Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments—a Review

Abstract

The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.

Spatial Heterogeneity of Vibrio spp. in Sediments of Chinese Marginal Seas

“…Vibrio spp. may evolve several adaptive strategies to survive in benthic environments, e.g., utilize a wide range of organic carbon sources, enter the VBNC state, or use sediments as reservoirs (3,16,52,53). Most Vibrio spp.…”

Spatio-Temporal Variations in Pathogenic Bacteria in the Surface Sediments of the Zuari Estuary, Goa, India

“…The re-suspension of sediment affects the quality of overlying water by addition of SPM, organic matter and pathogens which are hazardous to human health. The assessment of pathogenic bacteria in the sediment can improve our understanding of the behaviour, fate and mitigation of potential pathogens in the sediment as well as water body 46 . The abundance of TVC, TC, general Streptococci spp.…”

“…among allochthonous pathogens can be attributed to their adaptability and survival in the sediment. Pathogenic bacteria adsorbed to sediment particles protect themselves from UV light, phage attack and protozoan grazing and hence survive for longer time in the sediment [11][12][13]46 . The fecal indicator bacteria can even proliferate and regrow in organic matter and fine particle-rich sediments 51 .…”

Insights into the bacterial profiles and resistome structures following severe 2018 flood in Kerala, South India

“…In order to check the viability and resistance of pathogenic bacteria present on flooded sites, we performed a culture-based analysis using selective and differential agar media, which includes Eosin methylene blue agar (EMB agar), Salmonella 19 ( Supplementary Table S6), but the abundance of Enterococcus faecalis was reduced to more than half…”

“…Number of ARGs present in flooded sites is 3 times higher compared to non-flooded sites for each class of antibiotics and only 27 ARGs (26%) were found to be common. Among the major resistant classes, most of the ARGs present in flood-affected sites confer resistance to aminoglycoside(19), beta-lactams(29), tetracycline(29), fluoroquinolone (31), macrolide(24) and phenicol(16). 38% of the detected ARGs in flooded sites were multidrug-resistant, the most frequent being MexB, MexF and MuxB.…”