DOCSLIB.ORG

Genes and Microbes Impacting the Geochemistry of Arsenic Mobilised Aquifers in Bangladesh and Cambodia

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genes and Microbes Impacting the Geochemistry of Arsenic Mobilised Aquifers in Bangladesh and Cambodia Genes and Microbes Impacting the Geochemistry of Arsenic Mobilised Aquifers in Bangladesh and Cambodia A thesis submitted to The University of Manchester for the degree of Doctor of Philosophy in the Faculty of Science and Engineering 2017 Edwin Thadheu Gnanaprakasam School of Earth and Environmental Sciences 0 Table of Contents List of Figures …………………………………………………………………………………………………………….. 6 List of Tables ……………………………………………………………………………………………………………… 9 List of Abbreviations………………………………………………………………………………………………….. 11 Thesis Abstract …………………………………………………………………………………………………………. 13 Declaration ……………………………………………………………………………………………………………….. 14 Copyright Statement …………………………………………………………………………………………………. 15 Acknowledgements ………………………………………………………………………………………………….. 16 About the Author ……………………………………………………………………………………………………… 18 Chapter 1 : Introduction ............................................................................................................... 19 1.1. Project context ................................................................................................................. 19 1.2. Aims and objectives ....................................................................................................... 20 1.3. Thesis structure .............................................................................................................. 22 1.4. Paper status and author contributions ......................................................................... 25 Chapter 2 : Literature Review ...................................................................................................... 27 2.1. Arsenic general introduction ......................................................................................... 27 2.2. Arsenic geochemistry .................................................................................................... 30 2.2.1. Arsenic minerals and compounds ......................................................................... 30 2.2.2. Arsenic speciation ................................................................................................... 31 2.3. Arsenic bio-geochemical cycle ...................................................................................... 33 2.4. Geomicrobiology of arsenic mobilisation..................................................................... 35 2.4.1. Extracellular interaction ........................................................................................ 35 2.4.2. Intracellular interaction ........................................................................................ 36 2.4.2.1. Methylation and demethylation ..................................................................... 36 2.4.2.2. As(III) oxidation ............................................................................................. 38 2.4.2.3. As(V) reduction............................................................................................... 38 2.5. Role of other elements in the arsenic biogeochemical cycle ....................................... 40 2.6. Metagenomics of arsenic ............................................................................................... 41 2.6.1. 16S rRNA gene based community analysis ............................................................ 42 2.6.2. Functional genes analysis (targeted amplification and sequencing) .................. 44 2.6.3. Whole genome sequencing (WGS) based community analysis and gene annotation ....................................................................................................................... 50 2.7. Metatranscriptomic analysis of arsenic mRNAs ........................................................... 51 2.8. Metaproteomic analysis of arsenic proteins ................................................................. 52 2.9. Summary ........................................................................................................................ 54 1 Chapter 3 : Methodology ............................................................................................................. 55 3.1. Introduction ................................................................................................................... 55 3.2. Sampling methods ......................................................................................................... 55 3.3. General methods involved in the molecular analysis................................................... 57 3.3.1. DNA extraction ....................................................................................................... 57 3.3.2. RNA extraction ....................................................................................................... 58 3.3.3. Protein extraction .................................................................................................. 58 3.3.4. Primer design ......................................................................................................... 59 3.3.5. Thermal cycler and polymerase chain reaction (PCR) ......................................... 59 3.3.6. Gel electrophoresis and documentation ............................................................... 59 3.3.7. DNA and RNA quantification ................................................................................ 60 3.3.8. SequalPrep™ normalisation of PCR products ....................................................... 