Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea <i>Planctomycetes</i> bacteria.

Abstract

<i>Planctomycetes</i> bacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-sea <i>Planctomycetes</i> members have been cultivated, limiting our understanding of <i>Planctomycetes</i> in the deep biosphere. Here, we have successfully cultured a novel strain of <i>Planctomycetes</i> (strain ZRK32) from a deep-sea cold seep sediment. Our genomic, physiological, and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named: <i>Poriferisphaera heterotrophicis</i>. 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 cycle and the Embden-Meyerhof-Parnas 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. Overall, these findings expand our understanding of deep-sea <i>Planctomycetes</i> bacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.