DOCSLIB.ORG

Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

antibiotics Article Characterization of Environmental and Cultivable Antibiotic- Resistant Microbial Communities Associated with Wastewater Treatment Alicia Sorgen 1, James Johnson 2, Kevin Lambirth 2, Sandra M. Clinton 3 , Molly Redmond 1 , Anthony Fodor 2 and Cynthia Gibas 2,* 1 Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (A.S.); [email protected] (M.R.) 2 Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] (J.J.); [email protected] (K.L.); [email protected] (A.F.) 3 Department of Geography & Earth Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-704-687-8378 Abstract: Bacterial resistance to antibiotics is a growing global concern, threatening human and environmental health, particularly among urban populations. Wastewater treatment plants (WWTPs) are thought to be “hotspots” for antibiotic resistance dissemination. The conditions of WWTPs, in conjunction with the persistence of commonly used antibiotics, may favor the selection and transfer of resistance genes among bacterial populations. WWTPs provide an important ecological niche to examine the spread of antibiotic resistance. We used heterotrophic plate count methods to identify Citation: Sorgen, A.; Johnson, J.; phenotypically resistant cultivable portions of these bacterial communities and characterized the Lambirth, K.; Clinton, S.M.; composition of the culturable subset of these populations. Resistant taxa were more abundant in raw Redmond, M.; Fodor, A.; Gibas, C. sewage and wastewater before the biological aeration treatment stage. While some antibiotic-resistant Characterization of Environmental and Cultivable Antibiotic-Resistant bacteria (ARB) were detectable downstream of treated wastewater release, these organisms are not Microbial Communities Associated enriched relative to effluent-free upstream water, indicating efficient removal during treatment. with Wastewater Treatment. Combined culture-dependent and -independent analyses revealed a stark difference in community Antibiotics 2021, 10, 352. https:// composition between culturable fractions and the environmental source material, irrespective of doi.org/10.3390/antibiotics10040352 culturing conditions. Higher proportions of the environmental populations were recovered than predicted by the widely accepted 1% culturability paradigm. These results represent baseline Academic Editors: Luciana Migliore abundance and compositional data for ARB communities for reference in future studies addressing and Marco Maria D’Andrea the dissemination of antibiotic resistance associated with urban wastewater treatment ecosystems. Received: 2 March 2021 Keywords: culturability; antibiotic resistance; wastewater treatment Accepted: 22 March 2021 Published: 26 March 2021 Publisher’s Note: MDPI stays neutral 1. Introduction with regard to jurisdictional claims in published maps and institutional affil- Antibiotics are antimicrobial substances that can either kill or inhibit the growth and iations. replication of a bacterium [1]. Antibiotics have revolutionized the field of medicine; yet their increased use has exerted a selective pressure on susceptible bacteria, favoring the survival of antibiotic-resistant bacteria (ARB) and the proliferation of associated antibiotic resistance genes (ARGs) [2]. Some bacterial species are inherently resistant to certain antibiotics as a result of structural or functional characteristics [3,4]. Those not inherently resistant Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. can acquire resistance through mutations in chromosomal genes and via horizontal gene This article is an open access article transfer (HGT) furthering the development of resistance among previously susceptible distributed under the terms and organisms [5]. conditions of the Creative Commons Wastewater treatment plants (WWTP) are major sewage repositories that may receive Attribution (CC BY) license (https:// sewage from both residential and medical treatment facilities. The continuous inflow of pre- creativecommons.org/licenses/by/ existing ARB and antibiotic residues are important sources of resistance material [6,7]. The 4.0/). wastewater treatment process generally involves three stages of treatment where (1) large Antibiotics 2021, 10, 352. https://doi.org/10.3390/antibiotics10040352 https://www.mdpi.com/journal/antibiotics Antibiotics 2021, 10, x 2 of 20 Wastewater treatment plants (WWTP) are major sewage repositories that may re- ceive sewage from both residential and medical treatment facilities. The continuous in- Antibiotics 2021, 10, 352 flow of pre-existing ARB and antibiotic residues are important sources of resistance2 ofma- 19 terial [6,7]. The wastewater treatment process generally involves three