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The lichens species studied . ( A ) Lichina pygmaea (black fruticose gelatinous cyanolichen on rocky shores), ( B ) Lichina confinis (black fruticose gelatinous cyanolichen on rocky shores, white arrows) and ( C ) Roccella fuciformis (grey fruticose lichen on sheltered vertical rockfaces).
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Cultivable Actinobacteria are the largest source of microbially derived bioactive molecules. The high demand for novel antibiotics highlights the need for exploring novel sources of these bacteria. Microbial symbioses with sessile macro-organisms, known to contain bioactive compounds likely of bacterial origin, represent an interesting and underexp...
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... diversity of isolates. After the lichen sampling ( Fig. 1), serial dilutions of the washout and lichen homogenate (corresponding with bacteria on the surface and inside the thallus) were prepared. The bacterial inocula were plated on various media: marine agar (MA), actinomycete isolation agar (AIA) and International Streptomyces Project medium-2 (ISP 2) with nalidixic acid and cycloheximide ...
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This study aims to develop approaches for screening highly specific bacteriophages based on bio-informatic analysis of CRISPR-Cas structures of bacterial systems using the example of Corynebacterium diphtheriae. We proposed an algorithm for bioinformatic search and analysis of CRISPR-Cas structures of bacteria systems and phage screening through sp...
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... The compounds were duly identified according to their spectroscopic features, including based on their nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HR-MS) spectra, and using polarimetry for compounds with asymmetric carbons. Microbial (bacteria or fungal) metabolites were obtained after culture of the associated bacteria [30] or the endolichenic fungi previously isolated from lichens [31], which were then purified and identified in the same way as the lichen metabolites. ...
(1) Background: Since the emergence of SARS-CoV-2, responsible for the COVID-19 pandemic, efforts have been made to identify antiviral compounds against human coronaviruses. With the aim of increasing the diversity of molecule scaffolds, 42 natural compounds, of which 28 were isolated from lichens and 14 from their associated microorganisms (bacteria and fungi), were screened against human coronavirus HCoV-229E. (2) Methods: Antiviral assays were performed using HCoV-229E in Huh-7 and Huh-7/TMPRSS2 cells and SARS-CoV-2 in a Vero-81-derived clone with a GFP reporter probe. (3) Results: Four lichen compounds, including chloroatranol, emodin, perlatolic acid and vulpinic acid, displayed high activities against HCoV-229E (IC50 = 68.86, 59.25, 16.42 and 14.58 μM, respectively) and no toxicity at active concentrations. Kinetics studies were performed to determine their mode of action. The four compounds were active when added at the replication step. Due to their significant activity, they were further tested on SARS-CoV-2. Perlatolic acid was shown to be active against SARS-CoV-2. (4) Conclusions: Taken together, these results show that lichens are a source of interesting antiviral agents against human coronaviruses. Moreover, perlatolic acid might be further studied for its pan-coronavirus antiviral activity.
... Several of the genera identified in the 'core' community have been previously associated with lichens and mosses. These include the N-fixing cyanobacterial family Phormidiaceae (Bergman et al. 1997), which is associated with moss-covered biocrusts (Maier et al. 2018), as well as the lichen-associated bacterial genera Chthoniobacter (Aschenbrenner et al. 2017) and Nocardioides (Parrot et al. 2015). Almost half of the 'core' fungal genera were identified as lichenized fungi, including Cladonia, Stereocaulon (Park et al. 2015(Park et al. , 2018, Astroplaca (Arup et al. 2013) and Mastodia (Garrido-Benavent et al. 2017). ...
The majority of islands surrounding the Antarctic continent are poorly characterized in terms of microbial macroecology due to their remote locations, geographical isolation and access difficulties. The 2016/2017 Antarctic Circumnavigation Expedition (ACE) provided unprecedented access to a number of these islands. In the present study we use metagenomic methods to investigate the microbial ecology of soil samples recovered from 11 circum‐Antarctic islands as part of ACE, and to investigate the functional potential of their soil microbial communities. Comparisons of the prokaryote and lower eukaryote phylogenetic compositions of the soil communities indicated that the various islands harbored spatially distinct microbiomes with limited overlap. In particular, we identified a high prevalence of lichen‐associated fungal taxa in the soils, suggesting that terrestrial lichens may be one of the key drivers of soil microbial ecology on these islands. Differential abundance and redundancy analyses suggested that these soil microbial communities are also strongly shaped by multiple abiotic factors, including soil pH and average annual temperatures. Most importantly, we demonstrate that the islands sampled in this study can be clustered into three distinct large‐scale biogeographical regions in a conservation context, the sub‐, Maritime and Continental Antarctic, which are distinct in both environmental conditions and microbial ecology, but are consistent with the widely‐used regionalization applied to multicellular Antarctic terrestrial organisms. Functional profiling of the island soil metagenomes from these three broad biogeographical regions also suggested a degree of functional differentiation, reflecting their distinct microbial ecologies. Taken together, these results represent the most extensive characterization of the microbial ecology of Antarctic island soils to date.
