Genomic and transcriptomic evidence for scavenging of diverse organic compounds by widespread deep-sea archaea.

Meng Li,Brett J Baker,Karthik Anantharaman,Sunit Jain,John A Breier,Gregory J Dick

doi:10.1038/ncomms9933

Abstract

Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. However, little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans. Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Genome-enabled metabolic reconstructions and gene expression patterns show that these marine archaea are motile heterotrophs with extensive mechanisms for scavenging organic matter. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling.

Highlights

Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor
Four major groups of planktonic archaea have been reported in the global ocean, including Marine Group I Thaumarchaeota (MG-I)[2,3], Marine Group II Euryarchaeota (MG-II)[4], Marine Group III Euryarchaeota (MG-III)[4] and Marine Group IV Euryarchaeota (MG-IV)[5]
While MG-III and MG-IV are predominately found in the deep oceans at relatively low abundance[4,5], qualitative and quantitative studies suggest that MG-II are abundant in surface waters[4,6,7], whereas MG-I dominates at greater depths, sometimes constituting up to nearly 40% of marine microbial plankton[8]

Summary

Introduction

Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor. We present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins, carbohydrates, fatty acids and lipids as sources of carbon and energy at depths ranging from 800 to 4,950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins. Our results shed light on the ecological and physiological properties of ubiquitous marine archaea and highlight their versatile metabolic strategies in deep oceans that might play a critical role in global carbon cycling. We reconstructed 59 partial to near-completed genomes and transcriptomes of several ubiquitous uncultured archaea groups from deep-sea hydrothermal plumes and surrounding background seawater at three distinct locations. Our results reveal metabolic characteristics of these ubiquitous marine archaea and suggest that they play critical roles in modulating carbon cycle in deep oceans

Methods

Results

Conclusion