stages of treatment where (1) large solids are removed through physical processes before (2) entering a sedi- solidsmentation are removed tank in which through remaining physical processessuspended before solids (2) sink entering to form a sedimentation activated sludge tank and in whichwhere remainingbiological suspendedand chemical solids processes sink to are form employed activated to sludge remove and organic where matter biological [6]. andAny chemicaladditional processes organic areor chemical employed components to remove organic are removed matter using [6]. Any (3) additionaladditional organic treatment or chemicalprocesses components such as chemical are removed and biological-chemical using (3) additional contact treatment filters processes [8,9]. Prior such to as environ- chemi- calmental and biological-chemicalrelease, wastewater contact undergoes filters a [disinf8,9]. Priorection to stage environmental to eliminate release, harmful wastewater bacteria undergoesin the effluent a disinfection [10]. WWTPs stage are to considered eliminate harmful “hotspots” bacteria for resi in thestance effluent dissemination [10]. WWTPs due are to consideredthe sub-inhibitory “hotspots” concentrations for resistance of dissemination antibiotic compounds due to the sub-inhibitoryand the favorable concentrations conditions ofthat antibiotic promote compounds HGT [11–13]. and Insight the favorable into ARB conditions community that trends promote throughout HGT [11 the–13 treatment]. Insight intoprocess ARB can community help us understand trends throughout the effect the of treatment released process treated canwastewater help us understand on natural themi- effectcrobial of communities released treated [11–13]. wastewater on natural microbial communities [11–13]. AreasAreas withwith limitedlimited waterwater treatmenttreatment infrastructureinfrastructure havehave beenbeen shownshown toto passpass humanhuman microbialmicrobial resistomesresistomes intointo thethe environmentenvironment viavia mobilemobile geneticgenetic elementselements (MGEs),(MGEs), suchsuch asas plasmids,plasmids, transposons,transposons, and and integrons integrons [14 ,15[14,]. Even15]. Even in locations in locations with innovative with innovative wastew- aterwastewater treatment treatment systems, systems, the degree the degree of contaminant of contaminant removal removal depends depends on the on particularthe partic- technologyular technology and operatingand operating parameters parameters used, used, whether whether it be UV,it be chlorine, UV, chlorine, or microfiltration or microfil- disinfectiontration disinfection methods methods [16]. [16]. InIn thisthis study,study, wewe sampledsampled sitessites alongalong WWTP-associatedWWTP-associated urbanurban streams.streams. WeWe sampled sampled streamstream locationslocations upstreamupstream (UP)(UP) andand downstreamdownstream (DS)(DS) ofof thethe treatedtreated wastewaterwastewater releaserelease pointpoint toto understandunderstand thethe overalloverall impactimpact ofof treatedtreated waterwater releaserelease onon thethe streamstream microbialmicrobial communitycommunity (Figure(Figure1 1).). Inside Inside the the WWTP, WWTP, we we sampled sampled untreated untreated sewage sewage influent influent and and the the effluenteffluent ofof eacheach treatmenttreatment stagestage toto identifyidentify whichwhich taxataxa areare introducedintroduced toto thethe WWTPWWTP viavia influentinfluent andand whetherwhether theythey areare subsequentlysubsequently completelycompletely removed.removed. SamplesSamples pulledpulled atat eacheach sitesite withinwithin the the stream stream environment environment and and within within the the WWTP WWTP (as (as described described in Lambirthin Lambirth et al., et 2018)al., 2018) were were characterized characterized using using 16S rRNA16S rRNA amplicon amplicon and and metagenomic metagenomic sequencing. sequencing. FigureFigure 1.1. SchematicSchematic ofof thethe wastewaterwastewater treatment process and sampling sites utilized for this study. study. RawRaw sewagesewage from residential (RES) (RES) and and hospital hospital (HOS) (HOS) sources sources are are routed routed to toa main a main sewer sewer line. line. The combined raw influent (INF) is then passed through a physical screen to filter out large solids. The combined raw influent (INF) is then passed through a physical screen to filter out large solids. The screen-filtered wastewater (PCI) undergoes primary clarification. The primary clarifier efflu- The screen-filtered wastewater (PCI) undergoes primary clarification. The primary
Recommended publications
  • Succession and Persistence of Microbial Communities and Antimicrobial Resistance Genes Associated with International Space Stati

