Root Colonization and Systemic Spreading of Azoarcus Sp. Strain BH72 in Grasses
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Draft Genome Sequence of the Nitrogen-Fixing Endophyte Azoarcus Communis Swub3
Lawrence Berkeley National Laboratory Recent Work Title Draft Genome Sequence of the Nitrogen-Fixing Endophyte Azoarcus communis SWub3. Permalink https://escholarship.org/uc/item/2cd6v88c Journal Microbiology resource announcements, 7(13) ISSN 2576-098X Authors Zorraquino, Violeta Toubiana, David Yan, Dawei et al. Publication Date 2018-10-04 DOI 10.1128/mra.01080-18 Peer reviewed eScholarship.org Powered by the California Digital Library University of California GENOME SEQUENCES crossm Draft Genome Sequence of the Nitrogen-Fixing Endophyte Azoarcus communis SWub3 Violeta Zorraquino,a David Toubiana,a Dawei Yan,a Eduardo Blumwalda aDepartment of Plant Sciences, University of California, Davis, California, USA ABSTRACT Here we report a draft genome sequence of Azoarcus communis SWub3, a nitrogen-fixing bacterium isolated from root tissues of Kallar grass in Pakistan. iological nitrogen fixation is a process in which a living organism reduces atmo- Bspheric dinitrogen into two NH3 molecules. This reaction is catalyzed by the nitrogenase complex present exclusively in Bacteria and Archaea species. Plants can benefit from biological nitrogen fixation when they are in association with these nitrogen-fixing prokaryotes, either free living or as symbionts associated with their roots. Azoarcus is a bacterial genus that comprises species isolated from different environments, such as plant roots, sediments, aquifers, and contaminated soil (1–4). All Azoarcus species are Gram-negative rods with a strictly aerobic metabolism that can fix nitrogen microaerobically. The interest in this bacterial genus resides in its ability to efficiently infect several crops, including rice, which is a food staple for more than half of the world’s population (5–7). -
Identification of N2-Fixing Plant-And Fungus-Associated Azoarcus
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Nov. 1997, p. 4331–4339 Vol. 63, No. 11 0099-2240/97/$04.0010 Copyright © 1997, American Society for Microbiology Identification of N2-Fixing Plant- and Fungus-Associated Azoarcus Species by PCR-Based Genomic Fingerprints THOMAS HUREK, BIANCA WAGNER, AND BARBARA REINHOLD-HUREK* Max-Planck-Institut fu¨r Terrestrische Mikrobiologie, Arbeitsgruppe Symbioseforschung, D-35043 Marburg, Germany Received 14 February 1997/Accepted 30 August 1997 Most species of the diazotrophic Proteobacteria Azoarcus spp. occur in association with grass roots, while A. tolulyticus and A. evansii are soil bacteria not associated with a plant host. To facilitate species identification and strain comparison, we developed a protocol for PCR-generated genomic fingerprints, using an automated sequencer for fragment analysis. Commonly used primers targeted to REP (repetitive extragenic palindromic) and ERIC (enterobacterial repetitive intergenic consensus) sequence elements failed to amplify fragments from the two species tested. In contrast, the BOX-PCR assay (targeted to repetitive intergenic sequence elements of Streptococcus) yielded species-specific genomic fingerprints with some strain-specific differences. PCR profiles of an additional PCR assay using primers targeted to tRNA genes (tDNA-PCR, for tRNAIle) were more discriminative, allowing differentiation at species-specific (for two species) or infraspecies-specific level. Our protocol of several consecutive PCR assays consisted of 16S ribosomal DNA (rDNA)-targeted, genus- specific -
Microbial Community of a Gasworks Aquifer and Identification of Nitrate