62 3.3.9. Pooling ................................................................................................................... 62 3.3.10. Next generation sequencing ................................................................................. 62 3.3.10.1. Roche/454 (Pyrosequencing) ......................................................................... 63 3.3.10.2. MiSeq and HiSeq (Illumina) .......................................................................... 65 3.3.11. High performance computing (HPC) ................................................................... 66 3.3.12. Bioinformatics tools .............................................................................................. 66 3.4. Metagenomic methods .................................................................................................. 69 3.4.1. 16S rRNA gene based community analysis ............................................................ 70 3.4.1.1. Roche 454 pyrosequencing and QIIME pipeline ............................................ 70 3.4.1.2. MiSeq and the Amplicon analysis pipeline .................................................... 72 3.4.2. WGS based metagenomic analysis ........................................................................ 74 3.5. Metatranscriptomics methods ...................................................................................... 76 3.6. Proteomic methods ....................................................................................................... 77 3.7. Geochemical methods ................................................................................................... 78 3.7.1. pH and Eh ............................................................................................................... 78 3.7.2. Diffuse reflectance spectrum: ................................................................................ 79 3.7.3. X-Ray fluorescence ................................................................................................. 79 3.7.4. EXAFS spectra for iron and arsenic ....................................................................... 79 3.7.5. Analysis of trace elements ...................................................................................... 81 3.8. Statistical methods ........................................................................................................ 82 3.8.1. O2-PLS method (Orthogonal Projection to Latent Structure) ............................. 82 3.8.2. Spearman’s rank correlation ................................................................................. 83 2 Chapter 4 : Paper I - The microbial community structure and arsenic biogeochemistry in two arsenic impacted aquifers in Bangladesh…………………………… .............................................. 84 4.1. Introduction ................................................................................................................... 85 4.2. Materials and methods .................................................................................................. 89 4.2.1. Study site ................................................................................................................ 89 4.2.2. Sample collection ................................................................................................... 90 4.2.3. Sediment chemistry ................................................................................................ 91 4.2.3.1. X-Ray fluorescence ........................................................................................... 91 4.2.3.2. EXAFS spectra for iron and arsenic ................................................................ 92 4.2.4. Aqueous chemistry ................................................................................................ 94 4.2.5. Microbial Ecology .................................................................................................. 94 4.2.5.1. 16S rRNA Based Bacterial Community Analysis ............................................. 94 4.2.5.2. Functional Gene Analyses .............................................................................
Load more

Recommended publications
  • And Methane-Oxidizing Microorganisms in a Dutch Drinking Water Treatment Plant
    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.19.103440; this version posted May 20, 2020. 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. Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in a Dutch drinking water treatment plant Lianna Poghosyan, Hanna Koch, Jeroen Frank, Maartje A.H.J. van Kessel, Geert Cremers, Theo van Alen, Mike S.M. Jetten, Huub J.M. Op den Camp, Sebastian Lücker* 5 Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, the Netherlands *Correspondence: [email protected] Keywords Sand filtration; nitrification; comammox Nitrospira; methanotrophic bacteria; metagenomics 10 Highlights • Microbial distribution was mainly influenced by sampling location within the DWTP. • Clade A comammox Nitrospira were the most abundant nitrifying guild in samples from the primary sand filter, while clade B dominated in samples from wall biofilm and the secondary filter. 15 • A novel methanotrophic bacterium affiliated with the Methylophilaceae family comprised the largest bacterial fraction in the primary sand filter. bioRxiv preprint doi: https://doi.org/10.1101/2020.05.19.103440; this version posted May 20, 2020. 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. Abstract Elevated concentrations of ammonium and methane in groundwater can cause severe problems during drinking water production.
