Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) – Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration

Dziurzyński, Mikołaj; Górecki, Adrian; Pawłowska, Julia; Istel, Łukasz; Decewicz, Przemysław; Golec, Piotr; Styczyński, Michał; Poszytek, Krzysztof; Rokowska, Anna; Górniak, Dorota; Dziewit, Łukasz

doi:10.1016/j.scitotenv.2022.159072

Cited by 7 publications

(5 citation statements)

References 63 publications

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“…For isolation of microorganisms associated with the mesopelagic jellyfish P. periphylla , three different solid cultivation media, Marine agar (MA), Hastings medium (HS), and modified Wickerham medium (WSP), were used. MA is an oligotrophic medium supporting the growth of heterotrophic marine bacteria [ 33 ]. Modified Wickerham (WSP) and the nutrient rich Hastings (HS) media support the growth of both fungi and bacteria [ 34 , 35 ].…”

Section: Resultsmentioning

confidence: 99%

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla Periphylla

et al. 2023

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The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose–yeast–malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC50 values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms.

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Section: Resultsmentioning

confidence: 99%

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla Periphylla

et al. 2023

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“…This discrepancy is likely due to the greater diversity of plant communities that were studied in this work compared to that of [ 46 ]. A total of 115 amplicon sequence variants (ASVs) belonging to the basidiomycetes were identified in the soils of Spitsbergen, representing 13.07% of the total fungal diversity [ 47 ]. This represents a notable increase compared to our findings, although to some extent it can be attributed to the more diverse conditions under which the soil samples were collected for analysis.…”

Section: Discussionmentioning

confidence: 99%

Fauna and Ecology of Macromycetes (Basidiomycota) in the Arctic Tree and Shrub Ecosystems of Central Siberia

Kulakov,

Tatarintsev,

Demidko

et al. 2024

JoF

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The research was aimed at studying the taxonomic diversity, habitat specialization, and trophic characteristics of mycobiota, including Basidiomycota, in the northern ecosystems of the Krasnoyarsk Krai (Central Siberia) near Norilsk. Larch forests and woodlands in the Siberian permafrost zone are distinctive and Basidiomycota, as a component of these ecosystems, plays an essential role in their functioning. Currently, there is a paucity of information about this group in Arctic ecosystems, both in terms of floristic and ecological aspects. Seventy species of macromycetes belonging to different trophic groups were discovered and identified. Only 15% of species occur regularly, while most species are found rarely or only once. The identified species belong to 44 genera, 25 families, and 8 orders, which are included in the class Agaricomycetes. The leading families in terms of the number of species are Russulaceae, Polyporaceae, Tricholomataceae, Suillaceae, Strophariaceae, and Cortinariaceae. Mycorrhizal fungi and wood decay fungi dominate the structure of mycobiota of the study area (the total share is 71%). The rest of the species (29%) are fungal decomposers inhabiting plant litter, the forest floor, and humus. The largest number of species occur in forest ecosystems, which are dominated by mycorrhizal and wood decay fungi (up to 70%), which are trophically associated with woody plants and debris. The fungal decomposers inhabiting plant litter, the forest floor, and humus dominate (about 80%) in the species composition of tundra, where, in the absence of woody substrate, wood decay fungi have not been found at all. The species richness of tree and shrub Arctic ecosystems is low, yet the taxonomical and ecological structure of Basidiomycota is similar to that observed in taiga and temperate forests. These data permit a more comprehensive description of the biodiversity of the Arctic and may prove useful in studying biological processes in these ecosystems.

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“…Culturing approaches are known to only capture a small representation of the microbes present in the natural environment, which leaves most of the organisms unknown (Lloyd et al 2018 ). A recent study found that, of the microbial diversity of Svalbard permafrost observed through amplicon sequencing, only 6.37% of bacterial and 20% of fungal genera observed through amplicon sequencing were cultivable (Dziurzynski et al 2022 ). It is estimated that less than 1% of the total environmental microbial diversity can be cultivated under laboratory conditions (Kaeberlein et al 2002 ).…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have previously investigated the microbial communities of supraglacial habitats of the Greenland Ice Sheet through either culturing or culturing-independent approaches, or both (Musilova et al 2015 , Stibal et al 2015 , Cameron et al 2016 , Hauptmann et al 2017 , Perini et al 2019 , Mogrovejo et al 2020 , Poniecka et al 2020 , Millar et al 2021 ). Most papers, however, do not focus on comparing cultured diversity to diversity that is observed through sequencing, as was for instance done for Svalbard permafrost (Dziurzynski et al 2022 , Sipes et al 2022 ) and Tibetan glaciers (Liu et al 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches

Jaarsma,

Sipes,

Zervas

et al. 2023

FEMS Microbiology Ecology

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The microbiome of Greenland Ice Sheet supraglacial habitats is still under-investigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: 1) how microbial diversity differs between supraglacial habitats, 2) if obtained bacterial genomes reflect dominant community members, and 3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.

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Revealing the diversity of bacteria and fungi in the active layer of permafrost at Spitsbergen island (Arctic) – Combining classical microbiology and metabarcoding for ecological and bioprospecting exploration

Cited by 7 publications

References 63 publications

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla Periphylla

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla Periphylla

Fauna and Ecology of Macromycetes (Basidiomycota) in the Arctic Tree and Shrub Ecosystems of Central Siberia

Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches

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