Water Research 132 (2018) 146e157 Contents lists available at ScienceDirect Water Research journal homepage: www.elsevier.com/locate/watres Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation * Martin Sperfeld a, Charlotte Rauschenbach b, Gabriele Diekert a, Sandra Studenik a, a Institute of Microbiology, Friedrich Schiller University Jena, Department of Applied and Ecological Microbiology, Philosophenweg 12, 07743 Jena, Germany ® b JENA-GEOS -Ingenieurbüro GmbH, Saalbahnhofstraße 25c, 07743 Jena, Germany article info abstract Article history: We analyzed a coal tar polluted aquifer of a former gasworks site in Thuringia (Germany) for the Received 9 August 2017 presence and function of aromatic compound-degrading bacteria (ACDB) by 16S rRNA Illumina Received in revised form sequencing, bamA clone library sequencing and cultivation attempts. The relative abundance of ACDB 18 December 2017 was highest close to the source of contamination. Up to 44% of total 16S rRNA sequences were affiliated Accepted 18 December 2017 to ACDB including genera such as Azoarcus, Georgfuchsia, Rhodoferax, Sulfuritalea (all Betaproteobacteria) Available online 20 December 2017 and Pelotomaculum (Firmicutes). Sequencing of bamA, a functional gene marker for the anaerobic benzoyl-CoA pathway, allowed further insights into electron-accepting processes in the aquifer: bamA Keywords: Environmental pollutions sequences of mainly nitrate-reducing Betaproteobacteria were abundant in all groundwater samples, Microbial communities whereas an additional sulfate-reducing and/or fermenting microbial community (Deltaproteobacteria, Bioremediation Firmicutes) was restricted to a highly contaminated, sulfate-depleted groundwater sampling well. By Box pathway conducting growth experiments with groundwater as inoculum and nitrate as electron acceptor, or- Functional gene marker ganisms related to Azoarcus spp. -
Comparative Genomics Provides Insights Into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera
G C A T T A C G G C A T genes Article Comparative Genomics Provides Insights into the Taxonomy of Azoarcus and Reveals Separate Origins of Nif Genes in the Proposed Azoarcus and Aromatoleum Genera Roberto Tadeu Raittz 1,*,† , Camilla Reginatto De Pierri 2,† , Marta Maluk 3 , Marcelo Bueno Batista 4, Manuel Carmona 5 , Madan Junghare 6, Helisson Faoro 7, Leonardo M. Cruz 2 , Federico Battistoni 8, Emanuel de Souza 2,Fábio de Oliveira Pedrosa 2, Wen-Ming Chen 9, Philip S. Poole 10, Ray A. Dixon 4,* and Euan K. James 3,* 1 Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technical Education Sector—SEPT, UFPR, Curitiba, PR 81520-260, Brazil 2 Department of Biochemistry and Molecular Biology, UFPR, Curitiba, PR 81531-980, Brazil; [email protected] (C.R.D.P.); [email protected] (L.M.C.); [email protected] (E.d.S.); [email protected] (F.d.O.P.) 3 The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; [email protected] 4 John Innes Centre, Department of Molecular Microbiology, Norwich NR4 7UH, UK; [email protected] 5 Centro de Investigaciones Biológicas Margarita Salas-CSIC, Department of Biotechnology of Microbes and Plants, Ramiro de Maeztu 9, 28040 Madrid, Spain; [email protected] 6 Faculty of Chemistry, Biotechnology and Food Science, NMBU—Norwegian University of Life Sciences, 1430 Ås, Norway; [email protected] 7 Laboratory for Science and Technology Applied in Health, Carlos Chagas Institute, Fiocruz, Curitiba, PR 81310-020, Brazil; helisson.faoro@fiocruz.br 8 Department of Microbial Biochemistry and Genomics, IIBCE, Montevideo 11600, Uruguay; [email protected] Citation: Raittz, R.T.; Reginatto De 9 Laboratory of Microbiology, Department of Seafood Science, NKMU, Kaohsiung City 811, Taiwan; Pierri, C.; Maluk, M.; Bueno Batista, [email protected] M.; Carmona, M.; Junghare, M.; Faoro, 10 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; H.; Cruz, L.M.; Battistoni, F.; Souza, [email protected] E.d.; et al. -
Novel Clades of Soil Biphenyl Degraders Revealed by Integrating Isotope Probing, Multi-Omics, and Single-Cell Analyses
