Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on the global scale. Microorganisms play an important role in mineralizing them therein, yet to identify in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found the family Marinifilaceae occurred as one of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea of both marginal and oceanic areas. This taxa is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups based on the phylogenomic tree. We described the metabolic features and in situ metabolizing activities of different MF subgroups via the metagenomic and metatranscriptomic data. One representative subgroup MF-2 dominated plant detritus-enriched cultures and specialized in polysaccharide degradation and lignin oxidation. Intriguingly, they encode nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, those dominating the animal tissue-supported microbiomes were more diverse and formed three subgroups, which distinguished themselves from MF-2 in carbon and nitrogen metabolisms. Despite these metabolic divergences of MF lineages, they harbored anaerobic processes for energy conservation via organic fermentation, anaerobic respiration via iron and manganese reduction, and/or dimethyl sulfoxide reduction. These results highlight the role of Marinifilaceae bacteria neglected before in organic matter mineralizing in marine environments coupling carbon and nitrogen cycling with metals and other elements.