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.

Keywords: anthropogenic impacts; environmental microbiology; environmental pollutants; estuarine ecology; eutrophication; metagenomics; microbial ecology; microbiome.

Figure 1

Sampling locations within Sydney Harbor. Color of symbols indicates geographic regions of the estuary with large filled symbols indicating samples for which shotgun metagenomes were analzyed in addition to amplicon 16S rDNA libraries. Parramatta River, red symbols; Lane Cove, orange symbols; Middle Harbor, dark green symbols; Western-Harbor, cyan symbols; Eastern-Harbor, pale blue symbols; and Marine/Harbor Heads, dark blue symbols.

Figure 2

Variability in environmental variables in Sydney Harbor during high-rainfall (February 2013) and no rainfall (September 2013). Double circled symbols represent sites for which shotgun metagenomes were analyzed. Temperature (A,E), Salinity (B,F), pH (C,G), dissolved oxygen (DO) (D,H).

Figure 3

Variability in nutrient concentrations in Sydney Harbor during high-rainfall (February 2013) and no rainfall (September 2013). Double circled symbols represent sites for which shotgun metagenomes were analyzed. Nitrate+nitrite (A,E), Ammonium (B,F), Phosphate (C,G), Silicate (D,H).

Figure 4

Variation in total nutrient, chlorophyll, and suspended solid concentrations in Sydney Harbor during high-rainfall (February 2013) and no rainfall (September 2013). Double circled symbols represent sites for which shotgun metagenomes were analyzed. Chlorophyll-a (A,E), Total Suspended Solids (B,F), Total Nitrogen (C,G), Total Phosphorus (TP) (D,H).

Figure 5

MDS Ordination of (A) environmental variables and (B) microbial phylogenetic diversity and abundance in Sydney Harbor. Colors designate geographic regions of the estuary. Circles, February 2013 (High Rainfall); Triangles, September 2013 (Low Rainfall).

Figure 6

Relative abundance of microbial taxa (family level) in Sydney Harbor. Only families representing >0.1% abundance in any sample are shown. F, February 2013; S, September 2013.

Figure 7

Network analysis of associations between taxon abundances (family level) and nutrient concentration. Blue nodes indicate taxa with the width of the node proportional to the taxon's abundance. Green nodes indicate nutrients. Positive interactions are solid lines and negative are dashed, with the edge width proportional to the strength of the relationship (MIC score). Red node borders indicate top drivers identified using SIMPER analysis.

Figure 8

Pairwise comparison of functional profiles between Sydney Heads (PJ7, blue circles, positive differences between proportions on right-hand side of plot) and (A) Blackwattle Bay (PJ3; yellow circles) (B) Homebush Bay (P3; red circles). Corrected p-value is determined using Fisher's exact test with a Benjamini FDR multiple test correction. Pathways are level one of SEED metabolic hierarchy.

Figure 9

Heatmap displaying relative abundance of functional pathways involved in nutrient cycling (level one of the SEED hierarchy). Dendrogram clustering represents the Bray-Curtis similarity of profile.