Using IODP Borehole Observatories to Discover Microbial Functions: Genome Analysis of Candidate Phylum Aminicenantes

Abstract:

Little is known about the microbial life supported by subsurface environments such as the ocean crust. The ocean crust is composed of porous rock through which seawater circulates. As fluid circulates, water-rock interactions provide nutrients for microorganisms living in this extreme environment. This project studies candidate phylum Aminicenantes genomes found in the ocean crust which could contribute to information regarding new life strategies, a deeper understanding of branches within the genomic tree of life, and how these poorly understood microbes may contribute to subsurface nutrient cycling. Two research cruises in 2011 and 2019 sampled warm and anoxic crustal fluid from borehole observatories installed during IODP Expedition 327 on the eastern flank of the Juan de Fuca Ridge. Cells were isolated from crustal fluid samples using flow cytometry at the Facility for Aquatic Cytometry and genomic DNA was sequenced using single-cell genomic techniques at the Single Cell Genomics Center at Bigelow Laboratory for Ocean Science. Aminicenantes cells were identified in samples from both research cruises indicating that this bacteria is an active and consistent member of the ocean crust microbial community. This project investigated 16 crustal fluid Aminicenantes genomes aiming to learn what types of carbon this organism is utilizing. We found compelling evidence that ocean crust Aminicenantes use heterotrophic forms of carbon metabolism indicating that this bacterial phylum may be an active member in ocean crust carbon cycling. Additionally, this project used 16S rRNA phylogenetic analyses to review publically available Aminicenantes sequences to determine where the crustal fluid Aminicenantes cells fit within this phylum. Based on this comparison, the crustal fluid Aminicenantes genomes form two clades, one within a preexisting class and the other may form a new class. This research adds to the limited knowledge of the role Aminicenantes may play in ocean crust carbon cycling. Future work aims to identify genome differences that cause the crustal fluid Aminicenantes cells to form a new class within this phylum.