Substantial genetic potential for deep-sea chemoautotrophy extends beyond nitrifiers

Microbial chemoautotrophy has the potential to sustain ecosystems at depth, contribute to global carbon sequestration, and ameliorate the currently unbalanced marine carbon budget. However, an understanding of its mechanisms is still emerging, particularly beyond organisms performing nitrification. Here, we conduct a combined gene-based and genome-resolved analysis of 28 metagenomes from the Northeast Pacific Ocean to investigate the prevalence, distribution, and phylogenetic and metabolic diversity of marine chemoautotrophs. We find that organisms encoding marker genes for autotrophic dissolved inorganic carbon (DIC) fixation are abundant and widespread within our samples, comprising 11%-26% of microbial communities from 150 to 4,000 m water depth. Marker genes for the Calvin cycle and 3-hydroxypropionate bi-cycles are more prevalent than those for the 3-hydroxypropionate/4-hydroxybutyrate and reverse tricarboxylic acid cycles, the latter two of which are encoded by organisms conducting nitrification. We constructed and identified 128 putatively chemoautotrophic metagenome-assembled genomes (MAGs), spanning 13 phyla including the Proteobacteria, Actinobacteria, SAR324, and the Thermoproteota. These MAGs contain genes for the oxidation of carbon monoxide (77.3%), sulfur (69.5%), ammonia (5.5%), and/or methane (3.1%), suggesting that diverse catabolisms support deep-sea DIC fixation and an underappreciated potential role for aerobic carbon monoxide oxidation. Fifty percent of these MAGs encode multiple inorganic catabolic pathways, and 99% include genes for organic matter transport, suggesting catabolic flexibility and the use of externally produced organic matter, 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 marine carbon cycle plays a central role in regulating ecosystem productivity and the global climate. Chemoautotrophy, the microbial conversion of inorganic carbon (e.g., CO₂ or HCO₃^-) into cellular biomass, is an understudied process with the potential to significantly shift models of the marine carbon budget. While some marine chemoautotrophs are known, recent evidence suggests that the existing inventory is incomplete. Here, we find that microorganisms with the genetic potential for chemoautotrophy are more phylogenetically and metabolically diverse than previously appreciated. In particular, the prevalence of genes involved in CO oxidation suggests a potentially unrecognized role in supporting deep-sea chemoautotrophy. By identifying the potential microbial mediators and coupled energy sources, our results could aid future predictions of when, where, and how deep-sea chemoautotrophy occurs, and therefore its potential role in carbon cycling.