Cleaner approach for atrazine removal using recycling biowaste/waste in permeable barriers

This work addresses the rehabilitation of water contaminated with atrazine, entrapping it in a permeable and sustainable barrier designed with waste materials (sepiolite) and with biomaterials (cork and pine bark). Atrazine adsorption was assessed by kinetics and equilibrium assays and desorption was tested with different extraction solvents. Adsorbed atrazine was 100% recovered from sepiolite using 20% acetonitrile solution, while 40% acetonitrile was needed to leach it from cork (98%) and pine bark (94%). Continuous fixed-bed experiments using those sorbents as PRB were performed to evaluate atrazine removal for up-scale applications. The modified dose-response model properly described the breakthrough data. The highest adsorption capacity was achieved by sepiolite (23.3 (±0.8) mg/g), followed by pine bark (14.8 (±0.6) mg/g) and cork (13.0 (±0.9) mg/g). Recyclability of sorbents was evaluated by adsorption-desorption cycles. After two regenerations, sepiolite achieved 81% of atrazine removal, followed by pine with 78% and cork with 54%. Sepiolite had the best performance in terms of adsorption capacity/stability. SEM and FTIR analyses confirmed no significant differences in material morphology and structure. This study demonstrates that recycling waste/biowaste is a sustainable option for wastewater treatment, with waste valorization and environmental protection.Portuguese Foundation for Science and Technology (FCT) under the scope of the research project PTDC/AAG-TEC/5269/2014, the strategic funding of UID/BIO/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020—Programa Operacional Regional do Norte, Portugal. A. Lago thanks FCT for the concession of her PhD grant (SFRH/BD/132271/2017)info:eu-repo/semantics/publishedVersio

Biowaste valorization for emerging pollutant abatement in aqueous phase

The use of raw chemical- or thermal-modified pine bark (10 g/L) as a biosorbent to remove fluoxetine hydrochloride (FLX), carbamazepine (CRB) and atrazine (ATZ) from water at 5 mg/L each was explored in this work. The adsorption efficiency onto raw pine was as follows: FLX > ATZ > CRB. Pine oxidized with HNO3 revealed to be the best modified biosorbent in terms of overall sorbate entrapment capacity (1.95 mg/g). The performance of raw pine (as the most sustainable biosorbent) was assessed in a prepilot air-lift-type reactor as a rehabilitation system to treat contaminated water for upscale purposes.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the research project PTDC/AAG-TEC/5269/2014, the strategic funding of UID/BIO/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020—Programa Operacional Regional do Norte, Portugal. A. Lago thanks FCT for her PhD grant (SFRH/BD/132271/2017).info:eu-repo/semantics/publishedVersio

Trends in Helicobacter pylori resistance to clarithromycin: from phenotypic to genomic approaches

For a long time Helicobacter pylori infections have been treated using the macrolide antibiotic, clarithromycin. Clarithromycin resistance is increasing worldwide and is the most common cause of H. pylori treatment failure. Here we review the mechanisms of antibiotic resistance to clarithromycin, detailing the individual and combinations of point mutations found in the 23S rRNA gene associated with resistance. Additionally, we consider the methods used to detect clarithromycin resistance, emphasizing the use of high-throughput next-generation sequencing methods, which were applied to 17 newly sequenced pairs of H. pylori strains isolated from the antrum and corpus of a recent colonized paediatric population. This set of isolates was composed of six pairs of resistant strains whose phenotype was associated with two point mutations found in the 23S rRNA gene: A2142C and A2143G. Other point mutations were found simultaneously in the same gene, but, according to our results, it is unlikely that they contribute to resistance. Further, among susceptible isolates, genomic variations compatible with mutations previously associated with clarithromycin resistance were detected. Exposure to clarithromycin may select low-frequency variants, resulting in a progressive increase in the resistance rate due to selection pressure.F. F. V. is the recipient of a project grant (PTDC/BTM-SAL/28978/2017) from the Fundação para a Ciência e a Tecnologia (FCT), which supported this work. J. V.’s research group was financed by New England Biolabs, Inc. (USA).info:eu-repo/semantics/publishedVersio

Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates

Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.F.F.V. is funded by Fundação para a Ciência e a Tecnologia (FCT) through an Assistant Researcher grant CEECIND/03023/2017, and a project grant (PTDC/BTM-SAL/28978/2017) that supported this work. The work is partially supported by National funds from FCT, projects UIDB/04138/2020 and UIDP/04138/2020.info:eu-repo/semantics/publishedVersio