The ISME Journal https://doi.org/10.1038/s41396-021-01022-9 ARTICLE Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses 1 1 2,3 1 1 Song-Can Chen ● Rohit Budhraja ● Lorenz Adrian ● Federica Calabrese ● Hryhoriy Stryhanyuk ● 1 1 4 4,5 1 Niculina Musat ● Hans-Hermann Richnow ● Gui-Lan Duan ● Yong-Guan Zhu ● Florin Musat Received: 20 February 2021 / Revised: 12 May 2021 / Accepted: 21 May 2021 © The Author(s) 2021. This article is published with open access Abstract Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for aerobic biodegradation of biphenyl as a proxy for a large class of environmental pollutants, polychlorinated biphenyls. We used 13C-labeled biphenyl in contaminated soils and traced the flow of pollutant-derived carbon into active – 13 1234567890();,: 1234567890();,: cells using single-cell analyses and protein stable isotope probing. The detection of C-enriched proteins linked biphenyl biodegradation to the uncultured Alphaproteobacteria clade UBA11222, which we found to host a distinctive biphenyl dioxygenase gene widely retrieved from contaminated environments. The same approach indicated the capacity of Azoarcus species to oxidize biphenyl and suggested similar metabolic abilities for species of Rugosibacter. Biphenyl oxidation would thus represent formerly unrecognized ecological functions of both genera. -
Diversity and Function of the Microbial Community on Anodes of Sediment Microbial Fuel Cells Fueled by Root Exudates
Diversity and Function of the Microbial Community on Anodes of Sediment Microbial Fuel Cells fueled by Root Exudates Doctoral thesis Submitted in partial fulfillment of the requirement for a doctoral degree “Doktorgrad der Naturwissenschaften (Dr. rer. nat.)” to the faculty of biology – Philipps-Universität Marburg by Angela Cabezas da Rosa from Montevideo, Uruguay Marburg / Lahn | 2010 The research for the completion of this work was carried out from April 2007 to September 2010 at the Max-Planck Institute for Terrestrial Microbiology under the supervision of Prof. Michael W. Friedrich Thesis was submitted to the Faculty of Biology, Philipps-Universität, Marburg Doctoral thesis accepted on: 24.11.2010 Date of oral examination: 26.11.2010 First reviewer: Prof. Dr. Michael W. Friedrich Second reviewer: Prof. Dr. Wolfgang Buckel The following manuscripts originated from this work and were published or are in preparation: De Schamphelaire L, Cabezas A, Marzorati M, Friedrich MW, Boon N & Verstraete W (2010) Microbial Community Analysis of Anodes from Sediment Microbial Fuel Cells Powered by Rhizodeposits of Living Rice Plants. Applied and Environmental Microbiology 76: 2002-2008. Cabezas A, de Schamphelaire L, Boon N, Verstraete W, Friedrich MW. Rice root exudates select for novel electrogenic Geobacter and Anaeromyxobacter populations on sediment microbial fuel cell anodes. In preparation. Cabezas A, Köhler T, Brune A, Friedrich MW. Identification of β-Proteobacteria and Anaerolineae as active populations degrading rice root exudates on -
Whole-Genome Analysis of Azoarcus Sp. Strain CIB Provides Genetic
ManuscriptCORE Metadata, citation and similar papers at core.ac.uk Provided by Digital.CSIC Whole-genome analysis of Azoarcus sp. strain CIB 1 2 provides genetic insights to its different lifestyles and predicts 3 novel metabolic features 4 5 6 7 Zaira Martín-Moldes a1 , María Teresa Zamarro a1 , Carlos del Cerro a1 , Ana Valencia a, 8 Manuel José Gómez b2 , Aida Arcas b3 , Zulema Udaondo a4 , José Luis García a, Juan 9 a a a* 10 Nogales , Manuel Carmona , and Eduardo Díaz 11 a 12 Centro de Investigaciones Biológicas-CSIC, 28040 Madrid, Spain 13 b Centro de Astrobiología, INTA-CSIC, 28850 Torrejón de Ardoz, Madrid, Spain 14 15 1 16 These authors contributed equally to this work 17 18 19 2 Present address: Centro Nacional de Investigaciones Cardiovasculares, ISCIII, 20 Madrid, Spain 21 3 22 Present address: Instituto de Neurociencias, UMH -CSIC, Alicante, Spain 4 23 Present address: Abengoa Research, Sevilla, Spain 24 25 26 * 27 Corresponding author. Tel.: +34915611800. E-mail address : [email protected] 28 (E.Díaz) 29 30 31 32 33 34 35 36 Abbreviations : ANI, average nucleotide identity; BIMEs, bacterial interspersed mosaic 37 38 elements; IAA, indoleacetic acid; ICE, integrative and conjugative element ; REPs, 39 repeated extragenic palindrome sequences; ROS, reactive oxygen species; TAS, toxin - 40 antitoxin system; TMAO, trimethylamine N-oxide. 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 1 63 64 65 1 ABSTRACT 2 3 The genomic features of Azoarcus sp. CIB reflect its most distinguishing phenotypes as 4 5 a diazotroph, facultative anaerobe, capable of degrading either aerobically and/or 6 anaerobically a wide range of aromatic compounds, including some toxic hydrocarbons 7 such as toluene and m-xylene, as well as its endophytic lifestyle. -
