DOCSLIB.ORG

Microorganisms Involved in Anaerobic Benzene Degradation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Microorganisms Involved in Anaerobic Benzene Degradation Ann Microbiol (2015) 65:1201–1213 DOI 10.1007/s13213-014-0926-8 REVIEW ARTICLE Microorganisms involved in anaerobic benzene degradation Arturo Aburto-Medina & Andrew S. Ball Received: 17 March 2014 /Accepted: 29 May 2014 /Published online: 26 June 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract Benzene is a highly toxic compound. Moreover, Keywords Benzene . Benzene-contaminated groundwater . benzene-contaminated groundwater is a widespread problem Benzene-degrading microorganisms . Syntrophic interactions caused mainly by the lack of oxygen in the subsurface. Long- term exposure may cause leukaemia. However, pure cultures of microorganisms with the ability to degrade benzene anaer- Introduction obically have recently been isolated from novel enrichment cultures. The novel pure cultures include the hyperthermo- Benzene is derived from fossil fuels, cigarette smoke and philic archaeon Ferroglobus placidus and the Geobacter forest fires, among other sources. It is an important raw strains Ben and metallireducens which degrade benzene an- chemical used as an intermediate to produce a wide range of aerobically coupled to the reduction of Fe(III). Syntrophic products, such as plastics, resins, nylon, lubricants and pesti- interactions have been suggested in enrichments where mem- cides. Benzene is also highly toxic; it may cause acute mye- bers of the Peptococcaceae within the class Clostridia are the loid leukaemia, secondary aplastic anaemia and damage to the dominant organisms and suggested as being responsible for reproductive system. It can enter the body by skin contact, the first attack on the benzene ring. Laboratory enrichment inhalation or consumption of contaminated water. Benzene- studies have also resulted in the development of consortia contaminated groundwater is a widespread problem caused which degrade benzene, with different terminal electron ac- partially by its high solubility in water (1.8 g l−1 at 25°C) ceptors supporting the syntrophy. Other benzene-degrading relative to other organic compounds and partly to spills at microorganisms have been identified under methanogenic production sites and leaks in underground storage tanks. The- conditions, involving the reduction of humic acids by, for se leaks have been documented by studies of the environment example, the deltaproteobacterium Hasda-A and members of agencies in the USA and UK (Rudolph 1996;Atlas2005). the Betaproteobacteria, Gammaproteobacteria and Benzene is readily degraded under aerobic conditions Deltaproteobacteria, respectively. This review focuses on (Alvarez and Vogel 1991; Werlen et al. 1996; Fairlee et al. the microorganisms involved in anaerobic benzene degrada- 1997; Greene et al. 2000) by ubiquitous microorganisms, such tion under conditions involving several electron acceptors in as Pseudomonas sp. and Rhodococcus sp. (Fahy et al. 2006). recent years. Information related to the anaerobic degradation However contaminated groundwater is usually under anaero- of benzene is critical to understanding and predicting the fate bic conditions due to the rapid depletion of available oxygen of this contaminant in groundwater. in subterranean environments, which in turn decreases the redox potential, favouring the growth of denitrifying, sulphate-reducing, iron-reducing and methanogenic popula- * A. Aburto-Medina ( ) tions that may also degrade the contaminant. Therefore, in- Department of Environmental Sciences, Universidad Autónoma Metropolitana, Lerma 52006, Mexico formed knowledge of anaerobic microorganisms capable of e-mail: [email protected] benzene degradation is critical to understanding and predicting the fate of this contaminant. A. S. Ball Initial studies suggested the lack of benzene degradation School of Applied Sciences, Centre for Environment, Sustainability and Remediation, Royal Melbourne Institute of Technology, under anaerobic conditions (Barker et al. 1987;Kuhnetal. Bundoora, VIC 3083, Australia 1988; Acton and Barker 1992; Barbaro et al. 1992; Patterson 1202 Ann Microbiol (2015) 65:1201–1213 et al. 1993). However, laboratory-based and field studies in 2001). However, no anaerobic degradation genes were found the last 20 years have confirmed the degradation of this in the Dechloromonas aromatica RCB genome (Salinero et al. pollutant coupled to the reduction of nitrate (Burland and 2009), and subsequent data suggests the involvement of oxy- Edwards 1999;Coatesetal.2001; Chakraborty and Coates gen under nitrate-reducing conditions (Ettwig et al. 2010; 2005; Ulrich et al. 2005; Kasai et al. 2006;Jakoncicetal. Zhang et al. 2013). Nevertheless, recent studies have reported 2007), sulphate (Lovley et al. 1995; Phelps et al. 1996; Weiner the novel pure cultures archaeon Ferroglobus placidus and Lovley 1998a; Sublette et al. 2006; Musat and Widdel (Holmes et al. 2011)andaGeobacter metallireducens strain 2008; Berlendis et