Agromyces silvae sp. nov., Rathayibacter soli sp. nov., and Nocardioides terrisoli sp. nov., Isolated from Soil
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Three Gram-stain-positive, aerobic, rod-shaped, and non-motile bacteria, labelled as W11T , SW19T , and YR1T , were isolated from soil, and performed their polyphasic taxonomic investigation. The phylogenetic and 16S rRNA gene sequence analysis showed that strains W11T , SW19T , and YR1T belonged to the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Strain W11T was closely affiliated with Agromyces cavernae SYSU K20354T (98.1%), strain SW19T showed the closest affiliation with Rathayibacter rubneri ZW T2_19T (97.0%), and strain YR1T was most closely related to Nocardioides marmorisolisilvae KIS18-7T (98.0%). The genome sizes of strains W11T , SW19T , and YR1T were 4,181,720 bp, 4,740,677 bp, and 4,228,226 bp, respectively, with DNA G+C contents of 70.5%, 64.2%, and 69.7%, respectively. Average nucleotide identity and digital DNA–DNA hybridization values of W11T , SW19T , and YR1T with their respective reference species were <79.6% and <23.6%, respectively. The predominant cellular fatty acids detected in strain W11T were anteiso-C15:0, isoC16:0, and anteiso-C17:0. In strain SW19T , they were summed feature 9 (C16:0 10-methyl and/or isoC17:1ω 9c), anteiso-C17:0, and anteiso-C15:0. Strain YR1T exhibited C18:1ω 9c, C18:0 10-methyl, TBSA, and anteiso-C15:0 as its major cellular fatty acids. Overall, the polyphasic taxonomic comparisons indicated that strains W11T , SW19T , and YR1T represent novel species within the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Accordingly, we propose the names Agromyces silvae sp. nov., with the type strain W11T (=KCTC 49818T =NBRC 115999T ), Rathayibacter soli sp. nov., with the type strain SW19T (=KCTC 49860T =NBRC 116108T ), and Nocardioides terrisoli sp. nov., with the type strain YR1T (=KCTC 49863T =NBRC 116165T ).
Abstract
Three Gram-stain-positive, aerobic, rod-shaped, and non-motile bacteria, labelled as W11T , SW19T , and YR1T , were isolated from soil, and performed their polyphasic taxonomic investigation. The phylogenetic and 16S rRNA gene sequence analysis showed that strains W11T , SW19T , and YR1T belonged to the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Strain W11T was closely affiliated with Agromyces cavernae SYSU K20354T (98.1%), strain SW19T showed the closest affiliation with Rathayibacter rubneri ZW T2_19T (97.0%), and strain YR1T was most closely related to Nocardioides marmorisolisilvae KIS18-7T (98.0%). The genome sizes of strains W11T , SW19T , and YR1T were 4,181,720 bp, 4,740,677 bp, and 4,228,226 bp, respectively, with DNA G+C contents of 70.5%, 64.2%, and 69.7%, respectively. Average nucleotide identity and digital DNA–DNA hybridization values of W11T , SW19T , and YR1T with their respective reference species were <79.6% and <23.6%, respectively. The predominant cellular fatty acids detected in strain W11T were anteiso-C15:0, isoC16:0, and anteiso-C17:0. In strain SW19T , they were summed feature 9 (C16:0 10-methyl and/or isoC17:1ω 9c), anteiso-C17:0, and anteiso-C15:0. Strain YR1T exhibited C18:1ω 9c, C18:0 10-methyl, TBSA, and anteiso-C15:0 as its major cellular fatty acids. Overall, the polyphasic taxonomic comparisons indicated that strains W11T , SW19T , and YR1T represent novel species within the genera Agromyces, Rathayibacter, and Nocardioides, respectively. Accordingly, we propose the names Agromyces silvae sp. nov., with the type strain W11T (=KCTC 49818T =NBRC 115999T ), Rathayibacter soli sp. nov., with the type strain SW19T (=KCTC 49860T =NBRC 116108T ), and Nocardioides terrisoli sp. nov., with the type strain YR1T (=KCTC 49863T =NBRC 116165T ).
