecate bacterial strain, designated G-192T, was isolated from decaying biomass of a haloalkaliphilic cyanobacterium Geitlerinema sp. Z-T0701. The cells were aerobic, Gram-negative, non-endospore-forming and dimorphic, occurring either as sessile bacteria with a characteristic stalk or as motile flagellated cells. The strain utilized a limited range of substrates, mostly peptonaceous, but was able to degrade whole proteins. Growth occurred at 5-46 °C (optimum, 35-40 °C), pH 7.3-10.3 (optimum, pH 8.0-9.0), 0-14 % NaCl (v/w; optimum, 2.0-6.0 %, v/w). The G+C content of the genomic DNA of strain G-192T was 66.8%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain G-192T formed a distinct evolutionary lineage within the family Hyphomonadaceae. Strain G-192T showed the highest 16S rRNA sequence similarity to Glycocaulis profundi ZYF765T (95.2%), Oceanicaulis stylophorae GISW-4T (94.2%) and Marinicauda salina WD6-1T (95.5%). The major cellular fatty acids (>5% of the total) were C18:1 ω9c, C18:0 and 11-methyl-C18:1 ω7c. The major polar lipids were glycolipids and phospholipids. The only respiratory quinone was ubiquinone-10 (Q-10). Based on polyphasic results including phylogenomic data, the novel strain could be distinguished from other genera, which suggests that strain G-192T represents a novel species of a new genus, for which the name Alkalicaulis satelles gen. nov., sp. nov. is proposed. The type strain is G-192T (=VKM B-3306T=KCTC 72746T). The strain is the first representative of the stalked bacteria associated with a haloalkaliphilic cyanobacterium. Based on phylogenomic indices and phenotypic data, it is proposed to evolve two novel families Maricaulaceae fam. nov. and Robiginitomaculaceae fam. nov. out of the current family Hyphomonadaceae. In addition, it is proposed to place the first two families in the novel order Maricaulales ord. nov. and novel order Hyphomonadales ord. nov. is proposed to accommodate the family Hyphomonadaceae.
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Affiliation(s)
- Vadim Kevbrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | - Yulia Boltyanskaya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | - Veronika Koziaeva
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia.,Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | - Maria Uzun
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
| | - Denis Grouzdev
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2, Leninsky Ave., Moscow 119071, Russia
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20
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Sun J, Guo J, Lin TH, Feng X, Zhang R. Pseudopontixanthobacter vadosimaris gen. nov., sp. nov., isolated from shallow sea near Kueishan Island. Int J Syst Evol Microbiol 2020; 70:6444-6449. [PMID: 33174831 DOI: 10.1099/ijsem.0.004552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A Gram-stain-negative and aerobic bacterial strain, designated as JL3514T, was isolated from surface water of the hydrothermal system around Kueishan Island. The isolate formed red colonies and cells were non-flagellated, rod-shaped and contained methanol-soluble pigments. Growth was observed at 10-50 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum, pH 7.0) and in the presence of 0-9 % (w/v) NaCl (optimum, 2 %). Strain JL3514T was positive for catalase and weakly positive for oxidase. Results of 16S rRNA gene sequence analyses showed highest similarities to species in the family Erythrobacteraceae, namely Croceibacterium atlanticum (96.1 %), Pelagerythrobacter marensis (96.0 %), Tsuneonella rigui (96.0 %) and Altericroceibacterium xinjiangense (96.0 %). Phylogenetic analysis based on core gene sequences revealed that the isolate formed a distinct branch with the related species and it had a lower average amino acid identity value than the suggested threshold for genera boundaries. The major fatty acids (>5 %) were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, C17 : 1 ω6c, C14 : 0 2-OH and C12 : 0. The dominant polar lipids comprised diphosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, glycolipid, two unidentified lipids and one unidentified phospholipid. The main respiratory quinones were ubiquinone-10 (95.7 %) and ubiquinone-9 (4.3 %). The DNA G+C content from the genome was 63.0 mol%. Based on the presented data, we consider strain JL3514T to represent a novel genus of the family Erythrobacteraceae, with the name Pseudopontixanthobacter vadosimaris gen. nov., sp. nov. The type strain is JL3514T (=KCTC 62623T=MCCC 1K03561T).