Phylogenetic Analyses of a New Group of Denitrifiers Capable of Anaerobic Growth on Toluene and Description of Azoarcus Tolulyticus Sp
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1995, p. 500-506 Vol. 45, No. 3 0020-7713/95/$04.00 + 0 Copyright 0 1995, International Union of Microbiological Societies Phylogenetic Analyses of a New Group of Denitrifiers Capable of Anaerobic Growth on Toluene and Description of Azoarcus tolulyticus sp. nov. JIZHONG ZHOU,1,2 MARCOS R. FRIES,1.2 JOANNE C. CHEE-SANFORD,3 AND JAMES M. TIEDJE17273* Center For Microbial Ecology, Department of Crop and Soil Sciences, and Department of Microbiology, Michigan State University, East Lansing, Michigan 48824-1325 To understand the phylogeny and taxonomy of eight new toluene-degrading denitrifying isolates, we per- formed a 16s rRNA sequence analysis and a gas chromatographic analysis of their cellular fatty acids and examined some of their biochemical and physiological features. These isolates had 165 rRNA sequence signatures identical to those of members of the beta subclass of the Proteobacteria.The levels of similarity were as follows: 97.9 to 99.9% among the new isolates; 91.2 to 92.4%between the new isolates and Azoarcus sp. strain S5b2; 95.3 to 96.2% between the new isolates and Azoarcus sp. strain BH72; and 94.8 to 95.3% between the new isolates and Azoarcus indigens VB32T (T = type strain). Phylogenetic trees constructed by using the distance matrix, maximum-parsimony, and maximum-likelihood methods showed that our eight denitrifying isolates form a phylogenetically coherent cluster which represents a sister lineage of the previously described Azoarcus species. Furthermore, the fatty acid profiles, the cell morphology, and several physiological and nutritional characteristics of the eight isolates and the previously described members of the genus Azoarcus were also similar. -
Meta-Proteomic Analysis of Protein Expression Distinctive to Electricity
Chignell et al. Biotechnol Biofuels (2018) 11:121 https://doi.org/10.1186/s13068-018-1111-2 Biotechnology for Biofuels RESEARCH Open Access Meta‑proteomic analysis of protein expression distinctive to electricity‑generating bioflm communities in air‑cathode microbial fuel cells Jeremy F. Chignell1, Susan K. De Long2 and Kenneth F. Reardon1,3* Abstract Background: Bioelectrochemical systems (BESs) harness electrons from microbial respiration to generate power or chemical products from a variety of organic feedstocks, including lignocellulosic biomass, fermentation byproducts, and wastewater sludge. In some BESs, such as microbial fuel cells (MFCs), bacteria living in a bioflm use the anode as an electron acceptor for electrons harvested from organic materials such as lignocellulosic biomass or waste byprod- ucts, generating energy that may be used by humans. Many BES applications use bacterial bioflm communities, but no studies have investigated protein expression by the anode bioflm community as a whole. Results: To discover functional protein expression during current generation that may be useful for MFC optimiza- tion, a label-free meta-proteomics approach was used to compare protein expression in acetate-fed anode bioflms before and after the onset of robust electricity generation. Meta-proteomic comparisons were integrated with 16S rRNA gene-based community analysis at four developmental stages. The community composition shifted from dominance by aerobic Gammaproteobacteria (90.9 3.3%) during initial bioflm formation to dominance by Deltapro- teobacteria, particularly Geobacter (68.7 3.6%) in mature,± electricity-generating anodes. Community diversity in the intermediate stage, just after robust current± generation began, was double that at the early stage and nearly double that of mature anode communities. -
Suppl. Figure 1 (.Pdf)
