Freshwater Microbiology: Recent Updates and Prospects

Abstract

Along with bacteria, other microorganisms are also key components of microbiota structure of freshwater, and those include archaea, microbial eukaryotes, and viruses that together build the diverse community of microorganisms. All those microorganisms play key ecological functions and can have important impacts on animal, plant, and human health. The traditional culture-based microbiology methods have been mostly replaced, or complemented, by molecular methods, due to their accuracy, fast response, and capability to detect microorganisms that are quite difficult to grow in culture media. This chapter addresses some of the current tendencies on microbial structure and its analysis. Those methods included the “omic-based” DNA studies that allow better and more comprehensive characterization of bacterial communities, leading to metagenomic studies that help to elucidate the population structure of microbiomes in aquatic environments. Strategies for detecting water-borne pathogens are focused on detecting bacteria, protozoa, yeast, and virus in different water sources, and these methods can also be complemented by molecular tools such as molecular marker (RAPD, Microsatellites, RFLPs, and AFLPs). Those methods also allow to detect pathogenic bacteria, fungus, and viruses of public health interest, such as the enterovirus and, more recently, the coronavirus. Water bodies can also be important reservoirs of antibiotic-resistant bacteria, and the group of ESKAPE bacteria represents an important study model for antibiotic resistance and its distribution. The acronym “ESKAPE” is associated with this group due to their ability to escape antimicrobial activity and develop high levels of resistance to multiple antibiotics (multidrug resistance). Water bodies play a central role on the selective pressure and is the most important cause of the dissemination and extension of resistance and has contributed to the genetic diversification of resistance genes also affecting ecological microbial structures.