    [Show full text]
  • Alteration of the Immune Response and the Microbiota of the Skin During a Natural Infection by Vibrio Harveyi in European Seabass (Dicentrarchus Labrax)
    microorganisms Article Alteration of the Immune Response and the Microbiota of the Skin during a Natural Infection by Vibrio harveyi in European Seabass (Dicentrarchus labrax) María Cámara-Ruiz 1, Isabel M. Cerezo 2 , Francisco A. Guardiola 1 , José María García-Beltrán 1, M. Carmen Balebona 2 , Miguel Ángel Moriñigo 2 and María Ángeles Esteban 1,* 1 Immunobiology for Aquaculture Group, Department of Cell Biology and Histology, Faculty of Biology, Campus Regional de Excelencia Internacional “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain; [email protected] (M.C.-R.); [email protected] (F.A.G.); [email protected] (J.M.G.-B.) 2 Departamento de Microbiología, Universidad de Málaga, 29071 Málaga, Spain; [email protected] (I.M.C.); [email protected] (M.C.B.); [email protected] (M.Á.M.) * Correspondence: [email protected] Abstract: Disease outbreaks continue to represent one of the main bottlenecks for the sustainable development of the aquaculture industry. In marine aquaculture, many species from the Vibrio genus are serious opportunistic pathogens responsible for significant losses to producers. In this study, the effects on the immune response and the skin microbiota of European sea bass (Dicentrarchus labrax) were studied after a natural disease outbreak caused by V. harveyi. Data obtained from infected Citation: Cámara-Ruiz, M.; and non-infected fish were studied and compared. Regarding the local immune response (skin Cerezo, I.M.; Guardiola, F.A.; mucus) a decrease in the protease activity was observed in infected fish. Meanwhile, at a systemic García-Beltrán, J.M.; Balebona, M.C.; level, a decrease in protease and lysozyme activity was reported while peroxidase activity showed a Moriñigo, M.Á.; Esteban, M.Á.
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • Drylands Soil Bacterial Community Is Affected by Land Use Change and Different Irrigation Practices in the Mezquital Valley
    www.nature.com/scientificreports OPEN Drylands soil bacterial community is afected by land use change and diferent irrigation practices in the Received: 23 June 2017 Accepted: 3 January 2018 Mezquital Valley, Mexico Published: xx xx xxxx Kathia Lüneberg1, Dominik Schneider2, Christina Siebe1 & Rolf Daniel 2 Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater afects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specifc adaptations to drought and sodium content in specifc land use systems. Predicted functionality profles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles difered among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identifed potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profles provided extensive understanding of the short- term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands. Drylands are defned as regions with arid, semi-arid, and dry sub humid climate with an annual precipitation/ evapotranspiration potential ratio (P/PET)1 ranging from 0.05 to 0.652.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Fictibacillus Phosphorivorans Gen. Nov., Sp. Nov. and Proposal to Reclassify
    International Journal of Systematic and Evolutionary Microbiology (2013), 63, 2934–2944 DOI 10.1099/ijs.0.049171-0 Fictibacillus phosphorivorans gen. nov., sp. nov. and proposal to reclassify Bacillus arsenicus, Bacillus barbaricus, Bacillus macauensis, Bacillus nanhaiensis, Bacillus rigui, Bacillus solisalsi and Bacillus gelatini in the genus Fictibacillus Stefanie P. Glaeser,1 Wolfgang Dott,2 Hans-Ju¨rgen Busse3 and Peter Ka¨mpfer1 Correspondence 1Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, D-35392 Giessen, Germany Peter Ka¨mpfer 2Institut fu¨r Hygiene und Umweltmedizin, RWTH Aachen, Germany peter.kaempfer 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, Veterina¨rmedizinische Universita¨t, A-1210 Wien, @umwelt.uni-giessen.de Austria A Gram-positive-staining, aerobic, endospore-forming bacterium (Ca7T) was isolated from a bioreactor showing extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strain Ca7T was grouped in the genus Bacillus, most closely related to Bacillus nanhaiensis JSM 082006T (100 %), Bacillus barbaricus V2-BIII-A2T (99.2 %) and Bacillus arsenicus Con a/3T (97.7 %). Moderate 16S rRNA gene sequence similarities were found to the type strains of the species Bacillus gelatini and Bacillus rigui (96.4 %), Bacillus macauensis (95.1 %) and Bacillus solisalsi (96.1 %). All these species were grouped into a monophyletic cluster and showed very low sequence similarities (,94 %) to the type species of the genus Bacillus, Bacillus subtilis.Thequinonesystemof strain Ca7T consists predominantly of menaquinone MK-7. The polar lipid profile exhibited the major compounds diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. In addition, minor compounds of an unidentified phospholipid and an aminophospholipid were detected. No glycolipids were found in strain Ca7T, which was consistent with the lipid profiles of B.
