Streptomyces spinosus sp. nov. and Streptomyces shenzhenensis subsp. oryzicola subsp. nov. endophytic actinobacteria isolated from Jasmine rice and their genome mining for potential as antibiotic producers and plant growth promoters

Kaewkla, Onuma; Sukpanoa, Sudarat; Suriyachadkun, Chanwit; Chamroensaksi, Nitcha; Chumroenphat, Theeraphan; Franco, Christopher M. M.

doi:10.1007/s10482-022-01741-9

Cited by 9 publications

(8 citation statements)

References 87 publications

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“…The fatty acid profile of the strains is in agreement with reported Streptomyces species; for instance S. colonosanans MUSC 93J T , S. tardus P38-E01 T , S. spinosus SBTS01 T and S. shenzhenensis subsp. oryzicola W18L9 T , which contain anteiso-C 15:0 (21.3–26.6%) and iso-C 16:0 (15.1–30.0%) as major fatty acids ( Law et al, 2017 ; Králová et al, 2021 ; Kaewkla et al, 2022 ). The whole-cell sugars of G1–G3 were glucose and ribose ( Supplementary Figures S2A–C ).…”

Section: Resultsmentioning

confidence: 99%

“…The fatty acids profiles of G1-G3 are presented in Table 2. The major cellular fatty acids (percentage greater than 10%) in G1 and G2 were anteiso-C 15:0 (25.83 and 25.12%, respectively), iso-C 16:0 (18.28 and 15.90%) and C 16:0 (14.14 and 14.34%); ) and iso-C 16:0 (15.1-30.0%) as major fatty acids (Law et al, 2017;Králová et al, 2021;Kaewkla et al, 2022). The whole-cell sugars of G1-G3 were glucose and ribose (Supplementary Figures S2A-C).…”

Section: Chemotaxonomic Analysesmentioning

confidence: 99%

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Characterizing corn-straw-degrading actinomycetes and evaluating application efficiency in straw-returning experiments

Gong¹,

Yu²,

Hao³

et al. 2022

Front. Microbiol.

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Corn straw is an abundant lignocellulose resource and by-product of agricultural production. With the continuous increase in agricultural development, the output of corn straw is also increasing significantly. However, the inappropriate disposal of straw results in wasting of resources, and also causes a serious ecological crisis. Screening microorganisms with the capacity to degrade straw and understanding their mechanism of action is an efficient approach to solve such problems. For this purpose, our research group isolated three actinomycete strains with efficient lignocellulose degradation ability from soil in the cold region of China: Streptomyces sp. G1T, Streptomyces sp. G2T and Streptomyces sp. G3T. Their microbial properties and taxonomic status were assessed to improve our understanding of these strains. The three strains showed typical characteristics of the genus Streptomyces, and likely represent three different species. Genome functional annotation indicated that most of their genes were related to functions like carbohydrate transport and metabolism. In addition, a similar phenomenon also appeared in the COG and CAZyme analyses, with a large number of genes encoding carbohydrate-related hydrolases, such as cellulase, glycosidase and endoglucanase, which could effectively destroy the structure of lignocellulose in corn straw. This unambiguously demonstrated the potential of the three microorganisms to hydrolyze macromolecular polysaccharides at the molecular level. In addition, in the straw-returning test, the decomposing consortium composed of the three Streptomyces isolates (G123) effectively destroyed the recalcitrant bonds between the various components of straw, and significantly reduced the content of active components in corn straw. Furthermore, microbial diversity analysis indicated that the relative abundance of Proteobacteria, reportedly associated with soil antibiotic resistance and antibiotic degradation, was significantly improved with straw returning at both tested time points. The microbial diversity of each treatment was also dramatically changed by supplementing with G123. Taken together, G123 has important biological potential and should be further studied, which will provide new insights and strategies for appropriate treatment of corn straw.

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Section: Resultsmentioning

confidence: 99%

Section: Chemotaxonomic Analysesmentioning

confidence: 99%

Characterizing corn-straw-degrading actinomycetes and evaluating application efficiency in straw-returning experiments

Gong¹,

Yu²,

Hao³

et al. 2022

Front. Microbiol.

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“…A PCR-free library was prepared and sequenced as described by the previous protocol (Kaewkla et al, 2022 ). The reads were de novo assembled using Unicycler (0.4.8) (Wick et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

“…Whole-cell sugar of strain TML10 T was analyzed by the TLC method of Hasegawa et al ( 1983 ), and diaminopimelic acid (DAP) was detected by TLC using the method of O'Donnell et al ( 1985 ). The phospholipids were analyzed as described by Minnikin et al ( 1984 ) and Komagata and Suzuki ( 1987 ) using six spray reagents according to the previous study (Kaewkla et al, 2022 ). Extraction and purification of isoprenoid quinones have followed the method of Minnikin et al ( 1984 ) with analysis of the samples as described by Kaewkla et al ( 2022 ).…”

Section: Methodsmentioning

confidence: 99%

Description of Streptomyces naphthomycinicus sp. nov., an endophytic actinobacterium producing naphthomycin A and its genome insight for discovering bioactive compounds

Kaewkla,

Perkins,

Thamchaipenet

et al. 2024

Front. Microbiol.

