Antibiotics are among the most successful drugs used for human therapy. However, since they can challenge microbial populations, they must be considered as important pollutants as well. Besides being used for human therapy, antibiotics are extensively used for animal farming and for agricultural purposes. Residues from human environments and from farms may contain antibiotics and antibiotic resistance genes that can contaminate natural environments. The clearest consequence of antibiotic release in natural environments is the selection of resistant bacteria. The same resistance genes found at clinical settings are currently disseminated among pristine ecosystems without any record of antibiotic contamination. Nevertheless, the effect of antibiotics on the biosphere is wider than this and can impact the structure and activity of environmental microbiota. Along the article, we review the impact that pollution by antibiotics or by antibiotic resistance genes may have for both human health and for the evolution of environmental microbial populations. The article reviews the current knowledge on the effects that pollution by antibiotics and antibiotic resistance genes may have for the microbiosphere.

For phytoremediation of organic contaminants, plants have to host an efficiently degrading microflora. To assess the role of endophytes in alkane degradation, Italian ryegrass was grown in sterile soil with 0, 1 or 2% diesel and inoculated either with an alkane degrading bacterial strain originally derived from the rhizosphere of Italian ryegrass or with an endophyte. We studied plant colonization of these strains as well as the abundance and expression of alkane monooxygenase (alkB) genes in the rhizosphere, shoot and root interior. Results showed that the endophyte strain better colonized the plant, particularly the plant interior, and also showed higher expression of alkB genes suggesting a more efficient degradation of the pollutant. Furthermore, plants inoculated with the endophyte were better able to grow in the presence of diesel. The rhizosphere strain colonized primarily the rhizosphere and showed low alkB gene expression in the plant interior. Bacterial alkane degradation genes are expressed in the rhizosphere and in the plant interior.

The relationship between the microbial methylation of mercury and the microbial activities in sediments and water collected from the estuary of Bilbao (North of Spain) was studied in three different sampling points and in two different seasons. Three different cultures were prepared with a sediment slurry to distinguish between biotic and abiotic methylation pathways and the variations of the methylmercury concentration and the variations of the population of total number of bacteria (TDC), anaerobic heterotrophic bacteria (AHB), sulphate-reducing bacteria (SRB) and Desulfovibrio were measured. From this work, it can be concluded that the variation of MeHg concentrations is a result of the methylation/demethylation processes in the sediments, and that the abiotic processes have a negligible contribution to those processes. According to the statistical analysis of the results (partial least squares analysis) a significant statistical correlation was established between methylmercury and the SRB counts.The methylation of mercury follows a stationary pattern linked to the variation of sulphate-reducing bacteria.

Bacteria from this soil were cultured in mineral salt solution supplemented with mesotrione as sole source of carbon for the isolation of mesotrione-degrading bacteria. The bacterial community structure of the enrichment cultures was analyzed by temporal temperature gradient gel electrophoresis (TTGE). The TTGE fingerprints revealed that mesotrione had an impact on bacterial community structure only at its highest concentrations and showed mesotrione-sensitive and mesotrione-adapted strains. Two adapted strains, identified as Bacillus sp. and Arthrobacter sp., were isolated by colony hybridization methods. Biodegradation assays showed that only the Bacillus sp. strain was able to completely and rapidly biotransform mesotrione. Among several metabolites formed, 2-amino-4-methylsulfonylbenzoic acid (AMBA) accumulated in the medium. Although sulcotrione has a chemical structure closely resembling that of mesotrione, the isolates were unable to degrade it. A Bacillus sp. strain isolated from soil was able to completely and rapidly biotransform the triketone herbicide mesotrione.

Toxicity of nano-scaled aluminum, silicon, titanium and zinc oxides to bacteria (Bacillus subtilis, Escherichia coli and Pseudomonas fluorescens) was examined and compared to that of their respective bulk (micro-scaled) counterparts. All nanoparticles but titanium oxide showed higher toxicity (at 20 mg/L) than their bulk counterparts. Toxicity of released metal ions was differentiated from that of the oxide particles. ZnO was the most toxic among the three nanoparticles, causing 100% mortality to the three tested bacteria. Al2O3 nanoparticles had a mortality rate of 57% to B. subtilis, 36% to E. coli, and 70% to P. fuorescens. SiO2 nanoparticles killed 40% of B. subtilis, 58% of E. coli, and 70% of P. fluorescens. TEM images showed attachment of nanoparticles to the bacteria, suggesting that the toxicity was affected by bacterial attachment. Bacterial responses to nanoparticles were different from their bulk counterparts; hence nanoparticle toxicity mechanisms need to be studied thoroughly. Oxide nanoparticles show higher toxicity than their bulk counterparts.

