Aquatic Microbial Ecology 63:101
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Genomics 98 (2011) 370–375
Genomics 98 (2011) 370–375 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Whole-genome comparison clarifies close phylogenetic relationships between the phyla Dictyoglomi and Thermotogae Hiromi Nishida a,⁎, Teruhiko Beppu b, Kenji Ueda b a Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan b Life Science Research Center, College of Bioresource Sciences, Nihon University, Fujisawa, Japan article info abstract Article history: The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful Received 2 June 2011 enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Accepted 1 August 2011 Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene Available online 7 August 2011 sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its Keywords: evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence Whole-genome comparison Dictyoglomus comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a Bacterial systematics monophyletic group with Coprothermobacter proteolyticus (a constituent of the phylum Firmicutes) and Coprothermobacter proteolyticus Thermotogae. Our findings indicate that C. proteolyticus does not belong to the phylum Firmicutes and that the Thermotogae phylum Dictyoglomi is not closely related to either the phylum Firmicutes or Synergistetes but to the phylum Thermotogae. © 2011 Elsevier Inc. -
Vibrio Species in an Urban Tropical Estuary: Antimicrobial Susceptibility, Interaction with Environmental Parameters, and Possible Public Health Outcomes
microorganisms Article Vibrio Species in an Urban Tropical Estuary: Antimicrobial Susceptibility, Interaction with Environmental Parameters, and Possible Public Health Outcomes Anna L. B. Canellas 1 , Isabelle R. Lopes 1 , Marianne P. Mello 2, Rodolfo Paranhos 2, Bruno F. R. de Oliveira 1 and Marinella S. Laport 1,* 1 Laboratório de Bacteriologia Molecular e Marinha, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941902, Brazil; [email protected] (A.L.B.C.); [email protected] (I.R.L.); [email protected] (B.F.R.d.O.) 2 Departamento de Biologia Marinha, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941617, Brazil; [email protected] (M.P.M.); [email protected] (R.P.) * Correspondence: [email protected] Abstract: The genus Vibrio comprises pathogens ubiquitous to marine environments. This study evaluated the cultivable Vibrio community in the Guanabara Bay (GB), a recreational, yet heavily polluted estuary in Rio de Janeiro, Brazil. Over one year, 66 water samples from three locations along a pollution gradient were investigated. Isolates were identified by MALDI-TOF mass spectrometry, revealing 20 Vibrio species, including several potential pathogens. Antimicrobial susceptibility testing confirmed resistance to aminoglycosides, beta-lactams (including carbapenems and third-generation cephalosporins), fluoroquinolones, sulfonamides, and tetracyclines. Four strains were producers Citation: Canellas, A.L.B.; Lopes, of extended-spectrum beta-lactamases (ESBL), all of which carried beta-lactam and heavy metal I.R.; Mello, M.P.; Paranhos, R.; de resistance genes. The toxR gene was detected in all V. parahaemolyticus strains, although none carried Oliveira, B.F.R.; Laport, M.S. -
Genomic Signatures of Predatory Bacteria
The ISME Journal (2013) 7, 756–769 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE By their genes ye shall know them: genomic signatures of predatory bacteria Zohar Pasternak1, Shmuel Pietrokovski2, Or Rotem1, Uri Gophna3, Mor N Lurie-Weinberger3 and Edouard Jurkevitch1 1Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel; 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel and 3Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the ‘predatome,’ that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. -
Interactions Between the Human Pathogen Vibrio Parahaemolyticus and Common Marine Microalgae
Current Trends in Microbiology Vol. 12, 2018 Interactions between the human pathogen Vibrio parahaemolyticus and common marine microalgae Savannah L. Klein, Katherine E. Haney, Thomas M. Hornaday, India B. Gartmon and Charles R. Lovell* Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, 29208, USA. ABSTRACT KEYWORDS: Vibrio parahaemolyticus, tdh, trh, T3SS2, T6SS, microalgae. Vibrio parahaemolyticus is a gastrointestinal pathogen that is abundant in coastal marine environments. Elevated numbers of V. parahaemolyticus cells INTRODUCTION have been correlated with marine microalgae Vibrio parahaemolyticus, a common organism in blooms, particularly blooms of diatoms and coastal environments, is a significant and sometimes dinoflagellates, but the nature of the relationship pandemic human pathogen responsible for an between V. parahaemolyticus and microalgae is estimated 34,000 cases of seafood-associated unknown. We performed in vitro assays using 27 gastroenteritis per year in the United States [1]. Most environmental V. parahaemolyticus strains and cases of