al. 2010), iron (Lovley and Woodward named Ben (Zhang et al. 2012), both of which are capable of 1996;Kazumietal.1997; Rooney-Varga et al. 1999;Jahn anaerobic benzene degradation. The hyperthermophilic et al. 2005; Kunapuli et al. 2007), manganese (Villatoro- archaeon F. placidus is able to degrade benzene anaerobically Monzón et al. 2003, 2008), humic acids (Cervantes et al. under iron-reducing conditions, producing benzoate as the 2011) and methanogenesis (Vogel and Grbicgalic 1986; main metabolite, suggesting the carboxylation of benzene to Grbicgalic and Vogel 1987;Kazumietal.1997; Weiner and form benzoate (Holmes et al. 2011). The Geobacter strain Lovley 1998b; Caldwell and Suflita 2000;Ulrichand Ben, isolated from sediments within the ferric ion [Fe(III)]- Edwards 2003; Chang et al. 2005; Da Silva and Alvarez reducing zone in a petroleum-contaminated aquifer in 2007; Sakai et al. 2009). Bemidji, USA, was found to degrade benzene with ferric iron Moreover, recent studies on the novel pure cultures of and anthraquinone-2,6-disulfonate (AQDS) as the only elec- Geobacter species and the archaeon Ferroglobus placidus tron acceptors. In addition, G. metallireducens is also able to have confirmed the degradation of benzene coupled to iron- degrade benzene coupled to the reduction of Fe(III); trace reducing conditions and have also provided information on amounts of phenol were detected during the degradation of the metabolites produced during growth on benzene (Holmes benzene, suggesting phenol as an intermediate. This finding is et al. 2011; Zhang et al. 2012). In addition, syntrophic asso- also supported by the inhibition of benzene degradation by the ciations are also suggested in enrichments capable of benzene deletion of genes involved in the metabolism of phenol and by degradation where members of the Peptococcaceae are the their upregulation during benzene oxidation (Zhang et al. key players (Taubert et al. 2012; van der Zaan et al. 2012). 2012; Zhang et al. 2013). Other microorganisms involved in the degradation of benzene under methanogenic conditions or coupled to the reduction of humic acids include the deltaproteobacterium Hasda-A and Microorganisms identified in recent anaerobic benzene two phylotypes of Gammaproteobacteria, respectively degradation studies (Cervantes et al. 2011;Masumotoetal.2012). In this review, we focus on the microorganisms which have been identified in Genera of the family Peptococcaceae (phylum anaerobic benzene degradation studies in recent years and the Firmicutes,classClostridia) have been identified as the possible terminal electron acceptors. It should be noted that main benzene degraders with most of the terminal elec- excellent reviews on the anaerobic degradation of hydrocar- tron acceptors [sulphate, nitrate, Fe(III), chlorate], and bons (Boll et al. 2002; Foght 2008; Fuchs et al. 2011; syntrophic interactions are strongly suggested. The most Meckenstock and Mouttaki 2011;Flanaganetal.2013; recent study by the Vogt group involved a sulphate- Heider and Schühle 2013;Bolletal.2014), anaerobic micro- reducing enrichment analysed by the protein-SIP tech- bial communities in hydrocarbon-contaminated aquifers nique, with their observations indicating syntrophy be- (Kleinsteuber et al. 2012), the use of stable isotope probing tween a benzene-fermenting clostridial group, a (SIP) to identify anaerobic benzene and toluene degraders sulphate-reducing deltaproteobacterial group that uses (Cupples 2011) and the degradation of benzene under anaer- the metabolites generated during benzene fermentation obic conditions (Lovley 2000; Coates et al. 2002; Weelink and a putative scavenger group from Bacteroidetes/ et al. 2010;Vogtetal.2011) have been published during the Chlorobi (Taubert et al. 2012). This result is consistent past 12 years. with that of a previous study on the same consortium where acetate and hydrogen were strongly suggested as intermediate metabolites in the anaerobic benzene degra- Pure cultures capable of anaerobic benzene degradation dation process (Rakoczy et al. 2011). Members of the Cryptanaerobacter/Pelotomaculum group are suggested Until a few years ago there were only a few pure cultures able to be the benzene-fermenting group, as has been indicated to degrade benzene anaerobically, and all of these were in other studies from the same group (Kleinsteuber et al. coupled to nitrate reduction: an Azoarcus strain DN11 and 2008;Herrmannetal.2010). Moreover, the syntrophic AN9 (Kasai et al. 2006), a Bacillus cereus strain (Dou et al. interactions and the presence of the Peptococcaceae mem- 2010)andDechloromonas strains JJ and
Load more

Recommended publications
  • Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
    microorganisms Article Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens Maryam Rezadehbashi and Susan A. Baldwin * Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-604-822-1973 Received: 2 January 2018; Accepted: 17 February 2018; Published: 23 February 2018 Abstract: Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.
