DOCSLIB.ORG

Biomineralization of Atrazine and Analysis of 16S Rrna and Catabolic Genes of Atrazine- Degraders in a Former Pesticide Mixing A

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Biomineralization of Atrazine and Analysis of 16S Rrna and Catabolic Genes of Atrazine- Degraders in a Former Pesticide Mixing A Biomineralization of atrazine and analysis of 16S rRNA and catabolic genes of atrazine- degraders in a former pesticide mixing and machinery washing area at a farm site and in a constructed wetland DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By James F. Douglass Graduate Program in Microbiology The Ohio State University 2015 Dissertation Committee: Dr. Olli H. Tuovinen, Advisor Dr. Michael Boehm Dr. Charles Daniels Dr. Michael Ibba Copyright by James F. Douglass 2015 Abstract Atrazine is one of the most widely used herbicides in the world. It is primarily used in the production of corn in the United States. Although it may marginally increase crop yields, atrazine is also an endocrine disruptor in non-target organisms. Its moderate solubility in water allows for atrazine to contaminate surface and ground waters far removed from the point of application to soil. Although atrazine can be degraded abiotically, its primary mode of attenuation in natural environments is through bacterial - + degradation. Full mineralization of atrazine to CO2, H2O, Cl and NH4 has been demonstrated in Pseudomonas ADP, which contains the complete suite of atz atrazine catabolic genes. The overall hypothesis of this study is that the microorganisms and catabolic pathways reported in the literature do not universally account for the atrazine biodegradation observed in different natural environments. Furthermore, it is hypothesized that in situ pre-enrichment methods yield atrazine degraders uncultivable by classical laboratory enrichment, including anaerobic bacteria. The discovery of atrazine catabolic genes other than those in the atz pathway and the demonstrated involvement of consortia of bacteria in atrazine biodegradation suggest that the full diversity of environmental atrazine biodegradation has yet to be elucidated. ii In order to further elucidate the bacteria and genes responsible for atrazine biodegradation in different environments, locations with different exposures to atrazine were chosen for study. Among them were a farm location that was the site of multiple pesticide spill events throughout its history and a constructed wetland that receives river water containing agricultural runoff. Samples from these sites were assessed for atrazine biomineralization via biometer studies. In addition to traditional environmental sampling, these sites were also sampled with Bio-Sep beads to allow for in situ pre-enrichment for atrazine-degrading microbes. Soil and sediment samples were enriched for atrazine- degraders in liquid media, which included atrazine as the sole source of energy, C and N. Atrazine-degrading mixed cultures were screened via 16S-rDNA-PCR-DGGE, and mixed cultures displaying unique banding patterns were chosen for 16S rDNA clone library formation and sequencing. These isolates were also screened for eight atrazine catabolic genes via PCR. Atrazine mineralization was demonstrated in the sampling sites, but never exceeded 30% total mineralization of the added [U-ring-14C]-atrazine. Atrazine degrading pure and mixed cultures were successfully retrieved, with Acidovorax, Hydrogenophaga, Ralstonia, Variovorax, and Xanthobacter most prevalent among the mixed culture clone libraries and Arthrobacter spp. dominating the isolate collection. iii Dedication This document is dedicated to Laura Ellen Douglass. iv Acknowledgments I would like to thank my dissertation committee: Dr. Boehm, Dr. Daniels, and Dr. Ibba. This entire process would have been impossible without their support and guidance, and their patience has been near limitless. Thank you also to every other faculty member that has been a part of prior incarnations of my committee, specifically Dr. Warren Dick, Dr. Mark Morrison and Dr. Zhongtang Yu. Thanks to Dr. Mark Radosevich and his lab at the University of Tennessee for helping me with all of the molecular biology techniques used in this study. My project and I benefitted greatly from your kind help. The work was funded through the USDA National Research Initiative, Grant no. 2004-35107-14884 and fellowship support from the Robert H. Edgerley Environmental Toxicology Fund, Division of Natural and Mathematical Sciences of the College of Arts and Sciences, Ohio State University. Finally, I would like to thank my advisor, Dr. Tuovinen, for letting me be a part of his lab and this project and for not giving up on me. v Vita 2002................................................................B.S. Biology, Youngstown State University 2012................................................................J.D., The Ohio State University 2015................................................................M.S. Microbiology, The Ohio State University 2004-2012, 2015 ...........................................Graduate