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The anti-inflammatory drug ibuprofen is considered to be an emerging contaminant because of its presence in different environments (from water bodies to soils) at concentrations with adverse effects on aquatic organisms due to cytotoxic and genotoxic damage, high oxidative cell stress, and detrimental effects on growth, reproduction, and behavior. Because of its high human consumption rate and low environmental degradation rate, ibuprofen represents an emerging environmental problem. Ibuprofen enters the environment from different sources and accumulates in natural environmental matrices. The problem of drugs, particularly ibuprofen, as contaminants is complicated because few strategies consider them or apply successful technologies to remove them in a controlled and efficient manner. In several countries, ibuprofen's entry into the environment is an unattended contamination problem. It is a concern for our environmental health system that requires more attention. Due to its physicochemical characteristics, ibuprofen degradation is difficult in the environment or by microorganisms. There are experimental studies that are currently focused on the problem of drugs as potential environmental contaminants. However, these studies are insufficient to address this ecological issue worldwide. This review focuses on deepening and updating the information concerning ibuprofen as a potential emerging environmental contaminant and the potential for using bacteria for its biodegradation as an alternative technology.

Laboratory tests in which a fluid or combination of fluids that are injected into a core rock are designed to determine oil reservoir rock petrophysical properties, understand the mobility of fluid flow in the porous samples, and calibrate porous media fluid flow models. The core material is extracted from the oil reservoir. However, the manufacture of core plugs is challenging because of the complexity of extracting natural rocks from the reservoir and their morphological and atypical heterogeneity. In addition, core flooding tests are essentially destructive, making it impossible to achieve experimental repeatability by using identical cores. The use of 3D printing in digital rock physics has permitted the production and replication of synthetic rock samples with the morphological characteristics of natural rocks for core analysis and core flooding tests. This study proposes the 3D manufacture of artificial core plugs from microcomputed tomography of Berea sandstone. The digital samples were constructed using a digital particle packing approach by systematically manipulating rock textural parameters, such as the grain size and shape, cementation pattern, and sorting grain, making it possible to obtain a core plug that fulfills experimental requirements. Before the 3D printing of the sample, the flow distribution through the porous media structure was numerically simulated using the Lattice Boltzmann method to obtain the core plug samples' permeability and porosity. The core plug was digitally embedded within a core holder to generate a stereolithography file for 3D printing of the core flooding setup, which can be used directly in conventional experiments. The permeabilities of the 3D printed plugs were experimentally determined to permit a direct comparison to the numerical results and evaluate the utility of printed plugs for displacement experiments., Competing Interests: No competing financial interests exist., (Copyright 2022, Mary Ann Liebert, Inc., publishers.)

