Genomics- and Metabolomics-Based Investigation of the Deep-Sea Sediment-Derived Yeast, Rhodotorula mucilaginosa 50-3-19/20B

Buedenbender, Larissa; Kumar, Abhishek; Blümel, Martina; Kempken, Frank; Taşdemir, Deniz

doi:10.3390/md19010014

Cited by 17 publications

(11 citation statements)

References 74 publications

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“…Rhodotorula mucilaginosa has been isolated from a sediment core at 3600 m depth and cultivated at atmospheric pressure. It is a fungal species of interest due to its ability to produce valuable natural products, such as lipids and carotenoids, with potential applications as surfactants, food additives, and pharmaceuticals [41]. Chytridiomycota have been defined as one of the dominant groups of parasites in aquatic ecosystems.…”

Section: Asv-specific Differences By Ecosystemmentioning

confidence: 99%

Fungal Diversity and Community Composition across Ecosystems

Debeljak

Baltar

2023

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Fungi have shaped the biosphere since the development of life on Earth. Despite fungi being present in all environments, most of the available fungal research has focused on soils. As a result, the role and composition of fungal communities in aquatic (marine and freshwater) environments remain largely unexplored. The use of different primers to characterise fungal communities has additionally complicated intercomparisons among studies. Consequently, we lack a basic global assessment of fungal diversity across major ecosystems. Here, we took advantage of a recently published 18S rRNA dataset comprising samples from major ecosystems (terrestrial, freshwater, and marine) to attempt a global assessment of fungal diversity and community composition. We found the highest fungal diversities for terrestrial > freshwater > marine environments, and pronounced gradients of fungal diversity along temperature, salinity, and latitude in all ecosystems. We also identified the most abundant taxa in each of these ecosystems, mostly dominated by Ascomycota and Basidiomycota, except in freshwater rivers where Chytridiomycota dominated. Collectively, our analysis provides a global analysis of fungal diversity across all major environmental ecosystems, highlighting the most distinct order and ASVs (amplicon sequencing variants) by ecosystem, and thus filling a critical gap in the study of the Earth’s mycobiome.

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Section: Asv-specific Differences By Ecosystemmentioning

confidence: 99%

Fungal Diversity and Community Composition across Ecosystems

Debeljak

Baltar

2023

JoF

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“…Chromatograms were acquired with a UPLC I-Class System coupled to a Xevo G2-XS QToF Mass Spectrometer (Waters®, Milford, MA, USA) using a modified protocol described previously [ 73 ]. Samples were injected at a concentration of 0.1 mg/mL with an injection volume of 1 µL.…”

Section: Methodsmentioning

confidence: 99%

Bioactivity and Metabolome Mining of Deep-Sea Sediment-Derived Microorganisms Reveal New Hybrid PKS-NRPS Macrolactone from Aspergillus versicolor PS108-62

et al. 2023

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Despite low temperatures, poor nutrient levels and high pressure, microorganisms thrive in deep-sea environments of polar regions. The adaptability to such extreme environments renders deep-sea microorganisms an encouraging source of novel, bioactive secondary metabolites. In this study, we isolated 77 microorganisms collected by a remotely operated vehicle from the seafloor in the Fram Strait, Arctic Ocean (depth of 2454 m). Thirty-two bacteria and six fungal strains that represented the phylogenetic diversity of the isolates were cultured using an One-Strain-Many-Compounds (OSMAC) approach. The crude EtOAc extracts were tested for antimicrobial and anticancer activities. While antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium was common for many isolates, only two bacteria displayed anticancer activity, and two fungi inhibited the pathogenic yeast Candida albicans. Due to bioactivity against C. albicans and rich chemical diversity based on molecular network-based untargeted metabolomics, Aspergillus versicolor PS108-62 was selected for an in-depth chemical investigation. A chemical work-up of the SPE-fractions of its dichloromethane subextract led to the isolation of a new PKS-NRPS hybrid macrolactone, versicolide A (1), a new quinazoline (−)-isoversicomide A (3), as well as three known compounds, burnettramic acid A (2), cyclopenol (4) and cyclopenin (5). Their structures were elucidated by a combination of HRMS, NMR, [α]D, FT-IR spectroscopy and computational approaches. Due to the low amounts obtained, only compounds 2 and 4 could be tested for bioactivity, with 2 inhibiting the growth of C. albicans (IC50 7.2 µg/mL). These findings highlight, on the one hand, the vast potential of the genus Aspergillus to produce novel chemistry, particularly from underexplored ecological niches such as the Arctic deep sea, and on the other, the importance of untargeted metabolomics for selection of marine extracts for downstream chemical investigations.

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“…Genome sequencing resulted in the identification of the genomic locus of a key enzyme involved in the biosynthesis of these metabolites. 238 Phenols 680 and 681 were isolated from Roussoella siamensis , 239 feeding of anthranilic acid and phthalimide to a Scedosporium apiospermum culture resulted in production of diphenylamine derivative 682 , 240 cyclic decapeptides 683–686 were obtained from Sesquicillium microsporum , 241 and soft coral-derived Symplicium strains yielded steroid derivatives 687–690 , 242 and nortriterpenoids 691–701 . 243…”

Section: Marine Microorganisms and Phytoplanktonmentioning

confidence: 99%