... Two novel Streptomyces species (strains RI104-LiC106 and RI104-LiB101) collected from the Risiri Island, Japan were found to be producing antimicrobial compounds such as 1,1-dichlorocyclopropane containing angucycline and butanolide (Motohashi et al., 2010). Delphine Parrot et al. (2015) studied the endolichenic actinobacterial diversity in 3 different littoral lichens (Lichina Confinis, L Pygmaea &Roccella Fuciformis). The rich diversified actinobacterial families isolated are Micrococcaceae, Brevibacteriaceae, Nocardiodaceae and Streptomycetacea were screened genetically for the production of bioactive metabolites. ...
... Recently Bacillus gibsonii, a hyperactive pigment-producing bacterial strain identified from the lichen D. aegialita (Dawoud et al., 2020). The novel actinobacterial isolation from various lichens have established that the unexplored coastal lichens could be a potential source for the isolation of rare actinomycetes (Parrot et al., 2015). Recently, the statistical optimization tool namely, Response Surface Methodology (RSM) has become an attractive approach for enhancing the bacterial metabolite production. ...
Actinomycete DARP-7 was isolated from the coastal foliose lichen Dirinaria aegilita (Afzel.ex Ach.) B.J.Moore and identified as Streptomyces sp. using 16S rRNA sequencing. Among the eight culture media used for antimicrobial metabolite production, the peptone yeast extract iron medium (ISP-6) showed higher production with the maximum zone of inhibition (12 mm) against Staphylococcus aureus. Further, the ISP-6 medium components were optimized through the Plackett-Burman design (PBD) followed by Response Surface Methodology (RSM). Yeast extract, sodium thiosulphate, and ferric ammonium citrate would play a significant role in antibiotic production. Further, the significant variables from PBD were optimized through Central Composite Design (CCD) of RSM for enhanced antibiotic production. The optimal medium components were found to be peptone - 15 (g/L), protease peptone - 5 (g/L), yeast extract - 2.915 (g/L), ferric ammonium citrate - 0.651 (g/L), K2HPO4 – 1 (g/L) and Na2S2O3– 0.155 (g/L), respectively. The optimized result was validated and the antibacterial activity against S. aureus increased upto 19.9 mm (66.7%). The resazurin dye based quantification of minimum inhibitory concentration of the DARP-7 crude extract was found to be 41.34 µg and 46.44 µg against S. aureus and E.coli, respectively. Further, the compound profiling was done using UV-VIS, FTIR, EEM and GC-MS confirming the presence of polyene conjugates. Thus, the study delivers coastal lichen could be promising source for isolating bioactive metabolites producing rare actinobacteria. Furthermore, the use of a statistical optimization tool to improve bioactive metabolite yield is discussed.
... Although lichen metabolites are considered exclusively of fungal origin, the metabolic interaction between photobiont and mycobionts is found to be crucial for the production of these unique metabolites (Brunauer et al., 2007) since the mycobionts grown without a photobiont does not produce the same array of metabolites (Fazio et al., 2009). Beyond lichenized fungi, recent research has highlighted the presence of several other associated organisms such as endolichenic fungi , cyanolichen (Kaasalainen et al., 2012), epilichenic and bacteria associated with lichens (Lee et al., 2014;Parrot et al., 2015;Suzuki et al., 2016). These associated organisms further increase the profile of lichen chemical diversity but currently the impact of these associated organisms on the complete biochemical profile of a lichen species is unclear. ...
... The actinobacterial families obtained includes Micrococcaceae, Brevibacteriaceae, Mycobacteriaceae, Cellulomonadaceae, Sanguibacteraceae, Gordoniaceae, Nocardioidaceae, Pseudonocardiaceae, Promicromonosporaceaen and Streptomycetaceae. Screening of genes coding for polyketide synthases types I and II further highlighted the littoral lichens are a source of diverse potentially bioactive Actinobacteria (Parrot et al., 2015). Similarly, Parrot et al., have isolated novel metabolites from two actinobacterial strains. ...
Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.
