Cross-feeding options define genome evolution and community assembly of deep groundwater microbiome

TL;DR

This study explores how deep groundwater microbes evolve and form communities based on their metabolic interactions in nutrient-poor environments.

Contribution

The study introduces new insights into how metabolic cross-feeding influences genome evolution and community assembly in deep groundwater microbiomes.

Findings

Larger-genomed lineages thrive in deep, nutrient-poor groundwater, while metabolically dependent lineages decline.

Similar ecological niches are occupied by distinct microbial lineages across different groundwater sites.

Metabolic cross-feeding is limited in deep groundwater ecosystems, affecting microbial community assembly.

Abstract

Deep groundwaters populated by diverse and active microbes are among the most energy and nutrient-limited ecosystems. Characteristics of this ecosystem (including nutrient and dispersal limitations, low cell densities, and an episodic growth strategy) interactively underpin the so far elusive eco-evolutionary dynamics of its microbiome. Here, we used genome-resolved modular metabolic analyses of disconnected deep groundwater sites in the Fennoscandian Shield to test how eco-evolutionary constraints in these deep groundwater ecosystems shape microbial genome architecture, metabolic versatility, and community assembly at different depths.

The analysis revealed that lineages with larger genomes (≥ 2.6 Mb) maintained higher population sizes in the deepest and most oligotrophic groundwaters, whereas lineages with known metabolic dependencies, such as and DPANN, declined in relative abundance with depth. This pattern was interpreted as consistent with limited opportunities for sustained metabolic cross-feeding in these ecosystems. Moreover, while similar ecological niches based on cross-feeding interactions and potential primary production were available across different boreholes, distinct microbial lineages appeared to occupy these niches at each site.

The findings provided new insights into the role of metabolic cross-feeding in genome evolution and community assembly of deep groundwater microbiomes. By extending the streamlining theory, this study underscores the critical influence of ecological interactions, particularly metabolic exchanges, in shaping microbial life under severe nutrient limitation, offering new insights into subsurface microbial communities.

The online version contains supplementary material available at 10.1186/s40793-026-00865-z.

Figures