Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria

  1. CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
  2. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
  3. Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
  4. College of Earth Science, University of Chinese Academy of Sciences, Beijing, China

Peer review process

Not revised: This Reviewed Preprint includes the authors’ original preprint (without revision), an eLife assessment, public reviews, and a response from the authors (if available).

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Editors

  • Reviewing Editor
    David Paz-Garcia
    Centro de Investigaciones Biológicas del Noroeste (CIBNOR), La Paz, Mexico
  • Senior Editor
    Bavesh Kana
    University of the Witwatersrand, Johannesburg, South Africa

Reviewer #1 (Public Review):

The authors of the manuscript cultivated a Planctomycetes strain affiliated with Phycisphaerae. The strain was one of the few Planctomycetes from deep-sea environments and demonstrated several unique characteristics, such as being the only known Phycisphaerae using a budding mode of division, extensive involvement in nitrate assimilation, and being able to release phage particles without cell death. The manuscript is generally well-written. However, a few issues need to be more clearly addressed, especially regarding the identification and characterization of the phage.

Reviewer #2 (Public Review):

Summary:

Planctomycetes encompass a group of bacteria with unique biological traits, the compartmentalized cells make them appear to be organisms in between prokaryotes and eukaryotes. However, only a few of the Planctomycetes bacteria are cultured thus far, and this hampers insight into the biological traits of these evolutionarily important organisms.

This work reports the methodology details of how to isolate the deep-sea bacteria that could be recalcitrant to laboratory cultivation, and further reveals the distinct characteristics of the new species of a deep-sea Planctomycetes bacterium, such as the chronic phage release without breaking the host and promote the host and related bacteria in nitrogen utilization. Therefore, the finding of this work is of importance in extending our knowledge of bacteria.

Strengths:

Through the combination of microscopic, physiological, genomics, and molecular biological approaches, this reports the isolation and comprehensive investigation of the first anaerobic representative of the deep-sea Planctomycetes bacterium, in particular in that of the budding division, and release phage without lysis of the cells. Most of the results and conclusions are supported by the experimental evidence.

Weaknesses:

1. While EMP glycolysis is predicted to be involved in energy conservation, no experimental evidence indicated any sugar utilization by the bacterium.
2. "anaerobic representative" is indicated in the Title, the contrary, TCA in energy metabolism is predicted by the bacterium.
3. The possible mechanisms of the chronic phage release without breaking the host are not discussed.

  1. Howard Hughes Medical Institute
  2. Wellcome Trust
  3. Max-Planck-Gesellschaft
  4. Knut and Alice Wallenberg Foundation