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. 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. 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.

中文翻译：

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微生物暗物质填充高盐微生物垫中的生态位。

澳大利亚的鲨鱼湾拥有最广泛和最多样化的活动微生物垫系统之一，据提议该系统可与地球上某些最早的生态系统类似。这些生态系统已显示出拥有大量不可培养的微生物。据推测，这些神秘的微生物共同被称为“微生物暗物质”（MDM），在现代微生物垫中起着关键作用。我们重建了MDM的115个元基因组组装基因组（MAG），跨越42个门。这项研究首次报道了新型微生物（Zixibacterial GN15）被认为参与了表面高盐环境的异化硫酸盐还原，以及阿斯加德古细菌中的新型真核生物标志蛋白。尽管基因组尺寸缩小，MDM MAG具有发酵和降解有机碳的能力，暗示了其在回收有机碳方面的作用。鉴定了几种形式的RuBisCo，允许推定的CO2掺入核苷酸挽救途径，这可以作为碳和磷的替代来源。在鲨鱼湾MDM中发现了高产氢能力。在细小细菌，阿斯加德古细菌，DPANN古细菌和水生古细菌中也鉴定出假定的精神分裂视紫红质，使这些成员有可能捕获光能。产生多样性的后代元素在DPANN古细菌中很重要，这可能有助于适应动态的，寄主依赖性的生活方式。这是首次重建和详细描述与高盐微生物垫中的微生物暗物质相关的元基因组组装基因组（MAG）的研究。我们的数据表明，这些微生物群是这些系统的主要参与者。根据我们的发现，我们建议将H2，核糖和CO / CO2作为这些垫系统中MDM社区的主要能源。