V. parahaemolyticus-induced gastroenteritis various phototrophs; a diatom, a dinoflagellate, are self-limiting and relatively mild, but infections unarmored and armored forms of a coccolithophore, can be deadly in immunocompromised individuals. and two species of cyanobacteria. The V. The common mode of transmission of this parahaemolyticus strains we employed contained bacterium to the human host is ingestion of raw or different combinations of virulence-correlated genes, undercooked shellfish, primarily oysters. In addition, the hemolysin genes tdh and trh, the Type III some strains of V. parahaemolyticus can infect Secretion System 2 (T3SS2) marker gene vscC2, wounds and some produce systemic infections, and the Type VI Secretion System (T6SS) marker while others are apparently non-pathogenic. -
Characterization and Genomic Analysis of a Diesel-Degrading Bacterium, Acinetobacter Calcoaceticus CA16, Isolated from Canadian Soil Margaret T
Ho et al. BMC Biotechnology (2020) 20:39 https://doi.org/10.1186/s12896-020-00632-z RESEARCH ARTICLE Open Access Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil Margaret T. Ho1,2, Michelle S. M. Li1, Tim McDowell3, Jacqueline MacDonald1 and Ze-Chun Yuan1,3* Abstract Background: With the high demand for diesel across the world, environmental decontamination from its improper usage, storage and accidental spills becomes necessary. One highly environmentally friendly and cost-effective decontamination method is to utilize diesel-degrading microbes as a means for bioremediation. Here, we present a newly isolated and identified strain of Acinetobacter calcoaceticus (‘CA16’) as a candidate for the bioremediation of diesel-contaminated areas. Results: Acinetobacter calcoaceticus CA16 was able to survive and grow in minimal medium with diesel as the only source of carbon. We determined through metabolomics that A. calcoaceticus CA16 appears to be efficient at diesel degradation. Specifically, CA16 is able to degrade 82 to 92% of aliphatic alkane hydrocarbons (CnHn +2; where n = 12–18) in 28 days. Several diesel-degrading genes (such as alkM and xcpR) that are present in other microbes were also found to be activated in CA16. Conclusions: The results presented here suggest that Acinetobacter strain CA16 has good potential in the bioremediation of diesel-polluted environments. Keywords: Microbial bioremediation, Acinetobacter calcoaceticus CA16, Diesel-degrading bacteria, Diesel bioremediation, Aliphatic hydrocarbons, n-alkanes Background can be mitigated by microbial bioremediation, which With the high demand for diesel around the world, se- uses microbes to remove pollutants from the environ- vere environmental and ecological problems have arisen ment [3, 4]. -
BACTERIAL and PHAGE INTERACTIONS INFLUENCING Vibrio Parahaemolyticus ECOLOGY
University of New Hampshire University of New Hampshire Scholars' Repository Master's Theses and Capstones Student Scholarship Spring 2016 BACTERIAL AND PHAGE INTERACTIONS INFLUENCING Vibrio parahaemolyticus ECOLOGY Ashley L. Marcinkiewicz University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/thesis Recommended Citation Marcinkiewicz, Ashley L., "BACTERIAL AND PHAGE INTERACTIONS INFLUENCING Vibrio parahaemolyticus ECOLOGY" (2016). Master's Theses and Capstones. 852. https://scholars.unh.edu/thesis/852 This Thesis is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Master's Theses and Capstones by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. BACTERIAL AND PHAGE INTERACTIONS INFLUENCING Vibrio parahaemolyticus ECOLOGY BY ASHLEY MARCINKIEWICZ Bachelor of Arts, Wells College, 2011 THESIS Submitted to the University of New Hampshire In Partial Fulfillment of The Requirements for the Degree of Master of Science in Microbiology May, 2016 This thesis has been examined and approved in partial fulfillment of the requirements for the degree of Masters of Science in Microbiology by: Thesis Director, Cheryl A. Whistler Associate Professor of Molecular, Cellular, and Biomedical Sciences Stephen H. Jones Research Associate Professor of Natural Resources and the Environment Jeffrey T. Foster Assistant Professor of Molecular, Cellular, and Biomedical Sciences On April 15th, 2016 Original approved signatures are on file with the University of New Hampshire Graduate School. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS………………………………………………………... vi LIST OF TABLES………………………………………………………………… vii LIST OF FIGURES…….………………………………………………………….. viii ABSTRACT………………………………………………………………………. -
S41598-020-68891-6.Pdf
