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Cycloalkanes are an abundant and toxic class of compounds in subsurface petroleum reservoirs and their fate is quantitatively important to ecosystems impacted by natural oil seeps and spills. In this study, we focus on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often the most abundant cycloalkanes observed in petroleum and a substantial portion of these compounds will dissolve into the water column when introduced at the seafloor via a spill or natural seep. Once dissolved into the water column, the environmental fate of MCH and MCP is presumably controlled by microbial consumption, but little is known about this environmental process. We conducted incubations using fresh Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations along a transect with a gradient in the influence of natural oil seepage. We observe microbial blooms via optical oxygen sensors that occur at all stations with bloom occurrence among replicate incubations impacted by the proximity of natural seepage. Within all incubations with active respiration of MCH and MCP, we find thatB045, a novel genus of bacteria belonging to thePorticoccaceaefamily dominates the microbial community. Using seven high-quality metagenome-assembled genomes recovered from microbial blooms on MCH and MCP, we reconstruct the biodegradation pathways and central carbon metabolism ofB045, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a key role in MCH and MCP metabolism. Through comparative analysis of 176 genomes, we parse the taxonomy of thePorticoccaceaefamily and find evidence suggesting the acquisition ofpmoand other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.

Small genes (40,000 small-gene families in ~2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.