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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]. -
Changes in the Bacterial Diversity of Human Milk During Late Lactation Period (Weeks 21 to 48)
foods Communication Changes in the Bacterial Diversity of Human Milk during Late Lactation Period (Weeks 21 to 48) Wendy Marin-Gómez ,Ma José Grande, Rubén Pérez-Pulido, Antonio Galvez * and Rosario Lucas Microbiology Division, Department of Health Sciences, Faculty of Experimental Sciences, University of Jaén, 23071 Jaén, Spain; [email protected] (W.M.-G.); [email protected] (M.J.G.); [email protected] (R.P.-P.); [email protected] (R.L.) * Correspondence: [email protected]; Tel.: +34-953-212160 Received: 19 July 2020; Accepted: 25 August 2020; Published: 27 August 2020 Abstract: Breast milk from a single mother was collected during a 28-week lactation period. Bacterial diversity was studied by amplicon sequencing analysis of the V3-V4 variable region of the 16S rRNA gene. Firmicutes and Proteobacteria were the main phyla detected in the milk samples, followed by Actinobacteria and Bacteroidetes. The proportion of Firmicutes to Proteobacteria changed considerably depending on the sampling week. A total of 411 genera or higher taxons were detected in the set of samples. Genus Streptococcus was detected during the 28-week sampling period, at relative abundances between 2.0% and 68.8%, and it was the most abundant group in 14 of the samples. Carnobacterium and Lactobacillus had low relative abundances. At the genus level, bacterial diversity changed considerably at certain weeks within the studied period. The weeks or periods with lowest relative abundance of Streptococcus had more diverse bacterial compositions including genera belonging to Proteobacteria that were poorly represented in the rest of the samples. Keywords: breast milk; biodiversity; lactic acid bacteria; late lactation; metagenomics 1. -
Volatiles from Serratia Marcescens, S. Proteamaculans, and Bacillus
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.07.286443; this version posted September 7, 2020. 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. RESEARCH ARTICLE 1 Volatiles from Serratia marcescens, S. 2 proteamaculans, and Bacillus subtilis 3 Inhibit Growth of Rhizopus stolonifer and 4 Other Fungi 5 Derreck Carter-House1, Joshua Chung1, Skylar McDonald1, Kerry Mauck2, Jason 6 E Stajich1,* 7 University of California-Riverside, Department of Microbiology and Plant Pathology, Riverside, CA, USA1; University 8 of California-Riverside, Department of Entomology, Riverside, CA, USA2 Compiled September 7, 2020 This is a draft manuscript, pre-submission 9 abstract The common soil bacteria Serratia marcescens, Serratia proteamaculans, Address correspondence to Jason Stajich, ja- [email protected]. 10 and Bacillus subtilis produce small molecular weight volatile compounds that are fungi- 11 static against multiple species, including the zygomycete mold Rhizopus stolonifer (Mu- 12 coromycota) and the model filamentous mold Neurospora crassa (Ascomycota). The 13 compounds or the bacteria can be exploited in development of biological controls to 14 prevent establishment of fungi on food and surfaces. Here, we quantified and identi- 15 fied bacteria-produced volatiles using headspace sampling and gas chromatography- 16 mass spectrometry. We found that each bacterial species in culture has a unique 17 volatile profile consisting of dozens of compounds. Using multivariate statistical ap- 18 proaches, we identified compounds in common or unique to each species. Our anal- 19 ysis suggested that three compounds, dimethyl trisulfide, anisole, and 2-undecanone, 20 are characteristic of the volatiles emitted by these antagonistic bacteria. -
Current Insights Into the Mechanisms and Management of Infection Stones
