Novel clostridial lineages recovered from metagenomes of a hot oil reservoir

Glenn D Christman,Rui Zhao,Zarath M Summers,Rosa I León-Zayas,Jennifer F Biddle

doi:10.1038/s41598-020-64904-6

Glenn D Christman, Rui Zhao + Show 3 more

Open Access

https://doi.org/10.1038/s41598-020-64904-6

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Abstract

Oil reservoirs have been shown to house numerous microbial lineages that differ based on the in-situ pH, salinity and temperature of the subsurface environment. Lineages of Firmicutes, including Clostridiales, have been frequently detected in oil reservoirs, but are typically not considered impactful or relevant due to their spore-forming nature. Here we show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales. These organisms form an oil-reservoir specific clade based on the phylogenies of both 16S rRNA genes and ribosomal proteins, which we propose to name UPetromonas tenebris, meaning they are single-celled organisms from dark rocks. Metagenome-assembled genomes (MAGs) of these Petromonas sp. were obtained and used to determine that these populations, while capable of spore-formation, were also likely replicating in situ in the reservoir. We compared these MAGs to closely related genomes and show that these subsurface Clostridiales differ, from the surface derived genomes, showing signatures of the ability to degrade plant-related compounds, whereas subsurface genomes only show the ability to process simple sugars. The estimation of in-situ replication from genomic data suggest that UPetromonas tenebris lineages are functional in-situ and may be specifically adapted to inhabit oil reservoirs.

Highlights

Oil reservoirs have been shown to house numerous microbial lineages that differ based on the insitu pH, salinity and temperature of the subsurface environment
Oil reservoirs are unique subsurface environments that can be hostile to life due to high temperatures, pressures, and salinity
Determining the indigenous microbial community structures in these reservoirs can be difficult because of the presence of pipeline and infrastructure contaminants, and the indigenous communities themselves can be altered in terms of member representation and activity by the injection of seawater or gases and chemical additives used for secondary recovery[4]

Summary

Introduction

Oil reservoirs have been shown to house numerous microbial lineages that differ based on the insitu pH, salinity and temperature of the subsurface environment. We show, using metagenomics, a high temperature oil reservoir of marine salinity contains a microbial population that is predominantly from within the Order Clostridiales. Were obtained and used to determine that these populations, while capable of spore-formation, were likely replicating in situ in the reservoir We compared these MAGs to closely related genomes and show that these subsurface Clostridiales differ, from the surface derived genomes, showing signatures of the ability to degrade plant-related compounds, whereas subsurface genomes only show the ability to process simple sugars. Many observed Clostridiales are spore formers, which may give them an advantage in persisting in these systems with high temperatures, pressures, and salinity This ability means that they are often overlooked in regards to their influence on the in-situ microbial community, as it is unknown if these organisms are active in the reservoir or present in a dormant, sporulated form. Few studies have assessed the portion of sporulated and vegetative cells of Clostridiales in oil reservoirs

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