{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T16:07:32Z","timestamp":1753891652170,"version":"3.41.2"},"reference-count":51,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T00:00:00Z","timestamp":1739923200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>The microbial community in desert ecosystems is a vital and highly active component. <jats:italic>Streptomyces<\/jats:italic>, one of the dominant genera within this community, exhibits significant capabilities in metabolic degradation and the synthesis of secondary metabolites.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>To investigate the metabolic potential of <jats:italic>Streptomyces desertis<\/jats:italic>, two strains of <jats:italic>Streptomyces<\/jats:italic> were isolated from rhizosphere soil samples of <jats:italic>Populus euphratica<\/jats:italic> in the Taklimakan Desert during the initial phase of this study, TRM 70351<jats:sup>T<\/jats:sup> and TRM 70361<jats:sup>T<\/jats:sup>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The identification of these strains as belonging to the genus <jats:italic>Streptomyces<\/jats:italic> was confirmed through 16S rRNA sequencing. All calculated Average Nucleotide Identity (ANI) values were below the 95% cut-off recommended for distinguishing distinct species, and the estimated digital DNA-DNA hybridization (dDDH) values were all below the suggested threshold of 70% for species delineation. Results from phylogenetic, genomic, phenotypic, and chemotaxonomic analyses confirmed that TRM 70351<jats:sup>T<\/jats:sup> and TRM 70361<jats:sup>T<\/jats:sup> represent two new species within the genus <jats:italic>Streptomyces<\/jats:italic>, designated as <jats:italic>Streptomyces solitudini<\/jats:italic>s sp. nov. and <jats:italic>Streptomyces rubellus<\/jats:italic> sp. nov. The type strain for <jats:italic>Streptomyces solitudinis<\/jats:italic> sp. nov. is TRM 70351<jats:sup>T<\/jats:sup> ( = CCTCC AA 2020049<jats:sup>T<\/jats:sup> = LMG 32404<jats:sup>T<\/jats:sup>), while the type strain for <jats:italic>Streptomyces rubellus<\/jats:italic> sp. nov. is TRM 70361<jats:sup>T<\/jats:sup> ( = CCTCC AA 2020043<jats:sup>T<\/jats:sup> = JCM 35793<jats:sup>T<\/jats:sup>). Notably, Among the identified gene clusters of TRM 70351<jats:sup>T<\/jats:sup>, cluster 12.1 was predicted to be the biosynthetic gene cluster responsible for producing the aminoglycoside compound streptomycin, exhibiting a similarity of 55%. In this study, HSQC-TOCSY was employed to detect the presence of aminoglycosides in fermentation medium No. 1, while LC-MS\/MS was utilized to analyze the molecular fragments of neomycin and streptomycin in the alkaline aqueous phase sample of the fermentation product. The mixture was eluted using methanol and ammonia water in a 3:1 ratio, leading to the further separation of the compounds daidzein and Tridec-1-ene.<\/jats:p><\/jats:sec><jats:sec><jats:title>Discussion<\/jats:title><jats:p>This study has enhanced the species resources of <jats:italic>Streptomyces deserticum<\/jats:italic> and the diversity of aminoglycoside compound-producing bacteria. TRM 70351<jats:sup>T<\/jats:sup> exhibited unique metabolic potential, indicating that further studies could be conducted in the future.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2025.1530786","type":"journal-article","created":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T16:54:27Z","timestamp":1739984067000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Isolated from Populus euphratica rhizosphere soil, and mining their metabolites"],"prefix":"10.3389","volume":"16","author":[{"given":"Jia-xin","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi-huang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinrong","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li-li","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao-xia","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2025,2,19]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1038\/s41429-017-0012-0","article-title":"Asenjonamides A-C, antibacterial metabolites isolated from Streptomyces asenjonii strain KNN 42.f from an extreme-hyper arid Atacama desert soil.","volume":"71","author":"Abdelkader","year":"2018","journal-title":"J. Antibiot."