Current insights into the mechanisms and management of infection stones Authors: Erika J. Espinosa-Ortiz, Brian H. Eisner, Dirk Lange, and Robin Gerlach The final publication is available at Springer via https://dx.doi.org/10.1038/s41585-018-0120-z. Espinosa-Ortiz, Erika J., Brian H. Eisner, Dirk Lange, and Robin Gerlach, “Current insights into the mechanisms and management of infection stones,” Nature Reviews Urology, November 2018, 16: 35-53. doi: 10.1038/s41585-018-0120-z. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Current insights into the mechanisms and management of infection stones Erika J. Espinosa-Ortiz1,2, Brian H. Eisner3, Dirk Lange4* and Robin Gerlach 1,2* Abstract | Infection stones are complex aggregates of crystals amalgamated in an organic matrix that are strictly associated with urinary tract infections. The management of patients who form infection stones is challenging owing to the complexity of the calculi and high recurrence rates. The formation of infection stones is a multifactorial process that can be driven by urine chemistry , the urine microenvironment, the presence of modulator substances in urine, associations with bacteria, and the development of biofilms. Despite decades of investigation, the mechanisms of infection stone formation are still poorly understood. A mechanistic understanding of the formation and growth of infection stones — including the role of organics in the stone matrix, microorganisms, and biofilms in stone formation and their effect on stone characteristics — and the medical implications of these insights might be crucial for the development of improved treatments. Tools and approaches used in various disciplines (for example, engineering, chemistry , mineralogy , and microbiology) can be applied to further understand the microorganism–mineral interactions that lead to infection stone formation. -
Characterization of Serratia Isolates from Soil, Ecological Implications and Transfer of Serratia Proteamaculans Subsp
International Journal of Systematic and Evolutionary Microbiology (2002), 52, 2281–2289 DOI: 10.1099/ijs.0.02263-0 Characterization of Serratia isolates from soil, ecological implications and transfer of Serratia proteamaculans subsp. quinovora Grimont et al. 1983 to Serratia quinivorans corrig., sp. nov. 1 Cardiff School of Kevin E. Ashelford,1 John C. Fry,1 Mark J. Bailey2 and Martin J. Day1 Biosciences, Cardiff University, PO Box 915, Cardiff CF10 3TL, UK Author for correspondence: John C. Fry. Tel: j44 29 2087 4190. Fax: j44 29 2087 4305. 2 Centre for Ecology and e-mail: fry!cardiff.ac.uk Hydrology – Oxford, Mansfield Road, Oxford OX1 3SR, UK Eleven strains of Serratia were isolated from different soils and the guts of invertebrates and characterized by their sensitivity to eight indigenous bacteriophages. They were also classified according to bacteriocin production and sensitivity, BiOLOG plate and API 20E strip profiles and 16S rRNA sequence information. One strain was thus identified as Serratia plymuthica, another as Serratia fonticola. The remaining strains were shown to be closely related to Serratia proteamaculans subsp. quinovora Grimont et al. 1983 after DNA–DNA cross-hybridization demonstrated relatedness greater than 70% with the type strain of this subspecies. From an ecological perspective, our results illustrated the wide variation in sensitivity that closely related Serratia strains have towards various indigenous soil phages and that these phages have broad host ranges within the genus. Furthermore, the phage and bacteriocin interactions within the Serratia strains examined were intricate and did not reflect phylogenetic relationships. These results together imply that complex interactions will occur in soil within the natural community of Serratia strains and their bacteriophages. -
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 -
A Genome-Scale Antibiotic Screen in Serratia Marcescens Identifies Ydgh As a Conserved Modifier of Cephalosporin and Detergent S
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.16.440252; this version posted April 17, 2021. 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 A genome-scale antibiotic screen in Serratia marcescens identifies YdgH as a conserved 2 modifier of cephalosporin and detergent susceptibility 3 Jacob E. Lazarus1,2,3,#, Alyson R. Warr2,3, Kathleen A. Westervelt2,3, David C. Hooper1,2, Matthew 4 K. Waldor2,3,4 5 1 Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Harvard 6 Medical School, Boston, MA, USA 7 2 Department of Microbiology, Harvard Medical School, Boston, MA, USA 8 3 Department of Medicine, Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard 9 Medical School, Boston, MA, USA 10 4 Howard Hughes Medical Institute, Boston, MA, USA 11 * Correspondence to [email protected] 12 13 Running Title: Antibiotic whole-genome screen in Serratia marcescens 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.16.440252; this version posted April 17, 2021. 