Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in “Pink Berry” Marine Microbial Aggregates
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Abstract
Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms.
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To assess the distribution of pink berry-associated bacteria and phages, genome-wide read coverages were analyzed for individual pink berry metagenomes
It would be nice to provide a summary of what % of reads from the metagenome map to the genomes in Figure 3, and what % are unmapped. And also if are large portion are unmapped, if you have an idea what they are (eg run some taxonomic analysis on the unmapped reads)
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NARBL
is this a commonly used tool/ are there better tools that might exist? Looking at the GitHub page associated with NARBL, the documentation seems extremely scarce and it makes me concerned about the reproducibility of using this
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these phages have persisted over seven years.
this is really cool!
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Co-assembly of the three pink berry metagenomes yielded 184 contigs totaling 4.35 Mb in length
Could you add a sentence here explaining how diverse pink berry microbial communities are? And a statement of whether this assembly size seems reasonable? Is it surprising that the total assembly is only 4.35 Mb (about 1 bacterial genome?) It might be nice to know what % of reads are represented in this assembly
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One such AMG was a darB-like antirestriction gene encoded on the Thiohalocapsa phage MD04 genome (Suppl. Data 1). Interestingly, darB has been shown to methylate phage DNA to resist host restriction modification (RM) systems (Iida et al., 1987; Iyer et al., 2017).
Because auxiliary metabolic genes (AMGs) more commonly reflects instances where phages enhance bacterial energy metabolisms, you might want to consider calling these methylases "anti-defense" genes to more accurately reflect their proposed ecological role.
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48 unique repeat sequences from four reference genomes for known pink berry-associated bacteria:
This level of repeat diversity is much larger that I would have expected and implies that each reference genome has an extremely large number of independent CRISPR-Cas systems. Alternativley, the the repeat finder is erroneously detecting CRISPR repeats. Can you please add more information about what types of CRISPR Cas systems you are finding in each of these reference genomes to contextualize this repeat diversity?
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The remaining five genomes of interest lacked sufficient protein similarity for a connection in the vConTACT network, indicating that these phages represent novel and undescribed diversity.
RefSeq is not a great representation of total viral diversity, making it difficult to evaluate viral novelty simply from Pink Berry phages not being closely related to RefSeq viruses.
Could you compare instead to viruses MAGs from ecologically similar samples - like other marshes - to determine their relative novelty?
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2,802 unique CRISPR spacer sequences
This is a really high number of unique CRISPR spacers. CRISPR arrays in bacteria tend to be small-ish (less than 50 or so spacers) while archaea can be have larger arrays (less than 100 or so). Since there are only 4 different bacterial strains present, retrieving thousands of spacers would require a huge number of independent CRISPR-Cas systems in these strains, and/or extremely rapid CRISPR adaptation. Can you add more information to contextualize this finding?
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Moreover, although most host spacers matched to a single virus, two spacers from the Rhodobacteraceae host aligned to Thiohalocapsa phage MD04 and Desulfofustis phage MD02
Can you clarify what % ID this match is?
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NARBL
is this a commonly used tool/ are there better tools that might exist? Looking at the GitHub page associated with NARBL, the documentation seems extremely scarce and it makes me concerned about the reproducibility of using this
-
Moreover, although most host spacers matched to a single virus, two spacers from the Rhodobacteraceae host aligned to Thiohalocapsa phage MD04 and Desulfofustis phage MD02
Can you clarify what % ID this match is?
-
2,802 unique CRISPR spacer sequences
This is a really high number of unique CRISPR spacers. CRISPR arrays in bacteria tend to be small-ish (less than 50 or so spacers) while archaea can be have larger arrays (less than 100 or so). Since there are only 4 different bacterial strains present, retrieving thousands of spacers would require a huge number of independent CRISPR-Cas systems in these strains, and/or extremely rapid CRISPR adaptation. Can you add more information to contextualize this finding?
-
To assess the distribution of pink berry-associated bacteria and phages, genome-wide read coverages were analyzed for individual pink berry metagenomes
It would be nice to provide a summary of what % of reads from the metagenome map to the genomes in Figure 3, and what % are unmapped. And also if are large portion are unmapped, if you have an idea what they are (eg run some taxonomic analysis on the unmapped reads)
-
48 unique repeat sequences from four reference genomes for known pink berry-associated bacteria:
This level of repeat diversity is much larger that I would have expected and implies that each reference genome has an extremely large number of independent CRISPR-Cas systems. Alternativley, the the repeat finder is erroneously detecting CRISPR repeats. Can you please add more information about what types of CRISPR Cas systems you are finding in each of these reference genomes to contextualize this repeat diversity?
-
these phages have persisted over seven years.
this is really cool!
-
The remaining five genomes of interest lacked sufficient protein similarity for a connection in the vConTACT network, indicating that these phages represent novel and undescribed diversity.
RefSeq is not a great representation of total viral diversity, making it difficult to evaluate viral novelty simply from Pink Berry phages not being closely related to RefSeq viruses.
Could you compare instead to viruses MAGs from ecologically similar samples - like other marshes - to determine their relative novelty?
-
Co-assembly of the three pink berry metagenomes yielded 184 contigs totaling 4.35 Mb in length
Could you add a sentence here explaining how diverse pink berry microbial communities are? And a statement of whether this assembly size seems reasonable? Is it surprising that the total assembly is only 4.35 Mb (about 1 bacterial genome?) It might be nice to know what % of reads are represented in this assembly
-
One such AMG was a darB-like antirestriction gene encoded on the Thiohalocapsa phage MD04 genome (Suppl. Data 1). Interestingly, darB has been shown to methylate phage DNA to resist host restriction modification (RM) systems (Iida et al., 1987; Iyer et al., 2017).
Because auxiliary metabolic genes (AMGs) more commonly reflects instances where phages enhance bacterial energy metabolisms, you might want to consider calling these methylases "anti-defense" genes to more accurately reflect their proposed ecological role.
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