Bacterial community structure and their changes in contaminated ecosystems

Within the different ecosystem compartments, bacterial diversity reflects the natural and stressed environmental conditions to which they are subject. The presence of contaminants can lead to the disappearance of key species and/or to the selection of microbial groups able to partially or completely remove such molecules. Environmental contamination may result in changes in the microbial ecology, possibly changing the types of bacteria that carry out important ecosystem processes such as nutrient transformation and biomass decomposition. Microbial biodiversity in fact has a functional importance in the maintenance of soil and water biological processes, because most of the transformation involved in biogeochemical cycles is mediated exclusively by microorganisms. It has been reported that shifts in bacterial community structure, associated with a reduction in microbial biodiversity, lead to losses of functional stability (Girvan et al., 2005). Owing to their small size, large numbers and ubiquitous distribution in the environment, microorganisms are valuable indicators of the occurrence of disturbances due to exogenous physical-chemical stressors. The assessment of variations in microbial community structure is of basic importance in making it possible to evaluate the impact of an environmental stressor. The presence of toxic chemicals in microbial ecosystems induces the synthesis of detoxifying or degradative enzymes and certain stress proteins. Effects due to chemical toxicity tend to narrow the spectrum of microbial diversity because organisms that are not capable of resisting the toxic effects either die or enter a static metabolic phase, leaving those that have evolved resistance mechanisms and are thus capable of utilizing the excess chemicals as nutrients, to proliferate and become dominant members of the impacted ecosystems (Ogunseitan, 2000). In recent years, it has been recognized that biodegradation and/or mineralization of some contaminant molecules is only possible through the presence of microorganisms able to transform them (Topp et al., 2013). Consequently, some relationships between microbial communities and pollutants have been established. Among pollutants, pharmaceuticals including antibiotics, for both human and veterinary use, are frequently found as microcontaminants both in water and in soil ecosystems. Pharmaceuticals are molecules designed to produce a therapeutic effect on the body, usually active at very low concentrations, can pass through biological membranes and persist in the body long enough to avoid being inactivated before having an effect. These compounds are excreted through feces and urine as a mixture of metabolites and substances which are often unchanged. The primary sources of pharmaceutical contamination are represented by domestic, urban, hospital, and industrial wastewater, as well as by effluents from sewage treatment plants (STPs), aquaculture, and intensive livestock farming. Moreover, re-use of solid and liquid livestock manure and sewage sludge in agriculture, in order to recycle nitrogen compounds as fertilizers, can contribute to the dispersion of pharmaceuticals into soil and, under certain conditions, into water bodies. At present, the presence of antibiotics, steroids, blood lipid regulators, estrogens, painkillers, anti-inflammatories, antiseptics, antihypertensive drugs, antiepileptics, antineoplastic agents and other substances in surface water bodies and in soils receiving livestock manure or sewage sludge, even at very low concentration (ng- ?g/L or Kg), is well-documented (Boxall, 2004). Percolation of pharmaceuticals into groundwater and their presence in sea coastal water have been detected as well. The environmental occurrence of these intrinsically and biologically active molecules may cause direct (toxicological effects on non-target organisms) and indirect effects such as antibiotic resistance (Bottoni et al., 2010). People can be exposed to pharmaceuticals through polluted water or by consumption of contaminated food. Non-PCR-based methods commonly used in environmental studies are epifluorescence microscopy techniques, such as Fluorescence In Situ Hybridization (FISH) (Barra Caracciolo et al., 2013; Barra Caracciolo et al., 2010). They make it possible to characterize in situ bacterial populations in their natural ecosystems. In particular, FISH investigates the overall taxonomic composition of bacterial communities by using rRNA-targeted fluorescent probes. This technique is also used for testing the efficient remediation of xenobiotic pollutants by microbial communities (Whiteley and Bailey, 2000). In fact, the ability to monitor diversity structuring, stability and long-term resilience during process management are key requirements for monitoring and predicting bioremediation efficiency.