    [Show full text]
  • Dehalobacter Restrictus PER-K23T
    Standards in Genomic Sciences (2013) 8:375-388 DOI:10.4056/sigs.3787426 Complete genome sequence of Dehalobacter restrictus T PER-K23 Thomas Kruse1*, Julien Maillard2, Lynne Goodwin3,4, Tanja Woyke3, Hazuki Teshima3,4, David Bruce3,4, Chris Detter3,4, Roxanne Tapia3,4, Cliff Han3,4, Marcel Huntemann3, Chia-Lin Wei3, James Han3, Amy Chen3, Nikos Kyrpides3, Ernest Szeto3, Victor Markowitz3, Natalia Ivanova3, Ioanna Pagani3, Amrita Pati3, Sam Pitluck3, Matt Nolan3, Christof Holliger2, and Hauke Smidt1 1 Wageningen University, Agrotechnology and Food Sciences, Laboratory of Microbiology, Dreijenplein 10, NL-6703 HB Wageningen, The Netherlands. 2 Ecole Polytechnique Fédérale de Lausanne (EPFL), School of Architecture, Civil and Environmental Engineering, Laboratory for Environmental Biotechnology, Station 6, CH- 1015 Lausanne, Switzerland. 3 DOE Joint Genome Institute, Walnut Creek, California, USA 4 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA *Corresponding author: Thomas Kruse ([email protected]) Keywords: Dehalobacter restrictus type strain, anaerobe, organohalide respiration, PCE, TCE, reductive dehalogenases Dehalobacter restrictus strain PER-K23 (DSM 9455) is the type strain of the species Dehalobacter restrictus. D. restrictus strain PER-K23 grows by organohalide respiration, cou- pling the oxidation of H2 to the reductive dechlorination of tetra- or trichloroethene. Growth has not been observed with any other electron donor or acceptor, nor has fermentative growth been shown. Here we introduce the first full genome of a pure culture within the ge- nus Dehalobacter. The 2,943,336 bp long genome contains 2,826 protein coding and 82 RNA genes, including 5 16S rRNA genes. Interestingly, the genome contains 25 predicted re- ductive dehalogenase genes, the majority of which appear to be full length.
    [Show full text]
  • Status Report on Innovative in Situ Treatment Technologies Available to Remediate Perchlorate- Contaminated Groundwater
    (ITRC, 2005) Status Report on Innovative In Situ Remediation Technologies Available to Treat Perchlorate-Contaminated Groundwater August 2006 Prepared By Jennifer Raye Hoponick National Network for Environmental Management Studies Fellow for U.S. Environmental Protection Agency Office of Superfund Remediation & Technology Innovation Technology Innovation & Field Services Division Washington, D.C. www.epa.gov www.clu-in.org Status Report on In Situ Treatment Technologies to Remediate Perchlorate-Contaminated Groundwater NOTICE This document was prepared by a National Network of Environmental Management studies grantee under a fellowship from the U.S. Environmental Protection Agency. This report was not subject to EPA peer review or technical review. The EPA makes no warranties, expressed or implied, including without limitation, warranty for completeness, accuracy, or usefulness of the information, warranties as to the merchantability, or fitness for a particular purpose. Moreover, the listing of any technology, corporation, company, person, or facility in this report does not constitute endorsement, approval, or recommendation by the EPA. The report contains information attained from a wide variety of currently available sources, including project documents, reports, periodicals, Internet websites, and personal communication with both academically and commercially employed sources. No attempts were made to independently confirm the resources used. It has been reproduced to help provide federal agencies, states, consulting engineering firms, private industries, and technology developers with information on the current status of this project. About the National Network for Environmental Management Studies The National Network for Environmental Management Studies (NNEMS) is a comprehensive fellowship program managed by the Environmental Education Division of EPA. The purpose of the NNEMS Program is to provide students with practical research opportunities and experiences.