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Affiliation(s)
- Jia Sun
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Jiaying Guo
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Ta-Hui Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xuejin Feng
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
| | - Rui Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519080, PR China.,State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, PR China
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21
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Xu L, Sun C, Fang C, Oren A, Xu XW. Genomic-based taxonomic classification of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2020; 70:4470-4495. [PMID: 32726199 PMCID: PMC7660246 DOI: 10.1099/ijsem.0.004293] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
The family Erythrobacteraceae, belonging to the order Sphingomonadales, class Alphaproteobacteria, is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter, Croceibacterium, Croceicoccus, Erythrobacter, Erythromicrobium, Porphyrobacter and Qipengyuania. As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter. This study is the first genomic-based study of the family Erythrobacteraceae, and will contribute to further insights into the evolution of this family.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Cong Sun
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Chen Fang
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- College of Oceanography, Hohai University, Nanjing 210000, PR China
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, PR China
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22
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Lee JC, Whang KS. Sphingomonas segetis sp. nov., isolated from spinach farming field soil. Int J Syst Evol Microbiol 2020; 70:3905-3911. [PMID: 32501785 DOI: 10.1099/ijsem.0.004257] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterium, designated strain YJ09T, was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09T were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09T belongs to the genus Sphingomonas with high sequence similarities to Sphingomonas parvus GP20-2 T (98.0 %), Sphingomonas agri HKS-06T (97.7 %) and Sphingomonas lutea JS5T (97.4 %). The results of phylogenetic analysis indicated that strain YJ09T formed a distinct phyletic line in the genus Sphingomonas and the results of DNA-DNA relatedness studies demonstrated that strain YJ09T could be separated from its closest relatives in the genus Sphingomonas. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18:1 ω7c, C16 : 0 and C16:1 ω7c and/or iso-C15 : 0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09T is considered to represent a novel species in the genus Sphingomonas, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09T (=KACC 19551T=NBRC 113247T).
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Affiliation(s)
- Jae-Chan Lee
- Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 35349, Republic of Korea
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23
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Xu Z, Zhang Y, Muhammad Y, Wang G. Sphingomonas montanisoli sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2020; 70:3606-3613. [DOI: 10.1099/ijsem.0.004187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A soil bacterium, designated ZX9611T, was isolated from Taihang Mountain in Henan province, PR China. The strain was Gram-stain-negative and strictly aerobic. The cells were motile, rod-shaped and formed light pink-colored colonies. The 16S rRNA gene sequence of ZX9611T shared the highest similarities with those of
Sphingomonas crocodyli
CCP-7T (97.0%),
Sphingomonas jatrophae
S5-249T (96.6%) and
Sphingomonas starnbergensis
382T (95.9%). Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that ZX9611T clustered with
S. crocodyli
CCP-7T,
S. jatrophae
S5-249T and
S. starnbergensis
382T. The average nucleotide identity (ANI) values between ZX9611T and two type strains (
S. crocodyli
BCRC 81096T and
S. jatrophae
DSM 27345T) were 88.3 and 68.6% respectively. ZX9611T exhibited genome-sequence-based digital DNA–DNA hybridization (dDDH) values of 53.3 % and 15.3 %, compared with
S. crocodyli
BCRC 81096T and
S
.
jatrophae
DSM 27345T, respectively. ZX9611T had a genome size of 4.12 Mb and an average DNA G+C content of 64.8 %. ZX9611T had major fatty acids (>5 %) including summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c), and the major polyamine was sym-homospermidine. The only respiratory quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZX9611T represents a novel species of genus Sphingomonas, for which the name Sphingomonas montanisoli sp. nov. is proposed. The type strain is ZX9611T (=KCTC 72622T=CCTCC AB 2019350T).
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Affiliation(s)
- Zixiao Xu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yuxiao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yasir Muhammad
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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24
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Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Göker M. Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria. Front Microbiol 2020; 11:468. [PMID: 32373076 PMCID: PMC7179689 DOI: 10.3389/fmicb.2020.00468] [Citation(s) in RCA: 259] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/04/2020] [Indexed: 11/13/2022] Open
Abstract
The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.
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Affiliation(s)
- Anton Hördt
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marina García López
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Marcel Schleuning
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Lisa-Maria Weinhold
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czechia
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Berkeley, CA, United States
| | - Markus Göker
- Department of Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
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25
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Wang M, Xie X, Wang M, Wu J, Zhou Q, Sun Y. The bacterial microbiota in florfenicol contaminated soils: The antibiotic resistome and the nitrogen cycle. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 259:113901. [PMID: 32023788 DOI: 10.1016/j.envpol.2019.113901] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/18/2019] [Accepted: 12/28/2019] [Indexed: 06/10/2023]
Abstract
Soil antibiotic resistome and the nitrogen cycle are affected by florfenicol addition to manured soils but their interactions have not been fully described. In the present study, antibiotic resistance genes (ARGs) and nitrogen cycle genes possessed by soil bacteria were characterized using real-time fluorescence quantification PCR (qPCR) and metagenomic sequencing in a short-term (30 d) soil model experiment. Florfenicol significantly changed in the abundance of genes conferring resistance to aminoglycosides, β-lactams, tetracyclines and macrolides. And the abundance of Sphingomonadaceae, the protein metabolic and nitrogen metabolic functions, as well as NO reductase, nitrate reductase, nitrite reductase and N2O reductase can also be affected by florfenicol. In this way, ARG types of genes conferring resistance to aminoglycosides, β-lactamases, tetracyclines, colistin, fosfomycin, phenicols and trimethoprim were closely associated with multiple nitrogen cycle genes. Actinobacteria, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia played an important role in spreading of ARGs. Moreover, soil physicochemical properties were important factors affecting the distribution of soil flora. This study provides a theoretical basis for further exploration of the transmission regularity and interference mechanism of ARGs in soil bacteria responsible for nitrogen cycle.