Polycyclic aromatic hydrocarbons (PAHs) constitute important soil contaminants derived from petroleum. Poz14 strain can degrade pyrene and naphthalene. Its genome presented 9333 genes, among them those required for PAHs degradation. By phylogenomic analysis, the strain might be assigned to Amycolatopsis nivea. The strain was grown in glucose, pyrene, and naphthalene to compare their proteomes; 180 proteins were detected in total, and 90 of them were exclusives for xenobiotic conditions. Functions enriched with the xenobiotics belonged to transcription, translation, modification of proteins and transport of inorganic ions. Enriched pathways were pentose phosphate, proteasome and RNA degradation; in contrast, in glucose were glycolysis/gluconeogenesis and glyoxylate cycle. Proteins proposed to participate in the upper PAHs degradation were multicomponent oxygenase complexes, Rieske oxygenases, and dioxygenases; in the lower pathways were ortho-cleavage of catechol, phenylacetate, phenylpropionate, benzoate, and anthranilate. The catechol dioxygenase activity was measured and found increased when the strain was grown in naphthalene. Amycolatopsis sp. Poz14 genome and proteome revealed the PAHs degradation pathways and functions helping to contend the effects of such process., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Purpose: The aim of the present work was to assess the electrogenic activity of bacteria from hydrothermal vent sediments achieved under sulfate reducing (SR) conditions in a microbial fuel cell design with acetate, propionate and butyrate as electron donors., Methods: Two different mixtures of volatile fatty acids (VFA) were evaluated as the carbon source at two chemical oxygen demand (COD) proportions. The mixtures of VFA used were: acetate, propionate and butyrate COD: 3:0.5:0.5 (stage 1) and acetate - butyrate COD: 3.5:0.5 (stage 2). Periodical analysis of sulfate (SO 4 -2 ), sulfide (HS - ) and COD were conducted to assess sulfate reduction (SR) and COD removal along with measurements of voltage and current to assess the global performance of the consortium in the system., Results: Percentage of SR was of 97.5 ± 0.7 and 74.3 ± 1.5% for stage 1 and 2, respectively. The % COD removal was of 91 ± 2.1 and 75.3 ± 9.6 for stage 1 and 2, respectively. Although SR and COD removal were higher at stage 1, in regards of energy, stage 2 presented higher current and power densities and Coulombic efficiency as follows: 741.7 ± 30.5 μA/m 2 , 376 ± 34.4 μW/m 2 and 5 ± 2.7%, whereas for stage 1 these values were: 419 ± 71 μA/m 2 , 52.7 ± 18 μW/m 2 and 0.02%, respectively. A metagenomic analysis - stage 2 - in the anodic chamber, demonstrated that SR was due to Dethiosulfovibrionaceae ( HA73 ), Desulfobacter and Desulfococcus and the electrogenic microorganisms were Planococcus , SHD-231 , Proteiniclasticum , vadinCA02 , and families Porphyromonadacea and Pseudomonadaceae ., Conclusions: It was demonstrated that microorganisms prevenient from hydrothermal vent sediments adapted to a microbial fuel cell system are able to generate electricity coupled to 74.3 ± 1.5 and 75.3 ± 9.6% of SR and COD removal respectively, with a mixture of acetate - butyrate., Competing Interests: Conflict of interestThe authors declare that there are no conflict of interest., (© Springer Nature Switzerland AG 2020.)

Background: Avocado is affected by Colletotrichum gloeosporioides causing anthracnose. Antagonistic microorganisms against C. gloeosporioides represent an alternative for biological control. Accordingly, in the present study, we focused on the isolation and characterization of potential antagonist bacteria against a member of the C. gloeosporioides species complex with respect to their possible future application., Results: Samples of avocado rhizospheric soil were aquired from an orchard located in Ocuituco, Morelos, Mexico, aiming to obtain bacterial isolates with potential antifungal activity. From the soil samples, 136 bacteria were isolated and they were then challenged against a member of the C. gloeosporioides species complex; only three bacterial isolates A1, A2 and A3 significantly diminished mycelial fungal growth by 75%, 70% and 60%, respectively. Two of these isolates were identified by 16S rRNA as Bacillus mycoides (A1 and A2) and the third was identified as Bacillus tequilensis (A3). Bacillus mycoides bacterial cell-free supernatant reduced the mycelial growth of a member of the C. gloeosporioides species complex isolated from avocado by 65%, whereas Bacillus tequilensis A3 supernatant did so by 25% after 3 days post inoculation. Bacillus tequilensis mycoides A1 was a producer of proteases, indolacetic acid and siderophores. Preventive treatment using a cell-free supernatant of B. mycoides A1 diminished the severity of anthracnose disease (41.9%) on avocado fruit., Conclusion: These results reveal the possibility of using B. mycoides A1 as a potential biological control agent. © 2020 Society of Chemical Industry., (© 2020 Society of Chemical Industry.)

