Antimicrobial Resistance in Environmental Waters

Total Page:16

File Type:pdf, Size:1020Kb

Antimicrobial Resistance in Environmental Waters Antimicrobial Resistance in Environmental Waters Edited by Karina Yew-Hoong Gin and Charmaine Ng Printed Edition of the Special Issue Published in Water www.mdpi.com/journal/water Antimicrobial Resistance in Environmental Waters Antimicrobial Resistance in Environmental Waters Special Issue Editors Karina Yew-Hoong Gin Charmaine Ng MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editors Karina Yew-Hoong Gin Charmaine Ng National University of Singapore National University of Singapore Singapore Singapore Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Water (ISSN 2073-4441) from 2017 to 2019 (available at: https://www.mdpi.com/si/water/ Antimicrobial-Resistance-Environmental-Waters). For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-608-0 (Pbk) ISBN 978-3-03897-609-7 (PDF) Cover image courtesy of Charmaine Ng. c 2019 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Special Issue Editors ..................................... vii Preface to ”Antimicrobial Resistance in Environmental Waters” .................. ix Charmaine Ng and Karina Yew-Hoong Gin Monitoring Antimicrobial Resistance Dissemination in Aquatic Systems Reprinted from: Water 2019, 11, 71, doi:10.3390/w11010071 ...................... 1 Kevin Lambirth, Matthew Tsilimigras, Anju Lulla, James Johnson, Abrar Al-Shaer, Orion Wynblatt, Shannon Sypolt, Cory Brouwer, Sandra Clinton, Olya Keen, Molly Redmond, Anthony Fodor and Cynthia Gibas Microbial Community Composition and Antibiotic Resistance Genes within a North Carolina Urban Water System Reprinted from: Water 2018, 10, 1539, doi:10.3390/w10111539 ..................... 8 Hsin-Chi Tsai, Ming-Yuan Chou, Yi-Jia Shih, Tung-Yi Huang, Pei-Yu Yang, Yi-Chou Chiu, Jung-Sheng Chen and Bing-Mu Hsu Distribution and Genotyping of Aquatic Acinetobacter baumannii Strains Isolated from the Puzi River and Its Tributaries Near Areas of Livestock Farming Reprinted from: Water 2018, 10, 1374, doi:10.3390/w10101374 ..................... 29 Asli Aslan, Zachariah Cole, Anunay Bhattacharya and Oghenekpaobor Oyibo Presence of Antibiotic-Resistant Escherichia coli in Wastewater Treatment Plant Effluents Utilized as Water Reuse for Irrigation Reprinted from: Water 2018, 10, 805, doi:10.3390/w10060805 ..................... 41 Pierangeli G. Vital, Enrico S. Zara, Cielo Emar M. Paraoan, Ma. Angela Z. Dimasupil, Joseth Jermaine M. Abello, I nigo˜ Teodoro G. Santos and Windell L. Rivera Antibiotic Resistance and Extended-Spectrum Beta-Lactamase Production of Escherichia coli Isolated from Irrigation Waters in Selected Urban Farms in Metro Manila, Philippines Reprinted from: Water 2018, 10, 548, doi:10.3390/w10050548 ..................... 52 Muhammad Raihan Jumat, Muhammad Fauzi Haroon, Nada Al-Jassim, Hong Cheng and Pei-Ying Hong An Increase of Abundance and Transcriptional Activity for Acinetobacter junii Post Wastewater Treatment Reprinted from: Water 2018, 10, 436, doi:10.3390/w10040436 ..................... 63 Junying Lu, Zhe Tian, Jianwei Yu, Min Yang and Yu Zhang Distribution and Abundance of Antibiotic Resistance Genes in Sand Settling Reservoirs and Drinking Water Treatment Plants across the Yellow River, China Reprinted from: Water 2018, 10, 246, doi:10.3390/w10030246 ..................... 87 Zheng Xu, Yue Jiang, Shu Harn Te, Yiliang He and Karina Yew-Hoong Gin The Effects of Antibiotics on Microbial Community Composition in an Estuary Reservoir during Spring and Summer Seasons Reprinted from: Water 2018, 10, 154, doi:10.3390/w10020154 ..................... 