Genetic characterization of fluoroquinolone resistant Escherichia coli from urban streams and municipal and hospital effluents

Escherichia coli with reduced susceptibility to ciprofloxacin, isolated from urban streams, wastewater treatment plants and hospital effluent between 2004 and 2012, were compared based on multilocus sequence typing (MLST), quinolone and beta-lactam resistance determinants and plasmid replicon type. Isolates from the different types of water and isolation dates clustered together, suggesting the persistence and capacity to propagate across distinct aquatic environments. The most prevalent MLST groups were ST10 complex and ST131. Almost all isolates (98%) carried mutations in the chromosomal genes gyrA and/or parC, and 10% possessed the genes qepA, aac(6('))-Ib-cr and/or qnrS1. Over 80% of the isolates were resistant to three or more classes of antibiotics (MDR ≥ 3). The most prevalent beta-lactamase encoding gene was blaTEM, followed by blaCTX-M-15, co-existing with plasmid mediated quinolone resistance. The plasmid replicon types of the group IncF were the most prevalent and distributed by different MLST groups. The genes aac(6('))-Ib-cr and/or qnrS1 could be transferred by conjugation in combination with the genes blaTEM,blaSHV-12 or blaOXA-1 and the plasmid replicon types I1-Iγ, K, HI2 and/or B/O. The potential of multidrug resistant E. coli with reduced susceptibility to ciprofloxacin, harboring mobile genetic elements and with ability to conjugate and transfer resistance genes, to spread and persist across different aquatic environments was demonstrated.

Wastewater reuse in irrigation: a microbiological perspective on implications in soil fertility and human and environmental health

The reuse of treated wastewater, in particular for irrigation, is an increasingly common practice, encouraged by governments and official entities worldwide. Irrigation with wastewater may have implications at two different levels: alter the physicochemical and microbiological properties of the soil and/or introduce and contribute to the accumulation of chemical and biological contaminants in soil. The first may affect soil productivity and fertility; the second may pose serious risks to the human and environmental health. The sustainable wastewater reuse in agriculture should prevent both types of effects, requiring a holistic and integrated risk assessment. In this article we critically review possible effects of irrigation with treated wastewater, with special emphasis on soil microbiota. The maintenance of a rich and diversified autochthonous soil microbiota and the use of treated wastewater with minimal levels of potential soil contaminants are proposed as sine qua non conditions to achieve a sustainable wastewater reuse for irrigation.

An overview on the advanced oxidation processes applied for the treatment of water pollutants defined in the recently launched Directive 2013/39/EU

Environmental pollution is a recognized issue of major concern since a wide range of contaminants has been found in aquatic environment at ngL(-1) to μgL(-1) levels. In the year 2000, a strategy was defined to identify the priority substances concerning aquatic ecosystems, followed by the definition of environmental quality standards (EQS) in 2008. Recently it was launched the Directive 2013/39/EU that updates the water framework policy highlighting the need to develop new water treatment technologies to deal with such problem. This review summarizes the data published in the last decade regarding the application of advanced oxidation processes (AOPs) to treat priority compounds and certain other pollutants defined in this Directive, excluding the inorganic species (cadmium, lead, mercury, nickel and their derivatives). The Directive 2013/39/EU includes several pesticides (aldrin, dichlorodiphenyltrichloroethane, dicofol, dieldrin, endrin, endosulfan, isodrin, heptachlor, lindane, pentachlorophenol, chlorpyrifos, chlorfenvinphos, dichlorvos, atrazine, simazine, terbutryn, diuron, isoproturon, trifluralin, cypermethrin, alachlor), solvents (dichloromethane, dichloroethane, trichloromethane and carbon tetrachloride), perfluorooctane sulfonic acid and its derivatives (PFOS), polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), nonylphenol and octylphenol, as well as the three compounds included in the recommendation for the first watch list of substances (diclofenac, 17-alpha-ethinylestradiol (EE2) and 17-beta-estradiol (E2)). Some particular pesticides (aclonifen, bifenox, cybutryne, quinoxyfen), organotin compounds (tributyltin), dioxins and dioxin-like compounds, brominated diphenylethers, hexabromocyclododecanes and di(2-ethylhexyl)phthalate are also defined in this Directive, but studies dealing with AOPs are missing. AOPs are recognized tools to destroy recalcitrant compounds or, at least, to transform them into biodegradable species. Diuron (a phenylurea herbicide) and atrazine (from the triazine chemical class) are the most studied pesticides from Directive 2013/39/EU. Fenton-based processes are the most frequently applied to treat priority compounds in water and their efficiency typically increases with the operating temperature as well as under UV or solar light. Heterogeneous photocatalysis is the second most used treatment to destroy pollutants defined in the Directive. Ozone alone promotes the partial oxidation of pollutants, and an increase in the effluent biodegradability, but complete mineralization of pollutants is difficult. To overcome this drawback, ozonation has been combined with heterogeneous catalysts, addition of H2O2, other AOPs (such as photocatalysis) or membrane technologies.

