Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem

Abstract

Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.

Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing

“…Taken together, our results highlight that, differently from other potential pathogens (Fonti et al 2021 ), members of the Vibrionaceae family retrieved at sea are unlikely to be related to wastewater inputs. Therefore, we suggest to carefully consider the inclusion of the genus Vibrio in the “blacklist” of potentially pathogenic genera in surveys of microbiological pollution in coastal waters (e.g., Paliaga et al 2017 ; Fonti et al 2021 ; Orel et al 2022 ), also in light of the fact that the distribution of pathogenic traits within a single species (e.g., V. parahaemolyticus , V. vulnificus ) carried by specific genes (e.g., tdh , trh , vcgC ) is highly variable (Fabbro et al 2010 ; Nigro et al 2022 ).…”

Diversity of Free-Living and Particle-Attached Prokaryotes in a River-Influenced Coastal Area of the Northern Adriatic Sea

“…The Northern Adriatic Sea is also exposed to various anthropogenic impacts such as different types of wastewater pollution and agricultural and urban runoff. These inputs can introduce allochthonous organic matter and microbes into the environment (Orel et al, 2021). It is reported that the abundance, composition, and activity of microbial communities in this area depend, to a large extent, on river discharges (Celussi et al, 2010;Mozetič et al, 2012), and the Northern Adriatic Sea receives significant freshwater inputs from several rivers, such as Adige, Brenta, Piave, and Po, along the northwestern coast of Italy.…”

Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

“…Multidrug-resistant bacteria and antibiotic resistance genes have been used as indicators of contamination in various water environments, such as coastal waters (Shinde et al, 2020;Orel et al, 2022;Zhao et al, 2022), rivers (Niestępski et al, 2020;Odubanjo et al, 2021;Allsing et al, 2022), or localised water environment, such as ponds, lakes or karsts (Stange and Thiem, 2020;Hou et al, 2021;Kalinowska et al, 2021;Zhang Y et al, 2021). Tarek and Garner (2023) proposed a framework for the identification of indicator genes with the objective of monitoring antibiotic resistance in wastewater.…”