99 Yue Jiang, Cong Xu, Xiaoyu Wu, Yihan Chen, Wei Han, Karina Yew-Hoong Gin and Yiliang He Occurrence, Seasonal Variation and Risk Assessment of Antibiotics in Qingcaosha Reservoir Reprinted from: Water 2018, 10, 115, doi:10.3390/w10020115 .....................118 v Yihan Chen, Hongjie Chen, Li Zhang, Yue Jiang, Karina Yew-Hoong Gin and Yiliang He Occurrence, Distribution, and Risk Assessment of Antibiotics in a Subtropical River-Reservoir System Reprinted from: Water 2018, 10, 104, doi:10.3390/w10020104 .....................133 Jennipher Quach-Cu, Bellanira Herrera-Lynch, Christine Marciniak, Scott Adams, April Simmerman and Ryan A. Reinke The Effect of Primary, Secondary, and Tertiary Wastewater Treatment Processes on Antibiotic Resistance Gene (ARG) Concentrations in Solid and Dissolved Wastewater Fractions Reprinted from: Water 2018, 10, 37, doi:10.3390/w10010037 ......................149 Joyce Seow Fong Chin, Sheetal Sinha, Anjaiah Nalaparaju, Joey Kuok Hoong Yam, Zhiqiang Qin, Luyan Ma, Zhao-Xun Liang, Lanyuan Lu, Surajit Bhattacharjya and Liang Yang Pseudomonas aeruginosa Psl Exopolysaccharide Interacts with the Antimicrobial Peptide LG21 Reprinted from: Water 2017, 9, 681, doi:10.3390/w9090681 .......................167 vi About the Special Issue Editors Karina Yew-Hoong Gin is an Associate Professor with the Department of Civil and Environmental Engineering, National University of Singapore. She received her Bachelor degree in Civil Engineering from the University of Melbourne in 1988 and her M.Eng Degree from the National University of Singapore in 1991. She obtained her Doctor of Science (ScD) Degree jointly from the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution in 1996. Her research specialization is in the area of water quality, fate and transport of emerging contaminants, and ecosystem processes. Charmaine Ng is a Research Fellow with the Department of Surgery, National University of Singapore. She graduated with a PhD in microbiology at the University of New South Wales, Australia in 2011. Her research interests include marine and freshwater microbial ecology, antimicrobial resistance, and the study of the human microbiome in relation to different disease states. vii Preface to ”Antimicrobial Resistance in Environmental Waters” In recent years, the emergence of antimicrobial resistance has drawn heightened global concern because of its severe ramifications on the treatment of microbial infections. In particular, the issue of antibiotic resistance arises due to the overuse and misuse of antibiotics in both developed and developing countries. Bacteria develop antibiotic resistance in the presence of residual levels of antibiotics, and these antibiotic-resistant bacteria are in turn able to spread their resistance to other bacteria through mechanisms such as horizontal gene transfer, mediated by mobile genetic elements (e.g., plasmids, integrons) or co-selecting agents such as biocides and toxic metals. There is a worrying trend that pathogens are developing antibiotic resistance to a degree where last-resort antibiotics are no longer effective. This, in turn, has severe implications for public health and healthcare costs. In an effort to better understand the rising levels of antimicrobial resistance, surveillance studies have been undertaken across countries in a common effort to explore the occurrence of antimicrobial resistance in both clinical and natural environments. Implementing such initiatives by assessing the types of antibiotics used, antibiotic-resistant bacteria (ARB) present, and associated antibiotic resistant