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Affiliation(s)
- Mei Wang
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Xiying Xie
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Mianzhi Wang
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Jing Wu
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Qin Zhou
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China
| | - Yongxue Sun
- The Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China; National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642, China.
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26
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Park S, Chen S, Yoon JH. Erythrobacter insulae sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2020; 70:1470-1477. [DOI: 10.1099/ijsem.0.003824] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a tidal flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus
Erythrobacter
. JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0–98.4 % to the type strains of
Erythrobacter longus
,
Erythrobacter aquimaris
,
Erythrobacter nanhaisediminis
,
Erythrobacter vulgaris
,
Erythrobacter seohaensis
,
Erythrobacter litoralis
and
Erythrobacter citreus
and 93.7–96.6 % to the type strains of the other species of the genus
Erythrobacter
. The ANI and dDDH values between JBTF-M21T and the type strains of
E. longus
,
E. nanhaisediminis
,
E. seohaensis
and
E. litoralis
were 70.83–72.93 % and 18.0–18.8 %, respectively. Mean DNA–DNA relatedness values between JBTF-M21T and the type strains of
E. aquimaris
,
E. vulgaris
and
E. citreus
were 12–24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus
Erythrobacter
with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus
Erythrobacter
, for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).
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Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Siyu Chen
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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27
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Ruan ZP, Cao WM, Zhang X, Liu JTY, Zhu JC, Hu B, Jiang JD. Rhizobium terrae sp. nov., Isolated from an Oil-Contaminated Soil in China. Curr Microbiol 2020; 77:1117-1124. [PMID: 31982965 DOI: 10.1007/s00284-020-01889-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 01/16/2020] [Indexed: 11/26/2022]
Abstract
A Gram-stain-negative, facultative aerobic, non-spore-forming, non-motile, non-flagellated, rod-shaped bacterium, designated strain NAU-18T was isolated from an oil-contaminated soil in China. Strain NAU-18T could grow at 10-42 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, 7.0) and in the presence of 0-2.0% (w/v) NaCl (optimum, 0.5% NaCl in R2A). The predominant fatty acids were C18:1ω7c (71.2%) and Summed feature 2 (5.1%), representing 76.3% of the total fatty acids. The major respiratory quinones were Q9 and Q10. The DNA G + C content of strain NAU-18T was 61.4 mol% based on its draft genome sequence. Genome annotation of strain NAU-18T predicted the presence of 6668 genes, of which 6588 are coding proteins and 80 are RNA genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NAU-18T was a member of the genus Rhizobium and showed 96.93% (with 93.2% coverage) and 96.81% (with 100% coverage) identities with those of Neorhizobium alkalisoli CCBAU 01393T and Rhizobium oryzicola ZYY136T, respectively. In the phylogenetic analysis, strain NAU-18T and R. oryzicola ZYY136T are consistently placed in the same branch. Strain NAU-18T represents a novel species within the genus Rhizobium, for which the name Rhizobium terrae sp. nov. is proposed, with the type strain NAU-18T (=KCTC 62418T = CCTCC AB 2018075T).
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Affiliation(s)
- Zhe-Pu Ruan
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei-Miao Cao
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Zhang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing-Tian-Yi Liu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Chun Zhu
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Experimental Biology Education Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Hu
- Experimental Biology Education Center, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian-Dong Jiang
- Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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28
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Li HP, Yao D, Shao KZ, Han QQ, Gou JY, Zhao Q, Zhang JL. Altererythrobacter rhizovicinus sp. nov., isolated from rhizosphere soil of Haloxylon ammodendron. Int J Syst Evol Microbiol 2020; 70:680-686. [DOI: 10.1099/ijsem.0.003817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hui-Ping Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Dan Yao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Kun-Zhong Shao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Qing-Qing Han
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Jing-Yi Gou
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Qi Zhao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
| | - Jin-Lin Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, Gansu Province, PR China
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Barnier C, Clerissi C, Lami R, Intertaglia L, Lebaron P, Grimaud R, Urios L. Description of Palleronia rufa sp. nov., a biofilm-forming and AHL-producing Rhodobacteraceae, reclassification of Hwanghaeicola aestuarii as Palleronia aestuarii comb. nov., Maribius pontilimi as Palleronia pontilimi comb. nov., Maribius salinus as Palleronia salina comb. nov., Maribius pelagius as Palleronia pelagia comb. nov. and emended description of the genus Palleronia. Syst Appl Microbiol 2020; 43:126018. [DOI: 10.1016/j.syapm.2019.126018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/15/2022]
