Abstract
Summary Particulate membrane‐associated hydrocarbon monooxygenases ( pHMOs ) are critical components of the aerobic degradation pathway for low molecular weight hydrocarbons, including the potent greenhouse gas methane. Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon‐rich hydrothermal plumes in the G uaymas B asin ( GB ) and nearby background waters in the deep G ulf of C alifornia. Seven distinct phylogenetic groups of pHMO were present and transcriptionally active in both plume and background waters, including several that are undetectable with currently available polymerase chain reaction ( PCR ) primers. The seven groups of pHMOs included those related to a putative ethane oxidizing M ethylococcaceae ‐like group, a group of the SAR 324 D eltaproteobacteria , three deep‐sea clades (Deep sea‐1/symbiont‐like, Deep sea‐2/ PS ‐80 and Deep sea‐3/ OPU 3) within gammaproteobacterial methanotrophs, one clade related to Group Z and one unknown group. Differential abundance of pHMO gene transcripts in plume and background suggests niche differentiation between groups. Corresponding 16 S rRNA genes reflected similar phylogenetic and transcriptomic abundance trends. The novelty of transcriptionally active pHMOs we recovered from a hydrocarbon‐rich hydrothermal plume suggests there are significant gaps in our knowledge of the diversity and function of these enzymes in the environment.