genes (ARGs) in microbiomes enables a better understanding of the impact of antibiotics in the medicine, agriculture, and aquaculture industries. Aquatic environments harbor diverse freshwater bacterial communities which may be subjected to anthropogenic pressures, while domestic wastewaters receive direct loads of antibiotics and pathogenic bacteria from human excretion. The nature of these environments allows them to function as hotspots for resistance through the selection of ARB and the circulation of ARGs through the stimulation of horizontal gene transfer between members of the microbiome. The aims of this Special Issue are to present current trends in antimicrobial/antibiotic resistance in diverse environmental waters, ranging from the detection and occurrence of antimicrobial factors (e.g., antimicrobials, antibiotics, ARB, ARGs) to their fate and transformations in different environments such as surface waters, groundwaters, biofilms, and water and wastewater treatment processes. This knowledge is needed to assist in the management and control of antimicrobial/antibiotic resistance and, ultimately, the protection of public health. Karina Yew-Hoong Gin, Charmaine Ng Special Issue Editors ix water Editorial Monitoring Antimicrobial Resistance Dissemination in Aquatic Systems Charmaine Ng 1 and Karina Yew-Hoong Gin 2,3,* 1 Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117411, Singapore; [email protected] 2 Department of Civil and Environmental Engineering, National University of Singapore, Singapore 138602, Singapore 3 NUS Environmental Research Institute (NERI), Singapore 138602, Singapore * Correspondence:
Recommended publications
  • A Novel Type of N-Acetylglutamate Synthase Is Involved in the First Step
    Petri et al. BMC Genomics 2013, 14:713 http://www.biomedcentral.com/1471-2164/14/713 RESEARCH ARTICLE Open Access A novel type of N-acetylglutamate synthase is involved in the first step of arginine biosynthesis in Corynebacterium glutamicum Kathrin Petri, Frederik Walter, Marcus Persicke, Christian Rückert and Jörn Kalinowski* Abstract Background: Arginine biosynthesis in Corynebacterium glutamicum consists of eight enzymatic steps, starting with acetylation of glutamate, catalysed by N-acetylglutamate synthase (NAGS). There are different kinds of known NAGSs, for example, “classical” ArgA, bifunctional ArgJ, ArgO, and S-NAGS. However, since C. glutamicum possesses a monofunctional ArgJ, which catalyses only the fifth step of the arginine biosynthesis pathway, glutamate must be acetylated by an as of yet unknown NAGS gene. Results: Arginine biosynthesis was investigated by metabolome profiling using defined gene deletion mutants that were expected to accumulate corresponding intracellular metabolites. HPLC-ESI-qTOF analyses gave detailed insights into arginine metabolism by detecting six out of seven intermediates of arginine biosynthesis. Accumulation of N-acetylglutamate in all mutants was a further confirmation of the unknown NAGS activity. To elucidate the identity of this gene, a genomic library of C. glutamicum was created and used to complement an Escherichia coli ΔargA mutant. The plasmid identified, which allowed functional complementation, contained part of gene cg3035, which contains an acetyltransferase domain in its amino acid sequence. Deletion of cg3035 in the C. glutamicum genome led to a partial auxotrophy for arginine. Heterologous overexpression of the entire cg3035 gene verified its ability to complement the E. coli ΔargA mutant in vivo and homologous overexpression led to a significantly higher intracellular N-acetylglutamate pool.
