# Differential Expression of Core Metabolic Functions in Candidatus Altiarchaeum Inhabiting Distinct Subsurface Ecosystems

## TL;DR

This study compares gene expression in two subsurface-dwelling Candidatus Altiarchaeum species to understand how they adapt to different environments.

## Contribution

The paper reveals how gene expression differences in Ca. Altiarchaeum are influenced by viruses and symbiotic interactions in distinct subsurface ecosystems.

## Key findings

- 130 out of 331 annotated gene clusters showed significant expression differences between the two ecosystems.
- Genes related to virus defense and energy metabolism were overexpressed in the sulfidic spring population.
- CRISPR-Cas and polysaccharide biosynthesis genes were more active in the high-CO2 groundwater population.

## Abstract

Candidatus Altiarchaea are widespread across aquatic subsurface ecosystems and possess a highly conserved core genome, yet adaptations of this core genome to different biotic and abiotic factors based on gene expression remain unknown. Here, we investigated the metatranscriptome of two Ca. Altiarchaeum populations that thrive in two substantially different subsurface ecosystems. In Crystal Geyser, a high‐CO2 groundwater system in the USA, Ca. Altiarchaeum crystalense co‐occurs with the symbiont Ca. Huberiarchaeum crystalense, while in the Muehlbacher sulfidic spring in Germany, an artesian spring high in sulfide concentration, Ca. A. hamiconexum is heavily infected with viruses. We here mapped metatranscriptome reads against their genomes to analyse the in situ expression profile of their core genomes. Out of 537 shared gene clusters, 331 were functionally annotated and 130 differed significantly in expression between the two sites. Main differences were related to genes involved in cell defence like CRISPR‐Cas, virus defence, replication, transcription and energy and carbon metabolism. Our results demonstrate that altiarchaeal populations in the subsurface are likely adapted to their environment while influenced by other biological entities that tamper with their core metabolism. We consequently posit that viruses and symbiotic interactions can be major energy sinks for organisms in the deep biosphere.

Major differences between Candidatus Altiarchaeum species living in two distinct subsurface ecosystems as determined via metatranscriptomics. Genes overly expressed in different Ca. Altiarchaea in Muehlbacher sufidic spring (magenta; MSI; Regensburg, Germany) and Crystal Geyser (turquise; CG; Utah, USA). Ca. Altiarchaeum hamiconexum communities in MSI overexpressed genes encoding for phage shock proteins, signal peptide peptidases and FtsZ compared to Ca. Altiarchaeum crystalense in CG. In CG, the latter has an episymbiont (Probst et al. 2018 Nature Microbiology 3: 328–336; Esser et al. 2023 Nature Microbiology 8: 1619–1633) and exhibited a comparatively higher expression of genes encoding for CRISPR‐Cas, polysaccharide biosynthesis proteins and modification methylase MboII.