A paramour factor limiting metal-microorganism interaction is the metal ion concentration, and the metal precipitation efficiency driven by microorganisms is sensitive to metal ion concentration. The aim of the work was to determine the tolerance of the sulfidogenic sludge generated from hydrothermal vent sediments at microcosms level to different concentrations of Fe, Cu and Zn and the effect on the microbial community. In this study the chemical oxygen demand (COD) removal, sulfate-reducing activity (SRA) determination, inhibition effect through the determination of IC 50 , and the characterization of the bacterial community´s diversity were conducted. The IC 50 on SRA was 34 and 81 mg/L for Zn and Cu, respectively. The highest sulfide concentration (H 2 S mg/L) and % of sulfate reduction obtained were: 511.30 ± 0.75 and 35.34 ± 0.51 for 50 mg/L of Fe, 482.48 ± 6.40 and 33.35 ± 0.44 for 10 mg/L of Cu, 442.26 ± 17.1 and 30.57 ± 1.18 for 10 mg/L of Zn, respectively. The COD removal rates were of 71.81 ± 7.6, 53.92 ± 1.07 and 57.68 ± 10.2 mg COD/ L d for Fe (50 mg/L), Cu (40 mg/L) and Zn (20 mg/L), respectively. Proteobacteria, Firmicutes, Chloroflexi and Actinobacteria were common phyla to four microcosms (stabilized sulfidogenic and added with Fe, Cu or Zn). The dsrA genes of Desulfotomaculum acetoxidans, Desulfotomaculum gibsoniae and Desulfovibrio desulfuricans were expressed in the microcosms supporting the SRA results. The consortia could be explored for ex-situ bioremediation purposes in the presence of the metals tested in this work.

Epidemiological studies comparing clinical and commensal Staphylococcus epidermidis isolates suggest that biofilm formation is a discriminant biomarker. A study showed that four non-biofilm-forming clinical S. epidermidis isolates could form an induced biofilm by trypsin treatment, suggesting that S. epidermidis can form biofilms in a protease-independent way and in a trypsin-induced way. In this study, the trypsin capacity to induce biofilm formation was evaluated in non-biofilm-forming S. epidermidis isolates (n = 133) in order to support this mechanism and to establish the importance of total biofilms (meaning the sum of protease-independent biofilm and trypsin-induced biofilm). Staphylococcus epidermidis isolates from ocular infections (OI; n = 24), prosthetic joint infections (PJI; n = 64), and healthy skin (HS-1; n = 100) were screened for protease-independent biofilm formation according to Christensen's method. The result was that there are significant differences (p < .0001) between clinical (43.2%) and commensal (17%) protease-independent biofilm producers. Meanwhile, non-biofilm-forming isolates were treated with trypsin, and biofilm formation was evaluated by the same method. The number of commensal trypsin-induced biofilm producers significantly increased from 17% to 79%. In contrast, clinical isolates increased from 43.2% to 72.7%. The comparison between clinical and commensal total biofilm yielded no significant differences (p = .392). A similar result was found when different isolation sources were compared (OI vs. HS-1 and PJI vs. HS-1). The genotype icaA - /aap + was associated with the trypsin-induced biofilm phenotype; however, no correlation was observed between aap mRNA expression and the level of trypsin-induced biofilm phenotype. Studying another group of commensal S. epidermidis non-biofilm-forming isolates (HS-2; n = 139) from different body sites, it was found that 70 isolates (60.3%) formed trypsin-induced biofilms. In conclusion, trypsin is capable of inducing biofilm production in non-biofilm-forming commensal S. epidermidis isolates with the icaA - /aap + genotype, and there is no significant difference in total biofilms when comparing clinical and commensal isolates, suggesting that total biofilms are not a discriminant biomarker., (© 2019 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)

Objectives: Staphylococcus epidermidis can cause prosthetic joint infections. Strategies to differentiate between healthy skin and prosthetic joint infections isolates are relatively ineffective, which makes necessary to search for new differential biomarkers. Staphylococcus epidermidis has eleven surface proteins, denoted as Ses proteins. In this work, ses genes are used as biomarkers to differentiate between prosthetic joint infections and healthy skin isolates., Methods: All prosthetic joint infections (n = 51) and healthy skin (n = 51) isolates were genotyped by pulsed-field gel electrophoresis. icaA, embp, sesA-I, and sdrF genes were determined by PCR. The phenotypic data included biofilm production and antibiotic resistance., Results: 10 pulsed-field gel electrophoresis profiles were identified: four profiles were exclusive of prosthetic joint infections isolates, three profiles presented a higher proportion in prosthetic joint infections isolates and three profiles presented a higher proportion in healthy skin isolates. sesA, sesB, sesC, sesD, sesE, sesG, and sesH genes were more prevalent in healthy skin isolates than in prosthetic joint infections isolates (p < .05). Prosthetic joint infections isolates were more resistant to oxacillin (78%), ciprofloxacin (60%), levofloxacin (60%), and moxifloxacin (57%). The principal coordinate analysis and a discriminant analysis found that prosthetic joint infections isolates had as discriminant biomarker the biofilm formation, the icaA gene, oxacillin, ciprofloxacin, levofloxacin, moxifloxacin, and gentamicin resistance. In contrast, the healthy skin isolates had as discriminant biomarkers the embp, sesA, sesB, sesC, sesD, sesE, sesG, and sesH genes., Conclusions: These data suggest that ses genes can be considered biomarkers to differentiate between S. epidermidis commensal and prosthetic joint infections clinical.

