Multilayered Horizontal Operon Transfers from Bacteria Reconstruct a Thiamine Salvage Pathway in Yeasts
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The Burkholderia Genus: Between Mutualism and Pathogenicity
The Burkholderia genus: between mutualism and pathogenicity El género Burkholderia: entre el mutualismo y la patogenicidad David Espinosa-Victoria*, Laboratorio Interacción Molecular Planta-Microorganismo, 1Programa de Edafo- logía Colegio de Postgraduados, Carretera México-Texcoco Km 36.5, Montecillo Estado de México, México, 56230; Lucía López-Reyes, Moisés Graciano Carcaño-Montiel, Laboratorio Microbiología de Suelos, Bene- mérita Universidad Autónoma de Puebla, Avenida San Claudio s/n, Ciudad Universitaria, La Hacienda, Puebla, Puebla, 72592; 1María Serret-López. *Autor para correspondencia: [email protected] Recibido: 28 de Abril, 2020. Aceptado: 04 de Junio, 2020. Espinosa-Victoria D, López-Reyes L, Carcaño-Montiel Abstract. Burkholderia is an ambivalent genus MG and Serret-López M. 2020. The Burkholderia ge- because some of its species establish symbiotic- nus: between mutualism and pathogenicity. Mexican Jo- mutualistic relationships with plants, and urnal of Phytopathology 38(3): 337-359. symbiotic-pathogenic relationships with plants, DOI: 10.18781/R.MEX.FIT.2004-5 animals, and humans. Since the phytopathogenic bacterium B. cepacia was reported as a nosocomial Primera publicación DOI: 17 de Junio, 2020. opportunist, associated with cystic fibrosis, the First DOI publication: June 17, 2020. concern about possible infections in humans arose. The objective of this contribution was to make an analysis of Burkholderia’s functional versatility Resumen. Burkholderia es un género ambivalen- and its effect on human health. Burkholderia te debido a que algunas de sus especies establecen harbored about 100 species and the B. cepacia relaciones simbiótico-mutualistas con las plantas, y complex (BCC) consisting of 22 species. At the simbiótico-patogénicas con plantas, animales y hu- beginning, the existence of two lineages within manos. -
Response of Heterotrophic Stream Biofilm Communities to a Gradient of Resources
The following supplement accompanies the article Response of heterotrophic stream biofilm communities to a gradient of resources D. J. Van Horn1,*, R. L. Sinsabaugh1, C. D. Takacs-Vesbach1, K. R. Mitchell1,2, C. N. Dahm1 1Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA 2Present address: Department of Microbiology & Immunology, University of British Columbia Life Sciences Centre, Vancouver BC V6T 1Z3, Canada *Email: [email protected] Aquatic Microbial Ecology 64:149–161 (2011) Table S1. Representative sequences for each OTU, associated GenBank accession numbers, and taxonomic classifications with bootstrap values (in parentheses), generated in mothur using 14956 reference sequences from the SILVA data base Treatment Accession Sequence name SILVA taxonomy classification number Control JF695047 BF8FCONT18Fa04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Cellvibrio(100);unclassified; Control JF695049 BF8FCONT18Fa12.b1 Bacteria(100);Proteobacteria(100);Alphaproteobacteria(100);Rhizobiales(100);Methylocystaceae(100);uncultured(100);unclassified; Control JF695054 BF8FCONT18Fc01.b1 Bacteria(100);Planctomycetes(100);Planctomycetacia(100);Planctomycetales(100);Planctomycetaceae(100);Isosphaera(50);unclassified; Control JF695056 BF8FCONT18Fc04.b1 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);Xanthomonadales(100);Xanthomonadaceae(100);uncultured(64);unclassified; Control JF695057 BF8FCONT18Fc06.b1 Bacteria(100);Proteobacteria(100);Betaproteobacteria(100);Burkholderiales(100);Comamonadaceae(100);Ideonella(54);unclassified; -
Burkholderia Cenocepacia Integrates Cis-2-Dodecenoic Acid and Cyclic Dimeric Guanosine Monophosphate Signals to Control Virulence
