Ecology of ultra-small prokaryotic and viral communities in the terrestrial subsurface

Abstract

Aquifers harbor a large fraction of microbial life, most of which remains poorly characterised, despite growing interest in this area. A multi-omics study was undertaken to characterize microbial communities over a wide range of aquifer groundwater chemistries. Results indicate that prokaryotes with ultra-small genomes (e.g., the recently described Patescibacteria or Candidate Phyla Radiation, Dependentiae and DPANN radiation) are a characteristic feature of the terrestrial subsurface, present in geochemically and lithologically diverse, and geographically widespread, aquifers. Community composition of the ultra-small fraction was largely shaped by water oxygen content, while site-specific relative abundance profiles were driven by a combination of factors. Phylogenetically diverse ultra-small organisms cooccurred across sites, indicating shared preferences for groundwater conditions. All ultra-small phyla lacked numerous biosynthetic pathways, consistent with a symbiotic lifestyle. Despite this, gene expression profiles provided evidence that these organisms are major contributors to groundwater community transcriptional activity. The genetic exchange of metabolic functions in the terrestrial subsurface is not well understood, particularly for streamlined prokaryotes such as Patescibacteria. Horizontal gene transfer events in Patescibacteria were investigated and compared to other groundwater taxa. Despite the reductive evolution of Patescibacteria, these organisms exhibited evidence of dynamic genetic exchange, primarily with one other, but also diverse donors across archaeal and bacterial domains. Metabolic functions encoded by horizontally acquired regions were diverse, but were mainly critical functions, such as transcription, translation and defense. To further characterise agents of gene exchange, hundreds of viral genomes were reconstructed and analysed. Most were taxonomically unclassified, indicating substantial unexplored viral diversity. Putative prokaryotic hosts of groundwater viruses were predicted in silico. Hosts included ultra-small phyla, and were diverse. Many hosts were associated with biogeochemical cycling of carbon, nitrogen and sulfur. Groundwater parameters (e.g. dissolved oxygen and total iron) were found to impact viral community compositions and host-virus pairs. Metabolic predictions identified numerous putative host-derived genes (auxiliary metabolic genes), involved in diverse processes such as carbohydrate metabolism and sulfur cycling. Findings in this thesis provide insights into underexplored groundwater viral and ultra-small prokaryotic communities, and their environmental preferences, illustrating their large contribution to diversity and biological processes in the terrestrial subsurface.