Trichloroethylene (TCE) is known as a toxic organic compound found as a pollutant in water streams around the world. The ultimate goal of the present work was to determine the TCE concentration that would be feasible to biodegrade on a long-term basis by a sulfidogenic sludge while maintaining sulfate reducing activity (SRA). Microcosms were prepared with sulfidogenic sludge obtained from a stabilized sulfidogenic UASB and amended with different TCE concentrations (100-300 µM) and two different proportions of volatile fatty acids (VFA) acetate, propionate and butyrate at COD of 2.5:1:1 and 1:1:1, respectively to evaluate the tolerance of the sludge. The overall results suggested that the continuous exposure of the microorganisms to TCE leads to inhibition of SRA; nonetheless, the SRA can be recovered after adequate supplementation of carbon sources and sulfate. The most suitable TCE concentration to operate on a long-term basis while preserving SRA was 26-35 mg L -1 (200-260 µM). A low level of expression of the mRNA of the sulfite reductase subunit alpha (dsrA) gene was obtained in the presence of the TCE and its intermediate products. This gene was associated to SRB belonging to the genera Desulfovibrio, Desulfosalsimonas, Desulfotomaculum, Desulfococcus, Desulfatiglans and Desulfomonas.

Purpose: Staphylococcus epidermidis ATCC12228 lipoteichoic acid (LTA) inhibits TNFα production from keratinocytes that are activated with poly I:C. However, this effect has not been proven in clinical or commensal isolates., Methodology: The <10 kDa fractions of S. epidermidis isolates from ocular infections (n=56), healthy skin (n=35) and healthy conjunctiva (n=32) were obtained. TNFα production was determined by elisa in HaCaT keratinocytes stimulated with poly I:C and with the <10 kDa fractions. LTA in the cytoplasmic membrane and in the <10 kDa fractions of the isolates was determined during bacterial growth by flow cytometry, Western blot and electrospray ionization mass spectrometry. The expression levels of ugtP, ltaA and ltaS were evaluated., Results: Two populations of isolates were found: a population that inhibited TNFα production (TNFα-inhibitor isolates) and a population that did not inhibit it (TNFα non-inhibitor isolates). The cells from the TNFα-inhibitor isolates had less LTA in the cytoplasmic membrane compared to the cells from the TNFα non-inhibitor isolates (P<0.05). Similarly, LTA was detected in the supernatants of TNFα-inhibitor isolates, and it was absent in TNFα non-inhibitor isolates. High expression levels of the ugtP and ltaA genes in the 1850I (TNFα-inhibitor isolate) and 37HS (TNFα non-inhibitor isolate) isolates were found during bacterial growth. However, the ltaS gene had a low expression level (P<0.05) in the 37HS isolate., Conclusion: The TNFα-inhibitor isolates release LTA due to high expression of the LTA synthesis genes. By contrast, TNFα non-inhibitor isolates do not release LTA due to low expression level of the ltaS gene.

Marine microorganisms that are obtained from hydrothermal vent sediments present a great metabolic potential for applications in environmental biotechnology. However, the work done regarding their applications in engineered systems is still scarce. Hence, in this work, the sulfate reduction process carried out by a marine microbial community in an upflow anaerobic sludge blanket (UASB) reactor was investigated for 190 days under sequential batch mode. The effects of 1000 to 5500 mg L -1 of SO 4 -2 and the chemical oxygen demand (COD)/SO 4 -2 ratio were studied along with a kinetic characterization with lactate as the electron donor. Also, the feasibility of using the sulfide produced in the UASB for copper precipitation in a second column was studied under continuous mode. The system presented here is an alternative to sulfidogenesis, particularly when it is necessary to avoid toxicity to sulfide and competition with methanogens. The bioreactor performed better with relatively low concentrations of sulfate (up to 1100 mg L -1 ) and COD/SO 4 -2 ratios between 1.4 and 3.6. Under the continuous regime, the biogenic sulfide was sufficient to precipitate copper at a removal rate of 234 mg L -1  day -1 . Finally, the identification of the microorganisms in the sludge was carried out; some genera of microorganisms identified were Desulfitobacterium and Clostridium.