    [Show full text]
  • DGGE) and PGR Cloning of 16S Rrna Genes
    THE UNIVERSITY OF NEW SOUTH thesis/Dissertation Sheet Surname or Family name:LE Rrst ^ I Other narne/s: Abbreviation for degree as given in the University calendar: MSc | ScliooliBiotechnolo^^^^^^ and Biomolecular ScienoBS Faculty: Science Title:Community analysis and physiological characterisation of bacterial isolates from a nitrifying membrane bioreactor Abstract This thesis focuses on the identification of early colonisers on membrane surfaces used in wastewater treatment, as well as the physiological characterisation of bacterial cultures isolated from different micro- environments of a membrane bioreactor (MBR). The bacterial community composition of early biofilms on membrane surfaces under different hydrodynamic conditions (pressurised and non-pressurised) and of the activated sludge in an MBR were examined by culture-independent, molecular-based methods of PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and PGR cloning of 16S rRNA genes. A bench-scale, nitrifying MBR treating artificial waste was employed. The hollow fibre ultrafiltration membrane was made of polypropylene with an average pore diameter of 0.04 \im. Analysis of DGGE profiles of the sessile communities on membrane surfaces revealed that Tetrasphaera elongata species were important colonisers due to their ability to bind to membrane surfaces irrespective of the hydrodynamic context and exposure time. Interactions between isolates from the bioreactor and membrane surfaces were further investigated by characterising the physiological traits important in biofilm initiation and proliferation on membrane surfaces such as motility, auto-aggregation, co-aggregation, hydrophobicity and quorum sensing. Bacterial strains were isolated from floes and supernatant phases of the activated sludge as well as from pressurised membrane surfaces. Microbacterium sp. were prevalent in all culture collections.
    [Show full text]
  • 非会員: 10,000 円 12,000 円 *要旨集(2,000 円)のみをご希望の方は, 大会事務局までご連絡下さい。
    A B C D 1990年12月18日 第4種郵便物認可 ISSN 0914-5818 2019 VOL. 33 NO. 1 C 2019 T VOL. 33 NO. 1 IN (公開用) O ACTINOMYCETOLOGICA M Y C E T O L O G 日 本 I 放 C 線 菌 学 http://www. actino.jp/ 会 日本放線菌学会誌 第28巻 1 号 誌 Published by ACTINOMYCETOLOGICA VOL.28 NO.1, 2014 The Society for Actinomycetes Japan SAJ NEWS Vol. 33, No. 1, 2019 Contents • Outline of SAJ: Activities and Membership S2 • List of New Scientific Names and Nomenclatural Changes in the Phylum Actinobacteria Validly Published in 2018 S3 • Award Lecture (Dr. Yasuhiro Igarashi) S50 • Publication of Award Lecture (Dr. Yasuhiro Igarashi) S55 • Award Lecture (Dr. Yuki Inahashi) S56 • Publication of Award Lecture (Dr. Yuki Inahashi) S64 • Award Lecture (Dr. Yohei Katsuyama) S65 • Publication of Award Lecture (Dr. Yohei Katsuyama) S72 • 64th Regular Colloquim S73 • 65th Regular Colloquim S74 • The 2019 Annual Meeting of the Society for Actinomycetes Japan S75 • Online access to The Journal of Antibiotics for SAJ members S76 S1 Outline of SAJ: Activities and Membership The Society for Actinomycetes Japan (SAJ) Annual membership fees are currently 5,000 yen was established in 1955 and authorized as a for active members, 3,000 yen for student mem- scientific organization by Science Council of Japan bers and 20,000 yen or more for supporting mem- in 1985. The Society for Applied Genetics of bers (mainly companies), provided that the fees Actinomycetes, which was established in 1972, may be changed without advance announce- merged in SAJ in 1990. SAJ aims at promoting ment.
