Diversity of the culturable lichen-derived actinobacteria and the taxonomy of Streptomyces parmotrematis sp. nov.

Somphong, Achiraya; Poengsungnoen, Vasun; Buaruang, Kawinnat; Suriyachadkun, Chanwit; Sripreechasak, Paranee; Tanasupawat, Somboon; Phongsopitanun, Wongsakorn

doi:10.1007/s10482-022-01744-6

“…Analysis of the actinobacterial community in lichens through a metagenomics approach revealed that, overall, 56,505 observed OTUs were assigned to actinobacteria (13.21% of total bacterial OTUs). Many of the actinobacterial OTUs correspond with previous studies 17,40,41 . Several genera of actinobacterial OTUs were found in all the lichen samples studied here.…”

Section: Discussionsupporting

confidence: 87%

Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria

Weeraphan

¹

,

Somphong

²

,

Poengsungnoen

³

et al. 2023

Sci Rep

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Ten samples of tropical lichens collected from Doi Inthanon, Thailand, were explored for the diversity of their bacterial microbiomes through 16S rRNA-based metagenomics analysis. The five predominant lichen-associated bacteria belonged to the phyla Proteobacteria (31.84%), Planctomycetota (17.08%), Actinobacteriota (15.37%), Verrucomicrobiota (12.17%), and Acidobacteriota (7.87%). The diversity analysis metric showed that Heterodermia contained the highest bacterial species richness. Within the lichens, Ramalina conduplicans and Cladonia rappii showed a distinct bacterial community from the other lichen species. The community of lichen-associated actinobacteria was investigated as a potential source of synthesized biologically active compounds. From the total Operational Taxonomic Units (OTUs) found across the ten different lichen samples, 13.21% were identified as actinobacteria, including the rare actinobacterial genera that are not commonly found, such as Pseudonocardia, Kineosporia, Dactylosporangium, Amycolatopsis, Actinoplanes, and Streptosporangium. Evaluation of the pretreatment method (heat, air-drying, phenol, and flooding) and isolation media used for the culture-dependent actinobacterial isolation revealed that the different pretreatments combined with different isolation media were effective in obtaining several species of actinobacteria. However, metagenomics analyses revealed that there were still several strains, including rare actinobacterial species, that were not isolated. This research strongly suggests that lichens appear to be a promising source for obtaining actinobacteria.

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“…The isolates, for instance, are characterized by the presence of glucose, mannose and ribose in whole-organism hydrolysates. In addition, the isolates were found to grow over a narrower pH range than the type strains of S. parmotrematis and S. rubrisoli, namely pH 5-7, compared with the corresponding range, pH 5-9 [30,61,62].…”

Section: Phenotypic Propertiesmentioning

confidence: 91%

“…It is evident from the MLSA and phylogenomic trees, the POCP data, and associated phenotypic properties that the isolates and the type strains of S. ferralitis [61], S. parmotrematis [30] and S. rubrisoli [62] are bona fide members of the family Streptomycetaceae [6,15]. It is also clear from the wealth of genomic, genotypic and phenotypic data that the isolates belong to a novel species which can be distinguished from its closest neighbour, S. parmotrematis NBRC 115203 T .…”

Section: Phenotypic Propertiesmentioning

confidence: 99%

See 1 more Smart Citation

Streptantibioticus silvisoli sp. nov., acidotolerant actinomycetes from pine litter, reclassification of Streptomyces cocklensis, Streptomyces ferralitis, Streptomyces parmotrematis and Streptomyces rubrisoli as Actinacidiphila cocklensis comb. nov., Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov., and emended descriptions of the genus Streptantibioticus, the family Streptomycetaceae and Streptomyces iconiensis