In the Staphylococcus aureus ATCC25923 strain, the flqB mutation in the 5'untranslated region (5'UTR) of the norA gene causes increased norA mRNA expression and high efflux activity (HEA). The involvement of the norA gene 5'UTR in HEA has not been explored in S. epidermidis; therefore, we examined the function of this region in S. epidermidis clinical isolates. The selection of isolates with HEA was performed based on ethidium bromide (EtBr) MIC values and efflux efficiency (EF) using the semi-automated fluorometric method. The function of the 5'UTR was studied by quantifying the levels of norA expression (RT-qPCR) and by identifying 5'UTR mutations by sequence analysis. Only 10 isolates from a total of 165 (6.1%) had HEA (EtBr MIC = 300 μg/ml and EF ranged from 48.4 to 97.2%). Eight of 10 isolates with HEA had the 5'UTR 95 Δ G mutation. Isolates carrying the 95 Δ G mutation had higher levels of norA expression compared with those that did not. To corroborate that the 95 Δ G mutation is involved in HEA, a strain adapted to EtBr was obtained in vitro. This strain also presented the 95 Δ G mutation and had a high level of norA expression and EF, indicating that the 95 Δ G mutation is important for the HEA phenotype. The 95 Δ G mutation produces a different structure in the Shine-Dalgarno region, which may promote better translation of norA mRNA. To our knowledge, this is the first report to demonstrate the participation of the 5'UTR 95 Δ G mutation of the norA gene in the HEA phenotype of S. epidermidis isolates. Here, we propose that the efflux of EtBr is caused by an increment in the transcription and/or translation of the norA gene., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Staphylococcus epidermidis is a common commensal of healthy conjunctiva and it can cause endophthalmitis, however its presence in conjunctivitis, keratitis and blepharitis is unknown. Molecular genotyping of S. epidermidis from healthy conjunctiva could provide information about the origin of the strains that infect the eye. In this paper two collections of S. epidermidis were used: one from ocular infection (n = 62), and another from healthy conjunctiva (n = 45). All isolates were genotyped by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec), detection of the genes icaA, icaD, IS256 and polymorphism type of agr locus. The phenotypic data included biofilm production and antibiotic resistance. The results displayed 61 PFGE types from 107 isolates and they were highly discriminatory. MLST analysis generated a total of 25 STs, of which 11 STs were distributed among the ocular infection isolates and lineage ST2 was the most frequent (48.4%), while 14 STs were present in the healthy conjunctiva isolates and lineage ST5 was the most abundant (24.4%). By means of a principal coordinates analysis (PCoA) and a discriminant analysis (DA) it was found that ocular infection isolates had as discriminant markers agr III or agr II, SCCmec V or SCCmec I, mecA gene, resistance to tobramycin, positive biofilm, and IS256+. In contrast to the healthy conjunctiva isolates, the discriminating markers were agr I, and resistance to chloramphenicol, ciprofloxacin, gatifloxacin and oxacillin. The discriminant biomarkers of ocular infection were examined in healthy conjunctiva isolates, and it was found that 3 healthy conjunctiva isolates [two with ST2 and another with ST9] (3/45, 6.66%) had similar genotypic and phenotypic characteristics to ocular infection isolates, therefore a small population from healthy conjunctiva could cause an ocular infection. These data suggest that the healthy conjunctiva isolates do not, in almost all cases, infect the eye due to their large genotypic and phenotypic difference with the ocular infection isolates.

