Viruses of Polar Aquatic Environments

Yau, Sheree; Seth-Pasricha, Mansha

doi:10.3390/v11020189

Cited by 39 publications

(43 citation statements)

References 86 publications

(181 reference statements)

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“…Little overlap of viral communities from Arctic and Antarctic samples has also been observed (23,43) at the species level (22). However, there may be convergence at higher taxonomic levels (22). Another factor to consider is that represented by the differences in methodology between the two studies, including differences in the sequencing platforms (454 pyrosequencing in Ace Lake versus Illumina HiSeq nextgeneration sequencing in this study) and sequencing depths, which can magnify small-scale variations and exaggerate divergences.…”

Section: Discussionmentioning

confidence: 81%

“…Although Lake A and Ace Lake share several physical and ecological properties, the lack of overlap is unsurprising given the pronounced differences in the histories and locations of the two ecosystems. Little overlap of viral communities from Arctic and Antarctic samples has also been observed (23,43) at the species level (22). However, there may be convergence at higher taxonomic levels (22).…”

Section: Discussionmentioning

confidence: 99%

“…Yet viruses in the polar regions have received little attention. Previous studies mostly focused on the Arctic Ocean and Antarctica, and few have used metagenomics to investigate viral diversity (22), with a recent notable exception (23). A study of six lakes and ponds in the island of Spitsbergen in the Svalbard region of Norway used metagenomics to reveal that most of the viral sequences examined had no similarity to those in public databases (24).…”

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confidence: 99%

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Extreme Viral Partitioning in a Marine-Derived High Arctic Lake

Labbé

Girard

Vincent

et al. 2020

mSphere

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High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic. IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation.

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Section: Discussionmentioning

confidence: 81%

Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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Extreme Viral Partitioning in a Marine-Derived High Arctic Lake

Labbé

Girard

Vincent

et al. 2020

mSphere

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“…When working with RNA viruses, a retro-transcription step is required previous to library preparation, and if the efficiency of the nucleic acid recovery is low, amplification strategies are required. Among these, phi29 polymerase-based multiple displacement amplification and random PCR using modified versions of Sequence Independent Single-Primer Amplification (SISPA) have been useful in the virome amplification in samples from hot acidic lakes, hot springs and polar aquatic environments (Diemer and Stedman, 2012; Mead et al, 2017; Yau and Seth-Pasricha, 2019). When the viral genome material is RNA, a Random-Priming SISPA (RP-SISPA) method is frequently used (Miranda et al, 2016).…”

Section: Perspectives On Sampling and Processing: Methodological Chalmentioning

confidence: 99%

A Review on Viral Metagenomics in Extreme Environments

et al. 2019

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Viruses are the most abundant biological entities in the biosphere, and have the ability to infect Bacteria, Archaea, and Eukaryotes. The virome is estimated to be at least ten times more abundant than the microbiome with 107 viruses per milliliter and 109 viral particles per gram in marine waters and sediments or soils, respectively. Viruses represent a largely unexplored genetic diversity, having an important role in the genomic plasticity of their hosts. Moreover, they also play a significant role in the dynamics of microbial populations. In recent years, metagenomic approaches have gained increasing popularity in the study of environmental viromes, offering the possibility of extending our knowledge related to both virus diversity and their functional characterization. Extreme environments represent an interesting source of both microbiota and their virome due to their particular physicochemical conditions, such as very high or very low temperatures and >1 atm hydrostatic pressures, among others. Despite the fact that some progress has been made in our understanding of the ecology of the microbiota in these habitats, few metagenomic studies have described the viromes present in extreme ecosystems. Thus, limited advances have been made in our understanding of the virus community structure in extremophilic ecosystems, as well as in their biotechnological potential. In this review, we critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and we discuss the potential for new discoveries, as well as methodological challenges and perspectives.

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“…Recent high-throughput sequencing metagenomic analysis of soil [ 14 , 15 , 16 ], lacustrine [ 17 , 18 , 19 , 20 , 21 , 22 ], marine [ 23 , 24 , 25 ], and ice-associated samples [ 26 ] in Antarctica have revealed robust viral profiles of genomes with novel characteristics. With an aim to uncover further viral diversity associated with penguins south of the Polar Front, we undertook a study to investigate the diversity of DNA viruses and viral-like circular molecules in four penguin species: The Adélie Penguin ( Pygoscelis adeliae ), Chinstrap Penguin ( P. antarcticus ), Gentoo Penguin ( P. papua ), and King Penguin ( Aptenodytes patagonicus ).…”

Section: Introductionmentioning

confidence: 99%

Identification and Distribution of Novel Cressdnaviruses and Circular Molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula

Levy

Fontenele

Harding

et al. 2020

Viruses

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There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins interface with a number of other biota in their roles as marine mesopredators and several species overlap in their ranges and habitats. To characterize the circular single-stranded viruses related to those in the phylum Cressdnaviricota from these environmental sentinel species, cloacal swabs (n = 95) were obtained from King Penguins in South Georgia, and congeneric Adélie Penguins, Chinstrap Penguins, and Gentoo Penguins across the South Shetland Islands and Antarctic Peninsula. Using a combination of high-throughput sequencing, abutting primers-based PCR recovery of circular genomic elements, cloning, and Sanger sequencing, we detected 97 novel sequences comprising 40 ssDNA viral genomes and 57 viral-like circular molecules from 45 individual penguins. We present their detection patterns, with Chinstrap Penguins harboring the highest number of new sequences. The novel Antarctic viruses identified appear to be host-specific, while one circular molecule was shared between sympatric Chinstrap and Gentoo Penguins. We also report viral genotype sharing between three adult-chick pairs, one in each Pygoscelid species. Sequence similarity network approaches coupled with Maximum likelihood phylogenies of the clusters indicate the 40 novel viral genomes do not fall within any known viral families and likely fall within the recently established phylum Cressdnaviricota based on their replication-associated protein sequences. Similarly, 83 capsid protein sequences encoded by the viruses or viral-like circular molecules identified in this study do not cluster with any of those encoded by classified viral groups. Further research is warranted to expand knowledge of the Antarctic virome and would help elucidate the importance of viral-like molecules in vertebrate host evolution.

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Viruses of Polar Aquatic Environments

Cited by 39 publications

References 86 publications

Extreme Viral Partitioning in a Marine-Derived High Arctic Lake

Extreme Viral Partitioning in a Marine-Derived High Arctic Lake

A Review on Viral Metagenomics in Extreme Environments

Identification and Distribution of Novel Cressdnaviruses and Circular Molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula

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