},{"key":"B2","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1021\/cb3005116","article-title":"Aminoglycoside antibiotics in the 21st century.","volume":"8","author":"Becker","year":"2013","journal-title":"ACS Chem. Biol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"2563","DOI":"10.1111\/j.1420-9101.2009.01869.x","article-title":"Correction of a bootstrap approach to testing for evolution along lines of least resistance.","volume":"22","author":"Berner","year":"2009","journal-title":"J. Evol. Biol."},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1016\/j.jep.2022.115046","article-title":"In vitro and in silico evaluation of antimicrobial properties of Delphinium cashmerianum L., a medicinal herb growing in Kashmir.","volume":"291","author":"Bhat","year":"2022","journal-title":"India. J. Ethnopharmacol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"W29","DOI":"10.1093\/nar\/gkab335","article-title":"AntiSmash 6.0: Improving cluster detection and comparison capabilities.","volume":"49","author":"Blin","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"B6","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1099\/ijsem.0.002516","article-title":"Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes.","volume":"68","author":"Chun","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B7","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1099\/00221287-100-2-221","article-title":"Distribution of menaquinones in actinomycetes and corynebacteria.","volume":"100","author":"Collins","year":"1977","journal-title":"J. Gen. Microbiol."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1016\/j.margen.2022.100949","article-title":"Complete genome analysis reveals secondary metabolite biosynthetic capabilities of Streptomyces sp. R527F isolated from the Arctic Ocean.","volume":"63","author":"Duan","year":"2022","journal-title":"Mar. Genomics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1146\/annurev.mi.32.100178.001153","article-title":"Formation, properties, and germination of actinomycete spores.","volume":"32","author":"Ensign","year":"1978","journal-title":"Annu. Rev. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: A maximum likelihood approach.","volume":"17","author":"Felsenstein","year":"1981","journal-title":"J. Mol. Evol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1038\/nrmicro2649","article-title":"Microbial ultraviolet sunscreens.","volume":"9","author":"Gao","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"journal-title":"Methods for General and Molecular Bacteriology.","year":"1994","author":"Gerhardt","key":"B12"},{"key":"B13","first-page":"32","article-title":"Optimization of streptomycin-producing medium for Streptomyces griseus.","volume":"18","author":"Han","year":"2008","journal-title":"Chinese Brewing"},{"key":"B14","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1007\/978-1-4939-1720-4_6","article-title":"The Illumina-solexa sequencing protocol for bacterial genomes.","volume":"1231","author":"Hu","year":"2015","journal-title":"Methods Mol. Biol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1101\/gr.214346.116","article-title":"ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter.","volume":"27","author":"Jackman","year":"2017","journal-title":"Genome Res."},{"journal-title":"Inter-Society Color Council - National Bureau of Standards Color Name Charts Illustrated with Centroid Colors.","year":"1964","author":"Kelly","key":"B16"},{"key":"B17","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1099\/00207713-49-2-507","article-title":"Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov.","volume":"49","author":"Kim","year":"1999","journal-title":"Int. J. Syst. Bacteriol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/BF01731581","article-title":"A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.","volume":"16","author":"Kimura","year":"1980","journal-title":"J. Mol. Evol."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.005370","article-title":"Resolution of housekeeping gene sequences used in MLSA for the genus Streptomyces and reclassification of Streptomyces anthocyanicus and Streptomyces tricolor as heterotypic synonyms of Streptomyces violaceoruber.","volume":"72","author":"Komaki","year":"2022","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular evolutionary genetics analysis across computing platforms.","volume":"35","author":"Kumar","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"B21","first-page":"8202","article-title":"Optimization of streptomycin-producing fermentation medium of Streptomyces griseus.","author":"Li","year":"2013","journal-title":"Sci. Technol. Eng."