Student, Department of Microbiology, The Ohio State University Publications Douglass, J.F., Radosevich, M., Tuovinen, O.H., 2015. Molecular analysis of atrazine- degrading bacteria and catabolic genes in the water column and sediment of a created wetland in an agricultural/urban watershed. Ecol. Eng. 83, 405-412. Douglass, J.F., Radosevich, M., Tuovinen, O.H., 2014. Mineralization of atrazine in the river water intake and sediments of a constructed flow-through wetland. Ecol. Eng. 72, 35-39. Field of Study Major Field: Microbiology vi Table of Contents Abstract ............................................................................................................................... ii Dedication .......................................................................................................................... iv Acknowledgments............................................................................................................... v Vita ..................................................................................................................................... vi List of Tables ..................................................................................................................... xi List of Figures ................................................................................................................. xvii Chapter 1: Introduction ................................................................................................... 1 1.1 Background .......................................................................................................... 1 1.2 Objectives ............................................................................................................. 6 Chapter 2: Mineralization of atrazine in the river water intake and sediments of a constructed flow-through wetland .................................................................................... 10 2.1 Introduction ........................................................................................................ 10 2.2 Materials and methods ....................................................................................... 12 2.2.1 Sampling ..................................................................................................... 12 2.2.2 Atrazine mineralization in biometer experiments ....................................... 12 2.3 Results and discussion ........................................................................................ 14 vii 2.3.1 Mineralization of atrazine in river water samples from the intake to the wetland ..................................................................................................................... 14 2.3.2 Mineralization of atrazine in sediments of the constructed wetland ........... 15 Chapter 3: Molecular analysis of atrazine-mineralizing bacteria and catabolic genes in the water column and sediment of a constructed wetland in an agricultural watershed ... 23 3.1 Introduction ........................................................................................................ 23 3.2 Materials and methods ....................................................................................... 25 3.2.1 Sampling ..................................................................................................... 25 3.2.2 [U-ring-14C]-atrazine mineralization .......................................................... 27 3.2.3 Enrichment culture conditions .................................................................... 27 3.2.4 HPLC analysis of enrichment cultures ....................................................... 28 3.2.5 Isolation of atrazine-degrading pure cultures ............................................. 29 3.2.6 DNA isolation and 16S rRNA gene amplification ..................................... 29 3.2.7 16S rDNA clone library formation and analysis......................................... 30 3.2.8 Atrazine catabolic gene detection in atrazine-degrading pure cultures ...... 31 3.3 Results and discussion ........................................................................................ 33 3.3.1 Measurement of atrazine mineralization with [U-ring-14C]-atrazine and Bio- Sep beads ................................................................................................................... 33 3.3.2 16S rRNA gene sequence based analysis of atrazine-degrading enrichment cultures and bacterial isolates from wetland samples ................................................ 34 viii 3.3.3 Detection of atz and trz catabolic genes ..................................................... 35 3.4 Conclusions
Load more

Recommended publications
  • Revised Taxonomy of the Family Rhizobiaceae, and Phylogeny of Mesorhizobia Nodulating Glycyrrhiza Spp