... Most of the species isolated from the media reproducing the lichen environment were previously reported from water reservoirs and polluted environments. For instance, Aquaspirillum arcticum, Erythrobacter sp., Klenkia taihuensis, Paracoccus chinensis, Microterricola gilva, and Kocuria polaris (Table 1) were previously isolated from marine environments [39][40][41][42], sediments [43,44], seaweed [45], or cyanobacteria [46]. It is important to note that various Erythrobacter, Paracoccus, Kocuria, Pseudomonas, or Gordonia species were isolated earlier from marine or maritime Brittany lichens. ...
... It is important to note that various Erythrobacter, Paracoccus, Kocuria, Pseudomonas, or Gordonia species were isolated earlier from marine or maritime Brittany lichens. Furthermore, P. helmanticensis was isolated from an Austrian lichen [42]. Geobacillus sp. and Gordonia sp., isolated in this study on lichen-based media, were described to grow in thermal areas and polluted and contaminated environments [47][48][49][50][51][52][53]. ...
... Our novel culturomic approach to lichen-associated bacteria provides a unique picture and database on diversified bacterial communities naturally colonizing R. geographicum. Most of the previous culture-dependent studies on lichens only used classic media, allowing isolating a small fraction of lichen-associated microbes [42]. In addition, only two studies explored the diversity of R. geographicum. ...
As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota
... As there is no standardized methodology for the isolation of lichen-associated microbiota, a protocol for lichen washing was used, based on Parrot et al. (2015) and Petrini (1991). Two techniques of isolation and 11 different media picked on DMSZ website (https:// www.dsmz.de/collection/catalogue/microorganisms/cul ...
Recently, the study of the interactions within a microcosm between hosts and their associated microbial communities drew an unprecedented interest arising from the holobiont concept. Lichens, a symbiotic association between a fungus and an alga, are redefined as complex ecosystems considering the tremendous array of associated microorganisms that satisfy this concept. The present study focuses on the diversity of the microbiota associated with the seashore located lichen Rhizocarpon geographicum, recovered by different culture‐dependent methods. Samples harvested from two sites allowed the isolation and the molecular identification of 68 fungal isolates distributed in 43 phylogenetic groups, 15 bacterial isolates distributed in five taxonomic groups and three microalgae belonging to two species. Moreover, for 12 fungal isolates belonging to 10 different taxa, the genus was not described in GenBank. These fungal species have never been sequenced or described and therefore non‐studied. All these findings highlight the novel and high diversity of the microflora associated with R. geographicum. While many species disappear every day, this work suggests that coastal and wild environments still contain an unrevealed variety to offer and that lichens constitute a great reservoir of new microbial taxa which can be recovered by multiplying the culture‐dependent techniques.
... e results infer that the average maximum variation is 1.121 ± 2.400, along with an average minimum similarity of 99.927 ± 0.158 based on multiple copies of 16S rRNA analysis [44]. Ten Streptomyces strains isolated from three different lichens were found to have similar 16S rRNA gene sequences [45,46]. e analysis of multiple copies of 16S rRNA in different Nocardia strains suggests that only BLAST analysis could not confirm the species present in the isolates [47]. ...
Antibiotics are widely used in the prevention and treatment of infectious diseases. The main sources of antibiotics are Streptomyces species, which are mostly isolated from soil and marine environment. They are the primary source of various bioactive compounds, including antibiotics. Streptomyces species under stress conditions may produce new secondary metabolites, including antibiotics. Soil samples were collected from different regions of Nepal. Streptomyces species were isolated on ISP4 (International Streptomyces Project medium 4) and were sub-cultured on the same media. To isolate metabolites, seed culture was performed in TSB (Tryptone Soya Broth) medium. Primary screening of Streptomyces species was carried out on MHA (Mueller Hinton Agar) plate by perpendicular sticking method against Staphylococcus aureus, Shigella sonnei, Eschericha coli, Klebsiells pneumonia, Salmonella typhi, and Acinetobacter baumani. The antimicrobial susceptibility test of isolates was executed on MHA plates by well diffusion method and was evaluated by measuring the inhibition zone. Large number of Streptomyces colonies were isolated from soil samples. Distinct colonies were selected from the primary screening. Out of 30 different colonies, only two colonies BT09 and BT29 showed strong antimicrobial activity against gram positive bacteria.
... About 30% of the strains showed antimicrobial activity against other microorganisms. The presence of some structurally identified bioactive molecules is reported for a few bacterial strains although there are many other strains of relevance (Cardinale et al., 2006;Liba et al., 2006;Selbmann et al., 2010;Pankratov, 2012;Kim et al., 2014;Lee et al., 2014;Sigurbjörnsdóttir et al., 2014;Cernava et al., 2015;Parrot et al., 2015). In the following paragraph, we summarize information about several lichen-associated bacteria producing already identified bioactive compounds. ...
Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L . pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont ( Dictyochloropsis reticulata ) and interspersed cyanobacterial cell clusters ( Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont’s contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.
... Similarly, several hundred Actinobacteria were isolated from intertidal, subtidal, and deep-sea sediments of different geographical locations (e.g., Claverías et al., 2015;Cumsille et al., 2017;Duncan et al., 2014;Ettoumi et al., 2016;Gozari et al., 2019;Jose and Jha, 2017;Undabarrena et al., 2016;Xiong et al., 2014). Additionally, different marine invertebrates, such as sponges (e.g., Cheng et al., 2015;Gozari et al., 2019;Liu et al., 2019), corals (Mahmoud and Kalendar, 2016), marine algae (e.g., Girão et al., 2019), and marine lichens (e.g., Parrot et al., 2015), have received attention as rich sources of diverse Actinobacteria. ...
Actinobacteria are well-recognised biosynthetic factories that produce an extensive spectrum of secondary metabolites. Recent genomic insights seem to impact the exploitation of these metabolically versatile bacteria in several aspects. Notably, from the isolation of novel taxa to the discovery of new compounds, different approaches evolve at a steady pace. Here, we systematically discuss the enduring importance of Actinobacteria in the field of drug discovery, the current focus of isolation efforts targeting bioactive Actinobacteria from diverse sources, recent discoveries of novel compounds with different bioactivities, and the relative employment of different strategies in the search for novel compounds. Ultimately, we highlight notable progress that will have profound impacts on future quests for secondary metabolites of Actinobacteria.
... Our main goal herein is to study the effect of UA on the bacterial growth and metabolism of different bacterial strains isolated from lichens. The strains studied belong to the three main bacterial phyla isolated from various lichens: Actinobacteria, Alphaproteobacteria and Firmicutes (Parrot et al., 2015a). The Alphaproteobacterium selected was Mabikibacter ruber (also labeled MOLA1416), a Gram-negative strain previously isolated from the lichen Lichina pygmaea (Lightf.) ...
... This highlights a putative means for lichen-associated bacterial strains to develop resistance against the antibiotic lichen metabolite present in their environmental ecosystem. It is interesting to note that S. cyaneofuscatus, producer of UA and sensitive to this antibiotic, was also isolated from L. confinis, the host of M. ruber, and from R. fuciformis, two other littoral lichens (Parrot et al., 2015a) found in the same environment as L. pygmaea. R. fuciformis, from which Nocardia-like strains (Nocardioides mesophilus) (Parrot et al., 2015a) were isolated, is a well-known lichen producer of orsellinic derivatives (montagnetol, erythrin, etc.) (Parrot et al., 2015b). ...
... It is interesting to note that S. cyaneofuscatus, producer of UA and sensitive to this antibiotic, was also isolated from L. confinis, the host of M. ruber, and from R. fuciformis, two other littoral lichens (Parrot et al., 2015a) found in the same environment as L. pygmaea. R. fuciformis, from which Nocardia-like strains (Nocardioides mesophilus) (Parrot et al., 2015a) were isolated, is a well-known lichen producer of orsellinic derivatives (montagnetol, erythrin, etc.) (Parrot et al., 2015b). These derivatives possess the same biosynthetic tetraketide precursor as UA (Taguchi et al., 1969). ...
Lichens are specific symbiotic organisms harboring various microorganisms in addition to the two classic partners (algae or cyanobacterium and fungus). Although lichens produce many antibiotic compounds such as (+)-usnic acid, their associated microorganisms possess the ability to colonize an environment where antibiosis exists. Here, we have studied the behavior of several lichen-associated bacterial strains in the presence of (+)-usnic acid, a known antibiotic lichen compound. The effect of this compound was firstly evaluated on the growth and metabolism of three bacteria, thus showing its ability to inhibit Gram-positive bacteria. This inhibition was not thwarted with the usnic acid producer strain Streptomyces cyaneofuscatus. The biotransformation of this lichen metabolite was also studied. An ethanolamine derivative of (+)-usnic acid with low antibiotic activity was highlighted with chemical profiling, using HPLC-UV combined with low resolution mass spectrometry. These findings highlight the way in which some strains develop resistance mechanisms. A methylated derivative of (+)-usnic acid was annotated using the molecular networking method, thus showing the interest of this computer-based approach in biotransformation studies.