    [Show full text]
  • General Microbiota of the Soft Tick Ornithodoros Turicata Parasitizing the Bolson Tortoise (Gopherus flavomarginatus) in the Mapimi Biosphere Reserve, Mexico
    biology Article General Microbiota of the Soft Tick Ornithodoros turicata Parasitizing the Bolson Tortoise (Gopherus flavomarginatus) in the Mapimi Biosphere Reserve, Mexico Sergio I. Barraza-Guerrero 1,César A. Meza-Herrera 1 , Cristina García-De la Peña 2,* , Vicente H. González-Álvarez 3 , Felipe Vaca-Paniagua 4,5,6 , Clara E. Díaz-Velásquez 4, Francisco Sánchez-Tortosa 7, Verónica Ávila-Rodríguez 2, Luis M. Valenzuela-Núñez 2 and Juan C. Herrera-Salazar 2 1 Unidad Regional Universitaria de Zonas Áridas, Universidad Autónoma Chapingo, 35230 Bermejillo, Durango, Mexico; [email protected] (S.I.B.-G.); [email protected] (C.A.M.-H.) 2 Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, 35010 Gómez Palacio, Durango, Mexico; [email protected] (V.Á.-R.); [email protected] (L.M.V.-N.); [email protected] (J.C.H.-S.) 3 Facultad de Medicina Veterinaria y Zootecnia No. 2, Universidad Autónoma de Guerrero, 41940 Cuajinicuilapa, Guerrero, Mexico; [email protected] 4 Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, 54090 Tlalnepantla, Estado de México, Mexico; [email protected] (F.V.-P.); [email protected] (C.E.D.-V.) 5 Instituto Nacional de Cancerología, 14080 Ciudad de México, Mexico 6 Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54090 Tlalnepantla, Estado de México, Mexico 7 Departamento de Zoología, Universidad de Córdoba.Edificio C-1, Campus Rabanales, 14071 Cordoba, Spain; [email protected] * Correspondence: [email protected]; Tel.: +52-871-386-7276; Fax: +52-871-715-2077 Received: 30 July 2020; Accepted: 3 September 2020; Published: 5 September 2020 Abstract: The general bacterial microbiota of the soft tick Ornithodoros turicata found on Bolson tortoises (Gopherus flavomarginatus) were analyzed using next generation sequencing.
    [Show full text]
  • Deciphering the Genome of Polyphosphate Accumulating Actinobacterium Microlunatus Phosphovorus
    DNA RESEARCH 19, 383–394, (2012) doi:10.1093/dnares/dss020 Advance Access publication on 23 August 2012 Deciphering the Genome of Polyphosphate Accumulating Actinobacterium Microlunatus phosphovorus AKATSUKI Kawakoshi1,HIDEKAZU Nakazawa1,JUNJI Fukada1,MACHI Sasagawa1,YOKO Katano1, SANAE Nakamura1,AKIRA Hosoyama1,HIROKI Sasaki1,NATSUKO Ichikawa1,SATOSHI Hanada2, YOICHI Kamagata2,KAZUNORI Nakamura2,SHUJI Yamazaki1, and NOBUYUKI Fujita1,* Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan1 and Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan2 *To whom correspondence should be addressed. Tel. þ81 3-6686-2754. Fax. þ81 3-3481-8424. E-mail: [email protected] Edited by Katsumi Isono (Received 25 April 2012; accepted 24 July 2012) Abstract Polyphosphate accumulating organisms (PAOs) belong mostly to Proteobacteria and Actinobacteria and are quite divergent. Under aerobic conditions, they accumulate intracellular polyphosphate (polyP), while they typically synthesize polyhydroxyalkanoates (PHAs) under anaerobic conditions. Many ecological, physiological, and genomic analyses have been performed with proteobacterial PAOs, but few with actino- bacterial PAOs. In this study, the whole genome sequence of an actinobacterial PAO, Microlunatus phos- phovorus NM-1T (NBRC 101784T), was determined. The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases ( ppks), two polyP-dependent glucokinases ( ppgks), and three phosphate transporters ( pits). In contrast, it harbours only a single ppx gene for exopolyphosphatase, although two copies of ppx are generally present in other actinobacteria. Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H1 symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs.