},{"key":"B22","first-page":"50","article-title":"Application of nuclear magnetic resonance technique in the structural study of aminoglycoside antibiotics.","volume":"1","author":"Li","year":"2017","journal-title":"J. Changzhou Univer."},{"key":"B23","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1007\/s10482-018-1163-0","article-title":"Streptomyces desertarenae sp. nov., a novel actinobacterium isolated from a desert sample.","volume":"112","author":"Li","year":"2019","journal-title":"Antonie van Leeuwenhoek"},{"key":"B24","first-page":"328","article-title":"A new process for isolation and extraction of kanamycin from fermentation broth.","volume":"6","author":"Li","year":"2002","journal-title":"Chin. J. Antibiotics"},{"key":"B25","doi-asserted-by":"publisher","first-page":"203","DOI":"10.13995\/j.cnki.11-1802\/ts.023958","article-title":"Determination of nine aminoglycoside residues in honey by ultra performance liquid chromatography-tandem mass spectrometry.","volume":"18","author":"Ma","year":"2020","journal-title":"Food Fermentation Industry"},{"key":"B26","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1111\/1758-2229.12003","article-title":"Evidence of species recruitment and development of hot desert hypolithic communities.","volume":"5","author":"Makhalanyane","year":"2013","journal-title":"Environ. Microbiol. Rep"},{"key":"B27","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/0378-1119(92)90558-7","article-title":"Actinomycetes as agents of biodegradation in the environment\u2013A review.","volume":"115","author":"McCarthy","year":"1992","journal-title":"Gene"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1101\/pdb.top32","article-title":"Maximum parsimony method for phylogenetic prediction.","author":"Mount","year":"2008","journal-title":"CSH Protoc."},{"key":"B29","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1007\/s00792-012-0454-z","article-title":"Life at the hyperarid margin: Novel bacterial diversity in arid soils of the Atacama desert.","volume":"16","author":"Neilson","year":"2012","journal-title":"Chile. Extremophiles"},{"key":"B30","doi-asserted-by":"publisher","first-page":"6025","DOI":"10.1080\/14786419.2020.1815737","article-title":"Anticancer and antimicrobial compounds from Croton caudatus Gieseler and Eurya acuminata DC: Two edible plants used in the traditional medicine of the Kuki tribes.","volume":"35","author":"Neipihoi","year":"2021","journal-title":"Nat. Prod. Res."},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.3390\/biom14091084","article-title":"Genome mining for Diazo-synthesis-related genes in Streptomyces sp. CS057 unveiled the cryptic biosynthetic gene Cluster crx for the novel 3,4-AHBA-derived compound Crexazone 2.","volume":"14","author":"Prado-Alonso","year":"2024","journal-title":"Biomolecules"},{"key":"B32","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1128\/jb.56.1.107-114.1948","article-title":"The utilization of carbon compounds by some Actinomycetales as an aid for species determination.","volume":"56","author":"Pridham","year":"1948","journal-title":"J. Bacteriol."},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1038\/162820a0","article-title":"Utilization of wheat bran for streptomycin production by S. griseus.","volume":"162","author":"Rao","year":"1948","journal-title":"Nature"},{"key":"B34","doi-asserted-by":"publisher","first-page":"1365","DOI":"10.1099\/ijs.0.056614-0","article-title":"Streptomyces barkulensis sp. nov., isolated from an estuarine lake.","volume":"64","author":"Ray","year":"2014","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.006300","article-title":"Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes.","volume":"74","author":"Riesco","year":"2024","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B36","doi-asserted-by":"publisher","first-page":"1424","DOI":"10.1080\/14786419.2022.2140153","article-title":"Phytochemical analysis of Pithecellobium dulce (Roxb) Benth Bark via UPLC-ESI-MS\/MS and evaluation of its biological activity.","volume":"38","author":"Saeed Kotb","year":"2024","journal-title":"Nat. Prod. Res."