The Presence of Nitrate Dramatically Changed the Predominant Microbial

Total Page:16

File Type:pdf, Size:1020Kb

The Presence of Nitrate Dramatically Changed the Predominant Microbial Stepanov et al. BMC Microbiology 2014, 14:225 http://www.biomedcentral.com/1471-2180/14/225 RESEARCH ARTICLE Open Access The presence of nitrate dramatically changed the predominant microbial community in perchlorate degrading cultures under saline conditions Victor G Stepanov2†, Yeyuan Xiao1†, Quyen Tran2, Mark Rojas3, Richard C Willson2,4,5, Yuriy Fofanov3, George E Fox2,4 and Deborah J Roberts1* Abstract Background: Perchlorate contamination has been detected in both ground water and drinking water. An attractive treatment option is the use of ion-exchange to remove and concentrate perchlorate in brine. Biological treatment can subsequently remove the perchlorate from the brine. When nitrate is present, it will also be concentrated in the brine and must also be removed by biological treatment. The primary objective was to obtain an in-depth characterization of the microbial populations of two salt-tolerant cultures each of which is capable of metabolizing perchlorate. The cultures were derived from a single ancestral culture and have been maintained in the laboratory for more than 10 years. One culture was fed perchlorate only, while the other was fed both perchlorate and nitrate. Results: A metagenomic characterization was performed using Illumina DNA sequencing technology, and the 16S rDNA of several pure strains isolated from the mixed cultures were sequenced. In the absence of nitrate, members of the Rhodobacteraceae constituted the prevailing taxonomic group. Second in abundance were the Rhodocyclaceae. In the nitrate fed culture, the Rhodobacteraceae are essentially absent. They are replaced by a major expansion of the Rhodocyclaceae and the emergence of the Alteromonadaceae as a significant community member. Gene sequences exhibiting significant homology to known perchlorate and nitrate reduction enzymes were found in both cultures. Conclusions: The structure of the two microbial ecosystems of interest has been established and some representative strains obtained in pure culture. The results illustrate that under favorable conditions a group of organisms can readily dominate an ecosystem and yet be effectively eliminated when their advantage is lost. Almost all known perchlorate-reducing organisms can also effectively reduce nitrate. This is certainly not the case for the Rhodobacteraceae that were found to dominate in the absence of nitrate, but effectively disappeared in its presence. This study is significant in that it reveals the existence of a novel group of organisms that play a role in the reduction of perchlorate under saline conditions. These Rhodobacteraceae especially, as well as other organisms present in these communities may be a promising source of unique salt-tolerant enzymes for perchlorate reduction. Keywords: Perchlorate contamination, Nitrate, Metagenomic sequencing, Community analysis, Salt-tolerance * Correspondence: [email protected] †Equal contributors 1School of Engineering, University of British Columbia, EME 4261, 3333 University Way, Kelowna, BC, Canada Full list of author information is available at the end of the article © 2014 Stepanov et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Stepanov et al. BMC Microbiology 2014, 14:225 Page 2 of 10 http://www.biomedcentral.com/1471-2180/14/225 Background rRNA genes of several strains that have been isolated The perchlorate ion has been found to contaminate from the cultures and successfully cultivated in the la- ground and surface water, as well as food, vitamins, and boratory. The combination of these two approaches pro- drinking water [1-5]. Perchlorate is known to inhibit the vides new insight into the major and minor components sodium-iodide symporter, which is responsible for the of the cultures and their contribution to perchlorate and supply of iodine to the thyroid and to milk in the mam- nitrate removal from contaminated water. mary glands [6]. The environmentally stable perchlorate ion can be re- Results moved from contaminated water using ion-exchange in Pure culture isolation combination with a microbial treatment processes. Dur- Four pure strains were obtained using anaerobic incuba- ing bacterial respiration perchlorate acts as an electron tions: NW (white colonies) and NY (yellow colonies), acceptor and requires the addition of an electron donor originated from NP30; PW (white colonies) and PY (yel- [7-9]. Perchlorate is metabolized through a series of re- low colonies), originated from P30. Another four pure ductions to chlorite and then a dismutation to chloride strains were