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LEfSe cladogram showing taxonomic biomarkers of bacteria associated with the lichens collected from Signy Island (green) and the Syowa Station region (red). The innermost node corresponds to the domain Bacteria, followed by concentrically arranged nodes of phylum, class, order, family, genus and species. Red and green nodes/shades indicate taxa that are significantly higher in relative abundance. Diameter of each node circle is proportional to abundance of the taxon.
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Increased research attention is being given to bacterial diversity associated with lichens. Rock tripe lichens (Umbilicariaceae) were collected from two distinct Antarctic biological regions, the continental region near the Japanese Antarctic station (Syowa Station) and the maritime Antarctic South Orkney Islands (Signy Island), in order to compare...
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Context 1
... regional distinction in OTU diversity was driven by biomarker OTUs or biomarker taxa, which were identified by LEfSe and are represented in the phylogenetic cladogram (Figure 4). Among these, significant biomarkers having LDA scores >5 are listed in Table 6. ...
Context 2
... in Figure 4 Rank Biomarkers with LDA scores >4, including the 16 species-rank biomarkers, were further characterized by PICRUSt to predict metabolic features of lichen-associated bacteria in both sampling regions. The biomarker OTUs were projected on the LEGG metabolic map, and key metabolic features were visualized. ...
Citations
... Umbilicaria populations including Umbilicaria antarctica, U. kappeni, U. decussata, and U. umbilicarioides have colonized and re-lichenized in the Antarctic Peninsula multiple times independently [13]. Microbiomes of maritime and east Antarctic Umbilicaria exhibit bioclimatic variation [14]. Similarly, U. pustulata (syn. ...
... The products with the best amplification effect will be diluted in × 50, × 100, × 200, × 500, × 1000 again for the second PCR with the same protocols. This method is based on our previous experience, and it has a good effect on Umbilicaria thalli washed with ultrapure water [14]. ...
... Previous studies have reported the distribution of rock tripe lichens containing fungal partners (mycobionts) belonging to the Umbilicaria genus and algal partners (photobionts) belonging to the Trebouxia genus are distributed across diverse environments, even including Antarctic ice-free areas [12][13][14]. Given the relatively high resolution of the ITS region sequences, it was better to use in this study the sequences of the 18S rRNA gene only for the classification Content courtesy of Springer Nature, terms of use apply. ...
The diversity of bacteria associated with alpine lichens was profiled. Lichen samples belonging to the Umbilicariaceae family, commonly known as rock tripe lichens, were gathered from two distinct alpine fellfields: one situated on Mt. Brennkogel located in the Eastern European Alps (Austria), and the other on Mt. Stanley located in the Rwenzori mountains of equatorial Africa (Uganda). The primary aim of this research was to undertake a comparative investigation into the bacterial compositions, and diversities, identifying potential indicators and exploring their potential metabolisms, of these lichen samples. Bulk genomic DNA was extracted from the lichen samples, which was used to amplify the 18S rRNA gene by Sanger sequencing and the V3-V4 region of the 16S rRNA gene by Illumina Miseq sequencing. Examination of the fungal partner was carried out through the analysis of 18S rRNA gene sequences, belonging to the genus Umbilicaria (Ascomycota), and the algal partner affiliated with the lineage Trebouxia (Chlorophyta), constituted the symbiotic components. Analyzing the MiSeq datasets by using bioinformatics methods, operational taxonomic units (OTUs) were established based on a predetermined similarity threshold for the V3-V4 sequences, which were assigned to a total of 26 bacterial phyla that were found in both areas. Eight of the 26 phyla, i.e. Acidobacteriota, Actinomycota, Armatimonadota, Bacteroidota, Chloroflexota, Deinococcota, Planctomycetota, and Pseudomonadota, were consistently present in all samples, each accounting for more than 1% of the total read count. Distinct differences in bacterial composition emerged between lichen samples from Austria and Uganda, with the OTU frequency-based regional indicator phyla, Pseudomonadota and Armatimonadota, respectively. Despite the considerable geographic separation of approximately 5430 km between the two regions, the prediction of potential metabolic pathways based on OTU analysis revealed similar relative abundances. This similarity is possibly influenced by comparable alpine climatic conditions prevailing in both areas.
... Near-full-length 18S rDNA of lichen-forming fungi and algae were amplified on two TaKaRa Thermal Cyclers with the primer sets shown in Table 2 and using the thermal cycling described in the previous study [21]. The PCR amplicons were purified and Sanger-sequenced at the Department of Gene Science, Natural Science Center for Basic Research and Development (N-BARD), Hiroshima University [21]. ...
... Near-full-length 18S rDNA of lichen-forming fungi and algae were amplified on two TaKaRa Thermal Cyclers with the primer sets shown in Table 2 and using the thermal cycling described in the previous study [21]. The PCR amplicons were purified and Sanger-sequenced at the Department of Gene Science, Natural Science Center for Basic Research and Development (N-BARD), Hiroshima University [21]. [30] is the source of the map image. ...
... Thalli of a lichen sample were cleaned with autoclaved Milli-Q ultrapure water, cut into pieces, ground to finer fragments, and homogenized, one gram of which was used for DNA extraction by the method detailed in previous studies [20,21]. Although they were not examined under a microscope, cephalodia were not clearly visible. ...