Świecimska,

Golinska,

Sangal

et al. 2023

International Journal of Systematic and Evolutionary Microbiology

1

0

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Filamentous actinomycetes, designated SL13 and SL54T, were isolated from pine litter and their taxonomic status resolved using a polyphasic approach. The isolates exhibit chemotaxonomic and morphological properties consistent with their classification in the family Streptomycetaceae . They form extensively branched substrate mycelia bearing aerial hyphae that differentiate into straight chains of cylindrical spores. The whole-organism hydrolysates contain ll-diaminopimelic acid, glucose, mannose and ribose, the predominant isoprenologue is MK-9(H8), the polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and glycophospholipids, and the major fatty acids are anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic trees based on 16S rRNA gene sequences and multilocus gene sequences of conserved housekeeping genes show that the isolates form a well-supported lineage that is most closely related to Streptomyces parmotrematis NBRC 115203T. All of these strains form a well-defined clade in the multilocus sequence analysis tree together with Streptantibioticus cattleyicolor DSM 46488T, Streptomyces ferralitis DSM 41836T and Streptomyces rubrisoli DSM 42083T. Draft genomes assemblies of the isolates are rich in biosynthetic gene clusters predicted to produce novel specialized metabolites and stress-related genes which provide an insight into how they have adapted to the harsh conditions that prevail in pine litter. Phylogenomically, both isolates belong to the same lineage as the type strains of S. cattleyicolor, S. ferralitis , S. parmotrematis and S. rubrisoli ; these relationships are underpinned by high average amino acid identity, average nucleotide identity and genomic DNA–DNA hybridization values. These metrics confirm that isolates SL13 and SL54T belong to a novel species that is most closely related to S. parmotrematis NBRC 115203T and that these strains together with S. ferralitis DSM 41836T, S. rubrisoli DSM 42083T belong to the genus Streptantibioticus. Consequently, it is proposed that the isolates be recognized as a new Streptantibioticus species, Streptantibioticus silvisoli comb. nov., with isolate SL54T (=DSM 111111T=PCM3044T) as the type strain, and that S. ferralitis , S. parmotrematis and S. rubrisoli be transferred to the genus Streptantibioticus as Streptantibioticus ferralitis comb. nov., Streptantibioticus parmotrematis comb. nov. and Streptantibioticus rubrisoli comb. nov. Emended descriptions are given for the genus Streptantibioticus, the family Streptomycetaceae and for Streptomyces iconiensis which was found to be a close relative of the isolates in the 16S rRNA gene sequence analyses. It is also proposed that Streptomyces cocklensis be transferred to the genus Actinacidiphila as Actinacidiphila cocklensis comb. nov based on its position in the MLSA and phylogenomic trees and associated genomic data.

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“…The genus Streptomyces belongs to the family Streptomycetaceae and was first proposed by Waksman and Henrici [1]. At the time of writing, the genus Streptomyces comprises of 697 species with validly published and correct names (https://lpsn.dsmz.de/genus/streptomyces), including the most recently described Streptomyces parmotrematis , which was isolated from lichens [2]. Members of the genus Streptomyces are Gram-stain-positive, non-acid-fast aerobic bacteria that form extensively branched substrate mycelia and develop aerial hyphae that naturally liberate spore chains in the mature stage.…”

Section: Introductionmentioning

confidence: 99%

Streptomyces humicola sp. nov., a novel actinobacterium isolated from peat swamp forest soil in Thailand

Klaysubun

¹

,

Srisuk

²

,

Duangmal

³

2022

International Journal of Systematic and Evolutionary Microbiology

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A polyphasic approach was used to describe strain RB6PN25T, an actinobacterium isolated from peat swamp forest soil in Rayong Province, Thailand. The strain was a Gram-stain-positive and filamentous bacterium that contained ll -diaminopimelic acid, mannose and ribose in whole-cell hydrolysates. MK-9(H8) was the major menaquinone. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, two unidentified glycophospholipids, two unidentified aminolipids and an unidentified phospholipid. The 16S rRNA gene sequences analysis indicated that it was most closely related to Streptomyces rubrisoli DSM 42083T (97.6 %) and Streptomyces palmae TBRC 1999T (97.4 %). Strain RB6PN25T exhibited low average nucleotide identity and digital DNA–DNA hybridization values with S. rubrisoli DSM 42083T (78.6 %, 23.2 %) and S. palmae TBRC 1999T (76.0 %, 22.6 %). The DNA G+C content of strain RB6PN25T was 69.9%. The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses reveal that strain RB6PN25T represents a novel species of the genus Streptomyces , for which the name Streptomyces humicola sp. nov. is proposed. The type strain is RB6PN25T (=TBRC 14819T=NBRC 115204T).

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Diversity of the culturable lichen-derived actinobacteria and the taxonomy of Streptomyces parmotrematis sp. nov.

Cited by 11 publications

References 32 publications

Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria

Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria

Streptomyces humicola sp. nov., a novel actinobacterium isolated from peat swamp forest soil in Thailand

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