Polysaccharides induce deep-sea Lentisphaerae strains to release chronic bacteriophages
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Curated by eLife
eLife assessment
This manuscript presents useful findings on several phage from deep sea isolates of Lentisphaerae strains WC36 and zth2 that further our understanding of deep sea microbial life. The manuscript's primary claim is that phage isolates augment polysaccharide use in Pseudomonas bacteria via auxiliary metabolic genes (AMGs). However, the strength of the evidence is incomplete and does not support the primary claims. Namely, there are not data presented to rule out phage contamination in the polysaccharide stock solution, AMGs are potentially misidentified, and there is missing evidence of successful infection.
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Abstract
Viruses are ubiquitous in nature and play key roles in various ecosystems. Notably, some viruses (e.g. bacteriophage) exhibit alternative life cycles, such as chronic infections without cell lysis. However, the impact of chronic infections and their interactions with the host organisms remains largely unknown. Here, we found for the first time that polysaccharides induced the production of multiple temperate phages infecting two deep-sea Lentisphaerae strains (WC36 and zth2). Through physiological assays, genomic analysis, and transcriptomics assays, we found these bacteriophages were released via a chronic style without host cell lysis, which might reprogram host polysaccharide metabolism through the potential auxiliary metabolic genes (AMGs). The findings presented here, together with recent discoveries made on the reprogramming of host energy-generating metabolisms by chronic bacteriophages, shed light on the poorly explored marine virus-host interaction and bring us closer to understanding the potential role of chronic viruses in marine ecosystems.
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eLife assessment
This manuscript presents useful findings on several phage from deep sea isolates of Lentisphaerae strains WC36 and zth2 that further our understanding of deep sea microbial life. The manuscript's primary claim is that phage isolates augment polysaccharide use in Pseudomonas bacteria via auxiliary metabolic genes (AMGs). However, the strength of the evidence is incomplete and does not support the primary claims. Namely, there are not data presented to rule out phage contamination in the polysaccharide stock solution, AMGs are potentially misidentified, and there is missing evidence of successful infection.
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Reviewer #1 (Public Review):
Summary:
This manuscript describes the identification and isolation of several phage from deep sea isolates of Lentisphaerae strains WC36 and zth2. The authors observe induction of several putative chronic phages with the introduction of additional polysaccharides to the media. The authors suggest that two of the recovered phage genomes encode AMGs associated with polysaccharide use. The authors also suggest that adding the purified phage to cultures of Pseudomonas stutzeri 273 increased the growth of this bacteria due to augmented polysaccharide use genes from the phage.
While the findings were of interest and relevance to the field, it is my opinion that several of the analysis fall short of supporting the key assertions presented.
Strengths:
Interesting isolate pf deep sea Lentisphaerae strains which will …
Reviewer #1 (Public Review):
Summary:
This manuscript describes the identification and isolation of several phage from deep sea isolates of Lentisphaerae strains WC36 and zth2. The authors observe induction of several putative chronic phages with the introduction of additional polysaccharides to the media. The authors suggest that two of the recovered phage genomes encode AMGs associated with polysaccharide use. The authors also suggest that adding the purified phage to cultures of Pseudomonas stutzeri 273 increased the growth of this bacteria due to augmented polysaccharide use genes from the phage.
While the findings were of interest and relevance to the field, it is my opinion that several of the analysis fall short of supporting the key assertions presented.
Strengths:
Interesting isolate pf deep sea Lentisphaerae strains which will undoubtedly further our understanding of deep sea microbial life.
Weaknesses:
Many of the findings are consistent with a phage contamination in the polysaccharide stock solution.
The genes presented as AMGs are largely well known and studied phage genes which play a role in infection cycles.
The evidence that the isolated phage can infect Pseudomonas stutzeri 273 is lacking, putting into question the dependent results.
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Reviewer #2 (Public Review):
Summary:
This paper investigates virus-host interactions in deep-sea bacteriophage systems which employ a seemingly mutualistic approach to viral replication in which the virus aids host cell polysaccharide import and utilization via metabolic reprogramming. The hypothesis being tested is supported with solid and convincing evidence and the findings are potentially generalizable with implications for our understanding of polysaccharide-mediated virus-host interactions and carbon cycles in marine ecosystems more broadly.
Strengths:
This paper synthesizes sequencing and phylogenic analyses of two Lentisphaerae bacteria and three phage genomes; electron microscopy imaging of bacterial/phage particles; differential gene expression analyses; differential growth curve analyses, and differential phage proliferation …
Reviewer #2 (Public Review):
Summary:
This paper investigates virus-host interactions in deep-sea bacteriophage systems which employ a seemingly mutualistic approach to viral replication in which the virus aids host cell polysaccharide import and utilization via metabolic reprogramming. The hypothesis being tested is supported with solid and convincing evidence and the findings are potentially generalizable with implications for our understanding of polysaccharide-mediated virus-host interactions and carbon cycles in marine ecosystems more broadly.
Strengths:
This paper synthesizes sequencing and phylogenic analyses of two Lentisphaerae bacteria and three phage genomes; electron microscopy imaging of bacterial/phage particles; differential gene expression analyses; differential growth curve analyses, and differential phage proliferation assays to extract insights into whether laminarin and starch can induce both host growth and phage proliferation. The data presented convincingly demonstrate that both host culture density and phage proliferation increase as a result having host, phage, and polysaccharide carbon source together in culture.
Weaknesses (suggestions for improvement):
The article would be strengthened by the following additional experiment: providing the phage proteins hypothesized to be aiding host cell growth (red genes from Figure 5...TonB system energizer ExbB, glycosidases, etc) individually or in combination on plasmids rather than within the context of the actual phage itself to see if such additional genes are necessary and sufficient to realize the boosts in host cell growth/saturation levels observed in the presence of the phages tested.
The paper would also benefit from additional experiments focused on determining how the polysaccharide processing, transport, and metabolism genes are being used by the phages to either directly increase viral infection/replication or else to indirectly do so by supporting the growth of the host in a more mutualistic manner (i.e. by improving their ability to import, degrade, and metabolize polysaccharides).
The introduction would benefit from a discussion of what is known regarding phage and/or viral entry pathways that utilize carbohydrate anchors during host entry. The discussion could also be improved by linking the work presented to the concept of "selfishness" in bacterial systems (see for instance Giljan, G., Brown, S., Lloyd, C.C. et al. Selfish bacteria are active throughout the water column of the ocean. ISME COMMUN. 3, 11 (2023) https://doi.org/10.1038/s43705-023-00219-7). The bacteria under study are gram negative and it was recently demonstrated (https://www.nature.com/articles/ismej201726) that "selfish" bacteria sequester metabolizable polysaccharides in their periplasm to advantage. It is plausible that the phages may be hijacking this "selfishness" mechanism to improve infectivity and ENTRY rather than helping their hosts to grow and profilerate so they can reap the benefits of simply having more hosts to infect. The current work does not clearly distinguish between these two distinct mechanistic possibilities. The paper would be strengthened by at least a more detailed discussion of this possibility as well as the author's rationale for interpreting their data as they do to favor the "mutualistic" interpretation. In the same light, the paper would benefit from a more careful choice of words which can also help to make such a distinction more clear/evident/intentional. As currently written the authors seem to be actively avoiding giving insights wrt this question.
Finally, I would be interested to know if the author's sequencing datasets might be used to inform the question raised above by using bacterial immunity systems such as CRISPR/Cas9. For example, if the phage systems studied are truly beneficial/mutualistic for the bacteria then it's less likely that there would be evidence of targeted immunity against that particular phage that has the beneficial genes that support polysaccharide metabolism.
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