Bombella intestini gen. nov., sp. nov., an acetic acid bacterium isolated from bumble bee crop

In the frame of a bumble bee gut microbiota study, acetic acid bacteria (AAB) were isolated using a combination of direct isolation methods and enrichment procedures. MALDI-TOF MS profiling of the isolates and a comparison of these profiles with profiles of established AAB species identified most isolates as Asaia astilbis or as ‘Commensalibacter intestini’, except for two isolates (R-52486 and LMG 28161T) that showed an identical profile. A nearly complete 16S rRNA gene sequence of strain LMG 28161T was determined and showed the highest pairwise similarity to Saccharibacter floricola S-877T (96.5 %), which corresponded with genus level divergence in the family Acetobacteraceae . Isolate LMG 28161T was subjected to whole-genome shotgun sequencing; a 16S–23S rRNA internal transcribed spacer (ITS) sequence as well as partial sequences of the housekeeping genes dnaK, groEL and rpoB were extracted for phylogenetic analyses. The obtained data confirmed that this isolate is best classified into a new genus in the family Acetobacteraceae . The DNA G+C content of strain LMG 28161T was 54.9 mol%. The fatty acid compositions of isolates R-52486 and LMG 28161T were similar to those of established AAB species [with C18 : 1ω7c (43.1 %) as the major component], but the amounts of fatty acids such as C19 : 0 cyclo ω8c, C14 : 0 and C14 : 0 2-OH enabled to differentiate them. The major ubiquinone was Q-10. Both isolates could also be differentiated from the known genera of AAB by means of biochemical characteristics, such as their inability to oxidize ethanol to acetic acid, negligible acid production from melibiose, and notable acid production from d-fructose, sucrose and d-mannitol. In addition, they produced 2-keto-d-gluconate, but not 5-keto-d-gluconate from d-glucose. Therefore, the name Bombella intestini gen nov., sp. nov. is proposed for this new taxon, with LMG 28161T ( = DSM 28636T = R-52487T) as the type strain of the type species.

Solar photocatalytic oxidation of recalcitrant natural metabolic by-products of amoxicillin biodegradation

The contamination of the aquatic environment by non-metabolized and metabolized antibiotic residues has brought the necessity of alternative treatment steps to current water decontamination technologies. This work assessed the feasibility of using a multistage treatment system for amoxicillin (AMX) spiked solutions combining: i) a biological treatment process using an enriched culture to metabolize AMX, with ii) a solar photocatalytic system to achieve the removal of the metabolized transformation products (TPs) identified via LC-MS, recalcitrant to further biological degradation. Firstly, a mixed culture (MC) was obtained through the enrichment of an activated sludge sample collected in an urban wastewater treatment plant (WWTP). Secondly, different aqueous matrices spiked with AMX were treated with the MC and the metabolic transformation products were identified. Thirdly, the efficiency of two solar assisted photocatalytic processes (TiO2/UV or Fe(3+)/Oxalate/H2O2/UV-Vis) was assessed in the degradation of the obtained TPs using a lab-scale prototype photoreactor equipped with a compound parabolic collector (CPC). Highest AMX specific biodegradation rates were obtained in buffer and urban wastewater (WW) media (0.10 ± 0.01 and 0.13 ± 0.07 g(AMX) g(biomass)(-1) h(-1), respectively). The resulting TPs, which no longer presented antibacterial activity, were identified as amoxicilloic acid (m/z = 384). The performance of the Fe(3+)/Oxalate/H2O2/UV-Vis system in the removal of the TPs from WW medium was superior to the TiO2/UV process (TPs no longer detected after 40 min (QUV = 2.6 kJ L(-1)), against incomplete TPs removal after 240 min (QUV = 14.9 kJ L(-1)), respectively).