    Division of Microbiology and Biotechnology Department of Food and Environmental Sciences University of Helsinki Finland Revised taxonomy of the family Rhizobiaceae, and phylogeny of mesorhizobia nodulating Glycyrrhiza spp. Seyed Abdollah Mousavi Academic Dissertation To be presented, with the permission of the Faculty of Agriculture and Forestry of the University of Helsinki, for public examination in lecture hall 3, Viikki building B, Latokartanonkaari 7, on the 20th of May 2016, at 12 o’clock noon. Helsinki 2016 Supervisor: Professor Kristina Lindström Department of Environmental Sciences University of Helsinki, Finland Pre-examiners: Professor Jaakko Hyvönen Department of Biosciences University of Helsinki, Finland Associate Professor Chang Fu Tian State Key Laboratory of Agrobiotechnology College of Biological Sciences China Agricultural University, China Opponent: Professor J. Peter W. Young Department of Biology University of York, England Cover photo by Kristina Lindström Dissertationes Schola Doctoralis Scientiae Circumiectalis, Alimentariae, Biologicae ISSN 2342-5423 (print) ISSN 2342-5431 (online) ISBN 978-951-51-2111-0 (paperback) ISBN 978-951-51-2112-7 (PDF) Electronic version available at http://ethesis.helsinki.fi/ Unigrafia Helsinki 2016 2 ABSTRACT Studies of the taxonomy of bacteria were initiated in the last quarter of the 19th century when bacteria were classified in six genera placed in four tribes based on their morphological appearance. Since then the taxonomy of bacteria has been revolutionized several times. At present, 30 phyla belong to the domain “Bacteria”, which includes over 9600 species. Unlike many eukaryotes, bacteria lack complex morphological characters and practically phylogenetically informative fossils. It is partly due to these reasons that bacterial taxonomy is complicated.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub
    US 2005O289672A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub. Date: Dec. 29, 2005 (54) BIOLOGICAL GENE TRANSFER SYSTEM Publication Classification FOR EUKARYOTC CELLS (75) Inventor: Richard A. Jefferson, Canberra (AU) (51) Int. Cl. ............................. A01H 1700; C12N 15/82 (52) U.S. Cl. .............................................................. 800,294 Correspondence Address: CAROL NOTTENBURG 81432ND AVE 5 SEATTLE, WA 98144 (US) (57) ABSTRACT (73) Assignee: CAMBIA Appl. No.: 10/954,147 This invention relates generally to technologies for the (21) transfer of nucleic acids molecules to eukaryotic cells. In Filed: Sep. 28, 2004 particular non-pathogenic Species of bacteria that interact (22) with plant cells are used to transfer nucleic acid Sequences. Related U.S. Application Data The bacteria for transforming plants usually contain binary vectors, Such as a plasmid with a Vir region of a Tiplasmid (60) Provisional application No. 60/583,426, filed on Jun. and a plasmid with a T region containing a DNA sequence 28, 2004. of interest. pEHA105 244981 bp M3REW M13Fw f1 origin accA W pEHA105::pWBE58 (Km, Ap) moaa. Patent Application Publication Dec. 29, 2005 Sheet 1 of 24 US 2005/0289672 A1 FIGURE 1A CLASS ALPHAPROTEOBACTERIA ORDER Rhizobiales family Rhizobiaceae bgenus Rhizobium (includes former Agrobacterium) bgenus Chelatobacter bgenus Sinorhizobium Dunclassified Rhizobiaceae family Bartonellaceae bgenus Bartonella Dunclassified Bartonellaceae family Brucellaceae
    [Show full text]
  • Diversity of Sulfur-Oxidizing Bacteria at the Surface of Cattle Manure
    Microbes Environ. 35(3), 2020 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME18066 Short Communication Diversity of Sulfur-oxidizing Bacteria at the Surface of Cattle Manure Composting Assessed by an Analysis of the Sulfur Oxidation Gene soxB Yumi Mori1,2, Chika Tada1, Yasuhiro Fukuda1, and Yutaka Nakai1*† 1Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku University, 232–3 Yomogida, Naruko-onsen, Osaki, Miyagi 989–6711, Japan; and 2Research Institute for Bioresource and Biotechnology, Ishikawa Prefectural University, 1–308 Suematsu, Nonoichi, Ishikawa 921–8836, Japan (Received May 7, 2018—Accepted June 16, 2020—Published online July 22, 2020) Sulfur-oxidizing bacterial diversity at the surface of cattle manure was characterized throughout the composting process using a sulfur oxidation gene (soxB) clone library approach. In the mesophilic phase, clones related to the genera Hydrogenophaga and Hydrogenophilus were characteristically detected. In the thermophilic phase, clones related to the genera Hydrogenophaga and Thiohalobacter were predominant. In the cooling phase, the predominant soxB sequences were related to the genus Pseudaminobacter and a new sulfur-oxidizing bacterium belonging to the class Alphaproteobacteria. The present study showed changes in the community composition of sulfur-oxidizing bacteria at the surface of compost throughout the composting process. Key words: cattle manure compost, cloning analysis, Proteobacteria, soxB, sulfur-oxidizing bacteria Chemolithotrophic sulfur-oxidizing bacteria (SOB) are post via sulfide oxidization (Beffa et al., 1995, 1996; Asano aerobic bacteria that belong to the phylum Proteobacteria et al., 2007). In addition, sulfate produced by SOB reduces and oxidize reduced inorganic sulfur compounds to sulfate the pH of compost, thereby decreasing the volatility of (Friedrich, 1997), thereby contributing to the sulfur cycle.
