Charting the diversity of uncultured viruses of Archaea and Bacteria

Coutinho, Felipe H.; Edwards, Robert A.; Rodrı́guez-Valera, Francisco

doi:10.1186/s12915-019-0723-8

Cited by 36 publications

(47 citation statements)

References 58 publications

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“…The taxonomical affiliation of CCS reads and assembled contigs was based on the annotation of coded proteins (>70 % must share the same taxon). To find the putative target, CRISPR spacers were aligned using the blastn-short algorithm against nearly 200,000 phages collected and classified in [110]. Only matches with >97% identity and 100% alignment were considered.…”

Section: Methodsmentioning

confidence: 99%

Long read metagenomics, the next step?

Haro-Moreno

López‐Pérez

Rodrı́guez-Valera

2020

Preprint

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BackgroundThird-generation sequencing has penetrated little in metagenomics due to the high error rate and dependence for assembly on short-read designed bioinformatics. However, 2nd generation sequencing metagenomics (mostly Illumina) suffers from limitations, particularly in allowing assembly of microbes with high microdiversity or retrieving the flexible (adaptive) compartment of prokaryotic genomes.ResultsHere we have used different 3rd generation techniques to study the metagenome of a well-known marine sample from the mixed epipelagic water column of the winter Mediterranean. We have compared Oxford Nanopore and PacBio last generation technologies with the classical approach using Illumina short reads followed by assembly. PacBio Sequel II CCS appears particularly suitable for cellular metagenomics due to its low error rate. Long reads allow efficient direct retrieval of complete genes (473M/Tb) and operons before assembly, facilitating annotation and compensates the limitations of short reads or short-read assemblies. MetaSPAdes was the most appropriate assembly program when used in combination with short reads. The assemblies of the long reads allow also the reconstruction of much more complete metagenome-assembled genomes, even from microbes with high microdiversity. The flexible genome of reconstructed MAGs is much more complete and allows rescuing more adaptive genes.ConclusionsFor most applications of metagenomics, from community structure analysis to ecosystem functioning, long-reads should be applied whenever possible. Particularly for in-silico screening of biotechnologically useful genes, or population genomics, long-read metagenomics appears presently as a very fruitful approach and can be used from raw reads, before a computing-demanding (and potentially artefactual) assembly step.

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Section: Methodsmentioning

confidence: 99%

Long read metagenomics, the next step?

Haro-Moreno

López‐Pérez

Rodrı́guez-Valera

2020

Preprint

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“…Finally, protein sequences extracted from the scaffolds were queried against the pVOGs database [32] using HMMER set to a maximum e value of 0.00001 [62]. For each scaffold, we calculated the added viral quotient (AVQ) as the sum of the viral quotients of each pVOG that hits with the proteins of each scaffold [63]. Scaffolds for which at least 20% of proteins mapped to pVOGs resulting in an AVQ ≥ 2 were considered putative viruses.…”

Section: Sequence Processing and Analysismentioning

confidence: 99%

New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

et al. 2020

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Background Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat, but the viral communities from this ecosystem have not been characterized in detail. Results Here, we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae, and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. Conclusions These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely, by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance.

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“…To add-on their captivating lifestyles, research on extremophilic archaea is receiving increasing attention due to the viruses that have been found associated with their populations. These observations suggest that viruses infecting archaea might represent the most diverse and abundant biological entities on earth [ 18 ].…”

Section: Viruses Of Extremophile Archaeamentioning

confidence: 99%

Viruses in Extreme Environments, Current Overview, and Biotechnological Potential

Gil¹,

Mesa²,

Estrada‐Ortiz³

et al. 2021

Viruses

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Virus research has advanced significantly since the discovery of the tobacco mosaic virus (TMV), the characterization of its infection mechanisms and the factors that determine their pathogenicity. However, most viral research has focused on pathogenic viruses to humans, animals and plants, which represent only a small fraction in the virosphere. As a result, the role of most viral genes, and the mechanisms of coevolution between mutualistic viruses, their host and their environment, beyond pathogenicity, remain poorly understood. This review focuses on general aspects of viruses that interact with extremophile organisms, characteristics and examples of mechanisms of adaptation. Finally, this review provides an overview on how knowledge of extremophile viruses sheds light on the application of new tools of relevant use in modern molecular biology, discussing their value in a biotechnological context.

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Charting the diversity of uncultured viruses of Archaea and Bacteria

Cited by 36 publications

References 58 publications

Long read metagenomics, the next step?

Long read metagenomics, the next step?

New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

Viruses in Extreme Environments, Current Overview, and Biotechnological Potential

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