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Endophytic actinobacteria are a group of bacteria living inside plant tissue without harmful effects, and benefit the host plant. Many can inhibit plant pathogens and promote plant growth. This study aimed to identify a strain of Streptomyces as a novel species and study its antibiotics production. An endophytic actinobacterium, strain TML10T was isolated from a surface-sterilized leaf of a Thai medicinal plant (Terminalia mucronata Craib and Hutch). As a result of a polyphasic taxonomy study, strain TML10T was identified as a member of the genus Streptomyces. Strain TML10T was an aerobic actinobacterium with well-developed substrate mycelia with loop spore chains and spiny surface. Chemotaxonomic data, including cell wall components, major menaquinones, and major fatty acids, confirmed the affiliation of strain TML10T to the genus Streptomyces. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with a genome comparison study, allowed the genotypic and phenotypic differentiation of strain TML10T and the closest related type strains. The digital DNA-DNA hybridization (dDDH), Average nucleotide identity Blast (ANIb), and ANIMummer (ANIm) values between strain TML10T and the closest type strain, Streptomyces musisoli CH5-8T were 38.8%, 88.5%, and 90.8%, respectively. The name proposed for the new species is Streptomyces naphthomycinicus sp. nov. (TML10T = TBRC 15050T = NRRL B-65638T). Strain TML10T was further studied for liquid and solid-state fermentation of antibiotic production. Solid-state fermentation with cooked rice provided the best conditions for antibiotic production against methicillin-resistant Staphylococcus aureus. The elucidation of the chemical structures from this strain revealed a known antimicrobial agent, naphthomycin A. Mining the genome data of strain TML10T suggested its potential as a producer of antbiotics and other valuable compounds such as ε-Poly-L-lysine (ε-PL) and arginine deiminase. Strain TML10T contains the arcA gene encoding arginine deiminase and could degrade arginine in vitro.

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“…All data were obtained during this study except for those for 'S. spinosus', which were obtained from Kaewkla et al[35], S. musisoli which were obtained from Duangupama et al[36] and 'S. argyrophyllae' which were obtained from Mo et al[37].…”

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confidence: 99%

Streptomyces pyxinae sp. nov. and Streptomyces pyxinicus sp. nov. isolated from lichen Pyxine cocoes (Sw.) Nyl.

Somphong,

Polyiam,

Suriyachadkun

et al. 2024

International Journal of Systematic and Evolutionary Microbiology

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Two novel actinobacteria, designated as LP05-1T and LP11T, were isolated from the lichen Pyxine cocoes (Sw.) Nyl. collected in Bangkok, Thailand. Genotypic and phenotypic analyses revealed that both strains represented members of the genus Streptomyces. The 16S rRNA gene of LP05-1T showed the highest similarity to the genome of Streptomyces gelaticus (98.41 %), while the 16S rRNA gene of LP11T was most similar to that of Streptomyces cinerochromogenes (98.93 %). The major menaquinones in LP05-1T were MK-9(H8), MK-9(H6), MK-9(H4) and MK-9(H2), and in LP11T, they were MK-9(H8) and MK-9(H6). Both strains exhibited the major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, with LP05-1T also possessing iso-C17 : 0. The polar lipids of LP05-1T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified lipid, while those of LP11T consisted of phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid and an unidentified glycolipid. The digital DNA–DNA hybridisation (dDDH) and average nucleotide identity (ANI) values indicated that both strains are distinct from each other with values below 70 and 95 %, respectively. dDDH, ANI by blast (ANIb) and ANI by MUMmer (ANIm) values between LP05-1T and its closely related type strains were 26.07–26.80 %, 81.24–82.01 % and 86.82–86.96 %, respectively, while those for LP11T and its closely related type strains were 30.70–31.70 %, 84.09–85.31 % and 88.02–88.39 %, respectively. The results of the taxonomic investigation, including dDDH and ANI values, indicate that LP05-1T and LP11T are novel type strains of two novel species within the genus Streptomyces. The names proposed are Streptomyces pyxinae sp. nov. for strain LP05-1T (=TBRC 15494T, =NBRC 115434T) and Streptomyces pyxinicus sp. nov. for strain LP11T (=TBRC 15493T, =NBRC 115421T).

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Streptomyces spinosus sp. nov. and Streptomyces shenzhenensis subsp. oryzicola subsp. nov. endophytic actinobacteria isolated from Jasmine rice and their genome mining for potential as antibiotic producers and plant growth promoters

Cited by 9 publications

References 87 publications

Characterizing corn-straw-degrading actinomycetes and evaluating application efficiency in straw-returning experiments

Characterizing corn-straw-degrading actinomycetes and evaluating application efficiency in straw-returning experiments

Description of Streptomyces naphthomycinicus sp. nov., an endophytic actinobacterium producing naphthomycin A and its genome insight for discovering bioactive compounds

Streptomyces pyxinae sp. nov. and Streptomyces pyxinicus sp. nov. isolated from lichen Pyxine cocoes (Sw.) Nyl.

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