# Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota

## TL;DR

This study reveals new diversity in the rare biosphere of marine sediments, focusing on the archaeal class Ca. Penumbrarchaeia and its potential role in organic matter degradation.

## Contribution

The study identifies three novel orders within Ca. Penumbrarchaeia and highlights their unique genetic and functional characteristics.

## Key findings

- Ca. Penumbrarchaeia is involved in organic matter degradation in anoxic, carbon-rich habitats.
- All six families of Ca. Penumbrarchaeia have high numbers of taxon-specific genes, indicating environmental adaptation.
- This group has the highest proportion of unknown genes in the Thermoplasmatota phylum, suggesting functional novelty.

## Abstract

Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.

In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.

In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa.

Video Abstract

Video Abstract

The online version contains supplementary material available at 10.1186/s40168-025-02140-8.