Modelling Free-Living and Particle-Associated Bacterial Assemblages across the Deep and Hypoxic Lower St. Lawrence Estuary

Abstract

The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada are among the largest and most productive coastal ecosystems in the world. Very little information on bacterial diversity exists, hampering our understanding of the relationships between bacterial community structure and biogeochemical function in the EGSL. During the productive spring period, we investigated free-living and particle-associated bacterial communities across the stratified waters of the Lower St. Lawrence Estuary, including the particle-rich surface and bottom boundary layers. Modelling of community structure based on 16S rRNA gene and transcript diversity identified bacterial assemblages specifically associated with four habitat types defined by water mass (upper water or lower water column) and size fraction (free living or particle associated). Assemblages from the upper waters represent sets of cooccurring bacterial populations that are widely distributed across Lower St. Lawrence Estuary surface waters and likely key contributors to organic matter degradation during the spring. In addition, we provide strong evidence that particles in deep hypoxic waters and the bottom boundary layer support a metabolically active bacterial community that is compositionally distinct from those of surface particles and the free-living communities. Among the distinctive features of the bacterial assemblage associated with lower-water particles was the presence of uncultivated lineages of Deltaproteobacteria, including marine myxobacteria. Overall, these results provide an important ecological framework for further investigations of the biogeochemical contributions of bacterial populations in this important coastal marine ecosystem. IMPORTANCE The Estuary and Gulf of St. Lawrence (EGSL) in eastern Canada is an appealing ecosystem for studying how microbial communities and metabolic processes are related to environmental change. Ocean and climate variability result in large spatiotemporal variations in environmental conditions and oceanographic processes. The EGSL is also exposed to a variety of additional human pressures that threaten its integrity and sustainable use, including shipping, aquiculture, coastal development, and oil exploration. To monitor and perhaps mitigate the impacts of these human activities on the EGSL, a comprehensive understanding of the biological communities is required. In this study, we provide the first comprehensive view of bacterial diversity in the EGSL and describe the distinct bacterial assemblages associated with different environmental habitats. This work therefore provides an important baseline ecological framework for bacterial communities in the EGSL useful for further studies on how these communities may respond to environmental change.

Abundance-Occupancy Relationships Along Taxonomic Ranks Reveal a Consistency of Niche Differentiation in Marine Bacterioplankton With Distinct Lifestyles

“…In accordance with earlier findings in marine and estuarine systems ( Crump et al, 1999 ; Salazar et al, 2015 ; Mestre et al, 2017 ; Cui et al, 2020 ), the composition of FL bacteria was both taxonomically and phylogenetically distinct from that of PA bacteria ( Figure 2B and Supplementary Figure 1 , Unifrac). Bacteroidetes, Planctomycetes, and Verrucomicrobia accounted for a larger proportion of the PA fraction than of the FL fraction.…”

“…Microbially mediated biogeochemical processes and taxon-specific metabolic pathways have been well-documented in the SLE ( Bourgoin and Tremblay, 2010 ; Thibodeau et al, 2010 ; Ramachandran and Walsh, 2015 ) but the catalog of whole microbial communities that inhabit the estuary has received less attention. A recent study characterized the PA and FL bacterial communities across the Lower SLE ( Cui et al, 2020 ) but little is known about the alpha-diversity or the relationships between the bacterial community and the environment, and therefore the mechanisms that underlie community assembly.…”

Abundance-occupancy relationships along taxonomic ranks reveal a consistency of niche differentiation in marine bacterioplankton with distinct lifestyles

“…For example, a strong particle affinity of members of Planctomycetes was reported for biofilm-forming communities on microplastic particles (Wiegand et al, 2020), in the low-saline communities of the Baltic Sea (Rieck et al, 2015), and in deep-sea prokaryotic assemblages (Salazar et al, 2015). In our study, Cyanobacteria were more abundant in the PA than in the FL fractions at all stations, consistent with previous reports of abundant cyanobacterial populations in the LSLE (Cui et al, 2020) but also in the GSL, where the salinity is higher. The presence of cyanobacterial populations on (sinking) particles was also described (Farnelid et al, 2018; Yang et al, 2019).…”

“…In accordance with earlier findings in marine and estuarine systems (Crump et al, 1999; Salazar et al, 2015; Mestre et al, 2017; Cui et al, 2020), the composition of FL bacteria was both taxonomically and phylogenetically distinct from that of PA bacteria (Figure 2B; Supplementary Figure S1). Bacteroidetes, Planctomycetes, and Verrucomicrobia accounted for a larger proportion of the PA fraction than of the FL fraction.…”

“…Microbially mediated biogeochemical processes and taxon-specific metabolic pathways have been well-documented in the SLE (Thibodeau et al, 2010; Bourgoin et al, 2010; Ramachandran and Walsh, 2015) but the catalogue of whole microbial communities that inhabit the estuary have received less attention. A recent study characterized the PA and FL bacterial communities across the Lower SLE (Cui et al, 2020) but little is known about the alpha-diversity or the relationships between the bacterial community and the environment, and therefore the mechanisms that underlie community assembly.…”