Burkholderia cenocepacia integrates cis-2-dodecenoic acid and cyclic dimeric guanosine monophosphate signals to control virulence Chunxi Yanga,b,c,d,1, Chaoyu Cuia,b,c,1, Qiumian Yea,b, Jinhong Kane, Shuna Fua,b, Shihao Songa,b, Yutong Huanga,b, Fei Hec, Lian-Hui Zhanga,c, Yantao Jiaf, Yong-Gui Gaod, Caroline S. Harwoodb,g,2, and Yinyue Denga,b,c,2 aState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; bGuangdong Innovative Research Team of Sociomicrobiology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; cIntegrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China; dSchool of Biological Sciences, Nanyang Technological University, Singapore 637551; eCenter for Crop Germplasm Resources, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; fState Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; and gDepartment of Microbiology, University of Washington, Seattle, WA 98195 Contributed by Caroline S. Harwood, October 30, 2017 (sent for review June 1, 2017; reviewed by Maxwell J. Dow and Tim Tolker-Nielsen) Quorum sensing (QS) signals are used by bacteria to regulate N-octanoyl homoserine lactone (C8-HSL). The two QS systems biological functions in response to cell population densities. Cyclic have both distinct and overlapping effects on gene expression diguanosine monophosphate (c-di-GMP) regulates cell functions in (16, 17). response to diverse environmental chemical and physical signals One of the ways in which QS systems can act is by controlling that bacteria perceive. In Burkholderia cenocepacia, the QS signal levels of intracellular cyclic diguanosine monophosphate (c-di-GMP) receptor RpfR degrades intracellular c-di-GMP when it senses the in bacteria (18–21). -
Short-Interval Reburns in the Boreal Forest Alter Soil Bacterial Communities, Reflecting Increased Ph and Poor Conifer Seedling
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.31.437944; this version posted April 1, 2021. 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 Short-interval reburns in the boreal forest alter soil bacterial communities, reflecting 2 increased pH and poor conifer seedling establishment 3 4 Jamie Wooleta,b, Ellen Whitmanc,d, Marc-André Parisienc, Dan K. Thompsonc, Mike D. 5 Flannigand, and Thea Whitmana* 6 a. Department of Soil Science, University of Wisconsin-Madison, 1525 Observatory Dr., 7 Madison, WI, 53706, USA 8 b. Department of Forest and Rangeland Stewardship, Colorado State University, 1001 Amy Van 9 Dyken Way, Fort Collins, CO, 80521, USA 10 c. Northern Forestry Centre, Canadian Forest Service, Natural Resources Canada, 5320 122 11 Street, Edmonton, AB, T6H 3S5, Canada 12 d. Department of Renewable Resources, University of Alberta, 751 General Services Building, 13 Edmonton, AB, T6G 2H1, Canada 14 * Corresponding author: [email protected]; 608.263.4947 15 16 Abstract: Increasing burn rates (percentage area burned annually) in some biomes are leading to 17 fires burning in close succession, triggering rapid vegetation change as well as altering soil 18 properties. Despite the importance of soil microbes for nutrient cycling and as plant symbionts, 19 the effects of increased fire frequency on belowground microbial communities remain largely 20 unknown. We present a study of the effects of short interval reburns (defined here as <20 years 21 between fires) on soil bacterial communities in the boreal forest of northwestern Canada, using a 22 paired site design that spans wetlands and uplands, with 50 sites total. -
Identification of Active Methylotroph Populations in an Acidic Forest Soil
Microbiology (2002), 148, 2331–2342 Printed in Great Britain Identification of active methylotroph populations in an acidic forest soil by stable- isotope probing Stefan Radajewski,1 Gordon Webster,2† David S. Reay,3‡ Samantha A. Morris,1 Philip Ineson,4 David B. Nedwell,3 James I. Prosser2 and J. Colin Murrell1 Author for correspondence: J. Colin Murrell. Tel: j44 24 7652 2553. Fax: j44 24 7652 3568. e-mail: cmurrell!bio.warwick.ac.uk 1 Department of Biological Stable-isotope probing (SIP) is a culture-independent technique that enables Sciences, University of the isolation of DNA from micro-organisms that are actively involved in a Warwick, Coventry CV4 7AL, UK specific metabolic process. In this study, SIP was used to characterize the active methylotroph populations in forest soil (pH 35) microcosms that were exposed 2 Department of Molecular 13 13 13 13 and Cell Biology, to CH3OH or CH4. Distinct C-labelled DNA ( C-DNA) fractions were resolved University of Aberdeen, from total