Historic shipwrecks function as habitats for benthic organisms by providing food, refuge, and structure. They also form islands of biodiversity on the seabed, shaping microbial ecology and ecosystem processes. This study examined two wooden deep‐sea shipwrecks at 525 and 1800 m water depth and probed their influence on sediment microbiomes and geochemistry. Microbiomes were investigated with 16S rRNA gene amplicon sequencing along 60 m transects extending in four directions from the hulls of the shipwrecks. Distance from shipwrecks and sediment depth both shaped microbiome structure. Archaeal alpha diversity was significantly and positively correlated with proximity to the deeper shipwreck while bacterial diversity was not to either. Archaeal community structure differed at both sites; the deeper site had a higher proportion of Bathyarchaeia and Lokiarchaeia proximate to shipwreck compared to the shallow location. Major bacterial communities were consistent at both sites, however, at the deeper site had higher abundance of Bacteroidetes, Chloroflexi, Desulfofarculales, and Desulfobacteriales. Core microbiome and differential abundance analyses revealed unique taxa nearest the shipwrecks compared to the surrounding seabed including organoheterotrophs, and cellulolytic and sulfur cycling taxa. Sediment carbon content influenced microbiome structure near the shipwrecks (5–10 m). We show that shipwrecks have a distinct sediment microbiome and form unique habitat patches on seabed, resembling those surrounding organic falls. The shipwreck influence was more pronounced at the deeper site, further from terrestrial influences signaling shipwrecks may be a significant source of organic matter in far‐shore oligotrophic settings.

The number of built structures on the seabed, such as shipwrecks, energy platforms, and pipelines, is increasing in coastal and offshore regions. These structures, typically composed of steel or wood, are substrates for microbial attachment and biofilm formation. The success of biofilm growth depends on substrate characteristics and local environmental conditions, though it is unclear which feature is dominant in shaping biofilm microbiomes. The goal of this study was to understand the substrate- and site-specific impacts of built structures on short-term biofilm composition and functional potential. Seafloor experiments were conducted wherein steel and wood surfaces were deployed for four months at distances extending up to 115 m away from three historic (>50 years old) shipwrecks in the Gulf of Mexico. DNA from biofilms on the steel and wood was extracted, and metagenomes were sequenced on an Illumina NextSeq. A bioinformatics analysis revealed that the taxonomic composition was significantly different between substrates and sites, with substrate being the primary determining factor. Regardless of site, the steel biofilms had a higher abundance of genes related to biofilm formation, and sulfur, iron, and nitrogen cycling, while the wood biofilms showed a higher abundance of manganese cycling and methanol oxidation genes. This study demonstrates how substrate composition shapes biofilm microbiomes and suggests that marine biofilms may contribute to nutrient cycling at depth. Analyzing the marine biofilm microbiome provides insight into the ecological impact of anthropogenic structures on the seabed.