Biodegradation of sulfamethoxazole and other sulfonamides by Achromobacter denitrificans PR1

This study aimed to isolate and characterize a microbial culture able to degrade sulfonamides. Sulfamethoxazole (SMX)-degrading microorganisms were enriched from activated sludge and wastewater. The resultant mixed culture was composed of four bacterial strains, out of which only Achromobacter denitrificans PR1 could degrade SMX. This sulfonamide was used as sole source of carbon, nitrogen and energy with stoichiometric accumulation of 3-amino-5-methylisoxazole. Strain PR1 was able to remove SMX at a rate of 73.6 ± 9.6 μmol SMX/gcell dryweighth. This rate more than doubled when a supplement of amino acids or the other members of the mixed culture were added. Besides SMX, strain PR1 was able to degrade other sulfonamides with anti-microbial activity. Other environmental Achromobacter spp. could not degrade SMX, suggesting that this property is not broadly distributed in members of this genus. Further studies are needed to shed additional light on the genetics and enzymology of this process.

Insights into the relationship between antimicrobial residues and bacterial populations in a hospital-urban wastewater treatment plant system

The relationship between antimicrobial residues, antibiotic resistance prevalence and bacterial community composition in hospital effluent and in the receiving wastewater treatment plant was studied. Samples from hospital effluent, raw inflow and final effluent of the receiving wastewater treatment plant were characterized for amoxicillin and ciprofloxacin resistance prevalence, content of heavy metals and antimicrobial residues and bacterial community structure, based on 16S rRNA gene PCR-DGGE analysis. The concentration of fluoroquinolones, arsenic and mercury was in general higher in hospital effluent than in raw inflow, while the opposite was observed for tetracyclines, sulfonamides and penicillin G. The prevalence of ciprofloxacin resistance was significantly higher in hospital effluent than in raw inflow. The concentration of antimicrobial residues was observed to be significantly correlated with the prevalence of antibiotic resistant bacteria and with variations in the bacterial community. Hospital effluent was confirmed as a relevant, although not unique, source of antimicrobial residues and antibiotic resistant bacteria to the wastewater treatment plant. Moreover, given the high loads of antibiotic residues and antibiotic resistant bacteria that may occur in hospital effluents, these wastewater habitats may represent useful models to study and predict the impact of antibiotic residues on bacterial communities.

Acetobacter sicerae sp. nov., isolated from cider and kefir, and identification of species of the genus Acetobacter by dnaK, groEL and rpoB sequence analysis

Five acetic acid bacteria isolates, awK9_3, awK9_4 ( = LMG 27543), awK9_5 ( = LMG 28092), awK9_6 and awK9_9, obtained during a study of micro-organisms present in traditionally produced kefir, were grouped on the basis of their MALDI-TOF MS profile with LMG 1530 and LMG 1531(T), two strains currently classified as members of the genus Acetobacter. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences as well as on concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB indicated that these isolates were representatives of a single novel species together with LMG 1530 and LMG 1531(T) in the genus Acetobacter, with Acetobacter aceti, Acetobacter nitrogenifigens, Acetobacter oeni and Acetobacter estunensis as nearest phylogenetic neighbours. Pairwise similarity of 16S rRNA gene sequences between LMG 1531(T) and the type strains of the above-mentioned species were 99.7%, 99.1%, 98.4% and 98.2%, respectively. DNA-DNA hybridizations confirmed that status, while amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) data indicated that LMG 1531(T), LMG 1530, LMG 27543 and LMG 28092 represent at least two different strains of the novel species. The major fatty acid of LMG 1531(T) and LMG 27543 was C18 : 1ω7c. The major ubiquinone present was Q-9 and the DNA G+C contents of LMG 1531(T) and LMG 27543 were 58.3 and 56.7 mol%, respectively. The strains were able to grow on D-fructose and D-sorbitol as a single carbon source. They were also able to grow on yeast extract with 30% D-glucose and on standard medium with pH 3.6 or containing 1% NaCl. They had a weak ability to produce acid from d-arabinose. These features enabled their differentiation from their nearest phylogenetic neighbours. The name Acetobacter sicerae sp. nov. is proposed with LMG 1531(T) ( = NCIMB 8941(T)) as the type strain.

