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He Z, Naganuma T, Melville HIAS. Bacteriomic Profiles of Rock-Dwelling Lichens from the Venezuelan Guiana Shield and the South African Highveld Plateau. Microorganisms 2024; 12:290. [PMID: 38399694 PMCID: PMC10892498 DOI: 10.3390/microorganisms12020290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Lichens are not only fungal-algal symbiotic associations but also matrices for association with bacteria, and the bacterial diversity linked to lichens has been receiving more attention in studies. This study compares the diversity and possible metabolism of lichen-associated bacteria from saxicolous foliose and fruticose taxa Alectoria, Canoparmelia, Crocodia, Menegazzia, Usnea, and Xanthoparmelia from the Venezuelan Guiana Shield and the South African Highveld Plateau. We used DNA extractions from the lichen thalli to amplify the eukaryotic 18S rRNA gene (rDNA) and the V3-V4 region of the bacterial 16S rDNA, of which amplicons were then Sanger- and MiSeq-sequenced, respectively. The V3-V4 sequences of the associated bacteria were grouped into operational taxonomic units (OTUs) ascribed to twelve bacterial phyla previously found in the rock tripe Umbilicaria lichens. The bacterial OTUs emphasized the uniqueness of each region, while, at the species and higher ranks, the regional microbiomes were shown to be somewhat similar. Nevertheless, regional biomarker OTUs were screened to predict relevant metabolic pathways, which implicated different regional metabolic features.
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Affiliation(s)
- Zichen He
- Graduate School of Integrated Science for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima 739-8528, Japan
| | - Takeshi Naganuma
- Graduate School of Integrated Science for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-hiroshima 739-8528, Japan
| | - Haemish I. A. S. Melville
- Department of Environmental Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Florida, 0-41 Calabash Building, Unisa Science Campus, cnr Pioneer Avenue and Christiaan de Wet Road, Florida 1710, Gauteng, South Africa;
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Somphong A, Weeraphan T, Poengsungnoen V, Suriyachadkun C, Sripreechasak P, Chaotham C, Tanasupawat S, Phongsopitanun W. Actinoplanes pyxinae sp. nov., a new lichen-derived rare actinobacterium exhibiting antimicrobial and anticancer activity. Int J Syst Evol Microbiol 2024; 74. [PMID: 38180333 DOI: 10.1099/ijsem.0.006215] [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: 01/06/2024] Open
Abstract
A novel lichen-derived actinobacterium, designated Pm04-4T, was isolated from Pyxine cocoes (Sw.) Nyl. lichen collected from Chaiyaphum, Thailand. A polyphasic approach was used to describe the taxonomic position of the strain. The strain had morphological and chemotaxonomic properties similar to members of the genus Actinoplanes. It produced sporangia on the substrate mycelia. Meso-diaminopimelic acid, galactose, glucose and mannose were detected in the whole-cell hydrolysate of the strain. The major menaquinone was MK-9(H4). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Strain Pm04-4T showed the highest 16S rRNA gene sequence similarity to Actinoplanes akusuensis TRM 8003T (99.0 %). In the phylogenomic tree, strain Pm04-4T was positioned close to A. aksuensis TRM88003T, A. maris M416T, A. polyasparticus TRM66264T, A. hotanensis TRM88002T, A. abujensis DSM 45518T, A. bogorensis NBRC 110975T, A. brasiliensis DSM 43805T, A. lichenicola LDG1-01T and A. ovalisporus LDG1-06T. The average nucleotide identity and digital DNA-DNA hybridization values between strain Pm04-4T and its closely related neighbours were below the threshold values for describing new species. Moreover, the strain could be distinguished from its closely related type strains by phenotypic properties. Based on genotypic and phenotypic evidence, it can be concluded that strain Pm04-4T is a representative of a new Actinoplanes species for which the name Actinoplanes pyxinae sp. nov. is proposed. The type strain is Pm04-4T (=TBRC 16207T=NBRC 115836T). The type strain exhibited activity against Staphylococcus aureus ATCC 25923 as well as four yeast strains, namely Candida albicans TISTR 5554, Candida glabrata TISTR 5006, Candida krusei TISTR 5351 and Candida parapsilosis TISTR 5007. It also showed cytotoxicity against Caco-2, MNT-1 and MCF-7 cancer cells.
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Affiliation(s)
- Achiraya Somphong
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok, 10330, Thailand
| | - Trinset Weeraphan
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vasun Poengsungnoen
- Lichen Research Unit, Department of Biology, Faculty of Science, Ramkhamhaeng University, Bangkok, 10240, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Klong Luang, Pathumthani 12120, Thailand
| | - Paranee Sripreechasak
- Office of Educational Affairs, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | - Chatchai Chaotham
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
- Natural Products and Nanoparticles Research Unit (NP2), Chulalongkorn University, Bangkok, 10330, Thailand
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