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.
Highlights
Estuaries are among the most urbanized coastal ecosystems (Line and White, 2007) and as a consequence experience substantial environmental pressures, including habitat loss, decreased biodiversity, harmful algal blooms, anoxia, and contamination by sewage, pesticides, polycyclic aromatic hydrocarbons, heavy metals and other organic and inorganic pollutants (Birch et al, 1999; Diaz and Rosenberg, 2008)
Dissolved oxygen (DO) and pH levels were generally higher across the estuary during February, but were more heterogeneous at this time, with some localized sites where DO levels were below 3 mg L−1
By combining measurements of physicochemical conditions with assessments of patterns in microbial diversity and functional potential, we have provided a first insight into the microbial ecology of the Sydney Harbor estuary
Summary
Estuaries are among the most urbanized coastal ecosystems (Line and White, 2007) and as a consequence experience substantial environmental pressures, including habitat loss, decreased biodiversity, harmful algal blooms, anoxia, and contamination by sewage, pesticides, polycyclic aromatic hydrocarbons, heavy metals and other organic and inorganic pollutants (Birch et al, 1999; Diaz and Rosenberg, 2008). While these anthropogenically derived pressures have negative influences felt throughout entire estuarine food webs, the most prominent impacts often occur among populations of planktonic and sediment-bound microorganisms. Microbial communities are extremely sensitive to rapid changes in the environment and can be used as indicators of stress (Paerl, 2006; Sun et al, 2012) as changes in the relative abundance of specific taxa or functional genes can be indicative of shifts in the physicochemical dynamics within estuaries and coastal systems (Smith et al, 2010; Fortunato et al, 2012, 2013; Gregoracci et al, 2012)
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