    [Show full text]
  • Pseudaminobacter Granuli Sp. Nov., Isolated from Granules Used in a Wastewater Treatment Plant
    Journal of Microbiology (2017) Vol. 55, No. 8, pp. 607–611 eISSN 1976-3794 DOI 10.1007/s12275-017-7257-y pISSN 1225-8873 Pseudaminobacter granuli sp. nov., isolated from granules used in a wastewater treatment plant Young Ki Hahn1, Minseok S. Kim2*, by Kämpfer et al. (1999). Members of the genus are Gram- 3,4 negative, rod-shaped, oxidase and catalase-positive. It con- and Wan-Taek Im * tains ubiquinone-10 (Q-10) as the predominant respiratory quinone. The major polyamines are spermidine, sys-homo- 1 Samsung Electronics, Seoul 06620, Republic of Korea spermidine and putrescine. The overall polar lipid patterns 2Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Republic of Korea are phosphatidylcholine (PC), phosphatidylglycerol (PG), 3Department of Biotechnology, Hankyong National University, phosphatidyl-dimethylethanolamine (PDE), phosphatidyl- Kyonggi-do 17579, Republic of Korea mono-methylethanolamine (PME), phosphatidyl-ethanol- 4 Center for Genetic Information, Graduate School of Bio and amine (PE), and diphosphatidylglycerol (DPG). At the time Information Technology, Hankyong National University, Kyonggi-do 17579, Republic of Korea of writing this manuscript, the genus consisted of 2 species with validly published names including the recently described (Received Jun 26, 2017 / Revised Jul 18, 2017 / Accepted Jul 18, 2017) species Pseudaminobacter defluvii and Pseudaminobacter salicylatoxidans (Kämpfer et al., 1999). The aim of this study was to determine the taxonomic posi- A Gram negative, aerobic, non-motile and rod-shaped bac- T terial strain designated as Gr-2T was isolated from granules tion of strain Gr-2 by performing phylogenetic analysis based used in a wastewater treatment plant in Korea, and its taxo- on the 16S rRNA gene sequence, and to analyze its chemo- taxonomic and phenotypic characteristics.
    [Show full text]
  • Characteristics of the Mucus Layer on the Surface of the Bluegill (Lepomis Macrochirus) and the Bacterial Flora in the Mucus
    Microbes Environ. Vol. 20, No. 1, 69–80, 2005 http://wwwsoc.nii.ac.jp/jsme2/ Characteristics of the Mucus Layer on the Surface of the Bluegill (Lepomis macrochirus) and the Bacterial Flora in the Mucus TAKEAKI HASHIZUME1, CHIKAKO TAKAI1, MANAMI NAITO1 and HISAO MORISAKI1* 1 Department of Bioscience and Biotechnology, Faculty of Science and Engineering, Ritsumeikan University, 1–1–1 Nojihigashi, Kusatsu, Shiga 525–8577, Japan (Received October 9, 2004—Accepted December 24, 2004) The layer of mucus on the surface of bluegills (Lepomis macrochirus) captured in Lake Biwa was character- ized as 1) large enough to host microbes (ca. 76 m thick), 2) a physically different environment from the sur- rounding lake water in viscosity and buffering capacity, and 3) chemically rich in organic substances, which may be utilized as nutrients. Based on DAPI staining and on the number of colonies formed respectively, it was found that ca. 103 times and 3 to 7 times the number of microbial cells were present in the mucus layer, as compared with the lake water. The bacterial flora of the mucus was greatly different from that of the lake water, according to a phylogenetic analysis. About 60% of the isolates from the mucus were Gram-positive. These Gram-positive isolates could be divided into two major groups. Each group consisted of strains sampled in one season, i.e., the strains sampled in July were closely related to the genus Staphylococcus, while the strains sampled in November were close to the genus Mycobacterium. In contrast, most isolates from the lake water were Gram-negative (72%); with all the strains closely related to - and -Proteobacteria sampled in July.