Biofilm formation on medical and surgical devices is the main virulence factor of Staphylococcus epidermidis. A recent study has shown that norspermidine inhibits and disassembles the biofilm in the wild-type Bacillus subtilis NCBI3610 strain. In this study, the effect of norspermidine on S. epidermidis biofilm formation of clinical or commensal strains was tested. Biofilm producing strains of S. epidermidis were isolated from healthy skin (HS; n = 3), healthy conjunctiva (HC; n = 9) and ocular infection (OI; n = 19). All strains were treated with different concentrations of norspermidine, spermidine, putrescine, and cadaverine (1, 10, 25, 50 and 100 μM), and the biofilm formation was tested on microtiter plate. Besides, cell-free supernatants of S. epidermidis growth at 4 h and 40 h were analyzed by gas chromatography coupled to mass spectrometry (GC-MS) to detect norspermidine. Results showed that norspermidine at 25 μM and 100 μM prevented the biofilm formation in 45.16% (14/31) and 16.13% (5/31), respectively; only in one isolate from OI, norspermidine did not have effect. Other polyamines as spermidine, putrescine and cadaverine did not have effect on the biofilm formation of the strains tested. Norspermidine was also capable to disassemble a biofilm already formed. Norspermidine was detected in the 40 h cell-free supernatant of S. epidermidis by GC-MS. Norspermidine inhibited the biofilm development of S. epidermidis on the surface of contact lens. In this work, it was demonstrated that S. epidermidis produces and releases norspermidine causing an inhibitory effect on biofilm formation. Moreover, this is the first time showing that clinical S. epidermidis strains have different sensitivity to norspermidine, which suggest that the composition and structure of the biofilms is varied. We propose that norspermidine could potentially be used in the pre-treating of medical and surgical devices to inhibit the biofilm formation., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Sulfidogenesis in reactors is mostly achieved through adaptation of predominantly methanogenic granular sludge to sulfidogenesis. In this work, an upflow anaerobic sludge blanket (UASB) reactor operated under sulfate-reducing conditions was inoculated with hydrothermal vent sediments to carry out sulfate reduction using volatile fatty acids (VFAs) as substrate and chemical oxygen demand (COD)/SO4 (-2) ratios between 0.49 and 0.64. After a short period of adaptation, a robust non-granular sludge was capable of achieving high sulfate reduction efficiencies while avoiding competence with methanogens and toxicity to the microorganisms due to high sulfide concentration. The highest sulfide concentration (2,552 mg/L) was obtained with acetate/butyrate, and sulfate reduction efficiencies were up to 98 %. A mixture of acetate/butyrate, which produced a higher yielding of HS(-), was preferred over acetate/propionate/butyrate since the consumption of COD was minimized during the process. Sludge was analyzed, and some of the microorganisms identified in the sludge belong to the genera Desulfobacterium, Marinobacter, and Clostridium. The tolerance of the sludge to sulfide may be attributed to the syntrophy among these microorganisms, some of which have been reported to tolerate high concentrations of sulfide. To the best of our knowledge, this is the first report on the analysis of the direct utilization of hydrothermal vent sediments as an alternate source of sludge for sulfate reduction under high sulfide concentrations.

Biofilm formation on medical and surgical devices is a major virulence determinant for Staphylococcus epidermidis. The bacterium S. epidermidis is able to produce biofilms on biotic and abiotic surfaces and is the cause of ocular infection (OI). Recent studies have shown that d-amino acids inhibit and disrupt biofilm formation in the prototype strains Bacillus subtilis NCBI3610 and Staphylococcus aureus SCO1. The effect of d-amino acids on S. epidermidis biofilm formation has yet to be tested for clinical or commensal isolates. S. epidermidis strains isolated from healthy skin (n = 3), conjunctiva (n = 9) and OI (n = 19) were treated with d-Leu, d-Tyr, d-Pro, d-Phe, d-Met or d-Ala and tested for biofilm formation. The presence of d-amino acids during biofilm formation resulted in a variety of patterns. Some strains were sensitive to all amino acids tested, while others were sensitive to one or more, and one strain was resistant to all of them when added individually; in this way d-Met inhibited most of the strains (26/31), followed by d-Phe (21/31). Additionally, the use of d-Met inhibited biofilm formation on a contact lens. The use of l-isomers caused no defect in biofilm formation in all strains tested. In contrast, when biofilms were already formed d-Met, d-Phe and d-Pro were able to disrupt it. In summary, here we demonstrated the inhibitory effect of d-amino acids on biofilm formation in S. epidermidis. Moreover, we showed, for the first time, that S. epidermidis clinical strains have a different sensitivity to these compounds during biofilm formation., (© 2014 The Authors.)