    Succession and Persistence of Microbial Communities and Antimicrobial Resistance Genes Associated with International Space Stati

    Singh et al. Microbiome (2018) 6:204 https://doi.org/10.1186/s40168-018-0585-2 RESEARCH Open Access Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces Nitin Kumar Singh1, Jason M. Wood1, Fathi Karouia2,3 and Kasthuri Venkateswaran1* Abstract Background: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms. Results: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii,andAspergillus lentulus.EventhoughRhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3.
  • Inactivation of CRISPR-Cas Systems by Anti-CRISPR Proteins in Diverse Bacterial Species April Pawluk1, Raymond H.J

    Inactivation of CRISPR-Cas Systems by Anti-CRISPR Proteins in Diverse Bacterial Species April Pawluk1, Raymond H.J

    LETTERS PUBLISHED: 13 JUNE 2016 | ARTICLE NUMBER: 16085 | DOI: 10.1038/NMICROBIOL.2016.85 Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species April Pawluk1, Raymond H.J. Staals2, Corinda Taylor2, Bridget N.J. Watson2, Senjuti Saha3, Peter C. Fineran2, Karen L. Maxwell4* and Alan R. Davidson1,3* CRISPR-Cas systems provide sequence-specific adaptive immu- MGE-encoded mechanisms that inhibit CRISPR-Cas systems. In nity against foreign nucleic acids1,2. They are present in approxi- support of this hypothesis, phages infecting Pseudomonas aeruginosa mately half of all sequenced prokaryotes3 and are expected to were found to encode diverse families of proteins that inhibit constitute a major barrier to horizontal gene transfer. We pre- the CRISPR-Cas systems of their host through several distinct viously described nine distinct families of proteins encoded in mechanisms4,5,17,18. However, homologues of these anti-CRISPR Pseudomonas phage genomes that inhibit CRISPR-Cas function4,5. proteins were found only within the Pseudomonas genus. Here, We have developed a bioinformatic approach that enabled us to we describe a bioinformatic approach that allowed us to identify discover additional anti-CRISPR proteins encoded in phages five novel families of functional anti-CRISPR proteins encoded in and other mobile genetic elements of diverse bacterial phages and other putative MGEs in species spanning the diversity species. We show that five previously undiscovered families of Proteobacteria. of anti-CRISPRs inhibit the type I-F CRISPR-Cas systems of The nine previously characterized anti-CRISPR protein families both Pseudomonas aeruginosa and Pectobacterium atrosepticum, possess no common sequence motifs, so we used genomic context to and a dual specificity anti-CRISPR inactivates both type I-F search for novel anti-CRISPR genes.
  • Comparative Genomics of the Aeromonadaceae Core Oligosaccharide Biosynthetic Regions

    Comparative Genomics of the Aeromonadaceae Core Oligosaccharide Biosynthetic Regions

    CORE Metadata, citation and similar papers at core.ac.uk Provided by Diposit Digital de la Universitat de Barcelona International Journal of Molecular Sciences Article Comparative Genomics of the Aeromonadaceae Core Oligosaccharide Biosynthetic Regions Gabriel Forn-Cuní, Susana Merino and Juan M. Tomás * Department of Genética, Microbiología y Estadística, Universidad de Barcelona, Diagonal 643, 08071 Barcelona, Spain; [email protected] (G.-F.C.); [email protected] (S.M.) * Correspondence: [email protected]; Tel.: +34-93-4021486 Academic Editor: William Chi-shing Cho Received: 7 February 2017; Accepted: 26 February 2017; Published: 28 February 2017 Abstract: Lipopolysaccharides (LPSs) are an integral part of the Gram-negative outer membrane, playing important organizational and structural roles and taking part in the bacterial infection process. In Aeromonas hydrophila, piscicola, and salmonicida, three different genomic regions taking part in the LPS core oligosaccharide (Core-OS) assembly have been identified, although the characterization of these clusters in most aeromonad species is still lacking. Here, we analyse the conservation of these LPS biosynthesis gene clusters in the all the 170 currently public Aeromonas genomes, including 30 different species, and characterise the structure of a putative common inner Core-OS in the Aeromonadaceae family. We describe three new genomic organizations for the inner Core-OS genomic regions, which were more evolutionary conserved than the outer Core-OS regions, which presented remarkable variability. We report how the degree of conservation of the genes from the inner and outer Core-OS may be indicative of the taxonomic relationship between Aeromonas species. Keywords: Aeromonas; genomics; inner core oligosaccharide; outer core oligosaccharide; lipopolysaccharide 1.
  • Identification of Glucose Non-Fermenting Gram Negative Rods

