Abstract

Candidatus Poribacteria is a little-known bacterial phylum, previously characterized by partial genomes from a single sponge host, but never isolated in culture. We have reconstructed multiple genome sequences from four different sponge genera and compared them to recently reported, uncharacterized Poribacteria genomes from the open ocean, discovering shared and unique functional characteristics. Two distinct, habitat-linked taxonomic lineages were identified, designated Entoporibacteria (sponge-associated) and Pelagiporibacteria (free-living). These lineages differed in flagellar motility and chemotaxis genes unique to Pelagiporibacteria, and highly expanded families of restriction endonucleases, DNA methylases, transposases, CRISPR repeats, and toxin–antitoxin gene pairs in Entoporibacteria. Both lineages shared pathways for facultative anaerobic metabolism, denitrification, fermentation, organosulfur compound utilization, type IV pili, cellulosomes, and bacterial proteosomes. Unexpectedly, many features characteristic of eukaryotic host association were also shared, including genes encoding the synthesis of eukaryotic-like cell adhesion molecules, extracellular matrix digestive enzymes, phosphoinositol-linked membrane glycolipids, and exopolysaccharide capsules. Complete Poribacteria 16S rRNA gene sequences were found to contain multiple mismatches to “universal” 16S rRNA gene primer sets, substantiating concerns about potential amplification failures in previous studies. A newly designed primer set corrects these mismatches, enabling more accurate assessment of Poribacteria abundance in diverse marine habitats where it may have previously been overlooked.

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Acknowledgements

We thank Dr. Michelle Schorn (Scripps Institution of Oceanography) and Dr. Eduardo Esquenazi and the Sirenas collection team (Sirenas Marine Discovery LLC) for sponge sample collection assistance. This work was supported by grants from NSF (MCB-1149552) to EEA and NSF (OCE-1313747) and NIEHS (P01-ES021921) to BSM and EEA.

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Affiliations

  1. Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA

    • Sheila Podell
    • , Jessica M. Blanton
    •  & Eric E. Allen
  2. Division of Biological Sciences, University of California, La Jolla, San Diego, CA, USA

    • Alexander Neu
    •  & Eric E. Allen
  3. School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA

    • Vinayak Agarwal
  4. Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA

    • Vinayak Agarwal
    • , Bradley S. Moore
    •  & Eric E. Allen
  5. University of Guam Marine Laboratory, UOG Station, Mangilao, Guam, USA

    • Jason S. Biggs
  6. Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, La Jolla, San Diego, CA, USA

    • Bradley S. Moore

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Correspondence to Eric E. Allen.

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https://doi.org/10.1038/s41396-018-0292-9