    [Show full text]
  • S41598-020-62411-2.Pdf
    www.nature.com/scientificreports OPEN Microbial Diversity and Metabolic Potential in the Stratifed Sansha Yongle Blue Hole in the South China Sea Peiqing He1,2,3*, Linping Xie1,2, Xuelei Zhang1,2, Jiang Li1,3, Xuezheng Lin1,3, Xinming Pu1,2, Chao Yuan1,2, Ziwen Tian4 & Jie Li5 The Sansha Yongle Blue Hole is the world’s deepest (301 m) underwater cave and has a sharp redox gradient, with oligotrophic, anoxic, and sulfdic bottom seawater. In order to discover the microbial communities and their special biogeochemical pathways in the blue hole, we analyzed the 16S ribosomal RNA amplicons and metagenomes of microbials from seawater depths with prominent physical, chemical, and biological features. Redundancy analysis showed that dissolved oxygen was the most important factor afecting the microbial assemblages of the blue hole and surrounding open sea waters, and signifcantly explained 44.7% of the total variation, followed by silicate, temperature, sulfde, ammonium, methane, nitrous oxide, nitrate, dissolved organic carbon, salinity, particulate organic carbon, and chlorophyll a. We identifed a bloom of Alteromonas (34.9%) at the primary nitrite maximum occurring in close proximity to the chlorophyll a peak in the blue hole. Genomic potential for nitrate reduction of Alteromonas might contribute to this maximum under oxygen decrease. Genes that would allow for aerobic ammonium oxidation, complete denitrifcation, and sulfur- oxidization were enriched at nitrate/nitrite-sulfde transition zone (90 and 100 m) of the blue hole, but not anammox pathways. Moreover, γ-Proteobacterial clade SUP05, ε-Proteobacterial genera Sulfurimonas and Arcobacter, and Chlorobi harbored genes for sulfur-driven denitrifcation process that mediated nitrogen loss and sulfde removal.
    [Show full text]
  • Chlorate Reduction by an Acetogenic Bacterium, Sporomusa Sp., Isolated from an Underground Gas Storage
    Appl Microbiol Biotechnol (2010) 88:595–603 DOI 10.1007/s00253-010-2788-8 ENVIRONMENTAL BIOTECHNOLOGY (Per)chlorate reduction by an acetogenic bacterium, Sporomusa sp., isolated from an underground gas storage Melike Balk & Farrakh Mehboob & Antonie H. van Gelder & W. Irene C. Rijpstra & Jaap S. Sinninghe Damsté & Alfons J. M. Stams Received: 12 March 2010 /Revised: 16 July 2010 /Accepted: 16 July 2010 /Published online: 3 August 2010 # The Author(s) 2010. This article is published with open access at Springerlink.com Abstract A mesophilic bacterium, strain An4, was isolated Keywords Sporomusa sp. Perchlorate . from an underground gas storage reservoir with methanol Underground gas storage as substrate and perchlorate as electron acceptor. Cells were Gram-negative, spore-forming, straight to curved rods, 0.5– 0.8 μm in diameter, and 2–8 μm in length, growing as Introduction single cells or in pairs. The cells grew optimally at 37°C, and the pH optimum was around 7. Strain An4 converted Perchlorate and chlorate are used in a wide range of various alcohols, organic acids, fructose, acetoin, and applications. Chlorate is used as an herbicide or defoliant. H2/CO2 to acetate, usually as the only product. Succinate Perchlorate salts have been manufactured in large quantities was decarboxylated to propionate. The isolate was able to and used as ingredients in solid rocket fuels, highway safety respire with (per)chlorate, nitrate, and CO2. The G+C flares, air bag inflators, fireworks, and matches (Renner content of the DNA was 42.6 mol%. Based on the 16S 1998; Logan 2001; Motzer 2001). Perchlorate is chemically rRNA gene sequence analysis, strain An4 was most closely very stable and has low reactivity even in highly reducing related to Sporomusa ovata (98% similarity).