},{"key":"B37","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1093\/oxfordjournals.molbev.a040454","article-title":"The neighbor-joining method: A new method for reconstructing phylogenetic trees.","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B39","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1099\/00207713-16-3-313","article-title":"Methods for characterization of Streptomyces species.","volume":"16","author":"Shirling","year":"1966","journal-title":"Int. J. Syst. Bacteriol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1084\/jem.63.1.95","article-title":"The colony morphology of tubercle bacilli : V. influence of the Ph of the culture medium on colony form.","volume":"63","author":"Smithburn","year":"1936","journal-title":"J. Exp. Mede"},{"key":"B41","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1016\/j.steroids.2004.03.015","article-title":"Synthesis of phytoestrogenic isoflavonoid disulfates.","volume":"69","author":"Soidinsalo","year":"2004","journal-title":"Steroids"},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.1016\/j.syapm.2020.126153","article-title":"Streptomyces alkaliterrae sp. nov., isolated from an alkaline soil, and emended descriptions of Streptomyces alkaliphilus. Streptomyces calidiresistens and Streptomyces durbertensis.","volume":"43","author":"\u015awiecimska","year":"2020","journal-title":"Syst. Appl. Microbiol."},{"key":"B43","first-page":"57","article-title":"Mezhrodovaia kon\u201diugatsiia Escherichia coli-Streptomyces kak sposob peredachi kon\u201diugativnykh plazmid v produtsenty antibiotikov khlortetratsiklina i bialafosa [Intergeneric Escherichia coli-Streptomyces conjugation as a means for the transfer of conjugative plasmids into producers of antibiotics chlortetracycline and bialaphos].","volume":"30","author":"Tabakov","year":"1994","journal-title":"Genetika"},{"journal-title":"The Actinomycetes. A Summary of Current Knowledge.","year":"1967","author":"Waksman","key":"B44"},{"key":"B45","doi-asserted-by":"publisher","first-page":"1807","DOI":"10.1007\/s10482-018-1069-x","article-title":"Streptomyces carminius sp. nov., a novel actinomycete isolated from Sophora alopecuroides in Xinjiang. China.","volume":"111","author":"Wang","year":"2018","journal-title":"Antonie van Leeuwenhoek."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.765531","article-title":"Actinobacteria from desert: Diversity and biotechnological applications.","volume":"12","author":"Xie","year":"2021","journal-title":"Front. Microbiol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1016\/j.heares.2011.05.008","article-title":"New developments in aminoglycoside therapy and ototoxicity.","volume":"281","author":"Xie","year":"2011","journal-title":"Hear. Res."},{"key":"B48","first-page":"1050","article-title":"Mass spectrometry analysis of 14 aminoglycoside antibiotics.","volume":"8","author":"Yang","year":"2006","journal-title":"J. Pharm. Anal."},{"key":"B49","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1007\/s10482-017-0844-4","article-title":"A large-scale evaluation of algorithms to calculate average nucleotide identity.","volume":"110","author":"Yoon","year":"2017","journal-title":"Antonie van Leeuwenhoek"},{"key":"B50","doi-asserted-by":"publisher","first-page":"3635","DOI":"10.1099\/ijsem.0.003047","article-title":"Streptomyces durbertensis sp. nov., isolated from saline-alkali soil.","volume":"68","author":"Yu","year":"2018","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1038\/s41429-018-0080-9","article-title":"Streptomyces qaidamensis sp. nov., isolated from sand in the Qaidam Basin. China.","volume":"71","author":"Zhang","year":"2018","journal-title":"J. Antibiot (Tokyo)"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1530786\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T16:54:33Z","timestamp":1739984073000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1530786\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,19]]},"references-count":51,"alternative-id":["10.3389\/fmicb.2025.1530786"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1530786","relation":{},"ISSN":["1664-302X"],"issn-type":[{"type":"electronic","value":"1664-302X"}],"subject":[],"published":{"date-parts":[[2025,2,19]]},"article-number":"1530786"}}