obtained from aerobically incubated plates and molecular oxygen [10]. In many cases, perchlorate is and designated as NWO, NYO, PWO and PYO follow- present in very low concentrations and must be treated ing the naming scheme for anaerobic isolates. When to even lower levels, e.g., 6 ppb in California [11], and these new strains were transferred back into P medium, 2 ppb in Massachusetts [12]. This makes biological treat- none of them could reduce perchlorate after 120 days’ ment very difficult as a stand-alone process since other incubation, although growth was observed. A single add- electron acceptors such as nitrate and oxygen are often itional isolate that can reduce perchlorate was obtained preferred. from the NP30 culture and characterized in detail as re- Ion-exchange processes have been used to remove per- ported elsewhere [24]. This strain was identified as Marino- chlorate to meet the required treatment goals, but the bacter sp. strain P4B1 a member of the Alteromonadaceae. perchlorate and other co-contaminant anions such as ni- 16S rDNA sequences were obtained for all the pure strains trate are merely transferred to a concentrated brine except the NW isolate, which produced heterogeneous se- stream, which in turn must be treated [13,14]. The com- quencing patterns. Table 1 presents a summary of the re- bination of ion-exchange to remove and concentrate the sults obtained by comparing the sequences obtained for perchlorate from the contaminated water source and the pure cultures with those from the NCBI nt database. biological treatment to remove the perchlorate from the All belong to the phylum Proteobacteria. Two of the brine is an attractive option for drinking water treat- NP30 strains were identified as members of the Rhodobac- ment. Since nitrate is often present with perchlorate and teraceae closely related to Stappia indica.Theother will also be concentrated in the ion-exchange brine, the was an Azoarcus like isolate close to the members of a re- biological system should also remove nitrate. cently discovered and vaguely defined genus Denitromo- The cultures examined here were initially enriched nas (Rhodocyclaceae). Three of the five P30 isolates were from marine sediment in the year 2001. The culture des- identified as Hyphomonas jannaschiana. The remaining ignated as P30 has been maintained continuously in the P30 isolate was identified as a Cellulomonas strain that be- laboratory in a defined 3% NaCl saline medium with longs to the Cellulomonadaceae and is closely related to perchlorate and acetate as the sole electron acceptor and the C. hominis type strain. donor respectively in a 1.5 L batch reactor [15]. In 2003, half of the P30 culture was transferred to a new reactor Comparative metagenomic analysis and fed with both nitrate and perchlorate as the electron Illumina sequencing of the two cultures yielded approxi- acceptors and acetate as the sole electron donor. This mately 7.5 million reads for P30 and 6.3 million for culture was designated as NP30. The cultures have been NP30. Table 2 summarizes the assembly of the metage- used as the basis for many published studies over the nomic contigs. The data analysis strategy yielded conver- last 10 years [13,15-23]. ging estimates for the taxonomic composition of the P30 In order to better understand these cultures, an initial and NP30 microbial communities at the family level and characterization of the microbial populations was ob- above (Additional files 1, 2 and 3). As shown in Figure 1, tained by cloning 16S rDNA genes and characterizing both mixed cultures were found to be dominated by them by either DGGE or 16S rDNA sequencing [21]. In Alpha, Beta, and Gamma Proteobacteria, while the pro- the work reported here, we further our understanding of portion of other phyla is substantially lower. As shown the biota in these cultures by characterizing the total in Figure 2, Alphaproteobacteria from the family Rhodo- community DNA of both the P30 and NP30 cultures bacteraceae constitute a prevailing taxonomic group in using Illumina DNA sequencing technology. This meta- the P30 culture (Figure 2, Additional file 4). The second genome analysis is supplemented by sequencing the 16S most abundant fraction is formed by Betaproteobacteria Stepanov et al. BMC Microbiology 2014, 14:225 Page 3 of 10 http://www.biomedcentral.com/1471-2180/14/225 Table 1 Sequencing summary for 16S rDNA from pure cultures ID Origin Accession Length Closest BLAST match in NCBI nt database*) Identity Bit Taxonomic affiliation number (bp) (%) score (excluding uncultured/environmental
Recommended publications
  • Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
    fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells.