Increasing contamination of soil and groundwater with benzene, toluene, and xylene (BTX) due to activities of the chemical and oil refinery industry has caused serious environmental damage. Efficient methods are required to isolate and degrade them. Microorganisms associated with rhizosphere soil are considered efficient agents to remediate hydrocarbon contamination. In this study, we obtained a stabilized bacterial consortium from the rhizosphere soil of Cyperus sp. grown in a petroleum-contaminated field in Southern Mexico. This consortium was able to completely degrade BTX in 14 days. Bacteria isolated from the consortium were identified by 16S rRNA gene sequence analysis as Ralstonia insidiosa, Cellulomonas hominis, Burkholderia kururiensis, and Serratia marcescens. The BTX-degradation capacity of the bacterial consortium was confirmed by the detection of genes pheA, todC1, and xylM, which encoded phenol hydroxylase, toluene 1,2-dioxygenase, and xylene monooxygenase, respectively. Our results demonstrate feasibility of BTX biodegradation by indigenous bacteria that might be used for soil remediation in Southern Mexico.

In ocular infections (OIs) caused by Staphylococcus epidermidis, biofilms composed mainly of poly-N-acetylglucosamine (PNAG) have been widely studied, but PNAG-independent biofilms have not. Therefore, we searched for a relationship between the ica operon (involved in PNAG-biofilm) and the biochemical composition of biofilms in isolates from OI. Isolates from OI (n = 62), from healthy conjunctiva (HC; n = 45) and from healthy skin (HS; n = 53), were used to detect icaA and icaD genes, and the insertion sequence 256 (IS256) using PCR. The compositions of the biofilms were determined by treatment with NaIO₄, proteinase K and DNase I. Multilocus sequence typing (MLST) was performed to characterize the isolates, and the expression of aap and embp genes was determined by real-time qPCR. A strong relationship between the icaA(-)/icaD(-)/IS256(-) genotype and protein- or protein/extracellular DNA (eDNA)-biofilm composition was found in the isolates from OI (53.6%), whereas the icaA(+)/icaD(+)/IS256(-) genotype and carbohydrate-biofilm was most prevalent in isolates from HC (25%) and HS (25%). Isolates with an icaA(-)/icaD(-)/IS256(-) genotype and protein-biofilm phenotype were predominantly of the ST2 lineage, while carbohydrate-biofilm-producing strains were mainly of the ST9 lineage. The protein-biofilm-producing strains had higher expression levels of aap gene than carbohydrate-biofilm-producing strains; while embp gene did not have the same pattern of expression. These results suggest that S. epidermidis strains with icaA(-)/icaD(-)/IS256(-) genotype and protein- or protein/eDNA-biofilms have a stronger ability to establish in the eye than S. epidermidis strains with icaA(+)/icaD(+)/IS256(-) genotype and PNAG-biofilms.

Staphylococcus aureus employs a heme sensing system (HssR-HssS) and a heme-regulated transporter efflux pump (HrtA-HrtB) to avoid the accumulation of heme, which is toxic at high concentrations. The detoxification system to heme has not been studied in Staphylococcus epidermidis . In this work, the hssR, hssS, hrtA, and hrtB genes were detected, and their expression when stimulated by hemin in S. epidermidis was explored. In silico genomic analyses exhibited that the genetic organization of the hssRS and hrtAB genes was identical in 11 Staphylococcus species analyzed, including S. epidermidis. Slight variations were found in their syntenic regions. The predicted secondary structure of HrtAB proteins from these species was almost identical to these of S. aureus. Additionally, hrtAB promoter sequences of some species were analyzed, and 1 or 2 different nucleotide substitutions were found in the downstream motif. Concentrations of hemin above 5 µmol/L inhibited S. epidermidis growth. However, S. epidermidis that was pre-exposed to a subinhibitory hemin concentration (1 µmol/L) was able to grow when inoculated into medium containing above 5 µmol/L hemin. The expression levels of hrtA and hrtB genes in S. epidermidis exhibited a significant difference when they were stimulated with hemin. Our results suggest that the HrtAB could be involved in hemin detoxification of S. epidermidis.

