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Yang G, Li S, Niu R, Hu M, Huang G, Pan D, Yan S, Liu T, Li X, Li F. Insights into nitrate-reducing Fe(II) oxidation by Diaphorobacter caeni LI3 T through kinetic, nitrogen isotope fractionation, and genome analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168720. [PMID: 38008321 DOI: 10.1016/j.scitotenv.2023.168720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 11/28/2023]
Abstract
Nitrate (NO3-)-reducing Fe(II) oxidation (NRFO) is prevalent in anoxic environments. However, it is uncertain in which step(s) the biological Fe(II) oxidation is coupled with denitrification during NRFO. In this study, a heterotrophic NRFO bacterium, Diaphorobacter caeni LI3T, was isolated from paddy soil and used to investigate the transformation of Fe(II) and nitrogen as well as nitrogen isotopic fractionation (δ15N-N2O) during NRFO. Fe(II) oxidation was observed in the Cell+NO3- +Fe(II), Cell+NO2- + Fe(II), and NO2- + Fe(II) treatments, resulting in precipitation of amorphous Fe(III) minerals and lepidocrocite on the surface and in the periplasm of cells. The presence of Fe(II) slightly accelerated microbial NO3- reduction in the Cell+NO3- + Fe(II) treatment relative to the Cell+NO3- treatment, but slowed down the NO2- reduction in the Cell+NO2- + Fe(II) treatment relative to the Cell+NO2- treatment likely due to cell encrustation that blocking microbial NO2- reduction in the periplasm. The δ15N-N2O results in the Cell+NO3- + Fe(II) treatment were close to those in the Cell+NO3- and Cell+NO2- treatments, indicating that the accumulative N2O is primarily of biological origin during NRFO. The genome analysis found a complete set of denitrification and oxidative phosphorylation genes in strain LI3T, the metabolic pathways of which were closely related with cyc2 and cytc as indicated by protein-protein interactions network analysis. It is proposed that Fe(II) oxidation is catalyzed by the outer membrane protein Cyc2, with the resulting electrons being transferred to the nitrite reductase NirS via CytC in the periplasm, and the CytC can also accept electrons from the oxidative phosphorylation in the cytoplasmic membrane. Overall, our findings provide new insights into the potential pathways of biological Fe(II) oxidation coupled with nitrate reduction in heterotrophic NRFO bacteria.
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Affiliation(s)
- Guang Yang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Shuang Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - Rumiao Niu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Min Hu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Guoyong Huang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Dandan Pan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Siyao Yan
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Tongxu Liu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaomin Li
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
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Visser AN, Wankel SD, Frey C, Kappler A, Lehmann MF. Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation. Front Microbiol 2022; 13:927475. [PMID: 36118224 PMCID: PMC9478938 DOI: 10.3389/fmicb.2022.927475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Natural-abundance measurements of nitrate and nitrite (NOx) isotope ratios (δ15N and δ18O) can be a valuable tool to study the biogeochemical fate of NOx species in the environment. A prerequisite for using NOx isotopes in this regard is an understanding of the mechanistic details of isotope fractionation (15ε, 18ε) associated with the biotic and abiotic NOx transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NOx reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO3–) and nitrite (NO2–) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that 15ε and 18ε values obtained for heterotrophic (15ε-NO3–: 17.6 ± 2.8‰, 18ε-NO3–:18.1 ± 2.5‰; 15ε-NO2–: 14.4 ± 3.2‰) vs. mixotrophic (15ε-NO3–: 20.2 ± 1.4‰, 18ε-NO3–: 19.5 ± 1.5‰; 15ε-NO2–: 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NOx reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics (15ε-NO2–: –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NOx reduction. The similar isotope effects detected during mixotrophic and heterotrophic NOx reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NOx reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.