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Identification and Characterization of a Halotolerant, Cold-Active Marine Endo–1,4-Glucanase by Using Functional Metagenomics
    Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota Marjolaine Martin, Sophie Biver, Sébastien Steels, Tristan Barbeyron, Murielle Jam, Daniel Portetelle, Gurvan Michel, Micheline Vandenbol To cite this version: Marjolaine Martin, Sophie Biver, Sébastien Steels, Tristan Barbeyron, Murielle Jam, et al.. Identi- fication and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota. Applied and Environmental Microbi- ology, American Society for Microbiology, 2014, 80 (16), pp.4958-4967. 10.1128/AEM.01194-14. hal-02138133 HAL Id: hal-02138133 https://hal.archives-ouvertes.fr/hal-02138133 Submitted on 23 May 2019 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. AEM Accepts, published online ahead of print on 6 June 2014 Appl. Environ. Microbiol. doi:10.1128/AEM.01194-14 Copyright © 2014, American Society for Microbiology. All Rights Reserved. 1 Functional screening
    [Show full text]
  • Distribution of Aerobic Anoxygenic Phototrophs in Freshwater Plateau Lakes
    Pol. J. Environ. Stud. Vol. 27, No. 2 (2018), 871-879 DOI: 10.15244/pjoes/76039 ONLINE PUBLICATION DATE: 2018-01-15 Original Research Distribution of Aerobic Anoxygenic Phototrophs in Freshwater Plateau Lakes Yingying Tian1, 2, Xingqiang Wu1*, Qichao Zhou3, Oscar Omondi Donde1, 2, 4, Cuicui Tian1, Chunbo Wang1, Bing Feng1, 2, Bangding Xiao1* 1Key Laboratory of Algal Biology of Chinese Academy of Sciences, Institute of Hydrobiology, University of Chinese Academy of Sciences, Wuhan 430072, China 2University of Chinese Academy of Sciences, Beijing 100101, China 3Yunnan Key Laboratory of Pollution Process and Management of Plateau Lake-Watershed, Yunnan Institute of Environmental Science (Kunming China International Research Center for Plateau Lake), Kunming 650034, China 4Egerton University, Department of Environmental Science, P. O. Box 536-20115, Egerton-Kenya Received: 13 February 2017 Accepted: 23 July 2017 Abstract Aerobic anoxygenic phototrophic (AAP) bacteria are known functionally as photoheterotrophic microbes. Though numerously reported from ocean habitats, their distribution in freshwater lakes is far less documented. In the present study we investigated the dynamics of AAP bacteria in freshwater plateau lakes. Results revealed a high abundance of AAP bacteria in eutrophic lakes. Moreover, AAP bacteria were positively correlated with TN, TP, and Chl a, but the variations of AAP bacterial proportion to potential total bacteria (AAPB%). Alphaproteobacteria-related sequences dominated lakes Luguhu, Erhai, and Chenghai at ratios of 93.9, 85.4, and 70.6%, respectively, and in total comprised eight clearly defined subgroups. Sequences affiliated with Beta- and Grammaproteobacteria were found to be rare taxa. Additionally, Alkalibacterium-like sequences belonging to Firmutes were assigned.
    [Show full text]
  • Microbial Diversity in Long-Term Water-Flooded Oil Reservoirs with Different in Situ Temperatures in China
    Microbial diversity in long-term water-flooded oil reservoirs with different SUBJECT AREAS: BIODIVERSITY in situ temperatures in China MICROBIOLOGY Fan Zhang1, Yue-Hui She2,3, Lu-Jun Chai1, Ibrahim M. Banat4, Xiao-Tao Zhang1, Fu-Chang Shu2, ECOLOGY Zheng-Liang Wang2, Long-Jiang Yu3 & Du-Jie Hou1 ENVIRONMENTAL SCIENCES 1The Key Laboratory of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism, Ministry of Education, China; Received School of Energy Resources, China University of Geosciences (Beijing), Beijing 100083, China, 2College of Chemistry and 1 August 2012 Environmental Engineering, Yangtze University, Jingzhou, Hubei 434023, China, 3College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430079, China, 4School of Biomedical Sciences, University of Ulster, Accepted Coleraine, BT52 1SA, N. Ireland, UK. 27 September 2012 Published Water-flooded oil reservoirs have specific ecological environments due to continual water injection and oil 23 October 2012 production and water recycling. Using 16S rRNA gene clone library analysis, the microbial communities present in injected waters and produced waters from four typical water-flooded oil reservoirs with different in situ temperatures of 256C, 406C, 556C and 706C were examined. The results obtained showed that the Correspondence and higher the in situ temperatures of the oil reservoirs is, the less the effects of microorganisms in the injected requests for materials waters on microbial community compositions in the produced waters is. In addition, microbes inhabiting in the produced waters of the four water-flooded oil reservoirs were varied but all dominated by should be addressed to Proteobacteria. Moreover, most of the detected microbes were not identified as indigenous.