    [Show full text]
  • 2Phd Lichtarge Lab 2006
    Pages 1–9 2phd Evolutionary trace report by report maker January 27, 2010 4.3.1 Alistat 8 4.3.2 CE 8 4.3.3 DSSP 8 4.3.4 HSSP 9 4.3.5 LaTex 9 4.3.6 Muscle 9 4.3.7 Pymol 9 4.4 Note about ET Viewer 9 4.5 Citing this work 9 4.6 About report maker 9 4.7 Attachments 9 1 INTRODUCTION From the original Protein Data Bank entry (PDB id 2phd): Title: Crystal structure determination of a salicylate 1,2- dioxygenase from pseudaminobacter salicylatoxidans CONTENTS Compound: Mol id: 1; molecule: gentisate 1,2-dioxygenase; chain: a, b, c, d; ec: 1.13.11.4; engineered: yes 1 Introduction 1 Organism, scientific name: Pseudaminobacter Salicylatoxidans; 2phd contains a single unique chain 2phdD (352 residues long) and 2 Chain 2phdD 1 its homologues 2phdA, 2phdC, and 2phdB. 2.1 Q67FT0 overview 1 2.2 Multiple sequence alignment for 2phdD 1 2.3 Residue ranking in 2phdD 1 2.4 Top ranking residues in 2phdD and their position on the structure 1 2.4.1 Clustering of residues at 25% coverage. 1 2 CHAIN 2PHDD 2.4.2 Overlap with known functional surfaces at 2.1 Q67FT0 overview 25% coverage. 2 2.4.3 Possible novel functional surfaces at 25% From SwissProt, id Q67FT0, 94% identical to 2phdD: coverage. 6 Description: Gentisate 1,2-dioxygenase. Organism, scientific name: Pseudaminobacter salicylatoxidans. 3 Notes on using trace results 7 Taxonomy: Bacteria; Proteobacteria; Alphaproteobacteria; Rhizo- 3.1 Coverage 7 biales; Phyllobacteriaceae; Pseudaminobacter. 3.2 Known substitutions 7 3.3 Surface 7 3.4 Number of contacts 8 3.5 Annotation 8 2.2 Multiple sequence alignment for 2phdD 3.6 Mutation suggestions 8 For the chain 2phdD, the alignment 2phdD.msf (attached) with 102 sequences was used.
    [Show full text]
  • High-Quality-Draft Genome Sequence of the Multiple Heavy Metal Resistant
    Xia et al. Standards in Genomic Sciences (2018) 13:29 https://doi.org/10.1186/s40793-018-0330-2 SHORTGENOMEREPORT Open Access High-quality-draft genome sequence of the multiple heavy metal resistant bacterium Pseudaminobacter manganicus JH-7T Xian Xia†, Jiahong Li†, Zijie Zhou, Dan Wang, Jing Huang and Gejiao Wang* Abstract Pseudaminobacter manganicus JH-7T (= KCTC 52258T = CCTCC AB 2016107T) is a Gram-staining-negative, aerobic and non-motile strain that was isolated from a manganese mine. The strain JH-7T shows multiple heavy metal resistance and can effectively remove Mn2+ and Cd2+. In addition, it is able to produce exopolysaccharides (EPS), which may contribute to metal remove/adsorption. Thus, strain JH-7T shows a great potential in bioremediation of heavy metal-contaminated environment. In this study, we report the draft genomic sequence of P. manganicus JH-7T and compare it to related genomes. Strain JH-7T has a 4,842,937 bp genome size with a G + C content of 61.2%, containing 4504 protein-coding genes and 71 RNA genes. A large number of putative genes associated with heavy metal resistance and EPS synthesis are found in the genome. Keywords: Cadmium, Exopolysaccharides, Heavy metal resistance and adsorption, Manganese,Pseudaminobacter Introduction genome of an atypical Pseudaminobacter strain Pseu- Genus Pseudaminobacter was established by Kämpfer daminobacter salicylatoxidans KCT001 has been se- et al. in 1999 and contains three species represented quenced [7]. Strain KCT001 can utilize tetrathionate by Pseudaminobacter salicylatoxidans BN12T (type as the substrate for sulfur-oxidizing chemolitho- species) [1], Pseudaminobacter defluvii THI 051T [1] trophic growth [8].
