Sulfate reduction is estimated to account for half of the organic carbon respiration in anoxic, organic-rich ocean sediments. Sulfate-reducing microorganisms (SRMs) typically oxidize simple carbon compounds, such as primary alcohols, or small fatty acids. However, much of the organic input to the seafloor is complex, driving interactions between terminal respirers, such as SRMs and methanogens, and primary degraders that initiate the breakdown of complex organic carbon. To explore how these interactions shape sediment microbiomes, we conducted multi-month microcosm experiments using serially diluted sediments in deep 96-well plates. Sediments from a former deep-sea whalefall site were amended with either the insoluble polymer chitin or its soluble monomer N-acetylglucosamine. The high replication in these experiments allowed us to evaluate the effects of complex versus labile carbon on degradation activity, microbial diversity, community structure, and functional redundancy over time. Geochemical analysis, combined with 16S rRNA gene sequencing and metagenomics, revealed that chitin addition preserved higher microbial diversity and increased predicted interactions among microorganisms. Despite anaerobic chitin degradation producing N-acetylglucosamine, microbial communities enriched by these substrates showed low nestedness over the 7-month experiment. Complex carbon inputs fostered unique microbial assemblages and functional interactions, including the emergence of diverse methanogenic lineages at medium to high dilutions-less apparent in monomer treatments. In microoxic sediments, methanogens and other rare biosphere members co-exist with SRM and dynamically respond to complex carbon inputs. Our results highlight the contribution of carbon complexity and recalcitrance in stimulating metabolically diverse community members in sediments, driving the assembly of functional microbial networks. Deep-sea sediments cover over 60% of the planet's surface and harbor diverse microbial communities that are important contributors to the carbon and nitrogen budget of the ocean. Despite their importance, the mechanisms by which these communities maintain diversity are poorly understood. In this work, we discuss the contribution of complex carbon to the community structure of marine sediment microbial consortia through the establishment of highly replicated anaerobic incubations provided with either the complex cosmopolitan carbon source chitin or its monomer N-acetylglucosamine.
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