Taxonomic and Functional Characterization Of
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Research Article Antimicrobial and Antioxidant Properties of a Bacterial
Hindawi International Journal of Microbiology Volume 2020, Article ID 9483670, 11 pages https://doi.org/10.1155/2020/9483670 Research Article Antimicrobial and Antioxidant Properties of a Bacterial Endophyte, Methylobacterium radiotolerans MAMP 4754, Isolated from Combretum erythrophyllum Seeds Mampolelo M. Photolo ,1 Vuyo Mavumengwana ,2 Lungile Sitole ,1 and Matsobane G. Tlou 3 1Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park Campus, Johannesburg, South Africa 2DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Campus, Cape Town, South Africa 3Department of Biochemistry, School of Physical and Chemical Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mafikeng Campus, South Africa Correspondence should be addressed to Matsobane G. Tlou; [email protected] Received 17 September 2019; Accepted 21 December 2019; Published 25 February 2020 Academic Editor: Karl Drlica Copyright © 2020 Mampolelo M. Photolo et al. -is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -is study reports on the isolation and identification of Methylobacterium radiotolerans MAMP 4754 from the seeds of the medicinal plant, Combretum -
1 Supplementary Figures 1 2 Fine-Scale Adaptations To
1 SUPPLEMENTARY FIGURES 2 3 FINE-SCALE ADAPTATIONS TO ENVIRONMENTAL VARIATION AND GROWTH 4 STRATEGIES DRIVE PHYLLOSPHERE METHYLOBACTERIUM DIVERSITY. 5 6 Jean-Baptiste Leducq1,2,3, Émilie Seyer-Lamontagne1, Domitille Condrain-Morel2, Geneviève 7 Bourret2, David Sneddon3, James A. Foster3, Christopher J. Marx3, Jack M. Sullivan3, B. Jesse 8 Shapiro1,4 & Steven W. Kembel2 9 10 1 - Université de Montréal 11 2 - Université du Québec à Montréal 12 3 – University of Idaho 13 4 – McGill University 14 1 15 Figure S1 - Validation of Methylobacterium group A subdivisions in nine clades. Distribution 16 of pairwise nucleotide similarity (PS) within and among Methylobacterium clades and 17 Microvirga (outgroup) estimated from the complete rpoB nucleotide sequence (4064 bp). PS was 18 calculated in MEGA7 (1, 2) from aligned nucleotide sequences as PS = 1-pdistance. 19 2 A1 A2 A3 A4 A5 A6 Within clades A9 B C Within Methylobacterium among A1−A9 between A and B between A and C between B and C within Microvirga between Methylobacterium and Microvirga 0.75 0.80 0.85 0.90 0.95 1.00 PS 20 Figure S2 - ASV rarefaction on diversity assessed by 16s barcoding in 46 phyllosphere 21 samples, 1 positive control (METH community) and 1 negative controls. a) Diversity in 22 METH community (positive control) and rare ASVs threshold definition. The METH community 23 consisted in mixed genomic DNAs from 18 Methylobacterium isolates representative of diversity 24 isolated in SBL and MSH in 2017 and 2018 (Table S6; Table S10), one Escherichia coli strain 25 and one Sphingomonas sp. isolate from MSH in 2017 (isolate DNA022; Table S6), also probably 26 contaminated with Thermotoga sp. -
Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes
microorganisms Article Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes Charlotte M. van der Graaf 1,* , Javier Sánchez-España 2 , Iñaki Yusta 3, Andrey Ilin 3 , Sudarshan A. Shetty 1 , Nicole J. Bale 4, Laura Villanueva 4, Alfons J. M. Stams 1,5 and Irene Sánchez-Andrea 1,* 1 Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands; [email protected] (S.A.S.); [email protected] (A.J.M.S.) 2 Geochemistry and Sustainable Mining Unit, Dept of Geological Resources, Spanish Geological Survey (IGME), Calera 1, Tres Cantos, 28760 Madrid, Spain; [email protected] 3 Dept of Mineralogy and Petrology, University of the Basque Country (UPV/EHU), Apdo. 644, 48080 Bilbao, Spain; [email protected] (I.Y.); [email protected] (A.I.) 4 NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Landsdiep 4, 1797 SZ ‘t Horntje, The Netherlands; [email protected] (N.J.B.); [email protected] (L.V.) 5 Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal * Correspondence: [email protected] (C.M.v.d.G.); [email protected] (I.S.