    [Show full text]
  • Kido Einlpoeto Aalbe:AIO(W H
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date (10) International Publication Number 18 May 2007 (18.05.2007) PCT WO 2007/056463 A3 (51) International Patent Classification: AT, AU, AZ, BA, BB, BU, BR, BW, BY, BZ, CA, CL CN, C12P 19/34 (2006.01) CO, CR, CU, CZ, DE, DK, DM, DZ, EC, FE, EU, ES, H, GB, GD, GE, GIL GM, UT, IAN, HIR, HlU, ID, IL, IN, IS, (21) International Application Number: JP, KE, KG, KM, KN, Kg KR, KZ, LA, LC, LK, LR, LS, PCT/US2006/043502 LI, LU, LV, LY, MA, MD, MG, MK, MN, MW, MX, MY, M, PG, P, PL, PT, RO, RS, (22) International Filing Date:NA, NG, , NO, NZ, (22 InterntionaFilin Date:.006 RU, SC, SD, SE, SG, SK, SL, SM, SV, SY, TJ, TM, TN, 9NR, TI, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GIL GM, KE, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, ZM, (30) Priority Data: ZW), Eurasian (AM, AZ, BY, KU, KZ, MD, RU, TJ, TM), 60/735,085 9 November 2005 (09.11.2005) US European (AT, BE, BU, CIL CY, CZ, DE, DK, EE, ES, H, FR, GB, UR, IJU, JE, IS, IT, LI, LU, LV, MC, NL, PL, PT, (71) Applicant (for all designated States except US): RO, SE, SI, SK, IR), GAPI (BE BJ, C, CU, CI, CM, GA, PRIMERA BIOSYSTEMS, INC.
    [Show full text]
  • Requirements for Efficient Thiosulfate Oxidation in Bradyrhizobium
    G C A T T A C G G C A T genes Article Requirements for Efficient Thiosulfate Oxidation in Bradyrhizobium diazoefficiens Sachiko Masuda 1,*, Hauke Hennecke 2 and Hans-Martin Fischer 2 1 RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan 2 ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland [email protected] (H.H.); fi[email protected] (H.-M.F.) * Correspondence: [email protected]; Tel.: +81-45-503-9574 Received: 8 November 2017; Accepted: 12 December 2017; Published: 15 December 2017 Abstract: One of the many disparate lifestyles of Bradyrhizobium diazoefficiens is chemolithotrophic growth with thiosulfate as an electron donor for respiration. The employed carbon source may be CO2 (autotrophy) or an organic compound such as succinate (mixotrophy). Here, we discovered three new facets of this capacity: (i) When thiosulfate and succinate were consumed concomitantly in conditions of mixotrophy, even a high molar excess of succinate did not exert efficient catabolite repression over the use of thiosulfate. (ii) Using appropriate cytochrome mutants, we found that electrons derived from thiosulfate during chemolithoautotrophic growth are preferentially channeled via cytochrome c550 to the aa3-type heme-copper cytochrome oxidase. (iii) Three genetic regulators were identified to act at least partially in the expression control of genes for chemolithoautotrophic thiosulfate oxidation: RegR and CbbR as activators, and SoxR as a repressor. Keywords: Bradyrhizobium diazoefficiens; thiosulfate; chemolithoautotroph; regulation; cytochrome 1. Introduction The α-proteobacterium Bradyrhizobium diazoefficiens, a facultative nitrogen fixer and root-nodule symbiont of soybean, is not only a versatile heterotroph but may also entertain a chemolithotrophic lifestyle in the non-symbiotic state.
    [Show full text]
  • Deep Ocean Metagenomes Provide Insight Into the Metabolic Architecture of Bathypelagic Microbial Communities ✉ Silvia G
    ARTICLE https://doi.org/10.1038/s42003-021-02112-2 OPEN Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities ✉ Silvia G. Acinas 1,26 , Pablo Sánchez 1,26, Guillem Salazar 1,2,26, Francisco M. Cornejo-Castillo 1,3,26, Marta Sebastián 1,4, Ramiro Logares 1, Marta Royo-Llonch 1, Lucas Paoli2, Shinichi Sunagawa 2, Pascal Hingamp5, Hiroyuki Ogata 6, Gipsi Lima-Mendez 7,8, Simon Roux 9,25, José M. González 10, Jesús M. Arrieta 11, Intikhab S. Alam 12, Allan Kamau 12, Chris Bowler 13,14, Jeroen Raes15,16, Stéphane Pesant17,18, Peer Bork 19, Susana Agustí 20, Takashi Gojobori12, Dolors Vaqué 1, Matthew B. Sullivan 21, Carlos Pedrós-Alió22, Ramon Massana 1, Carlos M. Duarte 23 & Josep M. Gasol 1,24 1234567890():,; The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeo- graphy. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both auto- trophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean.