    Identification of Glucose Non-Fermenting Gram Negative Rods

    UK Standards for Microbiology Investigations Identification of Glucose Non-Fermenting Gram Negative Rods REVIEW UNDER Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 17 | Issue no: 2.2 | Issue date: 11.03.14 | Page: 1 of 24 © Crown copyright 2014 Identification of Glucose Non-Fermenting Gram Negative Rods Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (PHE) working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website http://www.hpa.org.uk/SMI/Partnerships. SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see http://www.hpa.org.uk/SMI/WorkingGroups). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the Medical Editors for editing the medical content. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: http://www.hpa.org.uk/SMI UK Standards for Microbiology Investigations are produced in association with: REVIEW UNDER Bacteriology – Identification | ID 17 | Issue no: 2.2 | Issue date: 11.03.14 | Page: 2 of 24 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Glucose Non-Fermenting Gram Negative Rods Contents ACKNOWLEDGMENTS .......................................................................................................... 2 AMENDMENT TABLE ............................................................................................................. 4 UK STANDARDS FOR MICROBIOLOGY INVESTIGATIONS: SCOPE AND PURPOSE ......
  • (Batch Learning Self-Organizing Maps), to the Microbiome Analysis of Ticks

    (Batch Learning Self-Organizing Maps), to the Microbiome Analysis of Ticks

    Title A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks Nakao, Ryo; Abe, Takashi; Nijhof, Ard M; Yamamoto, Seigo; Jongejan, Frans; Ikemura, Toshimichi; Sugimoto, Author(s) Chihiro The ISME Journal, 7(5), 1003-1015 Citation https://doi.org/10.1038/ismej.2012.171 Issue Date 2013-03 Doc URL http://hdl.handle.net/2115/53167 Type article (author version) File Information ISME_Nakao.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks Ryo Nakao1,a, Takashi Abe2,3,a, Ard M. Nijhof4, Seigo Yamamoto5, Frans Jongejan6,7, Toshimichi Ikemura2, Chihiro Sugimoto1 1Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido University, Kita-20, Nishi-10, Kita-ku, Sapporo, Hokkaido 001-0020, Japan 2Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan 3Graduate School of Science & Technology, Niigata University, 8050, Igarashi 2-no-cho, Nishi- ku, Niigata 950-2181, Japan 4Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Königsweg 67, 14163 Berlin, Germany 5Miyazaki Prefectural Institute for Public Health and Environment, 2-3-2 Gakuen Kibanadai Nishi, Miyazaki 889-2155, Japan 6Utrecht Centre for Tick-borne Diseases (UCTD), Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands 7Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, 0110 Onderstepoort, South Africa aThese authors contributed equally to this work. Keywords: BLSOMs/emerging diseases/metagenomics/microbiomes/symbionts/ticks Running title: Tick microbiomes revealed by BLSOMs Subject category: Microbe-microbe and microbe-host interactions Abstract Ticks transmit a variety of viral, bacterial and protozoal pathogens, which are often zoonotic.
  • Potential of Bacterial Cellulose Chemisorbed with Anti-Metabolites, 3-Bromopyruvate Or Sertraline, to Fight Against Helicobacter Pylori Lawn Biofilm

    Potential of Bacterial Cellulose Chemisorbed with Anti-Metabolites, 3-Bromopyruvate Or Sertraline, to Fight Against Helicobacter Pylori Lawn Biofilm