community DNA by CsCl density-gradient centrifugation. Analysis of Institute of Medical 16S rDNA sequences amplified from the 13C-DNA revealed that bacteria related Sciences, Foresterhill, Aberdeen AB25 2ZD, UK to the genera Methylocella, Methylocapsa, Methylocystis and Rhodoblastus had assimilated the 13C-labelled substrates, which suggested that moderately 3 Department of Biological Sciences, University of acidophilic methylotroph populations were active in the microcosms. Essex, Wivenhoe Park, Enrichments targeted towards the active proteobacterial CH3OH utilizers were Colchester, Essex CO4 3SQ, successful, although none of these bacteria were isolated into pure culture. A UK parallel analysis of genes encoding the key enzymes methanol dehydrogenase 4 Department of Biology, and particulate methane monooxygenase reflected the 16S rDNA analysis, but University of York, PO Box 373, YO10 5YW, UK unexpectedly revealed sequences related to the ammonia monooxygenase of ammonia-oxidizing bacteria (AOB) from the β-subclass of the Proteobacteria. -
Microbial Community Response to Heavy and Light Crude Oil in the Great Lakes
Microbial Community Response to Heavy and Light Crude Oil in the Great Lakes Stephen Techtmann 10/24/19 Microbial Sensors Techtmann Lab @ MTU Investigating the applications of environmental microbial communities Hydraulic Fracturing Related Antibiotic Resistance Oil Bioremediation Techtmann Lab @ MTU Overview • Background on oil biodegradation • Microbial response to light and heavy crude oil in the Great Lakes • Machine learning for prediction of contamination in the Great Lakes. Oil Spills Deepwater Horizon Enbridge Line 6B Deepwater Horizon Oil Spill • 4,1000,000 bbl of oil released • Light Sweet Crude oil released • April 20, 2010 • 1101.7 miles of shoreline oiled Atlas and Hazen 2011 Enbridge Line 6B Spill – Marshall MI • 20,082 bbl of oil released • Diluted Bitumen • July 26, 2010 • 70 miles of shoreline oiled https://www.mlive.com/news/kalamazoo/2010/07/state_of_emergency_declared_as.html Oil Transmissions Pipelines in the Great Lakes Region Line 5: • 645 miles from Superior WI to Sarnia Ontario • 540,000 barrels per day • Light crude and natural gas liquids (NGLs) Crude oil Oil types and API Gravity Microbes and Biotechnology (Bioremediation) Low cost input Microbe High value output Decreased Cost Contaminant Increased Efficiency Carbon dioxide or non- toxic daughter products Carbon dioxide Microbial Biomass Petroleum Microbe Daughter Products Water Microbial Ecology and Biotechnology Low cost input Microbe High value output Decreased Cost/Increased Efficiency Complex input Input A Microbe Microbe Output A Input B Microbe Output -
Polyamine Profiles of Some Members of the Alpha Subclass of the Class Proteobacteria: Polyamine Analysis of Twenty Recently Described Genera
Microbiol. Cult. Coll. June 2003. p. 13 ─ 21 Vol. 19, No. 1 Polyamine Profiles of Some Members of the Alpha Subclass of the Class Proteobacteria: Polyamine Analysis of Twenty Recently Described Genera Koei Hamana1)*,Azusa Sakamoto1),Satomi Tachiyanagi1), Eri Terauchi1)and Mariko Takeuchi2) 1)Department of Laboratory Sciences, School of Health Sciences, Faculty of Medicine, Gunma University, 39 ─ 15 Showa-machi 3 ─ chome, Maebashi, Gunma 371 ─ 8514, Japan 2)Institute for Fermentation, Osaka, 17 ─ 85, Juso-honmachi 2 ─ chome, Yodogawa-ku, Osaka, 532 ─ 8686, Japan Cellular polyamines of 41 newly validated or reclassified alpha proteobacteria belonging to 20 genera were analyzed by HPLC. Acetic acid bacteria belonging to the new genus Asaia and the genera Gluconobacter, Gluconacetobacter, Acetobacter and Acidomonas of the alpha ─ 1 sub- group ubiquitously contained spermidine as the major polyamine. Aerobic bacteriochlorophyll a ─ containing Acidisphaera, Craurococcus and Paracraurococcus(alpha ─ 1)and Roseibium (alpha-2)contained spermidine and lacked homospermidine. New Rhizobium species, including some species transferred from the genera Agrobacterium and Allorhizobium, and new Sinorhizobium and Mesorhizobium species of the alpha ─ 2 subgroup contained homospermidine as a major polyamine. Homospermidine was the major polyamine in the genera Oligotropha, Carbophilus, Zavarzinia, Blastobacter, Starkeya and Rhodoblastus of the alpha ─ 2 subgroup. Rhodobaca bogoriensis of the alpha ─ 3 subgroup contained spermidine. Within the alpha ─ 4 sub- group, the genus Sphingomonas has been divided into four clusters, and species of the emended Sphingomonas(cluster I)contained homospermidine whereas those of the three newly described genera Sphingobium, Novosphingobium and Sphingopyxis(corresponding to clusters II, III and IV of the former Sphingomonas)ubiquitously contained spermidine. -
