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

Abstract

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.

In vitro and in vivo assessment of antimicrobial, enzymatic, and antifouling properties of self‐potent lichen symbiotic bacteria

“…This suggests that the variation in LAB may also be attributed to the type of lichen growth. 47 Antifouling compounds were isolated from the bacterial strain that was tested against biofouling bacteria, which is extracellular in nature. The bacterial extracts were extracted using ethyl acetate as a solvent and concentrated for performing the bioassay method, 6 showing the ability of the marine actinomycetes as a potential source for the development of antifouling compounds.…”

Isolation, Characterization, and Herbicidal Activity of Streptomyces spp. from Diseased Potato Scab Tubers

“…The G1 and SCA media, which were used to nd saccharolytic bacteria, including actinobacteria [18, 34,35], were mostly made of soluble starch which facilitated the mycelial extension and cell growth of actinomycetes as a sole carbon source [19].…”

Bacteriomic Profiles of Rock-Dwelling Lichens from the Venezuelan Guiana Shield and the South African Highveld Plateau

“…These are compared with microbiomes of Thai tropical lichens, whose top five families are Beijerinckiaceae, Chthoniobacteraceae At the family level, the overall top five families in this study were acidobacterial Acidobacteriaceae and Bryobacteraceae, and alphaproteobacterial Acetobacteraceae, Beijerinckiaceae, and Sphingomonadaceae (Figure S4). These are compared with microbiomes of Thai tropical lichens, whose top five families are Beijerinckiaceae, Chthoniobacteraceae (phylum Verrucomicrobiota), Acetobacteraceae, Gemmataceae (phylum Planctomycetota), and an unidentified family in the order Tepidisphaerales (phylum Planctomycetota) [57]. The difference in the top five families can be ascribed to biogeography as well as to host lichen species.…”