    [Show full text]
  • Syntrophic Butyrate and Propionate Oxidation Processes 491
    Environmental Microbiology Reports (2010) 2(4), 489–499 doi:10.1111/j.1758-2229.2010.00147.x Minireview Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanismsemi4_147 489..499 Nicolai Müller,1† Petra Worm,2† Bernhard Schink,1* a cytoplasmic fumarate reductase to drive energy- Alfons J. M. Stams2 and Caroline M. Plugge2 dependent succinate oxidation. Furthermore, we 1Faculty for Biology, University of Konstanz, D-78457 propose that homologues of the Thermotoga mar- Konstanz, Germany. itima bifurcating [FeFe]-hydrogenase are involved 2Laboratory of Microbiology, Wageningen University, in NADH oxidation by S. wolfei and S. fumaroxidans Dreijenplein 10, 6703 HB Wageningen, the Netherlands. to form hydrogen. Summary Introduction In anoxic environments such as swamps, rice fields In anoxic environments such as swamps, rice paddy fields and sludge digestors, syntrophic microbial communi- and intestines of higher animals, methanogenic commu- ties are important for decomposition of organic nities are important for decomposition of organic matter to matter to CO2 and CH4. The most difficult step is the CO2 and CH4 (Schink and Stams, 2006; Mcinerney et al., fermentative degradation of short-chain fatty acids 2008; Stams and Plugge, 2009). Moreover, they are the such as propionate and butyrate. Conversion of these key biocatalysts in anaerobic bioreactors that are used metabolites to acetate, CO2, formate and hydrogen is worldwide to treat industrial wastewaters and solid endergonic under standard conditions and occurs wastes. Different types of anaerobes have specified only if methanogens keep the concentrations of these metabolic functions in the degradation pathway and intermediate products low. Butyrate and propionate depend on metabolite transfer which is called syntrophy degradation pathways include oxidation steps of (Schink and Stams, 2006).
    [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]
  • Journal of Molecular Microbiology and Biotechnology "Special Issue
    1 Journal of Molecular Microbiology and Biotechnology "Special Issue - Anaerobic Hydrocarbon 2 Degradation" 3 Review article 4 5 Stable isotope probing approaches to study anaerobic hydrocarbon degradation and 6 degraders 7 8 Carsten Vogt1, Tillmann Lueders2, Hans H. Richnow1, Martin Krüger3, Martin von Bergen4,5,6, 9 Jana Seifert7* 10 11 1 UFZ - Helmholtz Centre for Environmental Research, Department of Isotope 12 Biogeochemistry, Leipzig, Germany 13 2 Helmholtz Zentrum München—German Research Center for Environmental Health, Institute 14 for Groundwater Ecology, Neuherberg, Germany 15 3 Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany 16 4 UFZ - Helmholtz Centre for Environmental Research, Department of Proteomics, Leipzig, 17 Germany 18 5 UFZ - Helmholtz Centre for Environmental Research, Department of Metabolomics, Leipzig, 19 Germany 20 6 Aalborg University, Department of Biotechnology, Chemistry and Environmental 21 Engineering, Aalborg University, Aalborg, Denmark 22 7 University of Hohenheim, Institute of Animal Science, Stuttgart, Germany 23 24 *corresponding author: 25 University of Hohenheim 26 Institute of Animal Science 27 Emil-Wolff-Str. 6-10 28 70599 Stuttgart, Germany 29 [email protected] 30 31 32 Abstract 33 Stable isotope probing (SIP) techniques have become state-of-the-art in microbial ecology 34 over the last ten years, allowing for the targeted detection and identification of organisms, 35 metabolic pathways, and elemental fluxes active in specific processes within complex 36 microbial communities. For studying anaerobic hydrocarbon degrading microbial communities, 37 four stable isotope techniques have been used so far: DNA/RNA-SIP, PFLA-SIP, protein-SIP, 38 and single cell-SIP by nanoSIMS or confocal Raman microscopy.
