New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake

Abstract

It is widely stated that viruses represent the most significant source of biodiversity on Earth, yet characterizing the diversity of viral assemblages in natural systems remains difficult. Viral diversity studies are challenging because viruses lack universally present, phylogenetically informative genes. Here, we developed an approach to estimate viral diversity using a series of functional and novel conserved genes. This approach provides direct estimates of viral assemblage diversity while retaining resolution at the level of individual viral populations in a natural system. We characterized viral assemblages in eight samples from hypersaline Lake Tyrrell (LT), Victoria, Australia, using 39,636 viral contigs. We defined viral operational taxonomic units (OTUs) in two ways. First, we used genes with three different functional predictions that were abundantly represented in the data set. Second, we clustered proteins of unknown function based on sequence similarity, and we chose genes represented by three clusters with numerous members to define OTUs. In combination, diversity metrics indicated between 412 and 735 sampled populations, and the number of populations remained relatively constant across samples. We determined the relative representation of each viral OTU in each sample and found that viral assemblage structures correlate with salinity and solution chemistry. LT viral assemblages were near-replicates from the same site sampled a few days apart but differed significantly on other spatial and temporal scales. The OTU definition approach proposed here paves the way for metagenomics-based analyses of viral assemblages using ecological models previously applied to bacteria and archaea.

Microbial diversity of hypersaline environments: a metagenomic approach

“…In lake Tyrrell about 1,000 dominant viral populations may be present at any specific time (an underestimate given RNA viruses were not analyzed), but they were stable only for days or a few weeks, and were demonstrated to be dynamic on timescales of months or years [42,43]. Such findings indicate that viral diversity studies based on one or a few samples are limited in their interpretation capabilities and that extensive sampling and sequencing is required for insightful ecological and evolutionary conclusions.…”

Prokaryotic and viral community of the sulfate‐rich crust from Peñahueca ephemeral lake, an astrobiology analogue

“…Overall, PH1‐SC virus metagenome (hereinafter metavirome) showed a high degree of novelty since less than 0.01% of the PH1‐SC metavirome reads matched viral assemblages from other hypersaline environments worldwide, such as Lake Tyrrell, in Victoria, Australia (Emerson et al, , b), Lake Retba in Senegal (Sime‐Ngando et al ., ), coastal salterns in San Diego in the USA (Rodriguez‐Brito et al ., ), Santa Pola in Spain (Santos et al ., ) and Sfax in Tunisia (Boujelben et al, , b).…”

Virus‐host interplay in high salt environments

“…In addition to lemon‐shaped, spherical and tailed icosahedral morphotypes, virus‐sized particles with helical morphology or various undefined morphologies have been observed (Oren et al ., ; Sime‐Ngando et al ., ). Culture‐independent studies of virus‐host dynamics indicate that viruses are diverse and highly active in hypersaline environments (Rodriguez‐Brito et al ., ; Santos et al ., ; Emerson et al, ; ). The described activity refers to comparisons of viral genomes (populations) constructed from metagenomic DNA and their presence in the samples during different time points (Emerson et al ., ) as well as to the expression of viral genes in the environmental community (Santos et al ., ).…”