High‐throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments

Abstract

Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.

RNA-Seq Analysis on the Microbiota Associated with the White Shrimp (Litopenaeus vannamei) in Different Stages of Development

“…Changes in the L. vannamei microbiome structure were observed in different stages of development, not only in the varying number of taxons but also in their proportion, which agrees with previous reports [2,3,10,39]. The changes in the microbiome are influenced by intrinsic factors of the host organism, environmental factors, lifestyle and nutrition [46,47]; due to the response capacity the microbiome composition is considered a reliable indicator for external changes. In this aspect the culture conditions of the aquaculture systems can promote the biomass formation of certain microbial groups [9,10,15,21].…”

“…A low transcript representation could be noted in the host and the microbiome of metabolic processes related to "Transport and Catabolism", "Posttranslational modification, protein turnover and chaperones" and "Signal transduction". Previous studies performed in different species have shown that a high representation of these metabolic processes is found in environmental stress conditions [32,40,55,56], the presence of chaperones and chaperonins have particularly been reported previously as stress markers given that their content increases under stress conditions [47]. The low proportion of these metabolic groups in L. vannamei and the microbiome suggests that the environmental variations during the culture of this species were present in a basal state which is common in non-stressed organisms.…”

“…In the case of lipids, they are supplied in the commercial formula in the form of crude fat from different origins (fish oil, plant oils), which are present in different proportions in each stage of development. Previous studies mention that the lipids are supplied in the form of highly unsaturated fatty acids (fish), phospholipids and sterols (plants, algae) [45,47]. In the present study the lipid metabolism was observed in both host and microbiome, these types of compounds could act as signaling molecules, in the maintenance of the intestinal tissue and in the synthesis of steroid hormones in juvenile and adult stages where several of these metabolic modules were observed (Figures S3C, S4D and S5C) and are important in further stages of development, mainly in the gonadal development.…”

Bacterial Microbiomes in the Sediments of Lotic Systems Ecologic Drivers and Role: A Case Study from the Mureş River, Transylvania, Romania

“…Microbial communities are an essential link in the lotic trophic chain. They are both shaped by the environment in which they live and, in turn, they shape their environment [148]. Our knowledge of the diversity of microorganisms in sediments from rivers is relatively limited for Romania.…”

“…The bio-ecological roles of the main identified taxa are diverse and complex, for example: Proteobacteria offer extreme metabolic diversity [148]; Actinobacteria play an essential role of recycling biomaterials by decomposing complex mixtures of polymers in dead plants and animals and fungal materials and in producing important bioactive natural metabolites [149]. The Firmicutes importance rely on their characteristic as biofertilizers, biocontrol agents, metals uptake enhancers [150] Chloroflexi provide the filamentous scaffolding around which flocs are formed, to feed on the debris from lysed bacterial cells, to ferment carbohydrates and to degrade other complex polymeric organic compounds to low molecular weight substrates to support their growth and that of other bacterial populations; also remove nitrogen and phosphorus [151], etc.…”