A modular reactor to simulate biofilm development in orthopedic materials

Surfaces of medical implants are generally designed to encourage soft- and/or hard-tissue adherence, eventually leading to tissue- or osseo-integration. Unfortunately, this feature may also encourage bacterial adhesion and biofilm formation. To understand the mechanisms of bone tissue infection associated with contaminated biomaterials, a detailed understanding of bacterial adhesion and subsequent biofilm formation on biomaterial surfaces is needed. In this study, a continuous-flow modular reactor composed of several modular units placed in parallel was designed to evaluate the activity of circulating bacterial suspensions and thus their predilection for biofilm formation during 72 h of incubation. Hydroxyapatite discs were placed in each modular unit and then removed at fixed times to quantify biofilm accumulation. Biofilm formation on each replicate of material, unchanged in structure, morphology, or cell density, was reproducibly observed. The modular reactor therefore proved to be a useful tool for following mature biofilm formation on different surfaces and under conditions similar to those prevailing near human-bone implants.

Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome

Water is one of the most important bacterial habitats on Earth. As such, water represents also a major way of dissemination of bacteria between different environmental compartments. Human activities led to the creation of the so-called urban water cycle, comprising different sectors (waste, surface, drinking water), among which bacteria can hypothetically be exchanged. Therefore, bacteria can be mobilized between unclean water habitats (e.g. wastewater) and clean or pristine water environments (e.g. disinfected and spring drinking water) and eventually reach humans. In addition, bacteria can also transfer mobile genetic elements between different water types, other environments (e.g. soil) and humans. These processes may involve antibiotic resistant bacteria and antibiotic resistance genes. In this review, the hypothesis that some bacteria may share different water compartments and be also hosted by humans is discussed based on the comparison of the bacterial diversity in different types of water and with the human-associated microbiome. The role of such bacteria as potential disseminators of antibiotic resistance and the inference that currently only a small fraction of the clinically relevant antibiotic resistome may be known is discussed.

Assessment of solar driven TiO2-assisted photocatalysis efficiency on amoxicillin degradation

The objective of this work was to evaluate the efficiency of a solar TiO2-assisted photocatalytic process on amoxicillin (AMX) degradation, an antibiotic widely used in human and veterinary medicine. Firstly, solar photolysis of AMX was compared with solar photocatalysis in a compound parabolic collectors pilot scale photoreactor to assess the amount of accumulated UV energy in the system (Q UV) necessary to remove 20 mg L(-1) AMX from aqueous solution and mineralize the intermediary by-products. Another experiment was also carried out to accurately follow the antibacterial activity against Escherichia coli DSM 1103 and Staphylococcus aureus DSM 1104 and mineralization of AMX by tracing the contents of dissolved organic carbon (DOC), low molecular weight carboxylate anions, and inorganic anions. Finally, the influence of individual inorganic ions on AMX photocatalytic degradation efficiency and the involvement of some reactive oxygen species were also assessed. Photolysis was shown to be completely ineffective, while only 3.1 kJUV L(-1) was sufficient to fully degrade 20 mg L(-1) AMX and remove 61% of initial DOC content in the presence of the photocatalyst and sunlight. In the experiment with an initial AMX concentration of 40 mg L(-1), antibacterial activity of the solution was considerably reduced after elimination of AMX to levels below the respective detection limit. After 11.7 kJUV L(-1), DOC decreased by 71%; 30% of the AMX nitrogen was converted into ammonium and all sulfur compounds were converted into sulfate. A large percentage of the remaining DOC was in the form of low molecular weight carboxylic acids. Presence of phosphate ions promoted the removal of AMX from solution, while no sizeable effects on the kinetics were found for other inorganic ions. Although the AMX degradation was mainly attributed to hydroxyl radicals, singlet oxygen also plays an important role in AMX self-photosensitization under UV/visible solar light.