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30
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Zhu D, Niu Y, Liu D, Wang G, Zheng S. Sphingomonas gilva sp. nov., isolated from mountain soil. Int J Syst Evol Microbiol 2019; 69:3472-3477. [DOI: 10.1099/ijsem.0.003645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Dahui Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yaxin Niu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dongmei Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Shixue Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
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31
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Suresh G, Lodha TD, Indu B, Sasikala C, Ramana CV. Taxogenomics Resolves Conflict in the Genus Rhodobacter: A Two and Half Decades Pending Thought to Reclassify the Genus Rhodobacter. Front Microbiol 2019; 10:2480. [PMID: 31736915 PMCID: PMC6834548 DOI: 10.3389/fmicb.2019.02480] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022] Open
Abstract
The genus Rhodobacter is taxonomically well studied, and some members are model organisms. However, this genus is comprised of a heterogeneous group of members. 16S rRNA gene-based phylogeny of the genus Rhodobacter indicates a motley assemblage of anoxygenic phototrophic bacteria (genus Rhodobacter) with interspersing members of other genera (chemotrophs) making the genus polyphyletic. Taxogenomics was performed to resolve the taxonomic conflicts of the genus Rhodobacter using twelve type strains. The phylogenomic analysis showed that Rhodobacter spp. can be grouped into four monophyletic clusters with interspersing chemotrophs. Genomic indices (ANI and dDDH) confirmed that all the current species are well defined, except Rhodobacter megalophilus. The average amino acid identity values between the monophyletic clusters of Rhodobacter members, as well as with the chemotrophic genera, are less than 80% whereas the percentage of conserved proteins values were below 70%, which has been observed among several genera related to Rhodobacter. The pan-genome analysis has shown that there are only 1239 core genes shared between the 12 species of the genus Rhodobacter. The polyphasic taxonomic analysis supports the phylogenomic and genomic studies in distinguishing the four Rhodobacter clusters. Each cluster is comprised of one to seven species according to the current Rhodobacter taxonomy. Therefore, to address this taxonomic discrepancy we propose to reclassify the members of the genus Rhodobacter into three new genera, Luteovulum gen. nov., Phaeovulum gen. nov. and Fuscovulum gen. nov., and provide an emended description of the genus Rhodobacter sensu stricto. Also, we propose reclassification of Rhodobacter megalophilus as a sub-species of Rhodobacter sphaeroides.
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Affiliation(s)
- G. Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Tushar D. Lodha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - B. Indu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ch. Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Hyderabad, India
| | - Ch. V. Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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32
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Lee SD, Kim YJ, Kim IS. Erythrobacter suaedae sp. nov., isolated from a rhizosphere mudflat of a halophyte (Suaeda japonica). Int J Syst Evol Microbiol 2019; 69:3287-3292. [DOI: 10.1099/ijsem.0.003625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Soon Dong Lee
- Present address: R&D Center, BioPS Co., Ltd., Daedeuk Valley Campus, Hannam University, Daejon 34054, Republic of Korea
- Faculty of Science Education, Jeju National University, Jeju 63243, Republic of Korea
| | - Young-Ju Kim
- Ilseong Landscaping Co., Ltd., Jeju 63242, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daej on 34054, Republic of Korea
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33
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Yoon J, Maharjan S, Choi H. Polyphasic taxonomic analysis of Paracoccus ravus sp. nov., an alphaproteobacterium isolated from marine sediment. FEMS Microbiol Lett 2019; 366:5565046. [DOI: 10.1093/femsle/fnz184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/04/2019] [Indexed: 01/20/2023] Open
Abstract
ABSTRACTPolyphasic taxonomic analysis was performed on a novel marine bacterium, designated as strain YJ057T, isolated from marine sediment collected in the Republic of Korea. The strain was Gram-negative, beige-colored, facultatively anaerobic, coccoid or ovoid-shaped and nonmotile. Preliminary 16S rRNA gene sequence-based phylogenetic analysis indicated that this novel marine isolate belongs to the family Rhodobacteraceae of the class Alphaproteobacteria, and has the greatest (96.2%) sequence similarity to Paracoccus aestuariivivens GHD-30T. Major (>10%) fatty acids of strain YJ057T were C16:0 and C18:1 ω7c, G+C content in the genomic DNA of the strain was 63.6 mol% and the sole respiratory quinone was ubiquinone Q-10. It had phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and some unidentified components (three aminolipids, a glycolipid, a phospholipid and two lipids). As per the distinct phylogenetic position and combination of phenotypic and genotypic traits, the strain is considered a novel species of the genus Paracoccus, and the name Paracoccus ravus sp. nov. is proposed.
