Vancomycin and/or Multidrug-Resistant Citrobacter Freundii Altered the Metabolic Pattern of Soil Microbial Community

Antibiotic residues in environment: antimicrobial resistance development, ecological risks, and bioremediation

The overuse of antibiotics and their disposal without processing are leading the environment and its inhabitants towards a serious health emergency. There is abundance of diverse antibiotic resistance genes and bacteria in environment, which demands immediate attention for the effective removal of antibiotics. There are physical and chemical methods for removal, but the generation of toxic byproducts has directed the efforts towards bioremediation for eco-friendly and sustainable elimination of antibiotics from the environment. Various effective and reliable bioremediation approaches have been used, but still antibiotic residues pose a major global threat. Recent developments in molecular and synthetic biology might offer better solution for engineering of microbe-metabolite biodevices and development of novel strains endowed with desirable properties. This review summarizes the impact of antibiotics on environment, mechanisms of resistance development, and different bioremediation approaches.

Land application of sewage sludge: Response of soil microbial communities and potential spread of antibiotic resistance

The effect of land application of sewage sludge on soil microbial communities and the possible spread of antibiotic- and metal-resistant strains and resistance determinants were evaluated during a 720-day field experiment. Enzyme activities, the number of oligotrophic bacteria, the total number of bacteria (qPCR), functional diversity (BIOLOG) and genetic diversity (DGGE) were established. Antibiotic and metal resistance genes (ARGs, MRGs) were assessed, and the number of cultivable antibiotic- (ampicillin, tetracycline) and heavy metal- (Cd, Zn, Cu, Ni) resistant bacteria were monitored during the experiment. The application of 10 t ha^-1 of sewage sludge to soil did not increase the organic matter content and caused only a temporary increase in the number of bacteria, as well as in the functional and structural biodiversity. In contrast to expectations, a general adverse effect on the tested microbial parameters was observed in the fertilized soil. The field experiment revealed a significant reduction in the activities of alkaline and acid phosphatases, urease and nitrification potential. Although sewage sludge was identified as the source of several ARGs and MRGs, these genes were not detected in the fertilized soil. The obtained results indicate that the effect of fertilization based on the recommended dose of sewage sludge was not achieved.

Application of Erythromycin and/or Raoultella sp. Strain MC3 Alters the Metabolic Activity of Soil Microbial Communities as Revealed by the Community Level Physiological Profiling Approach

Erythromycin (EM), a macrolide antibiotic, by influencing the biodiversity of microorganisms, might change the catabolic activity of the entire soil microbial community. Hence, the goal of this study was to determine the metabolic biodiversity in soil treated with EM (1 and 10 mg/kg soil) using the community-level physiological profiling (CLPP) method during a 90-day experiment. In addition, the effect of soil inoculation with antibiotic-resistant Raoultella sp. strain MC3 on CLPP was evaluated. The resistance and resilience concept as well as multifactorial analysis of data was exploited to interpret the outcomes obtained. EM negatively affected the metabolic microbial activity, as indicated by the values of the CLPP indices, i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon-Wiener (H) and evenness (E) indices and the AWCD values for the six groups of carbon substrate present in EcoPlates until 15 days. The introduction of strain MC3 into soil increased the degradative activity of soil microorganisms in comparison with non-inoculated control. In contrast, at the consecutive sampling days, an increase in the values of the CLPP parameters was observed, especially for EM-10 + MC3-treated soil. Considering the average values of the resistance index for all of the measurement days, the resistance of the CLPP indices and the AWCD values for carbon substrate groups were categorized as follows: E > H > R > AWCD and polymers > amino acids > carbohydrates > miscellaneous > amines > carboxylic acids. The obtained results suggest a low level of resistance of soil microorganisms to EM and/or strain MC3 at the beginning of the exposure time, but the microbial community exhibited the ability to recover its initial decrease in catabolic activity over the experimental period. Despite the short-term effects, the balance of the soil ecosystem may be disturbed.

Antibiotics in the Soil Environment-Degradation and Their Impact on Microbial Activity and Diversity

Antibiotics play a key role in the management of infectious diseases in humans, animals, livestock, and aquacultures all over the world. The release of increasing amount of antibiotics into waters and soils creates a potential threat to all microorganisms in these environments. This review addresses issues related to the fate and degradation of antibiotics in soils and the impact of antibiotics on the structural, genetic and functional diversity of microbial communities. Due to the emergence of bacterial resistance to antibiotics, which is considered a worldwide public health problem, the abundance and diversity of antibiotic resistance genes (ARGs) in soils are also discussed. When antibiotic residues enter the soil, the main processes determining their persistence are sorption to organic particles and degradation/transformation. The wide range of DT50 values for antibiotic residues in soils shows that the processes governing persistence depend on a number of different factors, e.g., physico-chemical properties of the residue, characteristics of the soil, and climatic factors (temperature, rainfall, and humidity). The results presented in this review show that antibiotics affect soil microorganisms by changing their enzyme activity and ability to metabolize different carbon sources, as well as by altering the overall microbial biomass and the relative abundance of different groups (i.e., Gram-negative bacteria, Gram-positive bacteria, and fungi) in microbial communities. Studies using methods based on analyses of nucleic acids prove that antibiotics alter the biodiversity of microbial communities and the presence of many types of ARGs in soil are affected by agricultural and human activities. It is worth emphasizing that studies on ARGs in soil have resulted in the discovery of new genes and enzymes responsible for bacterial resistance to antibiotics. However, many ambiguous results indicate that precise estimation of the impact of antibiotics on the activity and diversity of soil microbial communities is a great challenge.

Functional Diversity of Soil Microbial Communities in Response to the Application of Cefuroxime and/or Antibiotic-Resistant Pseudomonas putida Strain MC1

Cefuroxime (XM), the most commonly prescribed antibiotic from the cephalosporin group, may cause changes in the structure of the soil microbial community, and these changes may also be reflected in the alteration of its functionality. Therefore, due to the lack of studies on this topic, the scope of this study was to assess the functional diversity and catabolic activity of the microbial community in soil treated with XM (1 mg/kg and 10 mg/kg soil) using the community-level physiological profile (CLPP) approach during a 90-day experiment. In addition, the effect of antibiotic-resistant Pseudomonas putida strain MC1 (Ps) was also evaluated. The resistance/resilience concept and multifactorial analysis were used to interpret the data. The results showed that the introduction of XM and/or Ps into the soil caused changes in the catabolic activity and functional diversity of the microbial community. A decrease in the values of the CLPP indices (i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon-Wiener (H) and evenness (E) indices and the AWCD values for the six carbon substrate groups) for the XM-treated soil was generally detected up to 30 days. In turn, at the same time, the activity measured in the Ps-inoculated soil was higher compared to the control soil. A stimulatory effect of XM at 10 mg/kg (XM10) and XM10+Ps on the utilization pattern of each substrate group was found at the following sampling times (days 60 and 90). The AWCD values for the utilization of amines, amino acids, carbohydrates, carboxylic acids, miscellaneous compounds and polymers for these treatments were found to be up to 2.3-, 3.1-, 2.3-, 13-, 3.4- and 3.3-fold higher compared to the values for the nontreated control, respectively. The resistance of the CLPP indices and the AWCD values for the carbon substrate groups were categorized as follows: E > H > R > AWCD and amino acids = carbohydrates > polymers > amines > miscellaneous > carboxylic acids, respectively. The results suggest a low initial resistance of the soil microbial community to XM and/or Ps, and despite the short-term negative effect, the balance of the soil ecosystem may be disturbed.