Influence of the composition of the initial mixtures on the chemical composition, physicochemical properties and humic-like substances content of composts

The influence of the proportion of C- and N-rich raw materials (initial C/N ratio) and bulking agent on the chemical functional groups composition, humic-like substances (HS-like) content and physicochemical properties of composts was assessed. To achieve these goals, seven initial mixtures (BA1-6 and C1) of dog food (N-rich raw material) were composted with wheat flour (C-rich raw material). Composts were analyzed in terms of chemical functional groups, physicochemical, maturity and stability parameters. The C-rich raw material favored the formation of oxidized organic matter (OM) during the composting process, as suggested by the variation of the ratios of the peaks intensity of FT-IR spectra, corresponding to a decrease of the polysaccharides and an increase of aromatic and carboxyl-containing compounds. However, although with high proportion of C-rich raw material, mixtures with low initial C/N seems to have favored the accumulation of partially oxidized OM, which may have contributed to high electrical conductivity values in the final composts. Therefore, although favoring the partial transformation of OM into stabilized HS-like, initial mixtures with high proportion of C-rich raw material but with low initial C/N led to unstable composts. On the other hand, as long as a high percentage of bulking agent was used to promote the structure of biomass and consequently improve of the aeration conditions, low initial C/N was not a limiting factor of OM oxidation into extractable stabilized humic-like acids.

Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing

Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data.

Influence of nanohydroxyapatite surface properties on Staphylococcus epidermidis biofilm formation

Nanohydroxyapatite (nanoHA), due to its chemical properties, has appeared as an exceptionally promising bioceramic to be used as bone regeneration material. Staphylococcus epidermidis have emerged as major nosocomial pathogens associated with infections of implanted medical devices. In this work, the purpose was to study the influence of the nanoHA surface characteristics on S. epidermidis RP62A biofilm formation. Therefore, two different initial inoculum concentrations (Ci) were used in order to check if these would affect the biofilm formed on the nanoHA surfaces. Biofilm formation was followed by the enumeration of cultivable cells and by scanning electron microscopy. Surface topography, contact angle, total surface area and porosimetry of the biomaterials were studied and correlated with the biofilm data. The surface of nanoHA sintered at 830℃ (nanoHA830) showed to be more resistant to S. epidermidis attachment and accumulation than that of nanoHA sintered at 1000℃ (nanoHA1000). The biofilm formed on nanoHA830 presented differences in terms of structure, surface coverage and EPS production when compared to the one formed on nanoHA1000 surface. It was observed that topography and surface area of nanoHA surfaces had influence on the bacterial attachment and accumulation. Ci influenced bacteria attachment and accumulation on nanoHA surfaces over time. The choice of the initial inoculum concentration was relevant proving to have an effect on the extent of adherence thus being a critical point for human health if these materials are used in implantable devices. This study showed that the initial inoculum concentration and surface material properties determine the rate of microbial attachment to substrata and consequently are related to biofilm-associated infections in biomaterials.

Insights into solar TiO2-assisted photocatalytic oxidation of two antibiotics employed in aquatic animal production, oxolinic acid and oxytetracycline

