Microbial dark matter filling the niche in hypersaline microbial mats
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RESEARCH
Open Access
Microbial dark matter filling the niche in hypersaline microbial mats Hon Lun Wong1,2, Fraser I. MacLeod1,2, Richard Allen White III2,3,4, Pieter T. Visscher2,5,6 and Brendan P. Burns1,2*
Abstract Background: Shark Bay, Australia, harbours one of the most extensive and diverse systems of living microbial mats that are proposed to be analogs of some of the earliest ecosystems on Earth. These ecosystems have been shown to possess a substantial abundance of uncultivable microorganisms. These enigmatic microbes, jointly coined as ‘microbial dark matter’ (MDM), are hypothesised to play key roles in modern microbial mats. Results: We reconstructed 115 metagenome-assembled genomes (MAGs) affiliated to MDM, spanning 42 phyla. This study reports for the first time novel microorganisms (Zixibacterial order GN15) putatively taking part in dissimilatory sulfate reduction in surface hypersaline settings, as well as novel eukaryote signature proteins in the Asgard archaea. Despite possessing reduced-size genomes, the MDM MAGs are capable of fermenting and degrading organic carbon, suggesting a role in recycling organic carbon. Several forms of RuBisCo were identified, allowing putative CO2 incorporation into nucleotide salvaging pathways, which may act as an alternative carbon and phosphorus source. High capacity of hydrogen production was found among Shark Bay MDM. Putative schizorhodopsins were also identified in Parcubacteria, Asgard archaea, DPANN archaea, and Bathyarchaeota, allowing these members to potentially capture light energy. Diversity-generating retroelements were prominent in DPANN archaea that likely facilitate the adaptation to a dynamic, host-dependent lifestyle. Conclusions: This is the first study to reconstruct and describe in detail metagenome-assembled genomes (MAGs) affiliated with microbial dark matter in hypersaline microbial mats. Our data suggests that these microbial groups are major players in these systems. In light of our findings, we propose H2, ribose and CO/CO2 as the main energy currencies of the MDM community in these mat systems.
Introduction A vast ‘known-unknown’ and even ‘unknown-unknown’, many microorganisms have yet to be unlocked from a majority of Earth’s ecosystems. These uncultured microbial community members represent a vast untapped and uncharacterised resource of biological information, representing the ‘microbial dark matter’ (MDM) of many microbial ecosystems [1, 2]. Despite the majority of these unexplored lineages possessing reduced genome sizes * Correspondence: [email protected] 1 School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia 2 Australian Centre for Astrobiology, University of New South Wales, Sydney, Australia Full list of author information is available at the end of the article
and minimal biosynthetic capacity, they were proposed to represent a major uncharacterised portion of microbial diversity and inhabiting every possible metabolic niche, that cover diverging metabolic n
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