Size-Fractionated Microbiome Structure in Subarctic Rivers and a Coastal Plume Across DOC and Salinity Gradients

Abstract

Little is known about the microbial diversity of rivers that flow across the changing subarctic landscape. Using amplicon sequencing (rRNA and rRNA genes) combined with HPLC pigment analysis and physicochemical measurements, we investigated the diversity of two size fractions of planktonic Bacteria, Archaea and microbial eukaryotes along environmental gradients in the Great Whale River (GWR), Canada. This large subarctic river drains an extensive watershed that includes areas of thawing permafrost, and discharges into southeastern Hudson Bay as an extensive plume that gradually mixes with the coastal marine waters. The microbial communities differed by size-fraction (separated with a 3-μm filter), and clustered into three distinct environmental groups: (1) the GWR sites throughout a 150-km sampling transect; (2) the GWR plume in Hudson Bay; and (3) small rivers that flow through degraded permafrost landscapes. There was a downstream increase in taxonomic richness along the GWR, suggesting that sub-catchment inputs influence microbial community structure in the absence of sharp environmental gradients. Microbial community structure shifted across the salinity gradient within the plume, with changes in taxonomic composition and diversity. Rivers flowing through degraded permafrost had distinct physicochemical and microbiome characteristics, with allochthonous dissolved organic carbon explaining part of the variation in community structure. Finally, our analyses of the core microbiome indicated that while a substantial part of all communities consisted of generalists, most taxa had a more limited environmental range and may therefore be sensitive to ongoing change.

Environmental niches and seasonal succession of phytoplankton assemblages in a subarctic coastal bay: Applications to remote sensing estimates

“…The seven clusters revealed relevant characteristics associated to the following groups (Figure 3; Table S1): prasinophytes and dinoflagellates (PraD); prymnesiophytes and dinoflagellates (PryD); cyanobacteria (Cy); diatoms (Dia); cryptophytes (Cry); cryptophytes and prasinophytes (CryP); and chlorophytes (Chlo). These phytoplankton assemblages have been reported elsewhere in subarctic and temperate estuaries and coastal areas (Roy et al, 1996;Vallières et al, 2008;Vaulot et al, 2008;Blais et al, 2022). However, the nomenclature adopted in this study reflects pigment ratios characteristics used to distinguish the major phytoplankton assemblages but are not necessarily related to higher biomass or numerical dominance of one or another taxonomic class.…”

“…The seasonal variability of surface nutrients followed the general pattern of the Gulf of St. Lawrence, especially regarding the establishment of nitrate-depleted conditions in summer (Tremblay et al, 2000;Blais et al, 2019). Nutrient concentrations in the nearshore and coastal areas of the Bay of Sept-I ̂les were consistently lower than those of upwelled waters in the Lower St. Lawrence Estuary (AZMP buoy, Blais et al, 2019).…”

Size‐dependent community patterns differ between microbial eukaryotes and bacteria in a permafrost lake–river–sea continuum

“…Samples for total suspended sediments (TSS) were filtered until clogging and onto preweighed GF/F (Whatman) filters that were dried and reweighed. Bacterial and phytoplanktonic abundance were determined by flow cytometry using a BD Accuri™ C6 flow cytometer (BD Biosciences) as in Blais et al (2022 a ). Colored dissolved organic matter (CDOM) absorbance was measured between 200 and 800 nm using a LAMBDA 850 UV/Vis Spectrophotometer (PerkinElmer).…”

“…Water for microbial community analysis was filtered sequentially through a 3‐ μ m pore size, 47‐mm diameter polycarbonate filter (large fraction), and 0.22‐ μ m Sterivex™ filter units (Millipore; small fraction) using a peristaltic pump. DNA was extracted from both filter fractions (one sample from each site) using the AllPrep DNA/RNA Mini Kit (Qiagen) as described in Blais et al (2022 a ). The V4 region of the SSU rRNA gene was amplified using primers E572F/E1009R (Comeau et al 2011) for microbial eukaryotes and 515F (Parada)/806R (Apprill) for Bacteria (Apprill et al 2015; Parada et al 2016) and sequenced on an Illumina MiSeq system at the Plateforme d'analyses génomiques (IBIS, Laval University).…”

Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus

“…First-year sea ice formations are characterized by a one-meter-thick shell on top of Hudson Bay’s water during winter, creating a highly dynamic freezing/melting cycle in the water–ice interface where nutrients and microbes accumulate 71 . A river system (Great Whale River) is relatively close to, discharges into and influences the surface bay waters with freshwater inputs, as commonly found in Arctic coastal marine systems 72 . The ice and the interface water (water just beneath the ice) of the sampled point in Hudson Bay are considered analogs to the water–ice interface environment found in Europa and Enceladus (water bodies perched in ice) owing to the low thickness of the first-year sea ice (1 m).…”