Conventional microbiological culture techniques are frequently insufficient to confirm endophthalmitis clinical cases which could require urgent medical attention because it could lead to permanent vision loss. We are proposing PCR-DGGE and 16S rRNA gene libraries as an alternative to improve the detection and identification rate of bacterial species from endophthalmitis cases.

In this study, the bacterial communities associated with the rhizospheres of pioneer plants Bahia xylopoda and Viguiera linearis were explored. These plants grow on silver mine tailings with high concentration of heavy metals in Zacatecas, Mexico. Metagenomic DNAs from rhizosphere and bulk soil were extracted to perform a denaturing gradient gel electrophoresis analysis (DGGE) and to construct 16S rRNA gene libraries. A moderate bacterial diversity and twelve major phylogenetic groups including Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Firmicutes, Verrucomicrobia, Nitrospirae and Actinobacteria phyla, and divisions TM7, OP10 and OD1 were recognized in the rhizospheres. Only 25.5% from the phylotypes were common in the rhizosphere libraries and the most abundant groups were members of the phyla Acidobacteria and Betaproteobacteria (Thiobacillus spp., Nitrosomonadaceae). The most abundant groups in bulk soil library were Acidobacteria and Actinobacteria, and no common phylotypes were shared with the rhizosphere libraries. Many of the clones detected were related with chemolithotrophic and sulfur-oxidizing bacteria, characteristic of an environment with a high concentration of heavy metal-sulfur complexes, and lacking carbon and organic energy sources.

The aim of this study was to assess the bacterial diversity associated with a corrosive biofilm in a steel pipeline from the Gulf of Mexico used to inject marine water into the oil reservoir. Several aerobic and heterotrophic bacteria were isolated and identified by 16S rRNA gene sequence analysis. Metagenomic DNA was also extracted to perform a denaturing gradient gel electrophoresis analysis of ribosomal genes and to construct a 16S rRNA gene metagenomic library. Denaturing gradient gel electrophoresis profiles and ribosomal libraries exhibited a limited bacterial diversity. Most of the species detected in the ribosomal library or isolated from the pipeline were assigned to Proteobacteria (Halomonas spp., Idiomarina spp., Marinobacter aquaeolei, Thalassospira sp., Silicibacter sp. and Chromohalobacter sp.) and Bacilli (Bacillus spp. and Exiguobacterium spp.). This is the first report that associates some of these bacteria with a corrosive biofilm. It is relevant that no sulfate-reducing bacteria were isolated or detected by a PCR-based method. The diversity and relative abundance of bacteria from water pipeline biofilms may contribute to an understanding of the complexity and mechanisms of metal corrosion during marine water injection in oil secondary recovery.

Molecular techniques were used to compare the compositions of the bacterial communities of the 2 following lagoons from the former soda Texcoco Lake, Mexico: the restored Facultativa lagoon and the Nabor Carrillo lagoon. Ribosomal intergenic spacer analysis (RISA) revealed that bacterial communities of the 2 lagoons were different and presented a relatively low diversity. Clone libraries of 16S rDNA genes were constructed, and significant phylotypes were distinguished by restriction fragment length polymorphism (RFLP). A representative clone from each phylotype was partially sequenced. Molecular identification and phylogenetic analyses based on ribosomal sequences revealed that the Facultativa lagoon harbored mainly gamma- and beta-Proteobacteria, low G+C Gram-positive bacteria, and several members of the Halobacteriaceae family of archaea. The Nabor Carrillo lagoon mainly included typical halophilic and alkaliphilic low G+C Gram-positive bacteria, gamma-Proteobacteria, and beta-Proteobacteria similar to those found in other soda lakes. Several probably noncultured new bacterial species were detected. Three strains were isolated from the Nabor Carrillo lagoon, their partial 16S rDNA sequences were obtained. On this basis, they were identified as Halomonas magadiensis (H1), Halomonas eurihalina (H2), and Staphylococcus sciuri (H3). This is the first study that uses molecular techniques to investigate potential genetic diversity in the Texcoco lakes. In this preliminary evaluation, we infer the presence of alkalophilic, halophilic, or haloalkaliphilic bacteria potentially useful for biotechnology.