Supplementary web Figure 1. 16S rRNA-based phylogenetic trees showing the affiliation of all cultured and uncultured members of the nine “Rhodocyclales” lineages. The consensus tree is based on maximum-likelihood analysis (AxML) of full- length sequences (>1,300 nucleotides) performed with a 50% conservation filter for the “Betaproteobacteria”. Named type species are indicated by boldface type. Bar indicates 10% estimated sequence divergence. Polytomic nodes connect branches for which a relative order could not be determined unambiguously by applying neighbor- joining, maximum-parsimony, and maximum-likelihood treeing methods. Numbers at branches indicate parsimony bootstrap values in percent. Branches without numbers had bootstrap values of less than 75%. The minimum 16S rRNA sequence similarity for each “Rhodocyclales” lineage is shown. P+ sludge clone SBR1021, AF204250 P+ sludge clone GC152, AF204242 Kraftisried wwtp clone KRA42, AY689087 Kraftisried wwtp clone S28, AF072922 Kraftisried wwtp clone A13, AF072927 Kraftisried wwtp clone H23, AF072926 Kraftisried wwtp clone S40, AF234757 Sterolibacterium lineage 100 Kraftisried wwtp clone H12, AF072923 100 Kraftisried wwtp clone H20, AF072920 92.5% 89 rape root clone RRA12, AY687926 100 P+ sludge clone SBR1001, AF204252 P- sludge clone SBR2080, AF204251 P+ sludge clone GC24, AF204243 mine water clone I12, AY187895 100 93 denitrifying cholesterol-degrading bacterium 72Chol, Y09967 Sterolibacterium denitrificans, AJ306683 Kraftisried wwtp clone KRZ64, AY689092 Kraftisried wwtp clone KRZ70, -
Phylogenomics of Rhodocyclales and Its Distribution in Wastewater Treatment Systems Zhongjie Wang1, Wenqing Li2, Hao Li1, Wei Zheng1 & Feng Guo1*
www.nature.com/scientificreports OPEN Phylogenomics of Rhodocyclales and its distribution in wastewater treatment systems Zhongjie Wang1, Wenqing Li2, Hao Li1, Wei Zheng1 & Feng Guo1* Rhodocyclales is an abundant bacterial order in wastewater treatment systems and putatively plays key roles in multiple functions. Its phylogenomics, prevalence of denitrifying genes in sub-lineages and distribution in wastewater treatment plants (WWTPs) worldwide have not been well characterized. In the present study, we collected 78 Rhodocyclales genomes, including 17 from type strains, non-type strains and genome bins contributed by this study. Phylogenomics indicated that the order could be divided into fve family-level lineages. With only a few exceptions (mostly in Rhodocyclaceae), nirS- containing genomes in this order usually contained the downstream genes of norB and nosZ. Multicopy of denitrifying genes occurred frequently and events of within-order horizontal transfer of denitrifying genes were phylogenetically deduced. The distribution of Rhodocyclaceae, Zoogloeaceae and Azonexaceae in global WWTPs were signifcantly governed by temperature, mixed liquor suspended solids, etc. Metagenomic survey showed that the order generally ranked at the top or second for diferent denitrifying genes in wastewater treatment systems. Our results provided comprehensive genomic insights into the phylogeny and features of denitrifying genes of Rhodocyclales. Its contribution to the denitrifying gene pool in WWTPs was proved. Activated sludge, which is a widely utilized biological process for the treatment of municipal and industrial waste- waters around the world for over a century1,2, relies on a complex consortium of microorganisms to remove pollutants and facilitate separation of focs and water3. A key functional microbial taxon in wastewater treatment systems is Rhodocyclales, which is dominant in activated sludge samples according to the relative abundance of 16S rRNA genes and hybridization approach4,5. -
Where Nitrite Respiration Meets Electrotrophy: Diversity Studies and Functional Characterization of Autotrophic Bacterial Isolates from Bioelectrochemical Systems
WHERE NITRITE RESPIRATION MEETS ELECTROTROPHY: DIVERSITY STUDIES AND FUNCTIONAL CHARACTERIZATION OF AUTOTROPHIC BACTERIAL ISOLATES FROM BIOELECTROCHEMICAL SYSTEMS Ariadna Vilar Sanz Per citar o enllaçar aquest document: Para citar o enlazar este documento: Use this url to cite or link to this publication: http://hdl.handle.net/10803/383756 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art.