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.
... High-throughput sequencing techniques have become increasingly common when characterizing both mycobiont and photobiont molecular diversity [25,26]. Compared to conventional Sanger sequencing, HTS allows for a far more reliable determination of the sequences within a mixed sample, making it useful for studying both the main lichen components but also the underlying thalli-associated microbiome [27][28][29][30]. DNA metabarcoding approaches have shown a high potential for lichen biodiversity assessments [31,32]; although an additional consideration to the ones mentioned above is to take caution when discriminating the target lichenized fungi from the "noise" generated by the presence of secondary fungi, biological variation and sequencing artifacts [29,31,33]. ...
DNA barcoding is a powerful method for the identification of lichenized fungi groups for which the diversity is already well-represented in nucleotide databases, and an accurate, robust taxonomy has been established. However, the effectiveness of DNA barcoding for identification is expected to be limited for understudied taxa or regions. One such region is Antarctica, where, despite the importance of lichens and lichenized fungi identification, their genetic diversity is far from characterized. The aim of this exploratory study was to survey the lichenized fungi diversity of King George Island using a fungal barcode marker as an initial identification tool. Samples were collected unrestricted to specific taxa in coastal areas near Admiralty Bay. Most samples were identified using the barcode marker and verified up to the species or genus level with a high degree of similarity. A posterior morphological evaluation focused on samples with novel barcodes allowed for the identification of unknown Austrolecia, Buellia, and Lecidea s.l. species. These results contribute to better represent the lichenized fungi diversity in understudied regions such as Antarctica by increasing the richness of the nucleotide databases. Furthermore, the approach used in this study is valuable for exploratory surveys in understudied regions to guide taxonomic efforts towards species recognition and discovery.
... The active part of the Jardine Peak community was less 460 diverse than that of the Penguin Rookery. In the lichen Umbillicaria rhizinata the opposite was 461 observed, with the coastal (and nitrogen fertilized) specimens hosting a less diverse community than 462 the inland ones (He et al., 2022). However, similarly to our U. antarctica samples, the coastal/nitrogen 463 enriched specimens harbored taxa affiliated with nitrophilic lichens (Armatimonadetes, Bacteroidetes), 464 while the inland lichens were dominated by Proteobacteria (He et al., 2022). ...
... In the lichen Umbillicaria rhizinata the opposite was 461 observed, with the coastal (and nitrogen fertilized) specimens hosting a less diverse community than 462 the inland ones (He et al., 2022). However, similarly to our U. antarctica samples, the coastal/nitrogen 463 enriched specimens harbored taxa affiliated with nitrophilic lichens (Armatimonadetes, Bacteroidetes), 464 while the inland lichens were dominated by Proteobacteria (He et al., 2022). Thus, shifting of the 465 bacterial community structure in nitrogen-tolerant lichens (or any wide amplitude lichens) may be the 466 basis for their efficient adaptability to changing environmental conditions. ...
Recently, lichens came once more into the scientific spotlight due to their unique relations with Prokaryotes. Several temperate region lichen species have been thoroughly explored in this regard yet, the information on Antarctic lichens and their associated bacteriobiomes is somewhat lacking. In this paper we assessed the phylogenetic structure of the whole and active fractions of bacterial communities housed by Antarctic lichens growing in different environmental conditions by targeted 16S rRNA gene amplicon sequencing. Bacterial communities associated with lichens procured from a nitrogen enriched site were very distinct from the communities isolated from lichens of a nitrogen depleted site. The former were characterized by substantial contributions of Bacteroidetes phylum members and the elusive Armatimonadetes. At the nutrient-poor site the lichen-associated bacteriobiome structure was unique for each lichen species, with chlorolichens being occupied largely by Proteobacteria. Lichen species with a pronounced discrepancy in diversity between the whole and active fractions of their bacterial communities had the widest ecological amplitude, hinting that the non-active part of the community is a reservoir of latent stress coping mechanisms. This is the first investigation to make use of targeted metatranscriptomics to infer the bacterial biodiversity in Antarctic lichens.
Bacterial and fungal adhesins mediate microbial aggregation, biofilm formation, and adhesion to host. We divide these proteins into two major classes: professional adhesins and moonlighting adhesins that have a non-adhesive activity that is evolutionarily conserved. A fundamental difference between the two classes is the dissociation rate. Whereas moonlighters, including cytoplasmic enzymes and chaperones, can bind with high affinity, they usually dissociate quickly. Professional adhesins often have unusually long dissociation rates: minutes or hours. Each adhesin has at least three activities: cell surface association, binding to a ligand or adhesive partner protein, and as a microbial surface pattern for host recognition. We briefly discuss Bacillus subtilis TasA, pilin adhesins, gram positive MSCRAMMs, and yeast mating adhesins, lectins and flocculins, and Candida Awp and Als families. For these professional adhesins, multiple activities include binding to diverse ligands and binding partners, assembly into molecular complexes, maintenance of cell wall integrity, signaling for cellular differentiation in biofilms and in mating, surface amyloid formation, and anchorage of moonlighting adhesins. We summarize the structural features that lead to these diverse activities. We conclude that adhesins resemble other proteins with multiple activities, but they have unique structural features to facilitate multifunctionality.