    [Show full text]
  • Kiloniella Laminariae Gen. Nov., Sp. Nov., an Alphaproteobacterium from the Marine Macroalga Laminaria Saccharina
    International Journal of Systematic and Evolutionary Microbiology (2009), 59, 350–356 DOI 10.1099/ijs.0.001651-0 Kiloniella laminariae gen. nov., sp. nov., an alphaproteobacterium from the marine macroalga Laminaria saccharina Jutta Wiese, Vera Thiel, Andrea Ga¨rtner, Rolf Schmaljohann and Johannes F. Imhoff Correspondence Kieler Wirkstoff-Zentrum am Leibniz-Institut fu¨r Meereswissenschaften IFM-GEOMAR, Johannes F. Imhoff Du¨sternbrooker Weg 20, 24105 Kiel, Germany [email protected] A novel alphaproteobacterium, strain LD81T, was isolated from the marine macroalga Laminaria saccharina. The bacterium is mesophilic and shows a typical marine growth response. It is a chemoheterotrophic aerobe with the potential for denitrification. Growth optima are 25 6C, pH 5.5 and 3 % NaCl. Strain LD81T has a unique phylogenetic position, not fitting any of the known families of the Alphaproteobacteria. The 16S rRNA gene sequence revealed a distant relationship to species of several orders of the Alphaproteobacteria, with less than 90 % sequence similarity. Phylogenetically, strain LD81T is related to the type strains of Terasakiella pusilla (88.4 % 16S rRNA gene sequence similarity) and the three Thalassospira species (88.9– 89.2 %). It forms a cluster with these bacteria and a novel as-yet undescribed isolate (KOPRI 13522; 96.6 % sequence similarity). Strain LD81T has a relatively low DNA G+C content (51.1 mol%) and, due to its distant phylogenetic position from all other alphaproteobacteria, strain LD81T (5NCIMB 14374T 5JCM 14845T) is considered as the type strain of a novel species within a new genus, for which the name Kiloniella laminariae gen. nov., sp. nov. is proposed.
    [Show full text]
  • Global Association Between Thermophilicity and Vancomycin Susceptibility in Bacteria
    ORIGINAL RESEARCH published: 31 March 2016 doi: 10.3389/fmicb.2016.00412 Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria Chayan Roy 1, Masrure Alam 1, Subhrangshu Mandal 1, Prabir K. Haldar 1, Sabyasachi Bhattacharya 1, Trinetra Mukherjee 2, Rimi Roy 1, Moidu J. Rameez 1, Anup K. Misra 3, Ranadhir Chakraborty 4, Ashish K. Nanda 5, Subhra K. Mukhopadhyay 2 and Wriddhiman Ghosh 1* 1 Department of Microbiology, Bose Institute, Kolkata, India, 2 Department of Microbiology, The University of Burdwan, Burdwan, India, 3 Division of Molecular Medicine, Bose Institute, Kolkata, India, 4 Department of Biotechnology, University of North Bengal, Siliguri, India, 5 Department of Chemistry, University of North Bengal, Siliguri, India Exploration of the aquatic microbiota of several circum-neutral (6.0–8.5 pH) Edited by: mid-temperature (55–85◦C) springs revealed rich diversities of phylogenetic relatives Octavio Luiz Franco, of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. To Universidade Catolica de Brasilia, Brazil gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives Reviewed by: of Gram-negative mesophilic bacteria detected in culture-independent investigations Dmitri Debabov, we attempted pure-culture isolation by supplementing the enrichment media with NovaBay Pharmaceuticals, USA −1 Santi M. Mandal, 50 µg ml vancomycin. Surprisingly, this Gram-positive-specific antibiotic eliminated Vidyasagar University, India the entire culturable-diversity of chemoorganotrophic and sulfur-chemolithotrophic Celio De Faria Junior, bacteria present in the tested hot water inocula. Moreover, it also killed all the Central Public Health Laboratory (LACEN) of the Brazilian Federal Gram-negative hot-spring isolates that were obtained in vancomycin-free media.
    [Show full text]