Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns

Benjamin J Tully

doi:10.1038/s41467-018-07840-4

Abstract

Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world, and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present a comparative genomic analysis of 250 MGII genomes, providing a comprehensive investigation of these mesophilic archaea. This analysis identifies 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera reveals distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins, common in all other subclades.

Highlights

Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references
These genomic studies have revealed a number of reoccurring traits common to the MGII, including: proteorhodopsins in MGII sampled from the photic zone[13], genes targeting the degradation of high molecular weight (HMW) organic matter, such as proteins, carbohydrates, and lipids, and subsequent transport of constituent components into the cell[11,14,15,16], genes representative of particle-attachment[9,14], and genes for the biosynthesis of tetraether lipids[11,17]
The analysis of 250 non-redundant MGII genomes identifies the metabolic traits unique to the genomes derived from the MGIIa and MGIIb, providing new context for the ecological roles each clade plays in remineralization of HMW organic matter

Summary

Introduction

Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) remain a difficult group of organisms to study, lacking cultured isolates and genome references. Instead our current understanding of the role these organisms play is derived from interpretations of environmental sampling data (e.g., phytoplankton- and particle-associated) and a limited number of genomic fragments and reconstructed environmental genomes These genomic studies have revealed a number of reoccurring traits common to the MGII, including: proteorhodopsins in MGII sampled from the photic zone[13], genes targeting the degradation of high molecular weight (HMW) organic matter, such as proteins, carbohydrates, and lipids, and subsequent transport of constituent components into the cell[11,14,15,16], genes representative of particle-attachment[9,14], and genes for the biosynthesis of tetraether lipids[11,17]. The MGIIa and MGIIb can be assigned to 17 subclades, with distinct ecological patterns with respect to sample depth, particle size, temperature, and nutrient concentrations

Methods

Results

Conclusion