Burkholderia Cenocepacia Intracellular Activation of the Pyrin
Activation of the Pyrin Inflammasome by Intracellular Burkholderia cenocepacia Mikhail A. Gavrilin, Dalia H. A. Abdelaziz, Mahmoud Mostafa, Basant A. Abdulrahman, Jaykumar Grandhi, This information is current as Anwari Akhter, Arwa Abu Khweek, Daniel F. Aubert, of September 29, 2021. Miguel A. Valvano, Mark D. Wewers and Amal O. Amer J Immunol 2012; 188:3469-3477; Prepublished online 24 February 2012; doi: 10.4049/jimmunol.1102272 Downloaded from http://www.jimmunol.org/content/188/7/3469 Supplementary http://www.jimmunol.org/content/suppl/2012/02/24/jimmunol.110227 Material 2.DC1 http://www.jimmunol.org/ References This article cites 71 articles, 17 of which you can access for free at: http://www.jimmunol.org/content/188/7/3469.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 29, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2012 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Activation of the Pyrin Inflammasome by Intracellular Burkholderia cenocepacia Mikhail A. -
Microvirgula Aerodenitrificans Gen. Nov., Sp. Nov., a New Gram-Negative
International Journal of Systematic Bacteriology (1 998), 48, 77 5-782 Printed in Great Britain Microvirgula aerodenitrificans gen. nov., sp. nov., a new Gram-negative bacterium exhibiting co-respiration of oxygen and nitrogen oxides up to oxygen-saturated conditions Dominique Patureau, Jean-Jacques Godon, Patrick Dabert, Theodore Bouchez, Nicolas Bernet, Jean Philippe Delgenes and Rene Moletta Author for correspondence : Dominique Patureau. Tel : + 33 468 42 5 1 69. Fax : + 33 468 42 5 1 60. e-mail : [email protected] lnstitut National de la A denitrifier micro-organism was isolated from an upflow denitrifying filter Recherche Agronomique, inoculated with an activated sludge. The cells were Gram-negative, catalase- Laboratoire de Biotechnolog ie de and oxidase-positivecurved rods and very motile. They were aerobic as well as I'Environnement (LBE), anoxic heterotrophsthat had an atypical respiratory type of metabolism in Avenue des Etangs, 111 00 which oxygen and nitrogen oxides were used simultaneously as terminal Narbonne, France electron acceptors. The G+C content was 65 mol%. Our isolate was phenotypically similar to Cornamonas testosteroni, according to classical systematic classificationsystems. However, a phylogenetic analysis based on the 16s rRNA sequence showed that the aerobic denitrifier could not be assigned to any currently recognized genus. For these reasons a new genus and species, Microvirgula aerodenitrificans gen. nov., sp. nov., is proposed, for which SGLYZT is the type strain. Keywords: Microvirgula aerodenitriJicansgen. nov., sp. nov., co-respiration of oxygen and nitrogen oxides, Proteobacteria, fluorescent in situ hybridization, oligonucleotide probes I INTRODUCTION denitrifying filter. It exhibits an atypical behaviour towards oxygen and nitrate (16), since it is able to co- The denitrifiers are facultative anaerobic bacteria that respire oxygen and nitrogen oxides and produce N,. -
Supplementary Material 16S Rrna Clone Library