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. 14 Abstract: 15 Serratia marcescens, a member of the order Enterobacterales, is adept at colonizing healthcare 16 environments and an important cause of invasive infections. Antibiotic resistance is a daunting 17 problem in S. marcescens because in addition to plasmid-mediated mechanisms, most isolates 18 have considerable intrinsic resistance to multiple antibiotic classes. -
Ubiquity of the Symbiont Serratia Symbiotica in the Aphid Natural Environment
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.18.440331; this version posted April 19, 2021. 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 Ubiquity of the Symbiont Serratia symbiotica in the Aphid Natural Environment: 2 Distribution, Diversity and Evolution at a Multitrophic Level 3 4 Inès Pons1*, Nora Scieur1, Linda Dhondt1, Marie-Eve Renard1, François Renoz1, Thierry Hance1 5 6 1 Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, 1348, 7 Louvain-la-Neuve, Belgium. 8 9 10 * Corresponding author: 11 Inès Pons 12 Croix du Sud 4-5, bte L7.07.04, 1348 Louvain la neuve, Belgique 13 [email protected] 14 15 16 17 18 19 20 21 22 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.18.440331; this version posted April 19, 2021. 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. 25 ABSTRACT 26 Bacterial symbioses are significant drivers of insect evolutionary ecology. However, despite recent 27 findings that these associations can emerge from environmentally derived bacterial precursors, there 28 is still little information on how these potential progenitors of insect symbionts circulates in the trophic 29 systems. The aphid symbiont Serratia symbiotica represents a valuable model for deciphering 30 evolutionary scenarios of bacterial acquisition by insects, as its diversity includes intracellular host- 31 dependent strains as well as gut-associated strains that have retained some ability to live independently 32 of their hosts and circulate in plant phloem sap. -
Prodigiosin of Serratia Marcescens ZPG19 Alters the Gut Microbiota Composition of Kunming Mice
molecules Article Prodigiosin of Serratia marcescens ZPG19 Alters the Gut Microbiota Composition of Kunming Mice Xue Li 1 , Xinfeng Tan 1, Qingshuang Chen 1, Xiaoling Zhu 2, Jing Zhang 1,*, Jie Zhang 1,* and Baolei Jia 1,* 1 State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250000, China; [email protected] (X.L.); [email protected] (X.T.); [email protected] (Q.C.) 2 Shandong Academy of Agricultural Sciences, Jinan 250000, China; [email protected] * Correspondence: [email protected] (J.Z.); [email protected] (J.Z.); [email protected] (B.J.) Abstract: Prodigiosin is a red pigment produced by Serratia marcescens with anticancer, antimalarial, and antibacterial effects. In this study, we extracted and identified a red pigment from a culture of S. marcescens strain ZPG19 and investigated its effect on the growth performance and intestinal micro- biota of Kunming mice. High-performance liquid chromatography/mass spectrometry revealed that the pigment had a mass-to-charge ratio (m/z) of 324.2160, and thus it was identified as prodigiosin. To investigate the effect of prodigiosin on the intestinal microbiota, mice (n = 5) were administered 150 µg/kg/d prodigiosin (crude extract, 95% purity) via the drinking water for 18 days. Administra- tion of prodigiosin did not cause toxicity in mice. High-throughput sequencing analysis revealed that prodigiosin altered the cecum microbiota abundance and diversity; the relative abundance of Desulfovibrio significantly decreased, whereas Lactobacillus reuteri significantly increased. This finding indicates that oral administration of prodigiosin has a beneficial effect on the intestinal microbiota of mice. -
Comparative Analysis of the Core Proteomes Among The