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Affiliation(s)
- Anna-Neva Visser
- Aquatic and Isotope Biogeochemistry, Department of Environmental Sciences, Basel University, Basel, Switzerland
- *Correspondence: Anna-Neva Visser,
| | - Scott D. Wankel
- Stable Isotope Biogeochemistry, Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Falmouth, MA, United States
| | - Claudia Frey
- Aquatic and Isotope Biogeochemistry, Department of Environmental Sciences, Basel University, Basel, Switzerland
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, Eberhard Karls University, Tuebingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tuebingen, Germany
| | - Moritz F. Lehmann
- Aquatic and Isotope Biogeochemistry, Department of Environmental Sciences, Basel University, Basel, Switzerland
- Moritz F. Lehmann,
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An Approach to In Silico Dissection of Bacterial Intelligence Through Selective Genomic Tools. Indian J Microbiol 2018; 58:278-286. [PMID: 30013271 DOI: 10.1007/s12088-018-0726-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/10/2018] [Indexed: 01/31/2023] Open
Abstract
All the genetic potential and the intelligence a bacteria can showcase in a given environment are embedded in its genome. In this study, we have presented systematic guidelines to understand a bacterial genome with the relevant set of in silico tools using a novel bacteria as an example. This study presents a multi-dimensional approach from genome annotation to tracing genes and their network of metabolism operating in an organism. It also shows how the sequence can be used to mine the enzymes and construction of its 3-dimensional structure so that its functional behavior can be predicted and compared. The discriminating algorithm allows analysis of the promoter region and provides the insight in the regulation of genes in spite of the similarity in its sequences. The ecological niche specific bacterial behavior and adapted altered physiology can be understood through the presence of secondary metabolite, antibiotic resistance genes, and viral genes; and it helps in the valorization of genetic information for developing new biological application/processes. This study provides an in silico work plan and necessary steps for genome analysis of novel bacteria without any rigorous wet lab experiments.
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Jamieson J, Prommer H, Kaksonen AH, Sun J, Siade AJ, Yusov A, Bostick B. Identifying and Quantifying the Intermediate Processes during Nitrate-Dependent Iron(II) Oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5771-5781. [PMID: 29676145 PMCID: PMC6427828 DOI: 10.1021/acs.est.8b01122] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microbially driven nitrate-dependent iron (Fe) oxidation (NDFO) in subsurface environments has been intensively studied. However, the extent to which Fe(II) oxidation is biologically catalyzed remains unclear because no neutrophilic iron-oxidizing and nitrate reducing autotroph has been isolated to confirm the existence of an enzymatic pathway. While mixotrophic NDFO bacteria have been isolated, understanding the process is complicated by simultaneous abiotic oxidation due to nitrite produced during denitrification. In this study, the relative contributions of biotic and abiotic processes during NDFO were quantified through the compilation and model-based interpretation of previously published experimental data. The kinetics of chemical denitrification by Fe(II) (chemodenitrification) were assessed, and compelling evidence was found for the importance of organic ligands, specifically exopolymeric substances secreted by bacteria, in enhancing abiotic oxidation of Fe(II). However, nitrite alone could not explain the observed magnitude of Fe(II) oxidation, with 60-75% of overall Fe(II) oxidation attributed to an enzymatic pathway for investigated strains: Acidovorax ( A.) strain BoFeN1, 2AN, A. ebreus strain TPSY, Paracoccus denitrificans Pd 1222, and Pseudogulbenkiania sp. strain 2002. By rigorously quantifying the intermediate processes, this study eliminated the potential for abiotic Fe(II) oxidation to be exclusively responsible for NDFO and verified the key contribution from an additional, biological Fe(II) oxidation process catalyzed by NDFO bacteria.
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Affiliation(s)
- James Jamieson
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Henning Prommer
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- National Centre for Groundwater Research and Training, Adelaide, South Australia 5001, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- Corresponding Author: .
| | - Anna H. Kaksonen
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
- School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jing Sun
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Adam J. Siade
- School of Earth Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
- National Centre for Groundwater Research and Training, Adelaide, South Australia 5001, Australia
- CSIRO Land and Water, Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Anna Yusov
- Department of Chemistry, Barnard College, 3009 Broadway, New York, New York 10027, United States
| | - Benjamin Bostick
- Lamont-Doherty Earth Observatory, PO Box 1000, 61 Route 9W, Palisades, New York 10964, United States
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Hu M, Chen P, Sun W, Li F, Cui J. A novel organotrophic nitrate-reducing Fe(ii)-oxidizing bacterium isolated from paddy soil and draft genome sequencing indicate its metabolic versatility. RSC Adv 2017. [DOI: 10.1039/c7ra09328d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Physiological and genomic information of this strain provide preliminary evidence for nitrate-reduction coupled Fe(ii)-oxidation in microorganisms from paddy soil.