Kip et al. Biogeosciences (bg-2011-334) Supplementary Material 16S rRNA clone library To investigate the total bacterial community a clone library based on the 16S rRNA gene was performed of the pool Sphagnum mosses from Andorra peat, next to S. magellanicum some S. falcatulum was present in this pool and both these species were analysed. Both 16S clone libraries showed the presence of Alphaproteobacteria (17%), Verrucomicrobia (13%) and Gammaproteobacteria (2%) and since the distribution of bacterial genera among the two species was comparable an average was made. In total a 180 clones were sequenced and analyzed for the phylogenetic trees see Fig. A1 and A2 The 16S clone libraries showed a very diverse set of bacteria to be present inside or on Sphagnum mosses. Compared to other studies the microbial community in Sphagnum peat soils (Dedysh et al., 2006; Kulichevskaya et al., 2007a; Opelt and Berg, 2004) is comparable to the microbial community found here, inside and attached on the Sphagnum mosses of the Patagonian peatlands. Most of the clones showed sequence similarity to isolates or environmental samples originating from peat ecosystems, of which most of them originate from Siberian acidic peat bogs. This indicated that similar bacterial communities can be found in peatlands in the Northern and Southern hemisphere implying there is no big geographical difference in microbial diversity in peat bogs. Four out of five classes of Proteobacteria were present in the 16S rRNA clone library; Alfa-, Beta-, Gamma and Deltaproteobacteria. 42 % of the clones belonging to the Alphaproteobacteria showed a 96-97% to Acidophaera rubrifaciens, a member of the Rhodospirullales an acidophilic bacteriochlorophyll-producing bacterium isolated from acidic hotsprings and mine drainage (Hiraishi et al., 2000). -
Rational Construction of Genome-Reduced Burkholderiales Chassis Facilitates Efficient Heterologous Production of Natural Products from Proteobacteria
ARTICLE https://doi.org/10.1038/s41467-021-24645-0 OPEN Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria Jiaqi Liu1, Haibo Zhou1, Zhiyu Yang1, Xue Wang1, Hanna Chen1, Lin Zhong1, Wentao Zheng1, Weijing Niu1, Sen Wang2, Xiangmei Ren2, Guannan Zhong1, Yan Wang3, Xiaoming Ding4, Rolf Müller 5, Youming Zhang1 & ✉ Xiaoying Bian 1 1234567890():,; Heterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for het- erologous BGC expression, but its cells undergo early autolysis, hindering further applica- tions. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chit- inimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression. 1 Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, China. 2 Core Facilities for Life and Environmental Sciences, Shandong University, Qingdao, Shandong, China. 3 College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China. -
Environmental Adaptability and Stress Tolerance of Laribacter
Lau et al. Cell & Bioscience 2011, 1:22 http://www.cellandbioscience.com/content/1/1/22 Cell & Bioscience RESEARCH Open Access Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis Susanna KP Lau1,2,3,4*†, Rachel YY Fan4*, Tom CC Ho4, Gilman KM Wong4, Alan KL Tsang4, Jade LL Teng4, Wenyang Chen5, Rory M Watt5, Shirly OT Curreem4, Herman Tse1,2,3,4, Kwok-Yung Yuen1,2,3,4 and Patrick CY Woo1,2,3,4† Abstract Background: Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler’s diarrhea and it can reside in human, fish, frogs and water. In this study, we performed an in-depth annotation of the genes in its genome related to adaptation to the various environmental niches. Results: L. hongkongensis possessed genes for DNA repair and recombination, basal transcription, alternative s-factors and 109 putative transcription factors, allowing DNA repair and global changes in gene expression in response to different environmental stresses. For acid stress, it possessed a urease gene cassette and two arc gene clusters. For alkaline stress, it possessed six CDSs for transporters of the monovalent cation/proton antiporter-2 and NhaC Na+:H+ antiporter families. For heavy metals acquisition and tolerance, it possessed CDSs for iron and nickel transport and efflux pumps for other metals. For temperature stress, it possessed genes related to chaperones and chaperonins, heat shock proteins and cold shock proteins. For osmotic stress, 25 CDSs were observed, mostly related to regulators for potassium ion, proline and glutamate transport. For oxidative and UV light stress, genes for oxidant-resistant dehydratase, superoxide scavenging, hydrogen peroxide scavenging, exclusion and export of redox-cycling antibiotics, redox balancing, DNA repair, reduction of disulfide bonds, limitation of iron availability and reduction of iron-sulfur clusters are present.