참고문헌 (44)
- Gledhill WE, "Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia", Appl. Microbiol, 18, pp.340~349 (1969)
- Zgurskaya H, "Rathayibacter gen. nov., including the species Rathayibacter rathayi comb. nov., Rathayibacter tritici comb. nov., Rathayibacter iranicus comb. nov., and six strains from annual grasses", Int. J. Syst. Evol. Microbiol, 43, pp.143~149 (1993)
- Prauser H, "Nocardioides, a new genus of the order Actinomycetales", Int. J. Syst. Evol. Microbiol, 26, pp.58~65 (1976)
- Lee JC, "Agromyces humi sp. nov., actinobacterium isolated from farm soil", Int. J. Syst. Evol. Microbiol, 70, pp.5032~5039 (2020)
- Fang BZ, "Agromyces cavernae sp. nov., a novel member of the genus Agromyces isolated from a karstic cave in Shaoguan", Int. J. Syst. Evol. Microbiol, 72, pp.005503~ (2022)
- Heo J, "Agromyces protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis", Int. J. Syst. Evol. Microbiol, 70, pp.1259~1265 (2020)
- Yi Bf, "Agromyces agglutinans sp. nov., isolated from saline lake sediment", Int. J. Syst. Evol. Microbiol, 72, pp.005208~ (2022)
- Park EJ, "Agromyces atrinae sp. nov., isolated from fermented seafood", Int. J. Syst. Evol. Microbiol, 60, pp.1056~1059 (2010)
- Chen Z, "Agromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta", Int. J. Syst. Evol. Microbiol, 66, pp.2278~2283 (2016)
- Yoon JH, "Nocardioides aquiterrae sp. nov., isolated from groundwater in Korea", Int. J. Syst. Evol. Microbiol, 54, pp.71~75 (2004)
- Jiang ZK, "Marmoricola endophyticus sp. nov., an endophytic actinobacterium isolated from Thespesia populnea", Int. J. Syst. Evol. Microbiol, 67, pp.4379~4384 (2017)
- Li FN, "Marmoricola mangrovicus sp. nov., an endophytic actinobacterium isolated from Kandelia candel", Int. J. Syst. Evol. Microbiol, 69, pp.1343~1349 (2019)
- Stoll DA, "Rathayibacter rubneri sp. nov. isolated from Allium cepa var. Rijnsburger, an onion landrace", Int. J. Syst. Evol. Microbiol, 73, pp.005811~ (2023)
- Suzuki KI, "Agromyces mediolanus sp. nov., nom. rev., comb. nov., a species for “Corynebacterium mediolanum” Mamoli 1939 and for some aniline-assimilating bacteria which contain 2, 4-diaminobutyric acid in the cell wall peptidoglycan", Int. J. Syst. Evol. Microbiol, 46, pp.88~93 (1996)
- Chaudhary DK, "Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oilcontaminated soil", Int. J. Syst. Evol. Microbiol, 67, pp.2731~2738 (2017)
- Frank JA, "Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes", Appl. Environ. Microbiol, 74, pp.2461~2470 (2008)
- Yoon SH, "Introducing EzBioCloud : a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies", Int. J. Syst. Evol. Microbiol, 67, pp.1613~1617 (2017)
- Kumar S, "MEGA X : molecular evolutionary genetics analysis across computing platforms", Mol. Biol. Evol, 35, pp.1547~ (2018)
- Felsenstein J, "Evolutionary trees from DNA sequences : a maximum likelihood approach", J. Mol. Evol, 17, pp.368~376 (1981)
- Saitou N, "The neighbor-joining method : a new method for reconstructing phylogenetic trees", Mol. Biol. Evol, 4, pp.406~425 (1987)
- Fitch WM, "Toward defining the course of evolution : minimum change for a specific tree topology", Syst. Biol, 20, pp.406~416 (1971)
- Felsenstein J, "Confidence limits on phylogenies : an approach using the bootstrap", Evolution, 39, pp.783~791 (1985)
- Kimura M, "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences", J. Mol. Evol, 16, pp.111~120 (1980)
- Lee I, "ContEst16S : an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences", Int. J. Syst. Evol. Microbiol, 67, pp.2053~2057 (2017)
- Zhang Z, "A greedy algorithm for aligning DNA sequences", J. Comput. Biol, 7, pp.203~214 (2000)
- Tatusova T, "NCBI prokaryotic genome annotation pipeline", Nucleic Acids Res, 44, pp.6614~6624 (2016)
- Aziz RK, "The RAST Server : rapid annotations using subsystems technology", BMC Genomics, 9, pp.75~ (2008)
- Huerta-Cepas J, "eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences", Nucleic Acids Res, 44, pp.D286~D293 (2016)
- Sun J, "OrthoVenn3 : an integrated platform for exploring and visualizing orthologous data across genomes", Nucleic Acids Res, 51, pp.W397~W403 (2023)
- Meier-Kolthoff JP, "Genome sequence-based species delimitation with confidence intervals and improved distance functions", BMC Bioinformatics, 14, pp.60~ (2013)
- Yoon SH, "A large-scale evaluation of algorithms to calculate average nucleotide identity", Antonie Van Leeuwenhoek, 110, pp.1281~1286 (2017)
- Blin K, "antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation", Nucleic Acids Res, 51, pp.W46~W50 (2023)
- Meier-Kolthoff JP, "TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy", Nat. Commun, 10, pp.2182~ (2019)
- Lee H, "Paenibacillus caseinilyticus sp. nov., isolated forest soil", Int. J. Syst. Evol. Microbiol, 73, pp.006171~ (2023)
- Smibert RM, "Methods for general and molecular bacteriology", pp.607~654 (1994), ASM Press
- Bacterial identification by gas chromatographic analysis of fatty acid methyl esters (GC-FAME), "Sasser M", MIDI Inc, ~, pp.MIDI Technical Note 101 (1990)
- Staneck JL, "Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography", Appl. Microbiol, 28, pp.226~231 (1974)
- Collins MD, "Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication", Microbiol. Rev, 45, pp.316~354 (1981)
- Minnikin DE, "An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids", J. Microbiol. Methods, 2, pp.233~241 (1984)
- Komagata K, "4 Lipid and cell-wall analysis in bacterial systematics", Method Microbiol, 19, pp.161~207 (1988)
- Stackebrandt E, "Taxonomic parameters revisited : tarnished gold standards", Microbiol. Today, 33, pp.152~155 (2006)
- Yarza P, "The all-species living tree project : a 16S rRNA-based phylogenetic tree of all sequenced type strains", Syst. Appl. Microbiol, 31, pp.241~250 (2008)
- Richter M, "Shifting the genomic gold standard for the prokaryotic species definition", Proc. Natl. Acad. Sci. USA, 106, pp.19126~19131 (2009)
- Wayne LG, "Report of the ad hoc committee on reconciliation of approaches to bacterial systematics", Int. J. Syst. Evol. Microbiol, 37, pp.463~464 (1987)