Exploring Viral Communities Associated With Terrestrial Cyanobacteria Metagenomes
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Abstract
Viruses are exceedingly common, but little is known about how they behave in extreme environments, and whether viruses facilitate adaptation of their hosts to harsh conditions. To understanding of these understudied viral-host interactions, we analyzed metagenomes from 50 unialgal but nonaxenic Cyanobacteria cultures with 47 representing various terrestrial habitats, including desert soil and rock surfaces, tropical soil, and vernal pools. These cultures represent low diversity microbial consortia dominated by the terrestrial Cyanobacteria and its associated cyanosphere microbiome containing heterotrophic microbes. We identified viral sequences in metagenomes, grouped these into viral operational taxonomic units (vOTUs) and then placed vOTUs into viral clusters (VCs). We also calculated vOTU relative abundance and predicted possible bacterial hosts In total we predicted 814 viral sequences representing 726 vOTUs. We assigned putative taxonomy to 72 of the 814 putative viral sequences; these were distributed into 15 VCs — mostly assigned to the Caudovirales order of viruses. We found that metagenomes were dominated by unclassified and unclustered viral sequences. Furthermore, we predicted bacterial hosts for 211 vOTUs, with the majority of viruses predicted to infect a Proteobacteria host, and only 3 vOTUs predicted to infect a Cyanobacteria host. Overall, these results are consistent with the notion that viruses in extreme environments are underrepresented in reference datasets. This work increases knowledge of viral diversity and sets a foundation for future work on viruses associated with terrestrial Cyanobacteria and their heterotroph associates, such as connecting specific viruses to critical cycling processes and investigating their metabolic functions.
Importance
Relatively little is known about Cyanobacteria that live on land, or their associated viral communities. To begin to address this knowledge gap, we identified viruses from metagenomes of multi-species cultures which contain mainly Cyanobacteria, but also associated heterotrophic bacteria. The majority of surveyed viruses did not share similarity with reference viral genomes, potentially indicating some viral novelty. Further, we found that for the viruses where we could predict a putative bacterial host, most were not associated with the Cyanobacteria members in these cultures. These results highlight how little is known about land-based Cyanobacteria or their associated viruses. Given the role of some viruses in influencing ecosystem services and enhancing host fitness, surveying viruses is foundational to understanding how Cyanobacteria may have adapted to and survive in some of the most extreme environments on land.
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For example this paper assembled MAGs of the cyanobacteria Phormidium and three associated microorganisms from a biofilm forming industrial photobioreactor: https://journals.asm.org/doi/full/10.1128/mra.00447-22, which I would guess from the nature of the bioreactor setup has better nutrient resources than these harsh environments would. In this paper specifically they ran VirSorter as well and found a complete phage. But could be a cool comparison to include other datasets of this type to see if 1) you find viral contigs at all and if you do 2) how they compare to viral contigs from these harsh environments
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first used Prodigal v. 2.6.3 to predict open reading frames in vOTU representative genomes using the -p meta option
If you wanted to do phage functional annotation you could use https://github.com/deprekate/PHANOTATE, which could also give interesting results if you did a comparison of cyanobacterial viral composition of harsh vs not-harsh environments (like photobioreactors)
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To expand knowledge of Cyanobacteria viruses largely from terrestrial environments,
One of the hypotheses postulated in the abstract was that Cyanos from terrestrial environments have viruses that help them adapt to harsh environments. It would be cool to directly compare to cyano co-cultures or simple communities from aquatic or industrial settings, the latter of which probably has "comfier" resources for Cyanos to see how those viral communities differ or have some overlap?
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We clustered these 814 viral sequences
I think I'm interpreting here that regardless of quality results from CheckV that all 814 viral sequences were used for downstream steps? I know that programs like VIBRANT or other phage identification programs can give a lot of false positives and this curation is needed to toss these out...so I'm curious why this decision was made to keep all of them
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