    International Journal of Molecular Sciences Article Potential of Bacterial Cellulose Chemisorbed with Anti-Metabolites, 3-Bromopyruvate or Sertraline, to Fight against Helicobacter pylori Lawn Biofilm Paweł Krzy˙zek 1,* , Gra˙zynaGo´sciniak 1 , Karol Fijałkowski 2 , Paweł Migdał 3 , Mariusz Dziadas 4 , Artur Owczarek 5 , Joanna Czajkowska 6, Olga Aniołek 7 and Adam Junka 8 1 Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland; [email protected] 2 Department of Immunology, Microbiology and Physiological Chemistry, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 70-311 Szczecin, Poland; karol.fi[email protected] 3 Department of Environment, Hygiene and Animal Welfare, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland; [email protected] 4 Faculty of Chemistry, University of Wroclaw, 50-353 Wroclaw, Poland; [email protected] 5 Department of Drug Form Technology, Wroclaw Medical University, 50-556 Wroclaw, Poland; [email protected] 6 Laboratory of Microbiology, Polish Center for Technology Development PORT, 54-066 Wroclaw, Poland; [email protected] 7 Faculty of Medicine, Lazarski University, 02-662 Warsaw, Poland; [email protected] 8 Department of Pharmaceutical Microbiology and Parasitology, Wroclaw Medical University, 50-556 Wroclaw, Poland; [email protected] * Correspondence: [email protected] Received: 23 November 2020; Accepted: 11 December 2020; Published: 14 December 2020 Abstract: Helicobacter pylori is a bacterium known mainly of its ability to cause persistent inflammations of the human stomach, resulting in peptic ulcer diseases and gastric cancers. Continuous exposure of this bacterium to antibiotics has resulted in high detection of multidrug-resistant strains and difficulties in obtaining a therapeutic effect.
  • Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea Across Earth’S Biomes

    Cryptic Inoviruses Revealed As Pervasive in Bacteria and Archaea Across Earth’S Biomes

    ARTICLES https://doi.org/10.1038/s41564-019-0510-x Corrected: Author Correction Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes Simon Roux 1*, Mart Krupovic 2, Rebecca A. Daly3, Adair L. Borges4, Stephen Nayfach1, Frederik Schulz 1, Allison Sharrar5, Paula B. Matheus Carnevali 5, Jan-Fang Cheng1, Natalia N. Ivanova 1, Joseph Bondy-Denomy4,6, Kelly C. Wrighton3, Tanja Woyke 1, Axel Visel 1, Nikos C. Kyrpides1 and Emiley A. Eloe-Fadrosh 1* Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach lever- aging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem.
  • Downloaded 13 April 2017); Using Diamond

    Downloaded 13 April 2017); Using Diamond

    bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 Re-evaluating the salty divide: phylogenetic specificity of 6 transitions between marine and freshwater systems 7 8 9 10 Sara F. Pavera, Daniel J. Muratorea, Ryan J. Newtonb, Maureen L. Colemana# 11 a 12 Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA 13 b School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, Wisconsin, USA 14 15 Running title: Marine-freshwater phylogenetic specificity 16 17 #Address correspondence to Maureen Coleman, [email protected] 18 bioRxiv preprint doi: https://doi.org/10.1101/347021; this version posted June 14, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 19 Abstract 20 Marine and freshwater microbial communities are phylogenetically distinct and transitions 21 between habitat types are thought to be infrequent. We compared the phylogenetic diversity of 22 marine and freshwater microorganisms and identified specific lineages exhibiting notably high or 23 low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA 24 gene tag-sequencing datasets. As expected, marine and freshwater microbial communities 25 differed in the relative abundance of major phyla and contained habitat-specific lineages; at the 26 same time, however, many shared taxa were observed in both environments. 27 Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between 28 marine and freshwater sample pairs.
  • 1 Supplementary Information Ugly Ducklings – the Dark Side of Plastic

    1 Supplementary Information Ugly Ducklings – the Dark Side of Plastic

    Supplementary Information Ugly ducklings – The dark side of plastic materials in contact with potable water Lisa Neu1,2, Carola Bänziger1, Caitlin R. Proctor1,2, Ya Zhang3, Wen-Tso Liu3, Frederik Hammes1,* 1 Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland 2 Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland 3 Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, USA Table of contents Table S1 Exemplary online blog entries on biofouling in bath toys Figure S1 Images of all examined bath toys Figure S2 Additional images of bath toy biofilms by OCT Figure S3 Additional images on biofilm composition by SEM Figure S4 Number of bacteria and proportion of intact cells in bath toy biofilms Table S2 Classification of shared OTUs between bath toys Table S3 Shared and ‘core’ communities in bath toys from single households Table S4 Richness and diversity Figure S5 Classification of abundant OTUs in real bath toy biofilms Table S5 Comparison of most abundant OTUs in control bath toy biofilms Figure S6 Fungal community composition in bath toy biofilms Table S6 Conventional plating results for indicator bacteria and groups Table S7 Bioavailability of migrating carbon from control bath toys’ material Water chemistry Method and results (Table S8) Table S9 Settings for Amplification PCR and Index PCR reactions 1 Table S1: Exemplary online blog entries on biofouling inside bath toys Issue - What is the slime? Link Rub-a-dub-dub, https://www.babble.com/baby/whats-in-the-tub/ what’s in the tub? What’s the black stuff http://blogs.babycenter.com/momstories/whats-the-black- in your squeeze toys? stuff-in-your-squeeze-toys/ Friday Find: NBC’s http://www.bebravekeepgoing.com/2010/03/friday-find-nbcs- Today Show segment: today-show-segment-do.html Do bath toys carry germs? Yuck.
  • Acinetobacter Baumannii – a Neglected Pathogen in Veterinary and Environmental Health in Germany