-A.) Received: 30 June 2020; Accepted: 14 August 2020; Published: 21 August 2020 Abstract: Acidic pit lakes are abandoned open pit mines filled with acid mine drainage (AMD)—highly acidic, metalliferous waters that pose a severe threat to the environment and are rarely properly remediated. Here, we investigated two meromictic, oligotrophic acidic mine pit lakes in the Iberian Pyrite Belt (IPB), Filón Centro (Tharsis) (FC) and La Zarza (LZ). -
Antimicrobial and Antioxidant Properties of a Bacterial Endophyte, Methylobacterium Radiotolerans MAMP 4754, Isolated from Combretum Erythrophyllum Seeds
Hindawi International Journal of Microbiology Volume 2020, Article ID 9483670, 11 pages https://doi.org/10.1155/2020/9483670 Research Article Antimicrobial and Antioxidant Properties of a Bacterial Endophyte, Methylobacterium radiotolerans MAMP 4754, Isolated from Combretum erythrophyllum Seeds Mampolelo M. Photolo ,1 Vuyo Mavumengwana ,2 Lungile Sitole ,1 and Matsobane G. Tlou 3 1Department of Biochemistry, Faculty of Science, University of Johannesburg, Auckland Park Campus, Johannesburg, South Africa 2DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Campus, Cape Town, South Africa 3Department of Biochemistry, School of Physical and Chemical Sciences, Faculty of Natural and Agricultural Sciences, North-West University, Mafikeng Campus, South Africa Correspondence should be addressed to Matsobane G. Tlou; [email protected] Received 17 September 2019; Accepted 21 December 2019; Published 25 February 2020 Academic Editor: Karl Drlica Copyright © 2020 Mampolelo M. Photolo et al. -is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. -is study reports on the isolation and identification of Methylobacterium radiotolerans MAMP 4754 from the seeds of the medicinal plant, Combretum -
Biodiversity of Bacteria That Dechlorinate Aromatic Chlorides and a New Candidate, Dehalobacter Sp
Interdisciplinary Studies on Environmental Chemistry — Biological Responses to Contaminants, Eds., N. Hamamura, S. Suzuki, S. Mendo, C. M. Barroso, H. Iwata and S. Tanabe, pp. 65–76. © by TERRAPUB, 2010. Biodiversity of Bacteria that Dechlorinate Aromatic Chlorides and a New Candidate, Dehalobacter sp. Naoko YOSHIDA1,2 and Arata KATAYAMA1 1EcoTopia Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-0814, Japan 2Laboratory of Microbial Biotechnology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8224, Japan (Received 18 January 2010; accepted 27 January 2010) Abstract—Bacteria that dechlorinate aromatic chlorides have been received much attention as a bio-catalyst to cleanup environments polluted with aromatic chlorides. So far, a variety of dechlorinating bacteria have been isolated, which contained members in diverse phylogenetic group such as genera Desulfitobacterium and “Dehalococcoides”. In this review, we introduced the up-to date knowledge of bacteria that dechlorinate aromatic chlorides and new candidate, Dehalobacter spp., as promising bacteria that dechlorinate aromatic chlorides. Keywords: reductive dehalogenation, aromatic chlorides, Dehalobacter INTRODUCTION Aromatic chlorides such as chlorinated phenols, benzenes, biphenyls, and dibenzo- p-dioxins are compounds of serious environmental concern because of their widespread use and hazardous effects for animals and plants and frequently encountered as persistent pollutants -
Downloaded from Genbank