Rehabilitation of water contaminated with an organic solvent by an aerobic bacterium: tolerance and bioremoval assays

e Portuguese Foundation for Science and Technology (FCT) under the scope of the research project PTDC/AAG-TEC/5269/2014, the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norteinfo:eu-repo/semantics/publishedVersio

Optoelectronics and Bio Devices on Paper Powered by Solar Cells

The employment of printing techniques as cost-effective methods to fabricate low cost, flexible, disposable and sustainable solar cells is intimately dependent on the substrate properties and the adequate electronic devices to be powered by them. Among such devices, there is currently a growing interest in the development of user-oriented and multipurpose systems for intelligent packaging or on-site medical diagnostics, which would greatly benefit from printable solar cells as their energy source for autonomous operation

Potential of silicon fertilization in the resistance of chestnut plants toink disease(Phytophthora cinnamomi)

The European chestnut (Castanea sativa Mill.) is a specie with great economic importance in Europe that have been present for thousands of years. In Portugal, the chestnut helps to maintain a positive trade balance, by contributing to the gross national product (GDP). One of the biggest threats for the chestnut is the ink disease caused by Phytophthoracinnamomi, this disease is problematic to chestnut crop with a damaging impact. Silicon (Si) is classified as a beneficial nutrient, having the ability to make plants more resistant to attacks by pathogens. Studies on the effect of silicon on chestnut are practically non-existent, so the aim of this study was to evaluate the impact of silicon in the resistance of chestnut plants to P. cinnamomi. The plants were treated by 0 mM, 5 mM, 7.5mM and 10 mM SiK® with the analyzed mad at 0, 15 and 30 days after inoculation by P. cinnamomi. These findings showed that the Si-treated plants had higher survival rate resulted from the presence of phytoliths in root tissues, that acted as a mechanical barrier reducing the development of pathogenic structures and they arealso associated with the improvement on antioxidant activity through the increase of CAT and SOD, higher values of total phenols compounds and less oxidative damage. The presence of Si in PDA medium reduced the growth of P. cinnamomi all over the time, presenting high PI. This work shows that the Si fertilization in chestnut plants contributes to increase the resistance against P. cinnamomi infection

Antimicrobial activity of prophage endolysins against critical Enterobacteriaceae antibiotic-resistant bacteria

Enterobacteriaceae species are part of the 2017 World Health Organization antibiotic-resistant priority pathogens list for development of novel medicines. Multidrug-resistant Klebsiella pneumoniae is an increasing threat to public health and has become a relevant human pathogen involved in life-threatening infections. Phage therapy involves the use of phages or their lytic endolysins as bioagents for the treatment of bacterial infectious diseases. Gram-negative bacteria have an outer membrane, making difficult the access of endolysins to the peptidoglycan. Here, three endolysins from prophages infecting three distinct Enterobacterales species, Kp2948-Lys from K. pneumoniae, Ps3418-Lys from Providencia stuartii, and Kaer26608-Lys from Klebsiella aerogenes, were purified and exhibited antibacterial activity against their specific bacterium species verified by zymogram assays. These three endolysins were successfully associated to liposomes composed of dimyristoyl phosphatidyl choline (DMPC), dioleoyl phosphatidyl ethanolamine (DOPE) and cholesteryl hemisuccinate (CHEMS) at a molar ratio (4:4:2), with an encapsulation efficiency ranging from 24 to 27%. Endolysins encapsulated in liposomes resulted in higher antibacterial activity compared to the respective endolysin in the free form, suggesting that the liposome-mediated delivery system enhances fusion with outer membrane and delivery of endolysins to the target peptidoglycan. Obtained results suggest that Kp2948-Lys appears to be specific for K. pneumoniae, while Ps3418-Lys and Kaer26608-Lys appear to have a broader antibacterial spectrum. Endolysins incorporated in liposomes constitute a promising weapon, applicable in the several dimensions (human, animals and environment) of the One Health approach, against multidrug-resistant Enterobacteriaceae.F.F.V. was funded by Fundação para a Ciência e a Tecnologia (FCT) through a project grant (PTDC/BTM-SAL/28978/2017) that supported this work. The work is partially supported by National funds from FCT, projects UIDB/04138/2020, UIDP/04138/2020, UIDB/00211/2020 and UIDB/04046/2020 (DOI https://doi.org/10.54499/UIDB/0404 6/2020)info:eu-repo/semantics/publishedVersio

Cryptic Prophages Contribution for Campylobacter jejuni and Campylobacter coli Introgression