In this study, solar driven TiO2-assisted heterogeneous photocatalytic experiments in a pilot-plant with compound parabolic collectors (CPCs) were carried out to study the degradation of two authorized veterinary antibiotics with particular relevance in finfish aquaculture, oxolinic acid (OXA) and oxytetracycline (OTC), using pure solutions of individual or mixed antibiotics. Firstly, the influence of natural solar photolysis was assessed for each antibiotic. Secondly, photocatalytic degradation kinetic rate constants for individual and mixed antibiotics were compared, using a catalyst load of 0.5 g L(-1) and an initial pH around 7.5. Thirdly, for individually photocatalytic-treated OXA and OTC in the same conditions, the growth inhibition of Escherichia coli DSM 1103 was followed, and the mineralization extent was assessed by the residual dissolved organic carbon (DOC), low-molecular-weight carboxylate anions and inorganic ions concentration. Finally, the effect of inorganic ions, such as chlorides, sulfates, nitrates, phosphates, ammonium and bicarbonates, on the photocatalytic degradation of individual solutions of OXA and OTC was also evaluated and the formation of different reactive oxygen species were probed using selective scavengers. The removal profiles of each antibiotic, both as single component or in mixture were similar, being necessary 2.5 kJ L(-1) of solar UV energy to fully remove them, and 18 kJ(UV) L(-1) to achieve 73% and 81% mineralization, for OXA and OTC, respectively. The remaining organic carbon content was mainly due to low-molecular-weight carboxylate anions. After complete removal of the antibiotics, the remaining degradation by-products no longer showed antibacterial activity. Also, 10% and 55% of the nitrogen content of each antibiotic was converted to ammonium, while no conversion to nitrite or nitrate was detected. The presence of phosphates hindered considerably the removal of both antibiotics, whereas the presence of other inorganic ions did not substantially altered the antibiotics photocatalytic degradation kinetics.

Antibiotic resistance, antimicrobial residues and bacterial community composition in urban wastewater

This study was based on the hypothesis that the occurrence of antimicrobial residues and antibiotic resistant bacteria in the sewage could be correlated with the structure and composition of the bacterial community and the antibiotic resistance loads of the final effluent. Raw and treated wastewater composite samples were collected from an urban treatment plant over 14 sampling dates. Samples were characterized for the i) occurrence of tetracyclines, penicillins, sulfonamides, quinolones, triclosan, arsenic, cadmium, lead, chromium and mercury; ii) antibiotic resistance percentages for tetracycline, sulfamethoxazole, ciprofloxacin and amoxicillin and iii) 16S rRNA gene-DGGE patterns. The data of corresponding samples, taking into account the hydraulic residence time, was analyzed using multivariate analysis. Variations on the bacterial community structure of the final effluent were significantly correlated with the occurrence of tetracyclines, penicillins, sulfonamides, quinolones and triclosan in the raw inflow. Members of the class Epsilonproteobacteria presented positive correlations with those antimicrobials, whereas negative correlations were observed with Beta and Gammaproteobacteria and Firmicutes. Antibiotic resistance percentages presented different trends of variation in heterotrophs/enterobacteria and in enterococci, varied over time and after wastewater treatment. Antibiotic resistance was positively correlated with the occurrence of tetracyclines residues and high temperature. A relationship between antibiotic residues, bacterial community structure and composition and antibiotic resistance is demonstrated. Further studies, involving more wastewater treatment plants may help to elucidate this complex relationship.

Recovery of humic-like susbtances from low quality composts

The quality of four commercial composts produced from poultry litter and municipal solid wastes was assessed based on their physic-chemical, stability and maturity parameters. These properties varied among the analysed composts; it was found that electric conductivity, heavy metals content and maturity were the parameters that limited the composts quality. Therefore, the feasibility of using them to obtain liquid fertilisers rich in humic-like substances (HS) was assessed. The HS yield, phytotoxicity, heavy metals co-extraction and chemical characterization were carried out. The linkage of the HS chemical composition with the compost properties was assessed by multivariate analysis. Among the compost properties, germination indices, Cr and Cu contents were the parameters that correlated most with the HS chemical composition. The low levels of metals and absence of phytotoxicity in all the analysed HS extracts indicate that composts with low quality may be used to produce liquid organic fertilisers, substituting those from natural resources.

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11(T), was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11(T) were Patulibacter ginsengiterrae CECT 7603(T) (96.8 % similarity), Patulibacter minatonensis DSM 18081(T) (96.6 %) and Patulibacter americanus DSM 16676(T) (96.6 %). Phenotypic characterization supports the inclusion of strain I11(T) within the genus Patulibacter (phylum Actinobacteria). However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11(T) ( = DSM 25962(T) = CECT 8141(T)).