www.nature.com/scientificreports OPEN Structure and co‑occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacifc white‑leg shrimp Penaeus vannamei aquaculture Yustian Rovi Alfansah1,2,3*, Sonja Peters1, Jens Harder4, Christiane Hassenrück1,7 & Astrid Gärdes1,5,6,7 Bacterial diseases cause production failures in shrimp aquacultures. To understand environmental conditions and bacterial community dynamics contributing to white faeces disease (WFD) events, we analysed water quality and compared bacterial communities in water as well as in intestines and faeces of healthy and diseased shrimps, respectively, via 16S rRNA gene sequencing and qPCR of transmembrane regulatory protein (toxR), thermolabile haemolysin (tlh), and thermostable direct haemolysin genes of pathogenic Vibrio parahaemolyticus as a proxy for virulence. WFD occurred when pH decreased to 7.71–7.84, and Alteromonas, Pseudoalteromonas and Vibrio dominated the aquatic bacterial communities. The disease severity further correlated with increased proportions of Alteromonas, Photobacterium, Pseudoalteromonas and Vibrio in shrimp faeces. These opportunistic pathogenic bacteria constituted up to 60% and 80% of the sequences in samples from the early and advances stages of the disease outbreak, respectively, and exhibited a high degree of co-occurrence. Furthermore, toxR and tlh were detected in water at the disease event only. Notably, bacterial community resilience in water occurred when pH was adjusted to 8. Then WFD ceased without a mortality event. In conclusion, pH was a reliable indicator of the WFD outbreak risk. Dissolved oxygen and compositions of water and intestinal bacteria may also serve as indicators for better prevention of WFD events. Bacterial diseases are a major problem for Penaeus vannamei pond aquaculture in Asia and Latin America. -
1 Marinobacter Hydrocarbonoclasticus
International Journal of Systematic Bacteriology (1998), 48, 1445-1 448 Printed in Great Britain ~ -~~~~~~ 1- Transfer of Pseudomonas nautica to L -~ 1 Marinobacter hydrocarbonoclasticus Cathrin Sproer, Elke Lang, Petra Hobeck, Jutta Burghardt, Erko Stackebrandt and B. J. Tindall Author for correspondence: B. J. Tindall. Tel: +49 531 2616 224. Fax: +49 531 2616 418. e-mail: bti@ gbf.de ~ DSMZ-Deutsche Sammlung A combination of genotypic and phenotypic properties (a polyphasic "On Mikroorganismen und taxonomic approach) was used to determine the relatedness between the type Zellkulturen GmbH, Mascheroder Weg 1b, strains of Pseudomonas nautica Bauman et a/. 1982 and Marinobacter D-38124 Braunschweig, hydrocarbonoc/asticusGauthier et a/. 1992, which were originally found to be Germany highly related by partial 16s rDNA sequence analysis. Analysis of genotypic properties, such as comparison of the almost complete 165 rDNA sequences, base composition of the total genomic DNA and DNA-DNA hybridization revealed that the two strains were highly similar and should be considered members of the same species. The phenotypic properties, such as the physiology and chemotaxonomic data (i.e. fatty acid composition, polar lipid patterns and respiratory lipoquinone content), confirmed the genotypic evaluation, and has lead to the proposal for a unification of the two species, Pseudomonas nautica (DSM 50418') and Marinobacter hydrocarbonodasticus (DSM 8798T)as Marinobacter hydrocarbonoclasticus. Keywords: Marinobacter hil~drocarbonoclasticus, Pseudomonas nautica, 16s rRN A sequence, chemotaxonomy, taxonomy Baumann et a/. (1972) described aerobic, oxidase- to members of the Pseudomonas aeruginosa rRNA positive. Gram-negative and motile strains which branch of the rRNA superfamily I (De Ley, 1978), showed a high degree of physiological similarity, but with the remaining species being transferred to other were different from other members of the genus genera, e .g . -
1 Microbial Transformations of Organic Chemicals in Produced Fluid From
Microbial transformations of organic chemicals in produced fluid from hydraulically fractured natural-gas wells Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Morgan V. Evans Graduate Program in Environmental Science The Ohio State University 2019 Dissertation Committee Professor Paula Mouser, Advisor Professor Gil Bohrer, Co-Advisor Professor Matthew Sullivan, Member Professor Ilham El-Monier, Member Professor Natalie Hull, Member 1 Copyrighted by Morgan Volker Evans 2019 2 Abstract Hydraulic fracturing and horizontal drilling technologies have greatly improved the production of oil and natural-gas from previously inaccessible non-permeable rock formations. Fluids comprised of water, chemicals, and proppant (e.g., sand) are injected at high pressures during hydraulic fracturing, and these fluids mix with formation porewaters and return to the surface with the hydrocarbon resource. Despite the addition of biocides during operations and the brine-level salinities of the formation porewaters, microorganisms have been identified in input, flowback (days to weeks after hydraulic fracturing occurs), and produced fluids (months to years after hydraulic fracturing occurs). Microorganisms in the hydraulically fractured system may have deleterious effects on well infrastructure and hydrocarbon recovery efficiency. The reduction of oxidized sulfur compounds (e.g., sulfate, thiosulfate) to sulfide has been associated with both well corrosion and souring of natural-gas, and proliferation of microorganisms during operations may lead to biomass clogging of the newly created fractures in the shale formation culminating in reduced hydrocarbon recovery. Consequently, it is important to elucidate microbial metabolisms in the hydraulically fractured ecosystem. -