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Affiliation(s)
- Min Hu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
| | - Pengcheng Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
- Guangzhou Institute of Geochemistry
| | - Weimin Sun
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
| | - Jianghu Cui
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental Science & Technology
- Guangzhou 510650
- P. R. China
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Ishii S, Joikai K, Otsuka S, Senoo K, Okabe S. Denitrification and Nitrate-Dependent Fe(II) Oxidation in Various Pseudogulbenkiania Strains. Microbes Environ 2016; 31:293-8. [PMID: 27431373 PMCID: PMC5017806 DOI: 10.1264/jsme2.me16001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 06/14/2016] [Indexed: 12/05/2022] Open
Abstract
Pseudogulbenkiania is a relatively recently characterized genus within the order Neisseriales, class Betaproteobacteria. This genus contains several strains that are capable of anaerobic, nitrate-dependent Fe(II) oxidation (NDFO), a geochemically important reaction for nitrogen and iron cycles. In the present study, we examined denitrification functional gene diversities within this genus, and clarified whether other Pseudogulbenkiania sp. strains perform denitrification and NDFO. Seventy strains were analyzed, including two type strains, a well-characterized NDFO strain, and 67 denitrifying strains isolated from various rice paddy fields and rice-soybean rotation fields in Japan. We also attempted to identify the genes responsible for NDFO by mutagenesis. Our comprehensive analysis showed that all Pseudogulbenkiania strains tested performed denitrification and NDFO; however, we were unable to obtain NDFO-deficient denitrifying mutants in our mutagenesis experiment. This result suggests that Fe(II) oxidation in these strains is not enzymatic, but is caused by reactive N-species that are formed during nitrate reduction. Based on the results of the comparative genome analysis among Pseudogulbenkiania sp. strains, we identified low sequence similarity within the nos gene as well as different gene arrangements within the nos gene cluster, suggesting that nos genes were horizontally transferred. Since Pseudogulbenkiania sp. strains have been isolated from various locations around the world, their denitrification and NDFO abilities may contribute significantly to nitrogen and iron biogeochemical cycles.
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Affiliation(s)
- Satoshi Ishii
- Department of Soil, Water, and Climate; BioTechnology Institute, University of Minnesota140 Gortner Laboratory, 1479 Gortner Ave., St. Paul, MN 55108–6106USA
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido UniversityKita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060–8628Japan
| | - Kazuki Joikai
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido UniversityKita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060–8628Japan
| | - Shigeto Otsuka
- Department of Applied Biological Chemistry, The University of Tokyo1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, The University of Tokyo1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657Japan
| | - Satoshi Okabe
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido UniversityKita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060–8628Japan
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Ng LM, Sudesh K. Identification of a new polyhydroxyalkanoate (PHA) producer Aquitalea sp. USM4 (JCM 19919) and characterization of its PHA synthase. J Biosci Bioeng 2016; 122:550-557. [PMID: 27132174 DOI: 10.1016/j.jbiosc.2016.03.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/28/2016] [Accepted: 03/31/2016] [Indexed: 11/28/2022]
Abstract
Aquitalea sp. USM4 (JCM 19919) was isolated from a freshwater sample at Lata Iskandar Waterfall in Perak, Malaysia. It is a rod-shaped, gram-negative bacterium with high sequence identity (99%) to Aquitalea magnusonii based on 16S rRNA gene analysis. Aquitalea sp. USM4 also possessed a PHA synthase gene (phaC), which had amino acid sequence identity of 77-78% to the PHA synthase of Chromobacterium violaceum ATCC12472 and Pseudogulbenkiania sp. NH8B. PHA biosynthesis results showed that wild-type Aquitalea sp. USM4 was able to accumulate up to 1.5 g/L of poly(3-hydroxybutyrate), [P(3HB)]. The heterologous expression of the PHA synthase gene of Aquitalea sp. USM4 (phaCAq) in Cupriavidus necator PHB-4 had resulted in PHA accumulation up to 3.2 g/L of P(3HB). It was further confirmed by 1H nuclear magnetic resonance (NMR) analysis that Aquitalea sp. USM4 and C. necator PHB-4 transformant were able to produce PHA containing 3-hydroxyvalerate (3HV), 4-hydroxybutyrate (4HB) and 3-hydroxy-4-methylvalerate (3H4MV) monomers from suitable precursor substrates. Interestingly, relatively high PHA synthase activity of 863 U/g and 1402 U/g were determined in wild-type Aquitalea sp. USM4 and C. necator PHB-4 transformant respectively. This is the first report on the member of genus Aquitalea as a new PHA producer as well as in vitro and in vivo characterization of a novel PHA synthase from Aquitalea sp. USM4.
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Affiliation(s)
- Lee-Mei Ng
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia; Centre for Chemical Biology, Universiti Sains Malaysia, 10 Persiaran Bukit Jambul, Bayan Lepas, 11900 Penang, Malaysia.