Methylotrophs and Methylotroph Populations for Chloromethane Degradation Françoise Bringel1*, Ludovic Besaury2, Pierre Amato3, Eileen Kröber4, Stefen Kolb4, Frank Keppler5,6, Stéphane Vuilleumier1 and Thierry Nadalig1 1Université de Strasbourg UMR 7156 UNISTR CNRS, Molecular Genetics, Genomics, Microbiology (GMGM), Strasbourg, France. 2Université de Reims Champagne-Ardenne, Chaire AFERE, INR, FARE UMR A614, Reims, France. 3 Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, Clermont-Ferrand, France. 4Microbial Biogeochemistry, Research Area Landscape Functioning – Leibniz Centre for Agricultural Landscape Research – ZALF, Müncheberg, Germany. 5Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany. 6Heidelberg Center for the Environment HCE, Heidelberg University, Heidelberg, Germany. *Correspondence: [email protected] htps://doi.org/10.21775/cimb.033.149 Abstract characterized ‘chloromethane utilization’ (cmu) Chloromethane is a halogenated volatile organic pathway, so far. Tis pathway may not be representa- compound, produced in large quantities by terres- tive of chloromethane-utilizing populations in the trial vegetation. Afer its release to the troposphere environment as cmu genes are rare in metagenomes. and transport to the stratosphere, its photolysis con- Recently, combined ‘omics’ biological approaches tributes to the degradation of stratospheric ozone. A with chloromethane carbon and hydrogen stable beter knowledge of chloromethane sources (pro- isotope fractionation measurements in microcosms, duction) and sinks (degradation) is a prerequisite indicated that microorganisms in soils and the phyl- to estimate its atmospheric budget in the context of losphere (plant aerial parts) represent major sinks global warming. Te degradation of chloromethane of chloromethane in contrast to more recently by methylotrophic communities in terrestrial envi- recognized microbe-inhabited environments, such ronments is a major underestimated chloromethane as clouds. -
Designing and Engineering Methylorubrum Extorquens AM1 for Itaconic Acid Production
fmicb-10-01027 May 8, 2019 Time: 14:44 # 1 ORIGINAL RESEARCH published: 09 May 2019 doi: 10.3389/fmicb.2019.01027 Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production Chee Kent Lim1, Juan C. Villada1, Annie Chalifour2†, Maria F. Duran1, Hongyuan Lu1† and Patrick K. H. Lee1* 1 School of Energy and Environment, City University of Hong Kong, Hong Kong, China, 2 Department of Chemistry, City Edited by: University of Hong Kong, Hong Kong, China Sabine Kleinsteuber, Helmholtz Centre for Environmental Research (UFZ), Germany Methylorubrum extorquens (formerly Methylobacterium extorquens) AM1 is a Reviewed by: methylotrophic bacterium with a versatile lifestyle. Various carbon sources including Volker Döring, acetate, succinate and methanol are utilized by M. extorquens AM1 with the latter Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), being a promising inexpensive substrate for use in the biotechnology industry. Itaconic France acid (ITA) is a high-value building block widely used in various industries. Given Norma Cecilia Martinez-Gomez, that no wildtype methylotrophic bacteria are able to utilize methanol to produce Michigan State University, United States ITA, we tested the potential of M. extorquens AM1 as an engineered host for this *Correspondence: purpose. In this study, we successfully engineered M. extorquens AM1 to express Patrick K. H. Lee a heterologous codon-optimized gene encoding cis-aconitic acid decarboxylase. The [email protected] engineered strain produced ITA using acetate, succinate and methanol as the carbon †Present address: Annie Chalifour, feedstock. The highest ITA titer in batch culture with methanol as the carbon source Swiss Federal Institute of Aquatic was 31.6 ± 5.5 mg/L, while the titer and productivity were 5.4 ± 0.2 mg/L and Science and Technology (EAWAG), 0.056 ± 0.002 mg/L/h, respectively, in a scaled-up fed-batch bioreactor under Überlandstrasse, Dübendorf, Switzerland 60% dissolved oxygen saturation. -
(REE)-Dependent Growth of Pseudomonas Putida KT2440
