Substantial genetic potential for deep-sea chemoautotrophy extends beyond nitrifiers

Abstract

I.Microbial chemoautotrophy in the deep sea has the potential to sustain ecosystems at depth, contribute to global carbon sequestration, and ameliorate the currently unbalanced deep-sea carbon budget. However, an understanding of its mechanisms and feasibility is still emerging, particularly beyond that fueled by nitrification. Here, we conduct both a gene-based and genome-resolved analysis of 28 metagenomes in the Northeast Pacific Ocean to investigate the prevalence, distribution, and phylogenetic and metabolic diversity of deep-sea chemoautotrophs. We find that organisms encoding marker genes for dissolved inorganic carbon (DIC) fixation are abundant and widespread at our study site, comprising 11-26% of microbial communities from 150-4000 m water depth. Marker genes for the Calvin cycle and 3-Hydroxypropionate (3HP) bi-cycles are more prevalent than those for the 3-Hydroxypropionate/4-Hydroxybutyrate (3HP/4HB) and reverse Tricarboxylic Acid (rTCA) cycles, the latter two of which are encoded by organisms conducting nitrification. We construct and identify 128 putatively chemoautotrophic metagenome-assembled genomes, spanning 14 phyla including the Proteobacteria, Actinobacteria, SAR324, and the Thermoproteota. They contained genes for the oxidation of carbon monoxide (77.3%), sulfur (68.8%), ammonia (5.5%), and/or methane (3.1%), suggesting diverse catabolisms fuel deep-sea DIC fixation and an underappreciated potential role for aerobic carbon monoxide oxidation. Fifty percent of these genomes encoded multiple inorganic catabolic pathways and 99% included genes for organic matter transport, suggesting catabolic flexibility and potentially facultative autotrophy, respectively. We create an inclusive inventory and map of potential chemoautotrophs at our study site, expanding their known phylogenetic breadth, metabolic repertoires, and potential to impact the carbon cycle. ImportanceThe deep-sea carbon cycle plays a central role regulating marine ecosystem productivity and the global climate. Chemoautotrophy, the microbial conversion of inorganic carbon (e.g., CO2 or HCO-3) into cellular biomass, is an understudied process with the potential to significantly shift models of the marine carbon budget. While some deep-sea chemoautotrophs are known, a wholistic analysis of organisms with the genetic potential for chemoautotrophy in the dark water column is lacking. Here, we find that microorganisms with the genetic potential for chemoautotrophy are widespread and abundant, and that they are more phylogenetically and metabolically diverse than previously appreciated. In particular, the prevalence of genes involved in CO oxidation suggests a currently unrecognized role in fueling deep-sea chemoautotrophy. By identifying the potential microbial mediators and coupled energy sources, our results allow for more accurate predictions of when, where, and how deep-sea chemoautotrophy occurs, and therefore its potential role in carbon cycling.