Urban microbial ecology of a freshwater estuary of Lake Michigan

Abstract

Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an "urban microbial signature," and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with potential long term impacts on the function of estuarine and nearshore ecosystems.

Figure 1. Map of sampling sites from Milwaukee stormwater outfalls, rivers, harbor and Lake Michigan

Our study area included stormwater outfalls and pipes, and surface water sites on three rivers within metropolitan Milwaukee and in Lake Michigan. The Kinnickinnic River, Menomonee River, and Milwaukee River converge in the Milwaukee estuary (Junction) just prior to discharging to Lake Michigan through the main opening in the harbor breakwall (Gap). A total of six lake sites were sampled offshore from the Milwaukee Harbor and Doctor’s Park. Stormwater outfall samples were collected from Holmes Avenue Creek, Wilson Park Creek, Honey Creek, Underwood Creek, and Menomonee River. doi: 10.12952/journal.elementa.000064.f001

Figure 2. Ordination of sample sites based on bacterial taxonomic composition

A non-metric multidimensional scaling plot based on Bray-Curtis dissimilarity of bacterial taxonomic composition across samples is illustrated. The run stress was 0.10, indicating a good fit. Ellipses indicate the dispersion of group based on a weighted covariance matrix of samples distance from the centroid. Individual samples are colored by environment: stormwater=coral, sewage=yellow-green, rivers=green, harbor=blue, lake=purple. doi: 10.12952/journal.elementa.000064.f002

Figure 3. Heat map of taxon relative abundance and hierarchical clustering of samples

Taxon relative abundance is represented by the heatmap. Values are scaled by taxon relative abundance across all samples: red indicates a taxon with skewed distribution, with the presence of a taxon concentrated in one or two samples; white indicates an even distribution among samples; and blue represents lower relative abundance or absence. Both the taxa and samples were clustered using Bray-Curtis dissimilarities. The colors on the cluster dendrogram correspond to the environments in the NMDS plot in Fig 2: coral = stormwater, yellow-green=sewage, green=rivers, blue=harbor, purple=lake. doi: 10.12952/journal.elementa.000064.f003

Figure 4. Venn diagram of biomarker taxa and cosmopolitan taxa from urban and aquatic environments

Venn diagrams show the distribution of biomarker signature taxa, and rare or nonpreferentially distributed taxa among A) rivers, harbor, and lake and among B) aquatic sources, sewage, and stormwater. The number of taxa identified by LEfSe analysis as biomarkers are shown as associated with their particular environment, although they may also be associated in lower abundance in other environments. The majority of taxa observed in the study had a cosmopolitan distribution, but low abundance in both urban and aquatic environments. doi: 10.12952/journal.elementa.000064.f004

Figure 5. Abundance of biomarker signature taxa

The relative abundance of signature taxa from A) lake, B) stormwater, and C) sewage is shown for individual samples. The total sequence reads that mapped to taxa reported as biomarkers from the LEfSe analysis were summed to create a “signature” for each type of environment. The twenty signature taxa with the highest rank abundance are colored uniquely and called out in the legend; the remaining signature taxa are grouped as “other.” doi: 10.12952/journal.elementa.000064.f005

Figure 6. Distribution of OTUs from urban signature taxa and percent urban signature in aquatic environments

Sequence-based analysis of 104 taxa within the urban infrastructure signature (stormwater taxa + nonfecal sewage taxa) identified 2,746 OTUs from over 8 million sequences; some OTUs were found exclusively in either urban (427; shown in grey) or aquatic (80; shown in blue) environments, but 2239 OTUs were found in both (pink). NMDS ordination of individual samples based on OTUs is overlaid to show how OTUs distributed in relation to samples and environments. doi: 10.12952/journal.elementa.000064.f006

Figure 7. The OTU-based percent urban signature for estuary and harbor samples collected under different weather conditions

Junction (estuary) samples are shown in brown; Gap (harbor) samples are shown in green. doi: 10.12952/journal.elementa.000064.f007