Rare Earth Element (REE)-Dependent Growth of Pseudomonas putida KT2440 Relies on the ABC-Transporter PedA1A2BC and Is Influenced by Iron Availability Matthias Wehrmann, Charlotte Berthelot, Patrick Billard, Janosch Klebensberger To cite this version: Matthias Wehrmann, Charlotte Berthelot, Patrick Billard, Janosch Klebensberger. Rare Earth El- ement (REE)-Dependent Growth of Pseudomonas putida KT2440 Relies on the ABC-Transporter PedA1A2BC and Is Influenced by Iron Availability. Frontiers in Microbiology, Frontiers Media, 2019, 10, 10.3389/fmicb.2019.02494. hal-02389228 HAL Id: hal-02389228 https://hal.archives-ouvertes.fr/hal-02389228 Submitted on 8 Jan 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial| 4.0 International License fmicb-10-02494 November 1, 2019 Time: 15:18 # 1 ORIGINAL RESEARCH published: 31 October 2019 doi: 10.3389/fmicb.2019.02494 Rare Earth Element (REE)-Dependent Growth of Pseudomonas putida KT2440 Relies on the ABC-Transporter PedA1A2BC and Is Influenced by Iron Availability Matthias Wehrmann1, Charlotte Berthelot2,3, Patrick Billard2,3* and Janosch Klebensberger1* 1 Edited by: Department of Technical Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 2 Hari S. -
Microbial Degradation of Organic Micropollutants in Hyporheic Zone Sediments
Microbial degradation of organic micropollutants in hyporheic zone sediments Dissertation To obtain the Academic Degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth by Cyrus Rutere Bayreuth, May 2020 This doctoral thesis was prepared at the Department of Ecological Microbiology – University of Bayreuth and AG Horn – Institute of Microbiology, Leibniz University Hannover, from August 2015 until April 2020, and was supervised by Prof. Dr. Marcus. A. Horn. This is a full reprint of the dissertation submitted to obtain the academic degree of Doctor of Natural Sciences (Dr. rer. nat.) and approved by the Faculty of Biology, Chemistry, and Geosciences of the University of Bayreuth. Date of submission: 11. May 2020 Date of defense: 23. July 2020 Acting dean: Prof. Dr. Matthias Breuning Doctoral committee: Prof. Dr. Marcus. A. Horn (reviewer) Prof. Harold L. Drake, PhD (reviewer) Prof. Dr. Gerhard Rambold (chairman) Prof. Dr. Stefan Peiffer In the battle between the stream and the rock, the stream always wins, not through strength but by perseverance. Harriett Jackson Brown Jr. CONTENTS CONTENTS CONTENTS ............................................................................................................................ i FIGURES.............................................................................................................................. vi TABLES .............................................................................................................................. -
Lanthanide Transport, Storage, and Beyond: Genes and Processes Contributing to Xoxf Function In
bioRxiv preprint doi: https://doi.org/10.1101/647677; this version posted May 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Lanthanide transport, storage, and beyond: genes and processes contributing to XoxF function in 2 Methylorubrum extorquens AM1 3 4 Paula Roszczenko-Jasińska,a,£ Huong N. Vu,b,*,£ Gabriel A. Subuyuj,b,* Ralph Valentine 5 Crisostomo,b,* James Cai,b Charumathi Raghuraman,b Elena M. Ayala,b Erik J. Clippard,b 6 Nicholas F. Lien,b Richard T. Ngo,b Fauna Yarza,b,* Caitlin A. Hoeber,b Norma C. Martinez- 7 Gomez,a# Elizabeth Skovranb# 8 9 10 aDepartment of Microbiology and Molecular Genetics, Michigan State University, East Lansing, 11 USA 12 bDepartment of Biological Sciences, San José State University, San José, California, USA 13 14 Running Head: Lanthanide transport and storage 15 £ Both authors contributed equally and share first authorship 16 # Address correspondence to: Elizabeth Skovran, [email protected] and N. Cecilia 17 Martinez-Gomez, [email protected] 18 * Present address: HNV: Department of Microbiology, University of Georgia, Athens, Georgia, 19 USA; GAS: Department of Microbiology and Molecular Genetics, University of California at 20 Davis, Davis, California, USA, RVC: Molecular Biology Institute, University of California at 21 Los Angeles, Los Angeles, California, USA; FY: Department of Biochemistry and Biophysics, 22 University of California at San Francisco, San Francisco, California, USA bioRxiv preprint doi: https://doi.org/10.1101/647677; this version posted May 24, 2019. -