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 42601, Republic of Korea
| | - Sailesh Maharjan
- College of Pharmacy, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 42601, Republic of Korea
| | - Hyukjae Choi
- College of Pharmacy, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 42601, Republic of Korea
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34
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Kämpfer P, Irgang R, Poblete-Morales M, Fernández-Negrete G, Glaeser SP, Fuentes-Messina D, Avendaño-Herrera R. Paracoccus nototheniae sp. nov., isolated from a black rock cod fish (Notothenia coriiceps) from the Chilean Antarctic. Int J Syst Evol Microbiol 2019; 69:2794-2800. [DOI: 10.1099/ijsem.0.003557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Rute Irgang
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | - Matías Poblete-Morales
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | | | - Stefanie P. Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Derie Fuentes-Messina
- Fraunhofer Chile Research Foundation, Center for Systems Biotechnology, Santiago, Chile
| | - Ruben Avendaño-Herrera
- Universidad Andrés Bello, Centro de Investigación Marina Quintay (CIMARQ), Quintay, Chile
- Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Viña del Mar, Chile
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35
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Park S, Won SM, Yoon JH. Erythrobacter marisflavi sp. nov., isolated from isolated from estuary water. Int J Syst Evol Microbiol 2019; 69:2696-2702. [DOI: 10.1099/ijsem.0.003510] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Sung Min Won
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, Republic of Korea
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36
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Yoon J. Isolation and polyphasic identification of Tateyamaria armeniaca sp. nov. FEMS Microbiol Lett 2019; 366:5553465. [DOI: 10.1093/femsle/fnz182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/21/2019] [Indexed: 11/14/2022] Open
Abstract
ABSTRACTA novel alphaproteobacterium, designated KMU-156T, was isolated from seawater collected on the coast of Jeju Island, Republic of Korea, and its phylogenetic position was determined using a polyphasic taxonomic approach. Strain KMU-156T was Gram-stain-negative, strictly aerobic, apricot-colored, rod-shaped, non-motile and chemoorganoheterotrophic. Phylogenetic study based on the 16S rRNA gene sequence revealed that the novel bacterium belongs to the family ‘Rhodobacteraceae’, of the class Alphaproteobacteria, and that it possessed the greatest sequence similarity (98.2%) with Tateyamaria omphalii MKT107T. DNA–DNA hybridization values between strains KMU-156T, T. omphalii KCTC 12333T and Tateyamaria pelophila DSM 17270T were less than 70%. The major isoprenoid quinone of the novel isolate was ubiquinone-10 (Q-10) and the major (> 10%) cellular fatty acids were C16:0 and C18:1 ω7c. The genomic DNA G + C content of strain KMU-156T was 59.3 mol%. The polar lipid profile of the strain KMU-156T had phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and two unidentified lipids. From the discriminative taxonomic features, the strain is considered to represent a novel species of the genus Tateyamaria for which the name Tateyamaria armeniaca sp. nov. is proposed. The type strain of T. armeniaca sp. nov. is KMU-156T (= KCCM 90321T = NBRC 113460T).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 42601, Republic of Korea
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37
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The name Bradyrhizobiaceae Garrity et al. 2006 contains Nitrobacter Winogradsky 1892 (Approved Lists 1980), the nomenclatural type of the family Nitrobacteraceae Buchanan 1917 (Approved Lists 1980), is illegitimate and proposals to alter the wording of Rule 54 of the International Code of Nomenclature of Prokaryotes to clarify the fact that the family name Bradyrhizobiaceae Garrity et al. 2006 is replaced by the family name Nitrobacteraceae Buchanan 1917 (Approved Lists 1980) the only correct name. Int J Syst Evol Microbiol 2019; 69:2609-2611. [DOI: 10.1099/ijsem.0.003253] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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38
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Hetharua B, Min D, Liao H, Guo W, Lin X, Xu H, Tian Y. Sphingosinithalassobacter portus gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from surface seawater. Int J Syst Evol Microbiol 2019; 69:2834-2840. [PMID: 31274398 DOI: 10.1099/ijsem.0.003566] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative strain, designated FM6T, was isolated from surface seawater sampled at the port in Xiamen, PR China. Strain FM6T showed less than 96.3 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FM6T belonged to the family Sphingomonadaceae and was closely related to species of the genera Sphingomonas (96.3 %) and Stakelama (96.0 %). Ubiquinone-10 was the predominant respiratory quinone. Cells were motile with a single polar flagellum. Growth occurred at temperatures from 20 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.0 (optimum, pH 7.0) and in 0-4.0 % (w/v) NaCl (optimum, 1.0-1.5 %). Predominant polar lipids were sphingoglycolipid, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, five unidentified glycolipids and five unidentified polar lipids. The major fatty acids were summed feature 8 (containing C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of the type strain was 63.8 mol%. On the basis of the results of phylogenetic analysis, combined with phenotypic and chemotaxonomic data, strain FM6T is considered to represent a novel species in a new genus in the family Sphingomonadaceae for which the name Sphingosinithalassobacter portus gen. nov., sp. nov. is proposed. The type strain of Sphingosinithalassobacter portus gen. nov., sp. nov. is FM6T (=MCCC 1K03501T=JCM 32714T).
