Climate-Endangered Arctic Epishelf Lake Harbors Viral Assemblages with Distinct Genetic Repertoires

Abstract

Milne Fiord, located on the coastal margin of the Last Ice Area (LIA) in the High Arctic (82°N, Canada), harbors an epishelf lake, a rare type of ice-dependent ecosystem in which a layer of freshwater overlies marine water connected to the open ocean. This microbe-dominated ecosystem faces catastrophic change due to the deterioration of its ice environment related to warming temperatures. We produced the first assessment of viral abundance, diversity, and distribution in this vulnerable ecosystem and explored the niches available for viral taxa and the functional genes underlying their distribution. We found that the viral community in the freshwater layer was distinct from, and more diverse than, the community in the underlying seawater and contained a different set of putative auxiliary metabolic genes, including the sulfur starvation-linked gene tauD and the gene coding for patatin-like phospholipase. The halocline community resembled the freshwater more than the marine community, but harbored viral taxa unique to this layer. We observed distinct viral assemblages immediately below the halocline, at a depth that was associated with a peak of prasinophyte algae and the viral family Phycodnaviridae. We also assembled 15 complete circular genomes, including a putative Pelagibacter phage with a marine distribution. It appears that despite its isolated and precarious situation, the varied niches in this epishelf lake support a diverse viral community, highlighting the importance of characterizing underexplored microbiota in the Last Ice Area before these ecosystems undergo irreversible change. IMPORTANCE Viruses are key to understanding polar aquatic ecosystems, which are dominated by microorganisms. However, studies of viral communities are challenging to interpret because the vast majority of viruses are known only from sequence fragments, and their taxonomy, hosts, and genetic repertoires are unknown. Our study establishes a basis for comparison that will advance understanding of viral ecology in diverse global environments, particularly in the High Arctic. Rising temperatures in this region mean that researchers have limited time remaining to understand the biodiversity and biogeochemical cycles of ice-dependent environments and the consequences of these rapid, irreversible changes. The case of the Milne Fiord epishelf lake has special urgency because of the rarity of this type of "floating lake" ecosystem and its location in the Last Ice Area, a region of thick sea ice with global importance for conservation efforts.

Keywords: Arctic; Caudovirales; Last Ice Area; Pelagibacter phage; Phycodnaviridae; auxiliary metabolic genes; epishelf lake; viruses.

FIG 1

(A) General location and local geography of the Milne Fiord epishelf lake in 2015 (adapted from reference 7). Gray areas of map indicate lake ice detected by RADARSAT-2 imagery. (B) Cartoon showing accumulation of freshwater behind Milne Ice Shelf and the bottom topography of Neige Bay.

FIG 2

Water column profiles of the Milne Fiord epishelf lake. Shown are (A) physical properties measured using a YSI probe and CTD sensors, (B) virus-like particle and cell counts, obtained by flow cytometry, and (C) chlorophyll a concentrations and mass ratios of photosynthetic pigments in the water column determined by HPLC analysis. See the interpretation of phytoplankton taxonomy in Results. Error bars in panels B and C show standard error (n = 3).

FIG 3

(A) Distribution of virus families by depth, as determined by VPF-Class. Relative abundance was calculated using the vOTU table standardized for contig sequence length. (B) Taxonomic composition of WGCNA modules.

FIG 4

Alpha diversity calculated as (A) richness, (B) inverse Simpson index, and (C) Shannon index for vOTUs at different depths of the Milne Fiord epishelf lake. Values for triplicate independent samples are shown (n = 3). Asterisks indicate depths with significantly different diversity (P < 0.05).

FIG 5

(A) Samples (three replicates per depth) clustered using Bray-Curtis distance on vOTU abundance data, normalized by sequence length and using Hellinger and log transformations; (B) number of vOTUs found at one depth only or at more than one depth. The bottom stacked bar groups vOTUs that are found both above and below the halocline, considered to be “euryhaline.”

FIG 6

(A) Distribution of WGCNA modules by depth. The number of vOTUs assigned to each module is given in parentheses. Relative abundance was calculated using the vOTU table, normalized by sequence length. (B) Modules clustered using Bray-Curtis distance on KEGG functional annotations. A heat map shows the proportion of contigs at each depth assigned to that module. (Note the nonlinear scale for the gradient.)

FIG 7

(A) Viral reads recruited to selected uncultivated viral genomes (UViGs) by depth; (B) genome organization of UViG NODE41_03 (outer ring) compared to a typical Pelagibacter phage, HTVC019P (inner ring), showing core genes for this viral genus. All coding is on the positive strand. Shared open reading frames (ORFs) are shown by dashed lines. The number of each ORF is shown within the arrow. A discussion of the genes, including abbreviations, may be found in the text.

FIG 8

Relative abundance of reads recruited to vOTUs carrying the tauD, patatin-like phospholipase (PLP), and integrase functional genes mapped by depth.