Qt4w8938g4 Nosplash 49C152
A physiological and genomic investigation of dissimilatory phosphite oxidation in Desulfotignum phosphitoxidans strain FiPS-3 and in microbial enrichment cultures from wastewater treatment sludge By Israel Antonio Figueroa A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Microbiology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor John D. Coates, Chair Professor Arash Komeili Professor David F. Savage Fall 2016 Abstract A physiological and genomic investigation of dissimilatory phosphite oxidation in Desulfotignum phosphitoxidans strain FiPS-3 and in microbial enrichment cultures from wastewater treatment sludge by Israel Antonio Figueroa Doctor of Philosophy in Microbiology University of California, Berkeley Professor John D. Coates, Chair 2- Phosphite (HPO3 ) is a highly soluble, reduced phosphorus compound that is often overlooked in biogeochemical analyses. Although the oxidation of phosphite to phosphate is a highly exergonic process (Eo’ = -650 mV), phosphite is kinetically stable and can account for 10-30% of the total dissolved P in various environments. Its role as a phosphorus source for a variety of extant microorganisms has been known since the 1950s and the pathways involved in assimilatory phosphite oxidation (APO) have been well characterized. More recently it was demonstrated that phosphite could also act as an electron donor for energy metabolism in a process known as dissimilatory phosphite oxidation (DPO). The bacterium described in this study, Desulfotignum phosphitoxidans strain FiPS-3, was isolated from brackish sediments and is capable of growing by coupling phosphite oxidation to the reduction of either sulfate or carbon dioxide. FiPS-3 remains the only isolated organism capable of DPO and the prevalence of this metabolism in the environment is still unclear. -
Candidatus Desulfomonile Palmitatoxidans”
fmicb-11-539604 December 11, 2020 Time: 20:59 # 1 ORIGINAL RESEARCH published: 17 December 2020 doi: 10.3389/fmicb.2020.539604 Long-Chain Fatty Acids Degradation by Desulfomonile Species and Proposal of “Candidatus Desulfomonile Palmitatoxidans” Joana I. Alves1, Andreia F. Salvador1, A. Rita Castro1, Ying Zheng2, Bart Nijsse2,3, Siavash Atashgahi2, Diana Z. Sousa1,2, Alfons J. M. Stams1,2, M. Madalena Alves1 and Ana J. Cavaleiro1* 1 Centre of Biological Engineering, University of Minho, Braga, Portugal, 2 Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands, 3 Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands Edited by: Microbial communities with the ability to convert long-chain fatty acids (LCFA) coupled Sabine Kleinsteuber, to sulfate reduction can be important in the removal of these compounds from Helmholtz Center for Environmental wastewater. In this work, an enrichment culture, able to oxidize the long-chain fatty Research (UFZ), Germany acid palmitate (C V ) coupled to sulfate reduction, was obtained from anaerobic Reviewed by: 16 0 Amelia-Elena Rotaru, granular sludge. Microscopic analysis of this culture, designated HP culture, revealed University of Southern Denmark, that it was mainly composed of one morphotype with a typical collar-like cell wall Denmark Anna Schnürer, invagination, a distinct morphological feature of the Desulfomonile genus. 16S rRNA Swedish University of Agricultural gene amplicon and metagenome-assembled genome (MAG) indeed confirmed that Sciences, Sweden the abundant phylotype in HP culture belong to Desulfomonile genus [ca. 92% 16S *Correspondence: rRNA gene sequences closely related to Desulfomonile spp.; and ca. 82% whole Ana J. Cavaleiro [email protected] genome shotgun (WGS)].