This article belongs to the Special Issue Bacteriophage Genomics.Campylobacter coli and C. jejuni, the causing agents of campylobacteriosis, are described to be undergoing introgression events, i.e., the transference of genetic material between different species, with some isolates sharing almost a quarter of its genome. The participation of phages in introgression events and consequent impact on host ecology and evolution remain elusive. Three distinct prophages, named C. jejuni integrated elements 1, 2, and 4 (CJIE1, CJIE2, and CJIE4), are described in C. jejuni. Here, we identified two unreported prophages, Campylobacter coli integrated elements 1 and 2 (CCIE1 and CCIE2 prophages), which are C. coli homologues of CJIE1 and CJIE2, respectively. No induction was achieved for both prophages. Conversely, induction assays on CJIE1 and CJIE2 point towards the inducibility of these prophages. CCIE2-, CJIE1-, and CJIE4-like prophages were identified in a Campylobacter spp. population of 840 genomes, and phylogenetic analysis revealed clustering in three major groups: CJIE1-CCIE1, CJIE2-CCIE2, and CJIE4, clearly segregating prophages from C. jejuni and C. coli, but not from human- and nonhuman-derived isolates, corroborating the flowing between animals and humans in the agricultural context. Punctual bacteriophage host-jumps were observed in the context of C. jejuni and C. coli, and although random chance cannot be fully discarded, these observations seem to implicate prophages in evolutionary introgression events that are modulating the hybridization of C. jejuni and C. coli species.F.F.V. is funded by Fundação para a Ciência e a Tecnologia (FCT) through an Assis tant Researcher grant CEECIND/03023/2017, and a project grant (PTDC/BTM-SAL/28978/2017) that supported this work. The work is partially supported by Na-tional funds from FCT, projects UIDB/04138/2020 and UIDP/04138/2020. Campylobacter strains were sequenced under the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020—Operational Programme for Competitiveness and Internationalization (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Oper-ational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by FCT. This work was also supported by Fundos FEDER through the Programa Op eracional Factores de Competitivida-de—COMPETE and by Fundos Nacionais through the FCT within the scope of the project UID/BIM/00009/2019 (Centre for Toxicogenomics and Human Health-ToxOmics).info:eu-repo/semantics/publishedVersio

Cryptic Prophages Contribution for Campylobacter jejuni and Campylobacter coli Introgression

Campylobacter coli and C. jejuni, the causing agents of campylobacteriosis, are described to be undergoing introgression events, i.e., the transference of genetic material between different species, with some isolates sharing almost a quarter of its genome. The participation of phages in introgression events and consequent impact on host ecology and evolution remain elusive. Three distinct prophages, named C. jejuni integrated elements 1, 2, and 4 (CJIE1, CJIE2, and CJIE4), are described in C. jejuni. Here, we identified two unreported prophages, Campylobacter coli integrated elements 1 and 2 (CCIE1 and CCIE2 prophages), which are C. coli homologues of CJIE1 and CJIE2, respectively. No induction was achieved for both prophages. Conversely, induction assays on CJIE1 and CJIE2 point towards the inducibility of these prophages. CCIE2-, CJIE1-, and CJIE4-like prophages were identified in a Campylobacter spp. population of 840 genomes, and phylogenetic analysis revealed clustering in three major groups: CJIE1-CCIE1, CJIE2-CCIE2, and CJIE4, clearly segregating prophages from C. jejuni and C. coli, but not from human- and nonhuman-derived isolates, corroborating the flowing between animals and humans in the agricultural context. Punctual bacteriophage host-jumps were observed in the context of C. jejuni and C. coli, and although random chance cannot be fully discarded, these observations seem to implicate prophages in evolutionary introgression events that are modulating the hybridization of C. jejuni and C. coli species.F.F.V. is funded by Fundação para a Ciência e a Tecnologia (FCT) through an Assistant Researcher grant CEECIND/03023/2017, and a project grant (PTDC/BTM-SAL/28978/2017) that supported this work. The work is partially supported by National funds from FCT, projects UIDB/04138/2020 and UIDP/04138/2020. Campylobacter strains were sequenced under the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020—Operational Programme for Competitiveness and Internationalization (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by FCT. This work was also supported by Fundos FEDER through the Programa Operacional Factores de Competitividade—COMPETE and by Fundos Nacionais through the FCT within the scope of the project UID/BIM/00009/2019 (Centre for Toxicogenomics and Human Health-ToxOmics).info:eu-repo/semantics/publishedVersio