With a pinch of salt : metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities

dc.contributor.authorMartinez-Alvarez, Laura
dc.contributor.authorRamond, Jean-Baptiste
dc.contributor.authorVikram, Surendra
dc.contributor.authorLeon-Sobrino, Carlos
dc.contributor.authorMaggs‑Kolling, Gillian
dc.contributor.authorCowan, Don A.
dc.contributor.emaildon.cowan@up.ac.zaen_US
dc.date.accessioned2024-02-07T09:10:03Z
dc.date.issued2023-11
dc.descriptionDATA AVAILABILITY : Metagenomic data generated in this work can be accessed through the IMG/M database (https://img.jgi.doe.gov/) under GOLD Sequencing Project ID: Gp0293142 and IMG Genome IDs: 3300023218, 3300023197, 3300022725, 3300023214, 3300023202, 3300022723, 3300022777, 3300022719, 3300022719 and 3300022719. The unassembled reads from all datasets analyzed are available in the SRA database under BioProject PRJNA943124, accession numbers: SRR23862440, SRR23862446, SRR23862438, SRR23862439, SRR23862444, SRR23862445, SRR23862443, SRR23862437, SRR23862441, SRR23862442en_US
dc.description.abstractSalt pans or playas, which are saline-rich springs surrounded by halite evaporates in arid environments, have played an essential role in landscape erosion during the formation of the Namib Desert and are numerous in its central region. In this study, we used shotgun metagenomics to investigate the phylogenetic and functional capacities of the microbial communities from two salt pans (namely, Eisefeld and Hosabes) located in central Namib Desert, located in Southwest Africa. We studied the source and sink sediment mat communities of the saline streams, as well as those from two halites (crystallized structures on the stream margins). The microbial assemblages and potential functions were distinct in both niches. Independently from their localization (Eisfeld vs Hosabes and source vs sink), the sediment mat communities were dominated by members of the Alpha- and Gamma-proteobacteria classes, while halites were Archaea dominated and also contained high abundances of the extremely halophilic bacterium Salinibacter sp. (phylum Bacteroidota). Photoheterotrophy and chemoheterotrophy were the principal lifestyles in both niches, with halite communities having a reduced diversity of metabolic pathways. Intense microbial-virus interactions in both niches were implied by the widespread detection of CRISPR-Cas defense systems. We identified a putatively novel clade of type II CRISPR-Cas systems, as well as novel candidate viral lineages of the class Caudoviricetes and of Halobacteriales-infecting haloviruses. Putative gene transfer agent-like sequences within the Alphaproteobacteria were identified in the sediment mat communities. These horizontal gene transfer elements have the potential to drive genome plasticity and evolution of the Alphaproteobacteria in the Namib Desert salt pan microbiomes.en_US
dc.description.departmentBiochemistryen_US
dc.description.departmentGeneticsen_US
dc.description.departmentMicrobiology and Plant Pathologyen_US
dc.description.embargo2024-05-16
dc.description.librarianhj2024en_US
dc.description.sdgSDG-15:Life on landen_US
dc.description.sponsorshipThe University of Pretoria and the National Research Foundation.en_US
dc.description.urihttp://aem.asm.orgen_US
dc.identifier.citationMartínez-Alvarez, L., Ramond, J.B., Vikram, S. et al. 2023, 'With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities', Applied and Environmental Microbiology, vol. 89, no. 12, doi : 10.1128/aem.00629-23.en_US
dc.identifier.issn0099-2240 (print)
dc.identifier.issn1098-5336 (online)
dc.identifier.other10.1128/aem.00629-23
dc.identifier.urihttp://hdl.handle.net/2263/94368
dc.language.isoenen_US
dc.publisherAmerican Society for Microbiologyen_US
dc.rights© 2023 American Society for Microbiology. All Rights Reserved.en_US
dc.subjectSalt pansen_US
dc.subjectPlayasen_US
dc.subjectNamib Deserten_US
dc.subjectCRISPR-Casen_US
dc.subjectFunctional diversityen_US
dc.subjectTaxonomic diversityen_US
dc.subjectMicrobial maten_US
dc.subjectHaliteen_US
dc.subjectHorizontal gene transferen_US
dc.subjectGene transfer agenten_US
dc.subjectVirus-host interactionsen_US
dc.subjectSDG-15: Life on landen_US
dc.titleWith a pinch of salt : metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communitiesen_US
dc.typePostprint Articleen_US

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