    Acinetobacter Baumannii – a Neglected Pathogen in Veterinary and Environmental Health in Germany

    Veterinary Research Communications (2019) 43:1–6 https://doi.org/10.1007/s11259-018-9742-0 REVIEW ARTICLE Acinetobacter baumannii – a neglected pathogen in veterinary and environmental health in Germany Gamal Wareth1 & Heinrich Neubauer1 & Lisa D. Sprague1 Received: 25 October 2018 /Accepted: 6 December 2018 /Published online: 27 December 2018 # The Author(s) 2018 Abstract The emergence and global spread of drug resistant Acinetobacter (A.) baumannii is a cause of great concern. The current knowledge on antibiotic resistance in A. baumannii from animal origin is mostly based on few internationally published case reports, investigations of strain collections and several whole genome analyses. This lack of data results in a somewhat sketchy picture on how to assess the possible impact of drug resistant A. baumannii strains on veterinary and public health in Germany. Consequently, there is an urgent need to intensify the surveillance of A. baumannii in pet animals, the farm animal population and wildlife. Keywords Acinetobacter baumannii . Review . Antibiotic resistance . Germany Introduction limited number of widespread clones appear to be responsible for hospital outbreaks in many countries (Diancourt et al. Acinetobacter (A.) baumannii is a gram-negative opportunis- 2010). Eight international clonal lineages have been described tic nosocomial pathogen belonging to the genus Acinetobacter so far and comparative typing of outbreak strains obtained all and a member of the family Moraxellaceae. Acinetobacter over Europe revealed the dominance of three clones, original- spp. are non-motile, non-fastidious Gram-negative, non- ly named European clones I-III (Dijkshoorn et al. 1996; Karah fermenting, catalase positive, oxidase negative, strictly aero- et al.
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater

    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
  • Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes Versicolor)

    Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes Versicolor)

    animals Article Environment-Dependent Variation in Gut Microbiota of an Oviparous Lizard (Calotes versicolor) Lin Zhang 1,2,*,† , Fang Yang 3,†, Ning Li 4 and Buddhi Dayananda 5 1 School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China 2 State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China 3 School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China; [email protected] 4 College of Food Science, Nanjing Xiaozhuang University, Nanjing 211171, China; [email protected] 5 School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; [email protected] * Correspondence: [email protected] † These authors contributed equally to this work. Simple Summary: The different gut sections potentially provide different habitats for gut microbiota. We found that Bacteroidetes, Firmicutes, and Proteobacteria were the three primary phyla in gut micro- biota of C. versicolor. The relative abundance of dominant phyla Bacteroidetes and Firmicutes exhibited an increasing trend from the small intestine to the large intestine, and there was a higher abun- dance of genus Bacteroides (Class: Bacteroidia), Coprobacillus and Eubacterium (Class: Erysipelotrichia), Parabacteroides (Family: Porphyromonadaceae) and Ruminococcus (Family: Lachnospiraceae), and Family Odoribacteraceae and Rikenellaceae in the hindgut, and some metabolic pathways were higher in the hindgut. Our results reveal the variations of gut microbiota composition and metabolic pathways in Citation: Zhang, L.; Yang, F.; Li, N.; different parts of the lizards’ intestine. Dayananda, B. Environment- Dependent Variation in Gut Abstract: Vertebrates maintain complex symbiotic relationships with microbiota living within their Microbiota of an Oviparous Lizard gastrointestinal tracts which reflects the ecological and evolutionary relationship between hosts and (Calotes versicolor).