    [Show full text]
  • Bacterial Diversity and Functional Analysis of Severe Early Childhood
    www.nature.com/scientificreports OPEN Bacterial diversity and functional analysis of severe early childhood caries and recurrence in India Balakrishnan Kalpana1,3, Puniethaa Prabhu3, Ashaq Hussain Bhat3, Arunsaikiran Senthilkumar3, Raj Pranap Arun1, Sharath Asokan4, Sachin S. Gunthe2 & Rama S. Verma1,5* Dental caries is the most prevalent oral disease afecting nearly 70% of children in India and elsewhere. Micro-ecological niche based acidifcation due to dysbiosis in oral microbiome are crucial for caries onset and progression. Here we report the tooth bacteriome diversity compared in Indian children with caries free (CF), severe early childhood caries (SC) and recurrent caries (RC). High quality V3–V4 amplicon sequencing revealed that SC exhibited high bacterial diversity with unique combination and interrelationship. Gracillibacteria_GN02 and TM7 were unique in CF and SC respectively, while Bacteroidetes, Fusobacteria were signifcantly high in RC. Interestingly, we found Streptococcus oralis subsp. tigurinus clade 071 in all groups with signifcant abundance in SC and RC. Positive correlation between low and high abundant bacteria as well as with TCS, PTS and ABC transporters were seen from co-occurrence network analysis. This could lead to persistence of SC niche resulting in RC. Comparative in vitro assessment of bioflm formation showed that the standard culture of S. oralis and its phylogenetically similar clinical isolates showed profound bioflm formation and augmented the growth and enhanced bioflm formation in S. mutans in both dual and multispecies cultures. Interaction among more than 700 species of microbiota under diferent micro-ecological niches of the human oral cavity1,2 acts as a primary defense against various pathogens. Tis has been observed to play a signifcant role in child’s oral and general health.
    [Show full text]
  • Molecular Phylogenetic Analyses of Diverse Cntl Alone (A) and Cntlm (B) Amino Acid Sequences from Bacteria
    Electronic Supplementary Material (ESI) for Metallomics. This journal is © The Royal Society of Chemistry 2020 Supplementary Figures A B 96 Paenibacillus amylolyticus NBRC-15957 100 Paenibacillus amylolyticus NBRC-15957 49 Paenibacillus pabuli NBRC13638 91 Paenibacillus pabuli NBRC13638 28 50 Bacillus gaemokensis BL3-6 Bacillus gaemokensis BL3-6 67 99 Paenibacillus mucilaginosus K02-(B2K11200) Paenibacillus mucilaginosus K02-(B2K11200) 56 Paenibacillus vortex V453 98 Paenibacillus vortex V453 Lysinibacillus sphaericus C3-41 Lysinibacillus sphaericus C3-41 73 97 99 Lysinibacillus xylanilyticus JKR-42 100 Lysinibacillus xylanilyticus JKR-42 Actinosynnema mirum DSM43827 Actinosynnema mirum DSM43827 Austwickia chelonae NBRC105200 Austwickia chelonae NBRC105200 97 100 99 100 91 Glutamicibacter mysorens NBRC103060 98 Glutamicibacter mysorens NBRC103060 100 Arthrobacter arilaitensis RE117 100 Arthrobacter arilaitensis RE117 Staphylococcus pseudintermedius LMG-22219 Staphylococcus pseudintermedius LMG-22219 Staphylococcus epidermidis ATCC-12228 Staphylococcus epidermidis ATCC-12228 100 100 99 Staphylococcus aureus Mu50 100 Staphylococcus aureus Mu50 100 100 Staphylococcus argenteus 3688STDY6125130 100 Staphylococcus argenteus 3688STDY6125130 100 Fusobacterium varium NCTC10560 Fusobacterium mortiferum ATCC-9817 96 Fusobacterium ulcerans NCTC12112 100 Fusobacterium varium NCTC10560 Fusobacterium mortiferum ATCC-9817 100 Fusobacterium ulcerans NCTC12112 100 Fictibacillus phosphorivorans Ca7 100 Fictibacillus phosphorivorans Ca7 61 Fictibacillus arsenicus
    [Show full text]
  • Repeated Anaerobic Microbial Redox Cycling of Iron †
    APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2011, p. 6036–6042 Vol. 77, No. 17 0099-2240/11/$12.00 doi:10.1128/AEM.00276-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved. Repeated Anaerobic Microbial Redox Cycling of Ironᰔ† Aaron J. Coby,1‡ Flynn Picardal,2 Evgenya Shelobolina,1 Huifang Xu,1 and Eric E. Roden1* Department of Geoscience, University of Wisconsin, Madison, Wisconsin 53706,1 and School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 474052 Received 7 February 2011/Accepted 28 June 2011 Some nitrate- and Fe(III)-reducing microorganisms are capable of oxidizing Fe(II) with nitrate as the electron acceptor. This enzymatic pathway may facilitate the development of anaerobic microbial communities that take advantage of the energy available during Fe-N redox oscillations. We examined this phenomenon in synthetic Fe(III) oxide (nanocrystalline goethite) suspensions inoculated with microflora from freshwater river floodplain sediments. Nitrate and acetate were added at alternate intervals in order to induce repeated cycles of microbial Fe(III) reduction and nitrate-dependent Fe(II) oxidation. Addition of nitrate to reduced, acetate- depleted suspensions resulted in rapid Fe(II) oxidation and accumulation of ammonium. High-resolution transmission electron microscopic analysis of material from Fe redox cycling reactors showed amorphous coatings on the goethite nanocrystals that were not observed in reactors operated under strictly nitrate- or Fe(III)-reducing conditions. Microbial communities associated with N and Fe redox metabolism were assessed using a combination of most-probable-number enumerations and 16S rRNA gene analysis. The nitrate- reducing and Fe(III)-reducing cultures were dominated by denitrifying Betaproteobacteria (e.g., Dechloromonas) and Fe(III)-reducing Deltaproteobacteria (Geobacter), respectively; these same taxa were dominant in the Fe cycling cultures.
    [Show full text]
  • Bacterial Community Dynamics During the Early Stages of Biofilm Formation
    Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration DOUTERELO, I., SHARPE, Rebecca <http://orcid.org/0000-0002-2783-9215> and BOXALL, J. Available from Sheffield Hallam University Research Archive (SHURA) at: http://shura.shu.ac.uk/9517/ This document is the author deposited version. You are advised to consult the publisher's version if you wish to cite from it. Published version DOUTERELO, I., SHARPE, Rebecca and BOXALL, J. (2014). Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration. Journal of applied microbiology, 117 (1), 286-301. Copyright and re-use policy See http://shura.shu.ac.uk/information.html Sheffield Hallam University Research Archive http://shura.shu.ac.uk Journal of Applied Microbiology ISSN 1364-5072 ORIGINAL ARTICLE Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration I. Douterelo1, R. Sharpe2 and J. Boxall1 1 Pennine Water Group, Department of Civil and Structural Engineering, University of Sheffield, Sheffield, UK 2 School of Civil and Building Engineering, Loughborough University, Loughborough, UK Keywords Abstract 16s rRNA sequencing, bacterial community structure, biofilm development, Aims: To characterize bacterial communities during the early stages of biofilm discolouration, drinking water distribution formation and their role in water discolouration in a fully representative, systems, terminal restriction fragment length chlorinated, experimental drinking water distribution systems (DWDS). polymorphism. Methods and Results: Biofilm development was monitored in an experimental DWDS over 28 days; subsequently the system was disturbed by raising hydraulic Correspondence conditions to simulate pipe burst, cleaning or other system conditions.
    [Show full text]