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Affiliation(s)
- Buce Hetharua
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Derong Min
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Hu Liao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Wei Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Xiaolan Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Hong Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, PR China
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39
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Liu YH, Fang BZ, Dong ZY, Li L, Mohamad OAA, Zhang YG, Egamberdieva D, Xiao M, Li WJ. Croceibacterium gen. nov., with description of Croceibacterium ferulae sp. nov., an endophytic bacterium isolated from Ferula sinkiangensis K. M. Shen and reclassification of Porphyrobacter mercurialis as Croceibacterium mercuriale comb. nov. Int J Syst Evol Microbiol 2019; 69:2547-2554. [PMID: 31215860 DOI: 10.1099/ijsem.0.003540] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel endophytic bacterium, designated strain SX2RGS8T, was isolated from the surface-sterilized roots of an endangered medicinal plant (Ferula sinkiangensis K. M. Shen) collected from Xinjiang, north-western PR China. The taxonomic position of the candidate was investigated using a polyphasic approach. Strain SX2RGS8T was found to be aerobic, Gram-stain-negative, oxidase-negative, catalase-positive and axiolitic-shaped. Strain SX2RGS8T grew at 4-45 °C (optimum, 28 °C), pH 4.0-10.0 (pH 7.0) and in the presence of 0-5 % (w/v) NaCl. The polar lipids detected for strain SX2RGS8T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified phosphoglycolipids, an unidentified phospholipid and unidentified lipids. The major respiratory quinone of strain SX2RGS8T was ubiquinone 10 and the major fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content was determined to be 66.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate belonged to the family Erythrobacteraceae and showed 99.2 % (Porphyrobacter mercurialis), 95.5 % (Porphyrobacter donghaensisi) and 95.4 % (Porphyrobacter colymbi) similarities to its closest relatives. The isolate contained carotenoids, but no bacteriochlorophyll a. On the basis of phenotypic, genotypic and phylogenetic data, strain SX2RGS8T represents a novel species of a novel genus in the family Erythrobacteraceae, for which the name Croceibacterium ferulae gen. nov., sp. nov. is proposed. The type strain is SX2RGS8T (=CGMCC 1.16402T=KCTC 62090T). In addition, Porphyrobacter mercurialis Coil et al. 2016 is proposed to be transferred to this new genus as Croceibacterium mercuriale comb. nov.
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Affiliation(s)
- Yong-Hong Liu
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Osama Abdalla Abdelshafy Mohamad
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China.,Environmental Science Department, Institute for Post Graduate Environmental Studies, Arish University, North-Sinai, 45511, Egypt
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Dilfuza Egamberdieva
- Department of Biotechnology and Microbiology, Faculty of Biology and Soil Science, National University of Uzbekistan, Tashkent 100174, Uzbekistan
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
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Yoon J, Ryu J. Altererythrobacter rubellus sp. nov., a marine alphaproteobacterium isolated from seawater. FEMS Microbiol Lett 2019; 366:5519857. [DOI: 10.1093/femsle/fnz131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-Gu, Daegu 42601, Republic of Korea
| | - Jaewon Ryu
- Department of Energy Convergence, Chosun University, 309 Pilmundaero, Dong-Gu, Gwangju 61452, Republic of Korea
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41
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Zhai TJ, Liu BT, Zhu RQ, Chen GJ, Du ZJ. Marinicauda salina sp. nov., isolated from a marine solar saltern. Int J Syst Evol Microbiol 2019; 69:2233-2238. [PMID: 31199230 DOI: 10.1099/ijsem.0.003441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic, oxidase-positive, motile, dimorphic rod bacterium, with a polar flagellum or a polar prostheca, designated as strain WD6-1T, was isolated from a sediment sample collected from a marine solar saltern located in Weihai, PR China. Growth of strain WD6-1T was observed at 15-45 °C (optimum, 37-40 °C). The pH range for growth was pH 6.0-9.5 (optimum, pH 7.0-7.5) while the NaCl concentration was 1.0-16.0 % (w/v; optimum, 5.0 %). The most closely related species was Marinicauda algicola (97.0 % 16S rRNA gene sequence similarity). The DNA G+C content of strain WD6-1T was 69.5 mol% and the sole respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acids (>10 %) of strain WD6-1T included summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C18 : 0 and C17 : 0, and the major polar lipids were glucuronopyranosyldiglyceride, monoglycosyldiglyceride and sulfo-quinovosyl diacylglycerol. Based on the results of phylogenetic, genotypic and phenotypic analyses, the isolate is representative of a new member of the genus Marinicauda, for which the name Marinicaudasalina sp. nov. is proposed. The type strain is WD6-1T (=KCTC 62348T=MCCC 1H00282T).
