The impact of urbanisation on community structure, gene abundance and transcription rates of microbes in upland swamps of Eastern Australia

Abstract

The Temperate Highland Peat Swamps on Sandstone of the Sydney Basin occur in the headwaters of Sydney's drinking water catchments and are listed as endangered ecosystems, yet they have suffered habitat losses and degradation due to human impacts such as urbanisation. Despite ongoing efforts to restore and better protect upland swamps, they remain poorly understood, potentially hindering the effectiveness of management efforts. Essential to overall ecosystem function and the provision of services for human and environmental benefit are the microbial component of wetland ecosystems. In the case of these swamps, the microbes, have not yet been studied. Here, we investigated differences in the microbial community of upland swamps in urbanised catchments compared to swamps from natural catchments in the Blue Mountains. A total of twelve swamps were sampled, six from within urbanised catchments and six with intact vegetation catchments, to compare sediment conditions and microbial community and genes expression and abundances. Catchment impervious area and number of stormwater drains entering a swamp, indicators for urbanisation, positively correlated with the pH and ammonium concentration of swamp sediment. Community analysis of the 16S rRNA gene (T-RFLP, qPCR) revealed the elevated pH of urbanised swamps coincided with changes to the abundance of bacteria and archaea. Furthermore, RT-qPCR revealed genes involved in carbon cycling (mcrA & pmoA) were more likely to be found in urbanised swamps. Taken together, our results indicate that urbanisation of the Blue Mountains is impacting the environmental services provided by the microbial community of upland swamps in the Sydney Basin.

Fig 1. Study site locations.

Red outlines are swamps in urbanised catchments and green outlines are swamps in intact catchments. Source: Basemaps produced with ArcGIS software by Esri. Sources: Esri, DigitalGlobe, GeoEye, Earthstar Geographics, CNES/Airbus DS, USDA, USGS, AeroGRID, IGN, and the GIS User Community. Swamp outlines taken from the Macquarie University, K Fryirs & G Hose 2016, THPSS mapping layer. 6 maps showing the spatial distribution of THPSS were produced for the following areas: Blue Mountains—VIS_ID 4480 Budderoo—VIS_ID 4481 Gosford—VIS_ID 4482 Newnes—VIS_ID 4483 Woronora—VIS_ID 4484 Penrose—VIS_ID 4485. Creative Commons license at: https://data.nsw.gov.au/data/dataset/temperate-highland-peat-swamps-on-sandstone-thpss-vegetation-maps-vis-ids-4480-to-4485.

Fig 2. Sediment parameters by catchment type and depth.

Mean (± Std dev) sediment quality parameters from surface (0 mm) and 50 cm depth in swamps with urbanised and intact catchments (n = 6). Different letters indicate statistical differences (p<0.05).

Fig 3. nMDS plot of bacteria DNA community.

Communities from intact catchment swamps are indicated by circles and those from urbanised catchments marked triangles. Open symbols represent surface samples and closed symbols represent samples from 50 cm depth. Soil Moist % = soil moisture as % dry weight, EC = electrical conductivity (μS/cm) and ammonium = ammonium concentration (mg/kg).

Fig 4. nMDS and dbRDA ordination plots of bacteria RNA community.

Communities from intact catchment swamps are indicated by circles and those from urbanised catchments marked triangles. Open symbols represent surface samples and closed symbols represent samples from 50 cm depth. Soil Moist % = soil moisture as % dry weight, EC = electrical conductivity (μS/cm) and ammonium = ammonium concentration (mg/kg).

Fig 5. nMDS and dbRDA ordination plots of archaeal DNA community.

Communities from intact catchment swamps are indicated by circles and those from urbanised catchments marked triangles. Open symbols represent surface samples and closed symbols represent samples from 50 cm depth. Soil Moist % = soil moisture as % dry weight, EC = electrical conductivity (μS/cm) and ammonium = ammonium concentration (mg/kg).

Fig 6. Gene and transcription abundances by catchment and depth.

Mean (± Std dev) number of DNA/RNA gene copies in sediment collected from the surface and at depth (50 cm) in swamps with urbanised and intact catchments. (n = 6).