Assessing the impact of sewage and wastewater on antimicrobial resistance in nearshore Antarctic biofilms and sediments

Abstract

Background: Despite being recognised as a global problem, our understanding of human-mediated antimicrobial resistance (AMR) spread to remote regions of the world is limited. Antarctica, often referred to as "the last great wilderness", is experiencing increasing levels of human visitation through tourism and expansion of national scientific operations. Therefore, it is critical to assess the impact that these itinerant visitors have on the natural environment. This includes monitoring human-mediated AMR, particularly around population concentrations such as visitor sites and Antarctic research stations. This study takes a sequencing discovery-led approach to investigate levels and extent of AMR around the Rothera Research Station (operated by the UK) on the Antarctic Peninsula.

Results: Amplicon sequencing of biofilms and sediments from the vicinity of Rothera Research Station revealed highly variable and diverse microbial communities. Analysis of AMR genes generated from long-reads Nanopore MinION sequencing showed similar site variability in both drug class and resistance mechanism. Thus, no site sampled was more or less diverse than the other, either in the biofilm or sediment samples. Levels of enteric bacteria in biofilm and sediment samples were low at all sites, even in biofilm samples taken from the station sewage treatment plant (STP). It would appear that incorporation of released enteric bacteria in wastewater into more established biofilms or associations with sediment was poor. This was likely due to the inactivation and vulnerability of these bacteria to the extreme environmental conditions in Antarctica.

Conclusions: Our results suggest minimal effect of a strong feeder source (i.e. sewage effluent) on biofilm and sediment microbial community composition, with each site developing its unique niche community. The factors producing these niche communities need elucidation, alongside studies evaluating Antarctic microbial physiologies. Our data from cultivated bacteria show that they are highly resilient to different environmental conditions and are likely to thrive in a warmer world. Our data show that AMR in the Antarctic marine environment is far more complex than previously thought. Thus, more work is required to understand the true extent of the Antarctic microbiota biodiversity, their associated resistomes and the impact that human activities have on the Antarctic environment.

Keywords: Bacteria; Biofilm; Drug class; Nanopore; Resistance mechanism; Sediment.

Fig. 1

AMR sampling sites. A: Position of Rothera Point on the Antarctic Peninsula; B: Closer detail of Adelaide Island including Rothera Point and the two furthest sampling sites, Hangar Cove and “Back Bay” Lagoon; C: Aerial photography image of the sampling sites at Rothera around the sewage treatment plant in North Cove. Background image is taken from the Rothera Minimum Snow Cover Survey 2019 aerial image, British Antarctic Survey. GIS co-ordinates available in Additional File 1

Fig. 2

Sewage treatment plant (STP) and surroundings at Rothera. A: Main building housing the STP; B: The pipe (covered in wooden ducting) from the STP to the discharge point in North Cove; C: Effluent discharging into a trough in the intertidal region of North Cove. Note there are two pipes, one discharging grey water and the other discharging macerated waste from the STP. NB: Biofilm samples from the STP outflow were taken from the bacterial film lining the latter pipe; D: Intertidal zone of North Cove, just below the STP outflow. The “Just below the STP” biofilm samples were taken from rocks under the outflow

Fig. 3

Phyla plot: Showing main Phyla in (A) biofilm samples and (B) sediment samples. Site abbreviations: BF = biofilm; Sed = sediment. STP: Sewage treatment plant; Out: Outflow pipe from the sewage treatment plant; JBSTP: sampled on rocks just below the sewage treatment plant outflow pipe; IT: intertidal; 100mE: 100 m east from the sewage treatment plant outflow pipe; 15mW: 15 m west from the sewage treatment plant outflow pipe; 15mWAn: anoxic sediment15m west from the sewage treatment plant outflow pipe; HC: Hangar Cove; BBL: Back Bay Lagoon Island (see Fig. 1 for map)

Fig. 4

Alpha diversity plot. (A) ASV richness of biofilm samples; (B) ASV richness of sediment samples; (C) Relative abundance of different genera in biofilm samples; (D) Relative abundance of different genera in sediment samples. See Fig. 3 for site abbreviations

Fig. 5

Drug class of ARGs identified at each site (A) Biofilm, (B) Sediment. Site abbreviations as per Fig. 3

Fig. 6

Resistance mechanism of ARGs identified at each site (A) Biofilm, (B) Sediment. Site abbreviations as per Fig. 3

Fig. 7

Number of unique ARGs per site. Percentage of unique ARGs between the different sites