    [Show full text]
  • Enhanced Nitrous Oxide Production in Denitrifying Dechloromonas Aromatica Strain RCB Under Salt Or Alkaline Stress Conditions
    W&M ScholarWorks VIMS Articles Virginia Institute of Marine Science 6-5-2019 Enhanced Nitrous Oxide Production in Denitrifying Dechloromonas aromatica Strain RCB Under Salt or Alkaline Stress Conditions H Han BK Song Virginia Institute of Marine Science MJ Song S Yoon Follow this and additional works at: https://scholarworks.wm.edu/vimsarticles Part of the Microbiology Commons Recommended Citation Han, H; Song, BK; Song, MJ; and Yoon, S, "Enhanced Nitrous Oxide Production in Denitrifying Dechloromonas aromatica Strain RCB Under Salt or Alkaline Stress Conditions" (2019). VIMS Articles. 1668. https://scholarworks.wm.edu/vimsarticles/1668 This Article is brought to you for free and open access by the Virginia Institute of Marine Science at W&M ScholarWorks. It has been accepted for inclusion in VIMS Articles by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. fmicb-10-01203 June 3, 2019 Time: 16:1 # 1 ORIGINAL RESEARCH published: 05 June 2019 doi: 10.3389/fmicb.2019.01203 Enhanced Nitrous Oxide Production in Denitrifying Dechloromonas aromatica Strain RCB Under Salt or Alkaline Stress Conditions Heejoo Han1, Bongkeun Song1,2, Min Joon Song1 and Sukhwan Yoon1* 1 Department of Civil and Environmental Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea, 2 Department of Biological Sciences, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA, United States Salinity and pH have direct and indirect impacts on the growth and metabolic activities of microorganisms. In this study, the effects of salt and alkaline stresses on the kinetic balance between nitrous oxide (N2O) production and consumption in the denitrification Edited by: pathway of Dechloromonas aromatica strain RCB were examined.
    [Show full text]
  • Desulfotomaculum Acetoxidans Type Strain (5575)
    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575). Permalink https://escholarship.org/uc/item/53z4r149 Journal Standards in genomic sciences, 1(3) ISSN 1944-3277 Authors Spring, Stefan Lapidus, Alla Schröder, Maren et al. Publication Date 2009-11-22 DOI 10.4056/sigs.39508 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2009) 1: 242-253 DOI:10.4056/sigs.39508 Complete genome sequence of Desulfotomaculum acetox- idans type strain (5575T) Stefan Spring1, Alla Lapidus2, Maren Schröder1, Dorothea Gleim1, David Sims3, Linda Meincke3, Tijana Glavina Del Rio2, Hope Tice2, Alex Copeland2, Jan-Fang Cheng2, Susan Lucas2, Feng Chen2, Matt Nolan2, David Bruce2,3, Lynne Goodwin2,3, Sam Pitluck2, Natalia Ivanova2, Konstantinos Mavromatis2, Natalia Mikhailova2, Amrita Pati2, Amy Chen4, Krish- na Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Patrick Chain2,6, Elizabeth Saunders2,3, Thomas Brettin2,3, John C. Detter2,3, Markus Göker1, Jim Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2, Nikos C Kyr- pides2, Hans-Peter Klenk1*, and Cliff Han2,3 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Labora- tory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 Lawrence Livermore National Laboratory, Livermore, California, USA 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: sulfate-reducer, hydrogen sulfide, piggery waste, mesophile, motile, sporulating, obligate anaerobic, Peptococcaceae, Clostridiales, Firmicutes.