    [Show full text]
  • FISH Handbook for Biological Wastewater Treatment
    ©2019 The Author(s) This is an Open Access book distributed under the terms of the Creative Commons Attribution Licence (CC BY 4.0), which permits copying and redistribution for non- commercial purposes, provided the original work is properly cited and that any new works are made available on the same conditions (http://creativecommons.org/licenses/by/4.0/). This does not affect the rights licensed or assigned from any third party in this book. This title was made available Open Access through a partnership with Knowledge Unlatched. IWA Publishing would like to thank all of the libraries for pledging to support the transition of this title to Open Access through the KU Select 2018 program. Downloaded from http://iwaponline.com/ebooks/book-pdf/521273/wio9781780401775.pdf by guest on 25 September 2021 Identification and quantification of microorganisms in activated sludge and biofilms by FISH and biofilms by sludge in activated Identification and quantification of microorganisms Treatment Wastewater Biological for Handbook FISH The FISH Handbook for Biological Wastewater Treatment provides all the required information for the user to be able to identify and quantify important microorganisms in activated sludge and biofilms by using fluorescence in situ hybridization (FISH) and epifluorescence microscopy. It has for some years been clear that most microorganisms in biological wastewater systems cannot be reliably identified and quantified by conventional microscopy or by traditional culture-dependent methods such as plate counts. Therefore, molecular FISH Handbook biological methods are vital and must be introduced instead of, or in addition to, conventional methods. At present, FISH is the most widely used and best tested of these methods.
    [Show full text]
  • Core Bacterial Taxon from Municipal Wastewater Treatment Plants
    ENVIRONMENTAL MICROBIOLOGY crossm Casimicrobium huifangae gen. nov., sp. nov., a Ubiquitous “Most-Wanted” Core Bacterial Taxon from Municipal Wastewater Treatment Plants Yang Song,a,b,c,d,g Cheng-Ying Jiang,a,b,c,d Zong-Lin Liang,a,b,c,g Bao-Jun Wang,a Yong Jiang,e Ye Yin,f Hai-Zhen Zhu,a,b,c,g Ya-Ling Qin,a,b,c,g Rui-Xue Cheng,a Zhi-Pei Liu,a,b,c,d Yao Liu,e Tao Jin,f Philippe F.-X. Corvini,h Korneel Rabaey,i Downloaded from Ai-Jie Wang,a,d,g Shuang-Jiang Liua,b,c,d,g aKey Laboratory of Environmental Biotechnology at Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China bState Key Laboratory of Microbial Resources at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China cEnvironmental Microbiology Research Center at Institute of Microbiology, Chinese Academy of Sciences, Beijing, China dRCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China eBeijing Drainage Group Co., Ltd., Beijing, China f BGI-Qingdao, Qingdao, China http://aem.asm.org/ gUniversity of Chinese Academy of Sciences, Beijing, China hUniversity of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland iCenter for Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium Yang Song and Cheng-Ying Jiang contributed equally to this work. Author order was determined by drawing straws. ABSTRACT Microorganisms in wastewater treatment plants (WWTPs) play a key role in the removal of pollutants from municipal and industrial wastewaters. A recent study estimated that activated sludge from global municipal WWTPs har- on June 19, 2020 by guest bors 1 ϫ 109 to 2 ϫ 109 microbial species, the majority of which have not yet been cultivated, and 28 core taxa were identified as “most-wanted” ones (L.