    [Show full text]
  • J. Gen. Appl. Microbiol., 48, 125-133 (2002)
    J. Gen. Appl. Microbiol., 48, 125–133 (2002) Full Paper Isolation and characterization of a Gram-positive polyphosphate-accumulating bacterium Shin Onda and Susumu Takii* Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192–0397, Japan (Received October 31, 2001; Accepted March 9, 2002) A Gram-positive polyphosphate-accumulating bacterium was isolated from phosphate-removal activated sludge using pyruvate-supplemented agar plates. The isolate was oval or coccobacilli 0.7؋0.5–1.0 mm) that occurred singly, in pairs or irregular clumps. Polyphosphate granules–0.4) in the cells were observed by toluidine blue staining. The pure culture of the isolate rapidly took up phosphate (9.2 mg-P/g-dry weight) in the 3-h aerobic incubation without organic substrates, after anaerobic incubation with organic substrates containing casamino acids. When acetate was the sole carbon source in the anaerobic incubation, the isolate did not remove phosphate. These physiological features of the isolate were similar to those of Microlunatus phosphovorus. However, unlike M. phosphovorus the P-removal ability of the isolate was relatively low and was not accelerated by repeating the anaerobic/aerobic incubation cycles. Phylogenetic analysis and comparison of several characteristics showed that the isolate was identified as Tetrasphaera elongata which was recently proposed as a new polyphosphate-accumulating species isolated from activated sludge. As the isolate contained menaquinone (MK)-8(H4) as the predominant iso- prenoid ubiquinone, it may be significantly responsible for phosphate removal, because MK- 8(H4) has reportedly been found in fairly high proportions in many phosphate-removing activated sludges.
    [Show full text]
  • View, 27(1): 99–127
    Journal of Environmental Sciences 21(2009) 223–228 Monitoring microbial community structure and succession of an A/O SBR during start-up period using PCR-DGGE WANG Xiuheng∗, ZHANG Kun, REN Nanqi, LI Nan, REN Lijiao State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China. E-mail: [email protected] Received 26 February 2008; revised 08 May 2008; accepted 16 May 2008 Abstract Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) protocol was employed for revealing microbial community structure and succession in a sequential anaerobic and aerobic reactor performing enhanced biological phosphorus removal (EBPR) during start-up period. High phosphorus removal was achieved after 15 d. On day 30, phosphorus removal efficiency reached to 83.2% and the start-up was finished. DGGE profiles of periodical sludge samples showed that dominant microbial species were 19 OTUs (operational taxonomy units). Unweighted pair-group method using arithmetic averages (UPGMA) clustering analysis revealed that rapid community succession correlated to low phosphorus removal rate and high phosphorus removal efficiency reflected on steady community structure. Sequencing results indicated that determined sequences (12 OTUs) belonged to Proteobacterium, Actinobacteria, Gemmatimonadales and unaffiliate group. Proteobacterium, Tetrasphaera elongate and Gemmatimonas aurantiaca may act important roles in phosphorus removal. With little amount as known glycogen accumulating organisms, Candidatus Competibacter phosphatis still at accumulating-phase had limited effect on microbial community structure. When climax community was obtained, dominant microbes were 14 OTUs. Microbes in a large amount were uncultured bacterium Thauera sp., uncultured γ-Proteobacterium and Tetrasphaera elongata. Key words: biological phosphorus removal; polyphosphate accumulating organisms; glycogen accumulating organisms DOI: 10.1016/S1001-0742(08)62255-X Introduction temperature also effect the microbial competition (Oehmen et al., 2007).