    [Show full text]
  • The Key Microorganisms for Anaerobic Degradation of Pentachlorophenol in Paddy Soil As Revealed by Stable Isotope Probing
    Journal of Hazardous Materials 298 (2015) 252–260 Contents lists available at ScienceDirect Journal of Hazardous Materials journal homepage: www.elsevier.com/locate/jhazmat The key microorganisms for anaerobic degradation of pentachlorophenol in paddy soil as revealed by stable isotope probing Hui Tong a,b,c, Chengshuai Liu d, Fangbai Li a,∗, Chunling Luo b, Manjia Chen a, Min Hu a a Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, PR China b Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, PR China c University of Chinese Academy of Sciences, Beijing 100049, PR China d State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550009, PR China highlights graphical abstract • SIP suggested that Dechloromonas can mineralize PCP in soil. • Methanosaeta and Methanocella acquired PCP-derived carbon. • Lactate enhanced microbial degrada- tion of PCP in soil. article info abstract Article history: Pentachlorophenol (PCP) is a common residual persistent pesticide in paddy soil and has resulted in harm- Received 3 March 2015 ful effect on soil ecosystem. The anaerobic microbial transformation of PCP, therefore, has been received Received in revised form 26 May 2015 much attentions, especially the functional microbial communities for the reductive transformation. How- Accepted 28 May 2015 ever, the key functional microorganisms for PCP mineralization in the paddy soil still remain unknown. In Available online 30 May 2015 this work, DNA-based stable isotope probing (SIP) was applied to explore the key microorganisms respon- sible for PCP mineralization in paddy soil.
    [Show full text]
  • D. Nigrificans and D. Carboxydivorans Are Gram- “Clostridium Nigrificans” by Werkman and Weaver Positive, Sulfate-Reducing, Rod Shaped Bacteria (1927) [2]
    Standards in Genomic Sciences (2014) 9:655-675 DOI:10.4056/sig s.4718645 Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans Michael Visser1, Sofiya N. Parshina2, Joana I. Alves3, Diana Z. Sousa1,3, Inês A. C. Pereira4, Gerard Muyzer5, Jan Kuever6, Alexander V. Lebedinsky2, Jasper J. Koehorst7, Petra Worm1, Caroline M. Plugge1, Peter J. Schaap7, Lynne A. Goodwin8,9, Alla Lapidus10,11, Nikos C. Kyrpides8, Janine C. Detter9, Tanja Woyke8, Patrick Chain 8,9, Karen W. Davenport8, 9, Stefan Spring 12, Manfred Rohde13, Hans Peter Klenk12, Alfons J.M. Stams1,3 1Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands 2Wingradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia 3Centre of Biological Engineering, University of Minho, Braga, Portugal 4Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal 5Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands 6Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany 7Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands 8DOE Joint Genome Institute, Walnut Creek, California, USA 9Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 10Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia 11 Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia 12Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany 13HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany Correspondence: Michael Visser ([email protected]) Keywords: Thermophilic spore-forming anaerobes, sulfate reduction, carboxydotrophic, Peptococcaceae, Clostr idiales.
    [Show full text]
  • Scientific Highlight April 2010
    Scientific Highlight April 2010 co-ordinated with the Director of the Institute Institute Institute of Groundwater Ecology PSP-Element: G-504300-002 Person to contact for further enquiries: Dr. Tillmann Lüders, [email protected], Tel. 3687 Title of the Highlight: DNA-SIP identifies sulfate-reducing Clostridia as important toluene-degraders in tar-oil-contaminated aquifer sediment Keywords: Groundwater resources, ecosystem services, natural attenuation, BTEX, microbial key-players Central statement of the Highlight in one sentence: We have proven that uncultured members of the Clostridia, classically considered as fermenters and often also pathogenic microbes, are responsible for toluene degradation under sulfate-reduction in a contaminated aquifer. Text of the Highlight: Groundwater is the most important drinking water resources of our society. Still, global groundwater resources are constantly challenged by a multitude of contaminants such as aromatic hydrocarbons. Especially in anaerobic habitats, a large diversity of unrecognized microbes is hypothesized to be responsible for their degradation. However, the true identity of these populations and the factors that control their activities in situ are still poorly understood. Here, by using innovative 13C-labelling technologies for DNA, we have identified the most active sulfate-reducing toluene degraders within a diverse aquifer microbial community from a former Gasworks site in Germany. Surprisingly, the identified key-players were related to Desulfosporosinus spp. within the Peptococcaceae (Clostridia). Up to now, members of the Clostridia have not been recognized as important sulfate-reducing contaminant degraders, rather they are classically considered as fermenters and often also pathogenic microbes. Also, carbon flow from the contaminant into degraders was unexpectedly low, pointing toward high ratios of heterotrophic CO2-fixation during assimilation of acetyl-CoA 1 from toluene, which may represent an important and unrecognized ecophysiological constraint for these degraders.
    [Show full text]
  • 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.
    [Show full text]