Many surface and ground waters in the continental US are contaminated with a variety of chemical pollutants, which are usually present in concentrations in the ppm and ppb range. The effects of these pollutants on coliform bacteria, which are prominent members of the aquatic flora, are poorly understood. Using a microtiter plate assay, isolates of Escherichia coli (from chicken intestine and fresh water), and an isolate of Klebsiella pneumoniae (from bovine milk) were exposed to varying concentrations of common pollutants over a 24 h period. The herbicides/pesticides simazine, atrazine, and diazinon; the VOCs trichloroethene and MTBE; the estrogens estradiol and estrone; and caffeine, all failed to inhibit bacterial growth at ppm levels. Only ethylene glycol, and the herbicide 2,4-D, significantly inhibited bacterial growth compared to controls. These results suggest that the replication of coliform bacteria in fresh waters is not adversely impacted by many common pollutants. Using a microtiter plate assay, E. coli and Klebsiella bacteria were exposed to a panel of common chemical pollutants of fresh water; only ethylene glycol and 2,4-D inhibited bacterial replication.

The potential of domestic wastewater treatment plants to contribute for the dissemination of ciprofloxacin-resistant bacteria was assessed. Differences on bacterial counts and percentage of resistance in the raw wastewater could not be explained on basis of the size of the plant or demographic characteristics of population served. In contrast, the treated effluent of the larger plants had significantly more heterotrophs and enterobacteria, including ciprofloxacin-resistant organisms, than the smaller (p < 0.01). Moreover, longer hydraulic retention times were associated with significantly higher percentages of resistant enterobacteria in the treated effluent (p < 0.05). Independently of the size or type of treatment used, domestic wastewater treatment plants discharged per day at least 10¹⁰-10¹⁴ colony forming units of ciprofloxacin-resistant bacteria into the receiving environment.

Fecal pollution from human and natural sources enters soil or watercourses, mixes, then reemerges as a nuisance of unknown origin. Before remediation is attempted, the sources and identities of pollution must be identified. Previous microbial source tracking studies have relied on traditional methods of microbiology such as selective media and biochemical characteristics to quantify fecal bacteria in water samples. This is successful when single sources are responsible for pollution. However, when multiple sources are present, numbers must be subdivided into categories of pollution to define relative importance and select appropriate methods of remediation which are very different for examples such as humans and avifauna pollution. Rather than depending on a single method, we recommend a tiered approach which takes advantage of ecological parameters and conventional microbiology to provide context for more precise DNA data and related statistics.

Naphthenic acids (NAs) are a complex group of naturally occurring oil sands constituents that constitute a significant portion of the dissolved organic carbon (DOC) pool available for microbial degradation in the process-related waste water associated with oil sands mine sites. One approach to understanding the biological fate of oil sands process-derived carbon and nitrogen in aquatic reclamation of the mine sites involves the use of stable isotope analyses. However, for stable isotope analyses to be useful in such field-based assessments, there is a need to determine how microbial degradation of a complex mixture of NAs might change the stable isotope values (δ ¹³C, δ ¹⁵N). In batch cultures and semi-continuous laboratory microcosms, utilization of a commercial mixture of NAs by oil sands-derived microbial cultures resulted in microbial biomass that was similar or slightly ¹³C enriched (1.4[per thousand] to 3.0[per thousand]) relative to the DOC source, depending on the length of incubation. Utilization of a NA-containing extract of oil sands processed water resulted in greater ¹³C enrichment of microbial biomass (8.5[per thousand]) relative to the DOC source. Overall, the δ ¹³C of the DOC comprised of complex mixtures of NAs showed minimal change (-0.5[per thousand] to -0.1[per thousand]) during the incubation period whereas the δ ¹³C of the dissolved inorganic carbon (DIC) was more variable (-5.0[per thousand] to +5.4[per thousand]). In tests where the concentration of available nitrogen was increased, the final biomass values were ¹⁵N enriched (3.8[per thousand] to 8.4[per thousand]) relative to the initial biomass. The isotope trends established in this study should enhance our ability to interpret field-based data from sites with hydrocarbon contamination, particularly in terms of carbon source utilization and ¹⁵N enrichment.

Advanced oxidation processes (AOPs) are among the most efficient methods for wastewater treatment. To achieve the degradation of persistent organic pollutants (POPs), AOPs have been developed that employ Fenton reactions promoted by ultrasound (US) or microwaves (MW). Integrated methods combining AOPs with biological treatments are also of great interest. The present paper describes such an integrated approach for the decontamination of water from nonylphenol (NP), a common pollutant that accumulates in aquatic organisms and is quite resistant to biodegradation. Polluted water (containing 1,000 ppm of NP) was sequentially subjected to a sonochemical Fenton reaction and biosorption by the filamentous fungus Paecilomyces lilacinus. Although these methods can be used separately, the sequential approach proved more advantageous. In 1 h the sonochemical oxidation, carried out in a 300 kHz US-reactor equipped with a cooling system, halved NP content in polluted water, as determined by GC-MS analysis. The water was then inoculated with pure cultures of the fungus, whose mycelial biomass further reduced NP content in 7 days. Thus an initial NP concentration of 1,000 ppm was reduced approximately by 90%.