    [Show full text]
  • Identification of Microorganisms for The
    IDENTIFICATION OF MICROORGANISMS FOR THE BIOREMEDIATION OF NITRATE AND MANGANESE IN MINNESOTA WATER A THESIS SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY EMILY ANDERSON IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE Satoshi Ishii AUGUST, 2018 © Emily Anderson 2018 ACKNOWLEDGEMENTS This work was supported by Minnesota Department of Agriculture (Project No. 108837), the Minnesota’s Discovery, Research and InnoVation Economy (MnDRIVE) initiative of the University of Minnesota, and the USDA North Central Region Sustainable Agriculture Research and Education (NCR-SARE) Graduate Student Grant Program. Additionally, I would like to thank my advisor, Satoshi Ishii, for taking me on as his first student and for his support and guidance throughout my degree program. I would also like to thank my committee members, Dr. Mike Sadowsky and Dr. Carl Rosen, as well as Dr. Gary Feyereisen for their time and advice towards achieving my degree. I am also grateful to the Ishii lab members for their support over the last two years, especially Jeonghwan Jang and Qian Zhang who have always been more than willing to help. I have enjoyed field and lab days in Willmar with the “woodchip team” (Ping Wang, Jeonghwan Jang, Ehsan Ghane, Ed Dorsey, Scott Schumacher, Todd Schumacher, Allie Arsenault, Hao Wang, Amanda Tersteeg) and others that were willing to volunteer with us (Nouf Aldossari, Stacy Nordstrom and Persephone Ma). For the manganese bioremediation project, I am grateful for the advice and encouragement from Dr. Cara Santelli and for the help from members of her lab. Luke Feeley had an important part in the manganese bioreactor establishment and maintenance as did Kimberly Hernandez and I am thankful for their contributions.
    [Show full text]
  • Physiology and Biochemistry of Aromatic Hydrocarbon-Degrading Bacteria That Use Chlorate And/Or Nitrate As Electron Acceptor
    Invitation for the public defense of my thesis Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic and biochemistry Physiology bacteria that use chlorate and/or nitrate as electron acceptor as electron nitrate and/or use chlorate that bacteria Physiology and biochemistry Physiology and biochemistry of aromatic hydrocarbon-degrading of aromatic hydrocarbon- degrading bacteria that bacteria that use chlorate and/or nitrate as electron acceptor use chlorate and/or nitrate as electron acceptor The public defense of my thesis will take place in the Aula of Wageningen University (Generall Faulkesweg 1, Wageningen) on December 18 2013 at 4:00 pm. This defense is followed by a reception in Café Carré (Vijzelstraat 2, Wageningen). Margreet J. Oosterkamp J. Margreet Paranimphs Ton van Gelder ([email protected]) Aura Widjaja Margreet J. Oosterkamp ([email protected]) Marjet Oosterkamp (911 W Springfield Ave Apt 19, Urbana, IL 61801, USA; [email protected]) Omslag met flap_MJOosterkamp.indd 1 25-11-2013 5:58:31 Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor Margreet J. Oosterkamp Thesis-MJOosterkamp.indd 1 25-11-2013 6:42:09 Thesis committee Thesis supervisor Prof. dr. ir. A. J. M. Stams Personal Chair at the Laboratory of Microbiology Wageningen University Thesis co-supervisors Dr. C. M. Plugge Assistant Professor at the Laboratory of Microbiology Wageningen University Dr. P. J. Schaap Assistant Professor at the Laboratory of Systems and Synthetic Biology Wageningen University Other members Prof. dr. L. Dijkhuizen, University of Groningen Prof. dr. H. J. Laanbroek, University of Utrecht Prof.
