Data Mining of Sediment Microbiomes of the Tibetan Plateau Revealed a Genomic Repository of Ancient Lineages and Adaptive Evolution of Asgardarchaeota

TL;DR

This study explores sediment microbiomes on the Tibetan Plateau, uncovering ancient microbial lineages and adaptive evolution in extreme environments.

Contribution

The study introduces a comprehensive microbial catalog and reveals the Tibetan Plateau as a genomic repository of ancient and adaptive microbes.

Findings

The Tibetan Plateau sediment microbiome contains over 90% novel species, expanding microbial diversity knowledge.

Sediments host a high proportion of ancient archaeal lineages, suggesting a microbial 'sedimentary archive'.

Asgardarchaeota in sediments show ancient divergence and adaptations to extreme environments.

Abstract

The extreme climatic conditions of the Tibetan Plateau foster unique microbial communities, especially in the sediment ecosystem. A thorough understanding of these communities could facilitate revealing their microbial diversity, biological resources, and response to climate change. Here, we have constructed the Tibetan Plateau Microbial Catalog of Sediment (TPMC-S) based on 248 metagenomic sediment samples from the Tibetan Plateau. We identified 511,056,752 nonredundant genes and recovered 13,696 metagenome-assembled genomes with enormous phylogenetic novelty (over 90% novel species), far exceeding other contemporary Tibetan microbial catalogs and expanding the microbial functional diversity. We also revealed that similarities of sediment microbial communities followed the distance–decay relationship. Furthermore, sediments contained a high proportion of evolutionarily “possible ancient species (PAS)” compared with paired aquatic samples, especially ancient archaeal lineages, suggesting a microbial “sedimentary archive” in sediment. Finally and most importantly, Asgardarchaeota, including 2 potentially novel genera, were identified from the sediments, and their latest divergence predated the uplift of the Tibetan Plateau, while they still gained functions to adapt to extreme environments. Our findings positioned the Tibetan Plateau as both a genomic repository of microbial antiquity, especially Asgardarchaeota, and an active arena for modern extremophile innovation, providing insights for deciphering microbial resilience strategies in climate-sensitive ecosystems and informing novel bioprospecting efforts.

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