Physiological and metabolic insights into the first cultured anaerobic representative of deep-seaPlanctomycetesbacteria

Planctomycetesbacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-seaPlanctomycetesmembers have been cultivated, limiting our understanding ofPlanctomycetesin the deep biosphere. Here, we have successfully cultured a novel strain ofPlanctomycetes(strain ZRK32) from a cold seep sediment, by using an enriched medium supplemented with rifampicin and different nitrogen sources. Our genomic, physiological and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named:Poriferisphaera heterotrophicis. We show that strain ZRK32 replicates using a budding mode of division. Based on the combined results from growth assays and transcriptomic analyses, we found that rich nutrients, or supplementation with NO₃^-or NH₄⁺promoted the growth of strain ZRK32 by facilitating energy production through the tricarboxylic acid (TCA) cycle and the Embden–Meyerhof–Parnas (EMP) glycolysis pathway. Moreover, supplementation with NO₃^-or NH₄⁺induced strain ZRK32 to release a bacteriophage in a chronic manner, without host cell lysis. This bacteriophage then enabled strain ZRK32, and another marine bacterium that we studied, to metabolize nitrogen through the function of auxiliary metabolic genes (AMGs). Overall, these findings expand our understanding of deep-seaPlanctomycetesbacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.