Diversity 2020, 12, 289 1 of 25 Article Comparative Analysis of the Core Proteomes among the Pseudomonas Major Evolutionary Groups Reveals Species‐Specific Adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis Marios Nikolaidis 1, Dimitris Mossialos 2, Stephen G. Oliver 3 and Grigorios D. Amoutzias 1,* 1 Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; [email protected] 2 Microbial Biotechnology‐Molecular Bacteriology‐Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500 Larissa, Greece; [email protected] 3 Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; [email protected] * Correspondence: [email protected]; Tel.: +30‐2410‐565289; Fax: +30‐2410‐565290 Received: 22 June 2020; Accepted: 22 July 2020; Published: 24 July 2020 Abstract: The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core‐orthologues. The subsequent phylogenomic analysis revealed two well‐defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus‐level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group‐specific core proteins were also identified, with P. -
Università Degli Studi Di Padova Dipartimento Di Biomedicina Comparata Ed Alimentazione
UNIVERSITÀ DEGLI STUDI DI PADOVA DIPARTIMENTO DI BIOMEDICINA COMPARATA ED ALIMENTAZIONE SCUOLA DI DOTTORATO IN SCIENZE VETERINARIE Curriculum Unico Ciclo XXVIII PhD Thesis INTO THE BLUE: Spoilage phenotypes of Pseudomonas fluorescens in food matrices Director of the School: Illustrious Professor Gianfranco Gabai Department of Comparative Biomedicine and Food Science Supervisor: Dr Barbara Cardazzo Department of Comparative Biomedicine and Food Science PhD Student: Andreani Nadia Andrea 1061930 Academic year 2015 To my family of origin and my family that is to be To my beloved uncle Piero Science needs freedom, and freedom presupposes responsibility… (Professor Gerhard Gottschalk, Göttingen, 30th September 2015, ProkaGENOMICS Conference) Table of Contents Table of Contents Table of Contents ..................................................................................................................... VII List of Tables............................................................................................................................. XI List of Illustrations ................................................................................................................ XIII ABSTRACT .............................................................................................................................. XV ESPOSIZIONE RIASSUNTIVA ............................................................................................ XVII ACKNOWLEDGEMENTS .................................................................................................... -
Pseudomonas/Brachypodium As a Model System for Studying Rhizosphere Plant Microbe Interactions Under Water Stress
The University of Southern Mississippi The Aquila Digital Community Master's Theses Fall 12-1-2018 Pseudomonas/Brachypodium as a Model System for Studying Rhizosphere Plant Microbe Interactions Under Water Stress Janiece McWilliams University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/masters_theses Recommended Citation McWilliams, Janiece, "Pseudomonas/Brachypodium as a Model System for Studying Rhizosphere Plant Microbe Interactions Under Water Stress" (2018). Master's Theses. 602. https://aquila.usm.edu/masters_theses/602 This Masters Thesis is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Master's Theses by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. PSEUDOMONAS/BRACHYPODIUM AS A MODEL SYSTEM FOR STUDYING RHIZOSPHERE PLANT-MICROBE INTERACTIONS UNDER WATER STRESS by Janiece Hutchins McWilliams A Thesis Submitted to the Graduate School, the College of Arts and Sciences and the School of Biological, Environmental, and Earth Sciences at The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Master of Science Approved by: Dr. Dmitri Mavrodi, Committee Chair Dr. Kevin Kuehn Dr. Micheal Davis ____________________ ____________________ ____________________ Dr. Dmitri Mavrodi Dr. Jake Schaefer Dr. Karen S. Coats Committee Chair Director of School Dean of the Graduate School December 2018 ABSTRACT In contrast to well-studied mechanisms of drought tolerance in plants, the interactions between plants and their microbiome during water stress are still poorly understood. This missing knowledge is crucial for the exploitation of beneficial microbial communities to improve the sustainability of agriculture under changing climatic conditions.