    [Show full text]
  • “Candidatus Propionivibrio Aalborgensis”: a Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants
    Aalborg Universitet “Candidatus Propionivibrio aalborgensis” A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants Albertsen, Mads; McIlroy, Simon Jon; Stokholm-Bjerregaard, Mikkel; Karst, Søren Michael; Nielsen, Per Halkjær Published in: Frontiers in Microbiology DOI (link to publication from Publisher): 10.3389/fmicb.2016.01033 Creative Commons License CC BY 4.0 Publication date: 2016 Document Version Publisher's PDF, also known as Version of record Link to publication from Aalborg University Citation for published version (APA): Albertsen, M., McIlroy, S. J., Stokholm-Bjerregaard, M., Karst, S. M., & Nielsen, P. H. (2016). “Candidatus Propionivibrio aalborgensis”: A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants. Frontiers in Microbiology, 7, [1033]. https://doi.org/10.3389/fmicb.2016.01033 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. ? Users may download and print one copy of any publication from the public portal for the purpose of private study or research. ? You may not further distribute the material or use it for any profit-making activity or commercial gain ? You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us at [email protected] providing details, and we will remove access to the work immediately and investigate your claim. fmicb-07-01033 June 30, 2016 Time: 16:42 # 1 ORIGINAL RESEARCH published: 04 July 2016 doi: 10.3389/fmicb.2016.01033 “Candidatus Propionivibrio aalborgensis”: A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants Mads Albertsen1†, Simon J.
    [Show full text]
  • Photosynthesis Is Widely Distributed Among Proteobacteria As Demonstrated by the Phylogeny of Puflm Reaction Center Proteins
    fmicb-08-02679 January 20, 2018 Time: 16:46 # 1 ORIGINAL RESEARCH published: 23 January 2018 doi: 10.3389/fmicb.2017.02679 Photosynthesis Is Widely Distributed among Proteobacteria as Demonstrated by the Phylogeny of PufLM Reaction Center Proteins Johannes F. Imhoff1*, Tanja Rahn1, Sven Künzel2 and Sven C. Neulinger3 1 Research Unit Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany, 2 Max Planck Institute for Evolutionary Biology, Plön, Germany, 3 omics2view.consulting GbR, Kiel, Germany Two different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Edited by: Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the Marina G. Kalyuzhanaya, phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria San Diego State University, United States employing this photosystem in nature. Almost complete pufLM gene sequences and Reviewed by: the derived protein sequences from 152 type strains and 45 additional strains of Nikolai Ravin, phototrophic Proteobacteria employing photosystem II were compared. The results Research Center for Biotechnology (RAS), Russia give interesting and comprehensive insights into the phylogeny of the photosynthetic Ivan A. Berg, apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as Universität Münster, Germany major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from *Correspondence: Caulobacterales (Brevundimonas subvibrioides).
    [Show full text]
  • Hirschia Baltica Type Strain (IFAM 1418T)
    Standards in Genomic Sciences (2011) 5:287-297 DOI:10.4056/sigs.2205004 Complete genome sequence of Hirschia baltica type strain (IFAM 1418T) Olga Chertkov1,2, Pamela J.B. Brown3, David T. Kysela3, Miguel A. DE Pedro4, Susan Lucas1, Alex Copeland1, Alla Lapidus1, Tijana Glavina Del Rio1, Hope Tice1, David Bruce1, Lynne Goodwin1,2, Sam Pitluck1, John C. Detter1,2, Cliff Han1,2, Frank Larimer2, Yun-juan Chang1,5, Cynthia D. Jeffries1,5, Miriam Land1,5, Loren Hauser1,5, Nikos C. Kyrpides1, Natalia Ivanova1, Galina Ovchinnikova1, Brian J. Tindall6, Markus Göker6, Hans-Peter Klenk6*, Yves V. Brun3* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 Indiana University, Bloomington, Indiana, USA 4 Universidad Autonoma de Madrid, Campus de Cantoblanco, Madrid, Spain 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany *Corresponding author: [email protected], [email protected] Keywords: aerobic, chemoheterotrophic, mesophile, Gram-negative, motile, budding, stalk- forming, Hyphomonadaceae, Alphaproteobacteria, CSP 2008 The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacte- ria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a published genome sequence. H. bal- tica is of special interest because it has a dimorphic life cycle and is a stalked, budding bacte- rium. The 3,455,622 bp long chromosome and 84,492 bp plasmid with a total of 3,222 pro- tein-coding and 44 RNA genes were sequenced as part of the DOE Joint Genome Institute Program CSP 2008.
    [Show full text]