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

Abstract

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.

Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland

“…Studies of eukaryotic microbial diversity in freshwater environments are not as abundant as in marine environments but have been carried out in, e.g., Arctic and Antarctic cryoconite holes ( Cameron et al, 2012 ; Jaarsma et al, 2023 ), Patagonian and Antarctic lakes ( Schiaffino et al, 2016 ), Lake Vostoc in the Antarctic ( Gura and Rogers, 2020 ) and ice-covered, freshwater lakes in Subarctic Russia ( Galachyants et al, 2023 ). The studies in general describe a rich eukaryotic diversity, including Ciliophora (ciliates), Cryptophyceae (flagellated algae), Dinophyceae (dinoflagellates), Bacillariophyceae (diatoms), Basidio- and Ascomycota (fungi), and Chlorophyta (green algae), which aligns well with our findings except that we, within the fungi, find Cryptomycota in much higher abundance that the Basidio- and Ascomycota.…”

“…Demultiplexed raw reads from Illumina metagenome sequencing were run through the in-house TotalRNA bioinformatics pipeline v1.1.0 2 in order to trim the reads, perform quality control and assemble full-length rRNA genes. Information about program versions and flags are presented in detail on the Github page and on recent publications ( Jaarsma et al, 2023 ; Scheel et al, 2023 ). Briefly, trimmed reads were sorted into a “Small Subunit” Pool with SortMeRNA ( Kopylova et al, 2012 ) and the SILVA 138.1 SSU Ref NR 99 database, before being assembled in full-length rRNA contigs using MetaRib ( Xue et al, 2020 ) and taxonomically classified with CREST4 ( Lanzen et al, 2012 ) as described elsewhere ( Anwar et al, 2019 ).…”

“…Metagenomes from Polar and high-altitude environments tend to be dominated by Pseudomonadota (Proteobacteria) and/or Actinomycetota (Actinobacteria; Glaring et al, 2015 ; Oh et al, 2019 ; Rai and Bhattacharjee, 2021 ; Zhang et al, 2021 ; Singh et al, 2022 ), indicating that these phyla are ubiquitously present in all cold habitats. Pseudomonadota, furthermore, seems to be relatively well represented among cultured isolates from polar regions in general ( Groudieva et al, 2004 ; Schmidt et al, 2006a ; García-Echauri et al, 2011 ; Sathyanarayana Reddy et al, 2016 ; Aguayo et al, 2017 ; Jaarsma et al, 2023 ). Attempts to bring more difficult-to-culture bacterial strains into culture have for years been carried out through, e.g., application of the iChip ( Nichols et al, 2010 ; Jaarsma et al, 2023 ) and similar co-culture approaches, where in situ nutrients and signaling molecules are made available to the microbial cultures through a diffusion membrane.…”

“…Pseudomonadota, furthermore, seems to be relatively well represented among cultured isolates from polar regions in general ( Groudieva et al, 2004 ; Schmidt et al, 2006a ; García-Echauri et al, 2011 ; Sathyanarayana Reddy et al, 2016 ; Aguayo et al, 2017 ; Jaarsma et al, 2023 ). Attempts to bring more difficult-to-culture bacterial strains into culture have for years been carried out through, e.g., application of the iChip ( Nichols et al, 2010 ; Jaarsma et al, 2023 ) and similar co-culture approaches, where in situ nutrients and signaling molecules are made available to the microbial cultures through a diffusion membrane. Other methods for bringing hard-to-culture microorganisms into culture comprise variants of the “dilution to extinction” or other cell separation approaches to reduce competition and fast-growing species ( Connon and Giovannoni, 2002 ; Stingl et al, 2008 ; Yadav et al, 2022 ) or through fabrication of artificial substrates with a nutrient or chemical composition as similar to the natural environment as possible ( Imazaki and Kobori, 2010 ; Rygaard et al, 2017 ; Mourad et al, 2018 ; Wu et al, 2020 ).…”

Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier

“…The prevalent Patescibacteria in supraglacial and proglacial sediment samples constitute an uncharacterized group frequently documented in cold environments (Kumar et al 2022 , Rathore et al 2022 ). Cyanobacteria, identified as the main primary producers in supraglacial habitats worldwide (Anesio et al 2017 , Rathore et al 2022 , Jaarsma et al 2023 ), was detected in the ERG surface sediments. Interestingly, Bdellovibrionota—a predatory bacterial group, occured in the supraglacial meltwater samples.…”