Bacterial diversity from the source to the tap: a comparative study based on 16S rRNA gene-DGGE and culture-dependent methods

This study aimed to assess the influence of water treatment and distribution on the bacterial communities with particular emphasis on tap water. Samples from the water treatment plant, the bulk supply distribution system and household taps, supplied by the same drinking water treatment plant, were analyzed using culture-dependent and culture-independent methods. Water treatment imposed alterations in the composition of the bacterial community, although this effect was more evident in the cultivable bacteria rather than among the total community assessed by 16S rRNA gene-denaturing gradient gel electrophoresis (DGGE) profiling. Water disinfection, mainly chlorination, promoted a reduction on bacterial diversity and cultivability, with a shift in the pattern of cultivable bacteria from predominantly Gram-negative to predominately Gram-positive and acid-fast. Downstream of the chlorination stages, tap water, in comparison with raw water, presented higher diversity indices and cultivability percentages. From the source to the tap, members of the Alpha-, Beta- and Gammaproteobacteria were the predominant lineages identified using 16S rRNA gene-DGGE analysis. Although with a lower coverage, the DGGE-based lineage identifications were in agreement with those found using 454-pyrosequencing analysis. Despite the effectiveness of water treatment to eliminate or inactivate most of the bacteria, Proteobacteria such as Acinetobacter, Bosea and Sphingomonadaceae may successfully colonize tap water.

Diversity and antibiotic resistance in Pseudomonas spp. from drinking water

Pseudomonas spp. are common inhabitants of aquatic environments, including drinking water. Multi-antibiotic resistance in clinical isolates of P. aeruginosa is widely reported and deeply characterized. However, the information regarding other species and environmental isolates of this genus is scant. This study was designed based on the hypothesis that members of the genus Pseudomonas given their high prevalence, wide distribution in waters and genetic plasticity can be important reservoirs of antibiotic resistance in drinking water. With this aim, the diversity and antibiotic resistance phenotypes of Pseudomonas isolated from different drinking water sources were evaluated. The genotypic diversity analyses were based on six housekeeping genes (16S rRNA, rpoD, rpoB, gyrB, recA and ITS) and on pulsed field gel electrophoresis. Susceptibility to 21 antibiotics of eight classes was tested using the ATB PSE EU (08) and disk diffusion methods. Pseudomonas spp. were isolated from 14 of the 32 sampled sites. A total of 55 non-repetitive isolates were affiliated to twenty species. Although the same species were isolated from different sampling sites, identical genotypes were never observed in distinct types of water (water treatment plant/distribution system, tap water, cup fillers, biofilm, and mineral water). In general, the prevalence of antibiotic resistance was low and often the resistance patterns were related with the species and/or the strain genotype. Resistance to ticarcillin, ticarcillin with clavulanic acid, fosfomycin and cotrimoxazol were the most prevalent (69-84%). No resistance to piperacillin, levofloxacin, ciprofloxacin, tetracycline, gentamicin, tobramycin, amikacin, imipenem or meropenem was observed. This study demonstrates that Pseudomonas spp. are not so widespread in drinking water as commonly assumed. Nevertheless, it suggests that water Pseudomonas can spread acquired antibiotic resistance, preferentially via vertical transmission.

Bacillus purgationiresistans sp. nov., isolated from a drinking-water treatment plant

A Gram-positive, aerobic, non-motile, endospore-forming rod, designated DS22T, was isolated from a drinking-water treatment plant. Cells were catalase- and oxidase-positive. Growth occurred at 15–37 °C, at pH 7–10 and with <8 % (w/v) NaCl (optimum growth: 30 °C, pH 7–8 and 1–3 % NaCl). The major respiratory quinone was menaquinone 7, the G+C content of the genomic DNA was 36.5 mol% and the cell wall contained meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis, strain DS22T was a member of the genus Bacillus. Its closest phylogenetic neighbours were Bacillus horneckiae NRRL B-59162T (98.5 % 16S rRNA gene sequence similarity), Bacillus oceanisediminis H2T (97.9 %), Bacillus infantis SMC 4352-1T (97.4 %), Bacillus firmus IAM 12464T (96.8 %) and Bacillus muralis LMG 20238T (96.8 %). DNA–DNA hybridization, and biochemical and physiological characterization allowed the differentiation of strain DS22T from its closest phylogenetic neighbours. The data supports the proposal of a novel species, Bacillus purgationiresistans sp. nov.; the type strain is DS22T ( = DSM 23494T = NRRL B-59432T = LMG 25783T).

Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost

Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).