Bacterioplankton Dynamics within a Large Anthropogenically Impacted Urban Estuary

Abstract

The abundant and diverse microorganisms that inhabit aquatic systems are both determinants and indicators of aquatic health, providing essential ecosystem services such as nutrient cycling but also causing harmful blooms and disease in impacted habitats. Estuaries are among the most urbanized coastal ecosystems and as a consequence experience substantial environmental pressures, providing ideal systems to study the influence of anthropogenic inputs on microbial ecology. Here we use the highly urbanized Sydney Harbor, Australia, as a model system to investigate shifts in microbial community composition and function along natural and anthopogenic physicochemical gradients, driven by stormwater inflows, tidal flushing and the input of contaminants and both naturally and anthropogenically derived nutrients. Using a combination of amplicon sequencing of the 16S rRNA gene and shotgun metagenomics, we observed strong patterns in microbial biogeography across the estuary during two periods: one of high and another of low rainfall. These patterns were driven by shifts in nutrient concentration and dissolved oxygen leading to a partitioning of microbial community composition in different areas of the harbor with different nutrient regimes. Patterns in bacterial composition were related to shifts in the abundance of Rhodobacteraceae, Flavobacteriaceae, Microbacteriaceae, Halomonadaceae, Acidomicrobiales, and Synechococcus, coupled to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons. Additionally, community beta-diversity was partitioned between the two sampling periods. This potentially reflected the influence of shifting allochtonous nutrient inputs on microbial communities and highlighted the temporally dynamic nature of the system. Combined, our results provide insights into the simultaneous influence of natural and anthropogenic drivers on the structure and function of microbial communities within a highly urbanized aquatic ecosystem.

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries

“…Further, within the groupings (brackish-euhaline and freshwater), samples clustered by season (Fig 4A), revealing temperature as a secondary driver of community drifts. This is in line with previous work showing that aside from salinity, temperature significantly influences the microbiomes of long and short estuaries, as well as estuaries under high or low anthropogenic pressures [2,4,6,20]. …”

“…Together, these factors cause bacteria to have a short residence time in surface waters. However, similar to the results shown in large estuaries [7,19,20], the bacterial communities of the Estuary of Bilbao were classified in two large groups according to salinity: brackish-euhaline communities (salinity > 5 ppt) and freshwater communities (salinity < 5 ppt) (Fig 4). Accordingly, the Spearman correlation values between OTUs and environmental features showed highest rho values when testing for salinity (rho = 0.72–0.85 for salinity and rho = 0.52–0.64 for temperature, S2 and S4 Tables).…”

“…The geomorphology of the Estuary of Bilbao contrasts to that of large estuaries characterized to date through amplicon sequencing (Mississippi [19], Sydney [20], etc.). The Estuary of Bilbao is short (~20 km) with low river discharge (max = 37 m 3 s -1 ) and a contrasting tidal fluxing rate (max = 700 m 3 s -1 in the outer zone and max = 10 m 3 s -1 in the inner zone) [13].…”

“…The use of amplicon sequencing to depict the makeup of bacterial communities in urban estuaries has been primarily focused on analyzing large estuaries with a well-defined salinity gradient (mixed or partially-mixed) like that of the Mississippi River in the United States [19], Sydney in Australia [20], and Kalama in Greece [21]. Although these estuaries are composed of dissimilar communities, common patterns can be observed throughout that point to salinity and temperature as main variables defining bacterial community changes in these large estuaries.…”

Abundant and Rare Bacterioplankton in Freshwater Lakes Subjected to Different Levels of Tourism Disturbances

“…Most studies did not differentiate the microbial community when exploring the diversity and composition of the microbial community in response to anthropogenic disturbances in aquatic ecosystems [25,26,52,53]. Considering possibly discrepant ecological roles in abundant and rare bacteria [31], we chose to divide the bacterioplankton community into two main components.…”