    [Show full text]
  • Genome-Based Taxonomic Classification of the Phylum
    ORIGINAL RESEARCH published: 22 August 2018 doi: 10.3389/fmicb.2018.02007 Genome-Based Taxonomic Classification of the Phylum Actinobacteria Imen Nouioui 1†, Lorena Carro 1†, Marina García-López 2†, Jan P. Meier-Kolthoff 2, Tanja Woyke 3, Nikos C. Kyrpides 3, Rüdiger Pukall 2, Hans-Peter Klenk 1, Michael Goodfellow 1 and Markus Göker 2* 1 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, 2 Department Edited by: of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Martin G. Klotz, Germany, 3 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Washington State University Tri-Cities, United States The application of phylogenetic taxonomic procedures led to improvements in the Reviewed by: Nicola Segata, classification of bacteria assigned to the phylum Actinobacteria but even so there remains University of Trento, Italy a need to further clarify relationships within a taxon that encompasses organisms of Antonio Ventosa, agricultural, biotechnological, clinical, and ecological importance. Classification of the Universidad de Sevilla, Spain David Moreira, morphologically diverse bacteria belonging to this large phylum based on a limited Centre National de la Recherche number of features has proved to be difficult, not least when taxonomic decisions Scientifique (CNRS), France rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft *Correspondence: Markus Göker genome sequences
    [Show full text]
  • Monashia Flava Gen. Nov., Sp. Nov., an Actinobacterium of the Family Intrasporangiaceae
    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 554–561 DOI 10.1099/ijsem.0.000753 Monashia flava gen. nov., sp. nov., an actinobacterium of the family Intrasporangiaceae Adzzie-Shazleen Azman,1 Nurullhudda Zainal,1,2 Nurul-Syakima Ab Mutalib,3 Wai-Fong Yin,2 Kok-Gan Chan2 and Learn-Han Lee1 Correspondence 1Biomedical Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Learn-Han Lee Monash University Malaysia, 46150 Bandar Sunway, Selangor Darul Ehsan, Malaysia [email protected] or 2Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, [email protected] University of Malaya, 50603 Kuala Lumpur, Malaysia 3UKM Medical Molecular Biology Institute (UMBI), UKM Medical Centre, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia A novel actinobacterial strain, MUSC 78T, was isolated from a mangrove soil collected from Peninsular Malaysia. The taxonomic status of this strain was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis revealed that strain MUSC 78T represented a novel lineage within the class Actinobacteria. Strain MUSC 78T formed a distinct clade in the family Intrasporangiaceae and was related most closely to members of the genera Terrabacter (98.3–96.8 % 16S rRNA gene sequence similarity), Intrasporangium (98.2– 96.8 %), Humibacillus (97.2 %), Janibacter (97.0–95.3 %), Terracoccus (96.8 %), Kribbia (96.6 %), Phycicoccus (96.2–94.7 %), Knoellia (96.1–94.8 %), Tetrasphaera (96.0–94.9 %) and Lapillicoccus (95.9 %). Cells were irregular rod-shaped or cocci and stained Gram- positive. The cell-wall peptidoglycan type was A3c, with LL-diaminopimelic acid as the diagnostic diamino acid.
    [Show full text]
  • Istanbul Technical University Institute of Science And
    İSTANBUL TECHNICAL UNIVERSITY INSTITUTE OF SCIENCE AND TECHNOLOGY MICROBIAL COMMUNITY AND METABOLISM OF ENHANCED BIOLOGICAL PHOSPHORUS REMOVAL Ph.D. Thesis by Gülsüm Emel ZENGİN Department : Environmental Engineering Programme : Environmental Engineering JANUARY 2009 İSTANBUL TECHNICAL UNIVERSITY INSTITUTE OF SCIENCE AND TECHNOLOGY MICROBIAL COMMUNITY AND METABOLISM OF ENHANCED BIOLOGICAL PHOSPHORUS REMOVAL Ph.D. Thesis by Gülsüm Emel ZENGİN, M.Sc. (501002355) Date of submission : 15 September 2008 Date of defence examination: 13 January 2009 Supervisor (Chairman) : Prof. Dr. Nazik ARTAN (ITU) Co-supervisor : Prof. Dr. Takashi MINO (UT) Members of the Examining Committee : Prof. Dr. Derin ORHON (ITU) Prof. Dr. Orhan YENİGÜN (BU) Prof. Dr. Rüya TAŞLI TORAMAN(ITU) Prof. Dr. Delya SPONZA (DEU) JANUARY 2009 İSTANBUL TEKNİK ÜNİVERSİTESİ FEN BİLİMLERİ ENSTİTÜSÜ BİYOLOJİK AŞIRI FOSFOR GİDERİMİNİN MİKROBİYAL TÜRLERİ VE METABOLİZMASI DOKTORA TEZİ Y. Müh. Gülsüm Emel ZENGİN (501002355) Tezin Enstitüye Verildiği Tarih : 15 Eylül 2008 Tezin Savunulduğu Tarih : 13 Ocak 2009 Tez Danışmanı : Prof. Dr. Nazik ARTAN (İTÜ) Eş Danışman : Prof. Dr. Takashi MINO (UT) Diğer Jüri Üyeleri : Prof. Dr. Derin ORHON (İTÜ) Prof. Dr. Orhan YENİGÜN (BÜ) Prof. Dr. Rüya TAŞLI TORAMAN (İTÜ) Prof. Dr. Delya SPONZA (DEÜ) OCAK 2009 ACKNOWLEDGMENT I would like to express my sincere gratitude and appreciation to my supervisors Prof. Dr. Nazik Artan and Prof. Dr. Takashi Mino for their effort in providing me their experience and knowledge, for the encouragement and support throughout my study and especially for their understanding. I would especially like to thank Prof. Dr. Derin Orhon for his sincere support, inputs for my study, and specially his encouragement and help for giving opportunity to study abroad.