Microbial Community Composition During Degradation of Organic Matter
TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Bodenökologie Microbial community composition during degradation of organic matter Stefanie Elisabeth Wallisch Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Univ.-Prof. Dr. A. Göttlein Prüfer der Dissertation: 1. Hon.-Prof. Dr. M. Schloter 2. Univ.-Prof. Dr. S. Scherer Die Dissertation wurde am 14.04.2015 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 03.08.2015 angenommen. Table of contents List of figures .................................................................................................................... iv List of tables ..................................................................................................................... vi Abbreviations .................................................................................................................. vii List of publications and contributions .............................................................................. viii Publications in peer-reviewed journals .................................................................................... viii My contributions to the publications ....................................................................................... viii Abstract -
Marinobacter Aquaeolei Sp. Nov., a Halophilic Bacterium Isolated from a Vietnamese Oil- Producing Well
lnternational Journal of Systematic Bacteriology (1999), 49, 367-375 Printed in Great Britain Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil- producing well Nguyen 6. Huu,' Ewald B. M. Denner,' Dang T. C. Ha,' Gerhard Wanner3 and Helga Stan-Lotter4 Author for correspondence: Helga Stan-Lotter. Tel: +43 662 8044 5756. Fax: +43 662 8044 144. e-mail : helgastan-lo tter @ sbg.ac.at 1 Institute of Biotechnology, Several strains of moderately halophilic and mesophilic bacteria were isolated National Center for at the head of an oil-producing well on an offshore platform in southern Natural Science and Technology, Nghia do, Tu Vietnam. Cells were Gram-negative, non-spore-forming, rod-shaped and motile liem, Hanoi, Vietnam by means of a polar f lagellum. Growth occurred at NaCl concentrations 2 lnstitut fur Mikrobiologie between 0 and 20%; the optimum was 5% NaCl. One strain, which was und Genetik, Universitdt designated VT8l, could degrade n-hexadecane, pristane and some crude oil Wien, Dr Bohrgasse 9, components. It grew anaerobically in the presence of nitrate on succinate, A-1030 Wien, Austria citrate or acetate, but not on glucose. Several organic acids and amino acids 3 Botanisches lnstitut der were utilized as sole carbon and energy sources. The major components of its Universitdt Munchen, Menzinger Str. 67, D-80638 cellular fatty acids were Clzr0 3-OH, c16:1 09c, c16:o and C18:1 w9c. The DNA G+C Munchen, Germany content was 557 mol0/o. 165 rDNA sequence analysis indicated that strain VT8T 4 lnstitut fur Genetik und was closely related to Marinobacter sp. -
Marinobacter Maroccanus Sp. Nov., a Moderately Halophilic Bacterium Isolated from a Saline Soil
Full PDF (including article, references, figures, tables) Click here to download Full PDF (including article, references, figures, tables) Marinobacter maroccanus.pdf 1 Marinobacter maroccanus sp. nov., a moderately halophilic bacterium 2 isolated from a saline soil 3 4 Nadia Boujida,1† Montserrat Palau,2† Saoulajan Charfi,1 Àngels Manresa,2 Nadia Skali 5 Senhaji,1 Jamal Abrini,1 David Miñana-Galbis2* 6 7 Author affiliations: 1Biotechnology and Applied Microbiology Research Group, 8 Department of Biology, Faculty of Sciences, University Abdelmalek Essaâdi, BP2121, 9 93002 Tetouan, Morocco; 2Secció de Microbiologia, Dept. Biologia, Sanitat i Medi 10 Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Av. 11 Joan XXIII, 27-31, 08028 Barcelona, Catalonia, Spain. 12 13 †These authors contributed equally to this work. 14 15 *Correspondence: David Miñana-Galbis, [email protected] 16 17 Keywords: Marinobacter maroccanus sp. nov.; halophilic bacterium. 18 19 The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and rpoD gene 20 sequences and the whole genome shotgun project of strain N4T are MG563241, 21 MG551593, and PSSX01000000, respectively. 22 1 23 Abstract 24 25 During the taxonomic investigation of exopolymer producing halophilic bacteria, a rod- 26 shaped, motile, Gram-stain-negative, aerobic, halophilic bacterium, designated strain 27 N4T, was isolated from a natural saline soil located in the northern Morocco. The optimal 28 growth of the isolate was at 30–37 ºC and at pH 6.0–9.0, in the presence of 5–7% (w/v) 29 NaCl. Useful tests for the phenotypic differentiation of strain N4T from other Marinobacter 30 species included α-chymotrypsin and α-glucosidase activities and the carbohydrate T 31 assimilation profile.