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Affiliation(s)
- Tong-Jie Zhai
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Bang-Tao Liu
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Ruo-Qi Zhu
- College of Marine Science, Shandong University, Weihai 264209, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University, Weihai 264209, PR China
- State key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zong-Jun Du
- State key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- College of Marine Science, Shandong University, Weihai 264209, PR China
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42
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Qu JH, Ma WW, Li HF, Wang XF, Lu BB, Luo Y. Altererythrobacter amylolyticus sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2019; 69:1231-1236. [DOI: 10.1099/ijsem.0.003299] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, motile, Gram-stain-negative bacterium, designated strain NS1T, was isolated from interfacial sediment from Taihu Lake, China. The strain formed yellow colonies on R2A medium. Cells were ovoid to rod-shaped and non-spore-forming. Growth occurred at 15–40 °C (optimum, 28 °C), at pH 5.0–10.5 (optimum, 6.5–7.5) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). Phylogenetic trees based on 16S rRNA gene sequences showed that strain NS1T represented a member of the genus
Altererythrobacter
and had the highest sequence similarity to
Altererythrobacter troitsensis
CCTCC AB 2015180T (97.1 %). The average nucleotide identity value between strain NS1T and the closest related strain based on their genomes was 78.6 %. The predominant ubiquinone was Q-10. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid, an unidentified glycolipid and six unidentified lipids. The genomic DNA G+C content was 66.6 mol%. On the basis of phenotypic and genotypic characteristics, strain NS1T represents a novel species of the genus
Altererythrobacter
, for which the name
Altererythrobacter
amylolyticus sp. nov. is proposed. The type strain is NS1T (=CGMCC 1.13679T=NBRC 113553T).
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Affiliation(s)
- Jian-Hang Qu
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, PR China
| | - Wen-Wen Ma
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, PR China
| | - Hai-Feng Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, PR China
| | - Xi-Feng Wang
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, PR China
| | - Bin-Bin Lu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450000, PR China
| | - Yu Luo
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450000, PR China
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43
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Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 2019; 8:e42535. [PMID: 30789345 PMCID: PMC6447387 DOI: 10.7554/elife.42535] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/21/2019] [Indexed: 11/13/2022] Open
Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
| | - Sebastian Hess
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
- Institute of ZoologyUniversity of CologneCologneGermany
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and GenomicsUniversité de MontréalMontrealCanada
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and GenomicsUniversité de MontréalMontrealCanada
| | - Edward Susko
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
- Department of Mathematics and StatisticsDalhousie UniversityHalifaxCanada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
| | - Andrew J Roger
- Department of Biochemistry and Molecular BiologyDalhousie UniversityHalifaxCanada
- Centre for Comparative Genomics and Evolutionary BioinformaticsDalhousie UniversityHalifaxCanada
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44
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Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E, Slamovits CH, Roger AJ. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. eLife 2019; 8. [PMID: 30789345 DOI: 10.7554/elife.42535.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/21/2019] [Indexed: 05/20/2023] Open
Abstract
The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Sebastian Hess
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Gertraud Burger
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - B Franz Lang
- Department of Biochemistry, Robert-Cedergren Center in Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Edward Susko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
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45
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Chen X, Liu J, Xu Y, Wang Y, Yan X. Erythrobacter nanhaiensis sp. nov., A Novel Member of the Genus Erythrobacter Isolated from the South China Sea. Curr Microbiol 2018; 76:57-62. [PMID: 30343327 DOI: 10.1007/s00284-018-1584-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/12/2018] [Indexed: 11/25/2022]
Abstract
A Gram-negative, motile, rod-shaped, aerobic bacterial strain with tufty polar flagella, JLT1363T, was isolated from the South China Sea. The bacteria formed yellow colonies on rich organic medium. The major cellular fatty acids present in JLT1363T were C18:1 ω7c and/or C18:1 ω6c (36.06%), C17:1 ω6c (17.04%), C14:0 2-OH (9.85%), and C16:0 (8.09%). The genome size was ~3.12 Mbps with a G+C content of 64.9%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JLT1363T fell within the genus Erythrobacter. The 16S rRNA gene sequence similarity between strain JLT1363T and the type strains of Erythrobacter species ranged from 95.0% (with Erythromicrobium ramosum) to 98.7% (with Erythrobacter lutimaris). The Average Nucleotide Identity (ANI) value between genome sequences of strain JLT1363T and Erythrobacter lutimaris KCTC 42109T was 82.2%. Strain JLT1363T lacked bacteriochlorophyll a, and the major polar lipids were sphingoglycolipids, diphosphatidylglycerol, phosphatidylcholine, and phosphatidylglycerol. Phylogenetic and phenotypic properties indicated that strain JLT1363T represents a novel species of the genus Erythrobacter, for which the name Erythrobacter nanhaiensis sp. nov. is proposed. The type strain is JLT1363T (=CGMCC 1.7293T = LMG 24872T).
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Affiliation(s)
- Xiao Chen
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, People's Republic of China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, People's Republic of China. .,State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361005, People's Republic of China.
| | - Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, People's Republic of China.,State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361005, People's Republic of China
| | - Yanan Wang
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, 361005, People's Republic of China.,Key Laboratory of Microbial Engineering at the Institute of Biology, Henan Academy of Sciences, Zhengzhou, 450008, People's Republic of China
| | - Xiaojun Yan
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
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46
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Hughes RA, Jin X, Zhang Y, Zhang R, Tran S, Williams PG, Lindsey JS, Miller ES. Genome sequence, metabolic properties and cyanobacterial attachment of Porphyrobacter sp. HT-58-2 isolated from a filamentous cyanobacterium–microbial consortium. Microbiology (Reading) 2018; 164:1229-1239. [DOI: 10.1099/mic.0.000706] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rebecca-Ayme Hughes
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
- 2Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA
| | - Xiaohe Jin
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Yunlong Zhang
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Ran Zhang
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Sabrina Tran
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
- 3Enloe Magnet High School, Raleigh, North Carolina 27610, USA
| | - Philip G. Williams
- 4Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96822-2275, USA
| | - Jonathan S. Lindsey
- 1Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-8204, USA
| | - Eric S. Miller
- 2Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695-7615, USA
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47
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Ma H, Ren H, Huang L, Luo Y. Altererythrobacter flavus sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2018; 68:2265-2270. [DOI: 10.1099/ijsem.0.002822] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hui Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems; Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Hao Ren
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems; Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Lingfeng Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems; Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
| | - Yuanrong Luo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems; Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, PR China
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48
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Lee H, Kim DU, Park S, Yoon JH, Ahn JH, Ka JO. Tardibacter chloracetimidivorans gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from an agricultural soil from Jeju Island in Republic of Korea. J Microbiol 2018; 56:324-330. [PMID: 29721829 DOI: 10.1007/s12275-018-7455-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 11/29/2022]
Abstract
A pale yellow bacterial strain, designated JJ-A5T, was isolated form an agricultural soil from Jeju Island in Republic of Korea. Cells of the strain were Gram-stain-negative, motile, flagellated and rod-shaped. The strain grew at 15-30°C, pH 6.0-9.0, and in the presence of 0-1.5% (w/v) NaCl. Growth occurred on R2A, but not on Luria-Bertani agar, nutrient agar, trypticase soy agar and MacConkey agar. The strain utilized alachlor as a sole carbon source for growth. The strain JJ-A5T showed 16S rRNA gene sequence similarities lower than 95.4% with members of the family Sphingomonadaceae. Phylogenetic analysis showed that the strain belongs to the family Sphingomonadaceae and strain JJ-A5T was distinctly separated from established genera of this family. The strain contained Q-10 as dominant ubiquinone and spermidine as major polyamine. The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c), 11-methyl C18:1ω7c, C16:0 and C14:0 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, and phosphatidylcholine. The DNA G + C content of the strain was 62.7 mol%. On the basis of the phenotypic, genomic and chemotaxonomic characteristics, strain JJ-A5T is considered to represent a novel genus and species within the family Sphingomonadaceae, for which the name Tardibacter chloracetimidivorans gen. nov., sp. nov. is proposed. The type strain of Tardibacter chloracetimidivorans is JJ-A5T (= KACC 19450T = NBRC 113160T).
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Affiliation(s)
- Hyosun Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dong-Uk Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jong-Ok Ka
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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49
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Dahal RH, Kim J. Altererythrobacter fulvus sp. nov., a novel alkalitolerant alphaproteobacterium isolated from forest soil. Int J Syst Evol Microbiol 2018. [DOI: 10.1099/ijsem.0.002697] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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50
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Dahal RH, Chaudhary DK, Kim J. Pinisolibacter ravus gen. nov., sp. nov., isolated from pine forest soil and allocation of the genera Ancalomicrobium and Pinisolibacter to the family Ancalomicrobiaceae fam. nov., and emendation of the genus Ancalomicrobium Staley 1968. Int J Syst Evol Microbiol 2018; 68:1955-1962. [PMID: 29683414 DOI: 10.1099/ijsem.0.002772] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated strain E9T, was isolated from pine forest soil of Kyonggi University (Suwon, Republic of Korea). Cells were facultatively anaerobic, Gram-staining-negative, catalase-negative, oxidase-positive, non-motile, non-spore-forming, rod-shaped and straw coloured. Prosthecae were absent. Glucose was fermented. The strain grew in the pH range of 5.0-10.0 (optimum, 6.5-8.5) and at 45 °C (optimum, 28-32 °C). E9T was sensitive to NaCl at low concentration and tolerated only 0.2 % NaCl (w/v). A phylogenetic analysis based on 16S rRNA gene sequences revealed that E9T formed a lineage within the phylum Proteobacteria that was distinct from various members of the order Rhizobiales, including Ancalomicrobium adetum DSM 4722T (94.76 % sequence similarity), 'Nitratireductor lucknowense' IITR-21 (92.72 %), Prosthecomicrobium hirschii 16T (92.66 %) and Kaistia soli DSM 19436T (92.53 %). The predominant isoprenoid quinone was Q-10. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidyl-N-methylethanolamine. Major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), and C16 : 0. The DNA G+C content of the type strain was 68.4 mol%. Polyphasic characterization indicated that strain E9T represented a novel species in a novel genus within a novel family, for which the name Pinisolibacter ravus gen. nov., sp. nov. is proposed. The type strain of Pinisolibacter ravus is E9T (=KEMB 9005-534T=KACC 19120T=NBRC 112686T). A formal allocation of the genus Ancalomicrobium to the family Ancalomicrobiaceae fam. nov. is also proposed.
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Affiliation(s)
- Ram Hari Dahal
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Dhiraj Kumar Chaudhary
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Jaisoo Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 16227, Republic of Korea
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