    [Show full text]
  • Population Dynamics and Metabolic Potential of a Pilot-Scale Microbial Community
    Population dynamics and metabolic potential of a pilot-scale microbial community performing enhanced biological phosphorus removal by CHRISTOPHER EVAN LAWSON B.A.Sc. (Civil Engineering), University of British Columbia, 2010 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF APPLIED SCIENCE in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Civil Engineering) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) September 2014 © Christopher Evan Lawson, 2014 Abstract Enhanced biological phosphorus removal (EBPR) is an environmental biotechnology of global importance, essential for protecting receiving waters from eutrophication and enabling phosphorus recovery. Current understanding of EBPR is largely based on empirical evidence and black-box models that fail to appreciate the driving force responsible for nutrient cycling and ultimate phosphorus removal, namely microbial communities. Accordingly, this thesis focused on understanding the microbial ecology of a pilot-scale microbial community performing EBPR to better link bioreactor processes to underlying microbial agents. Initially, temporal changes in microbial community structure and activity were monitored in a pilot-scale EBPR treatment plant by examining the ratio of small subunit ribosomal RNA (SSU rRNA) to SSU rRNA gene over a 120-day study period. Although the majority of operational taxonomic units (OTUs) in the EBPR ecosystem were rare, many maintained high potential activities, suggesting that rare OTUs made significant contributions to protein synthesis potential. Few significant differences in OTU abundance and activity were observed between bioreactor redox zones, although differences in temporal activity were observed among phylogenetically cohesive OTUs. Moreover, observed temporal activity patterns could not be explained by measured process parameters, suggesting that alternate ecological forces shaped community interactions in the bioreactor milieu.
    [Show full text]
  • Provided for Non-Commercial Research and Educational Use. Not for Reproduction, Distribution Or Commercial Use
    Provided for non-commercial research and educational use. Not for reproduction, distribution or commercial use. This article was originally published in the Encyclopedia of Microbiology published by Elsevier, and the attached copy is provided by Elsevier for the author’s benefit and for the benefit of the author’s institution, for non-commercial research and educational use including without limitation use in instruction at your institution, sending it to specific colleagues who you know, and providing a copy to your institution’s administrator. All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution’s website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier’s permissions site at: http://www.elsevier.com/locate/permissionusematerial E M Wellington. Actinobacteria. Encyclopedia of Microbiology. (Moselio Schaechter, Editor), pp. 26-[44] Oxford: Elsevier. Author's personal copy BACTERIA Contents Actinobacteria Bacillus Subtilis Caulobacter Chlamydia Clostridia Corynebacteria (including diphtheria) Cyanobacteria Escherichia Coli Gram-Negative Cocci, Pathogenic Gram-Negative Opportunistic Anaerobes: Friends and Foes Haemophilus Influenzae Helicobacter Pylori Legionella, Bartonella, Haemophilus Listeria Monocytogenes Lyme Disease Mycoplasma and Spiroplasma Myxococcus Pseudomonas Rhizobia Spirochetes Staphylococcus Streptococcus Pneumoniae Streptomyces
    [Show full text]