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Ullrich SR, Poehlein A, Tischler JS, González C, Ossandon FJ, Daniel R, Holmes DS, Schlömann M, Mühling M. Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum". PLoS One 2016; 11:e0146832. [PMID: 26808278 PMCID: PMC4725956 DOI: 10.1371/journal.pone.0146832] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/22/2015] [Indexed: 02/07/2023] Open
Abstract
Background Members of the genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) waters which are characterised by their high metal and sulfate loads. So far isolation and microbiological characterisation have only been successful for the designated type strain “Ferrovum myxofaciens” P3G. Thus, knowledge about physiological characteristics and the phylogeny of the genus “Ferrovum” is extremely scarce. Objective In order to access the wider genetic pool of the genus “Ferrovum” we sequenced the genome of a “Ferrovum”-containing mixed culture and successfully assembled the almost complete genome sequence of the novel “Ferrovum” strain JA12. Phylogeny and Lifestyle The genome-based phylogenetic analysis indicates that strain JA12 and the type strain represent two distinct “Ferrovum” species. “Ferrovum” strain JA12 is characterised by an unusually small genome in comparison to the type strain and other iron oxidising bacteria. The prediction of nutrient assimilation pathways suggests that “Ferrovum” strain JA12 maintains a chemolithoautotrophic lifestyle utilising carbon dioxide and bicarbonate, ammonium and urea, sulfate, phosphate and ferrous iron as carbon, nitrogen, sulfur, phosphorous and energy sources, respectively. Unique Metabolic Features The potential utilisation of urea by “Ferrovum” strain JA12 is moreover remarkable since it may furthermore represent a strategy among extreme acidophiles to cope with the acidic environment. Unlike other acidophilic chemolithoautotrophs “Ferrovum” strain JA12 exhibits a complete tricarboxylic acid cycle, a metabolic feature shared with the closer related neutrophilic iron oxidisers among the Betaproteobacteria including Sideroxydans lithotrophicus and Thiobacillus denitrificans. Furthermore, the absence of characteristic redox proteins involved in iron oxidation in the well-studied acidophiles Acidithiobacillus ferrooxidans (rusticyanin) and Acidithiobacillus ferrivorans (iron oxidase) indicates the existence of a modified pathway in “Ferrovum” strain JA12. Therefore, the results of the present study extend our understanding of the genus “Ferrovum” and provide a comprehensive framework for future comparative genome and metagenome studies.
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Affiliation(s)
- Sophie R. Ullrich
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
- * E-mail: (SRU); (MM)
| | - Anja Poehlein
- Georg-August-University Göttingen, Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Grisebachstraße 8, Göttingen, Germany
| | - Judith S. Tischler
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
| | - Carolina González
- Center for System Biotechnology, Bio-Computing Division and Applied Genetics Division, Fraunhofer Chile Research Foundation, Avenida Mariano Sánchez Fontecilla 310, Santiago, Chile, and Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482, and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Francisco J. Ossandon
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482 and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Rolf Daniel
- Georg-August-University Göttingen, Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Grisebachstraße 8, Göttingen, Germany
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Fundación Ciencia y Vida, Zañartu 1482 and Facultad de Ciencias Biologicas, Universidad Andres Bello, Avenida Los Leones 745, Santiago, Chile
| | - Michael Schlömann
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
| | - Martin Mühling
- Institute of Biological Sciences, TU Bergakademie Freiberg, Leipziger Straße 29, Freiberg, Germany
- * E-mail: (SRU); (MM)
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9
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O'Reilly E, Iglesias C, Ghislieri D, Hopwood J, Galman JL, Lloyd RC, Turner NJ. A regio- and stereoselective ω-transaminase/monoamine oxidase cascade for the synthesis of chiral 2,5-disubstituted pyrrolidines. Angew Chem Int Ed Engl 2014; 53:2447-50. [PMID: 24478044 PMCID: PMC4227563 DOI: 10.1002/anie.201309208] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/11/2013] [Indexed: 11/18/2022]
Abstract
Biocatalytic approaches to the synthesis of optically pure chiral amines, starting from simple achiral building blocks, are highly desirable because such motifs are present in a wide variety of important natural products and pharmaceutical compounds. Herein, a novel one-pot ω-transaminase (TA)/monoamine oxidase (MAO-N) cascade process for the synthesis of chiral 2,5-disubstituted pyrrolidines is reported. The reactions proceeded with excellent enantio- and diastereoselectivity (>94 % ee; >98 % de) and can be performed on a preparative scale. This methodology exploits the complementary regio- and stereoselectivity displayed by both enzymes, which ensures that the stereogenic center established by the transaminase is not affected by the monoamine oxidase, and highlights the potential of this multienzyme cascade for the efficient synthesis of chiral building blocks.
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Affiliation(s)
- Elaine O'Reilly
- School of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN (UK)
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10
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O'Reilly E, Iglesias C, Ghislieri D, Hopwood J, Galman JL, Lloyd RC, Turner NJ. A Regio- and Stereoselective ω-Transaminase/Monoamine Oxidase Cascade for the Synthesis of Chiral 2,5-Disubstituted Pyrrolidines. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309208] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Fe(II) oxidation is an innate capability of nitrate-reducing bacteria that involves abiotic and biotic reactions. J Bacteriol 2013; 195:3260-8. [PMID: 23687275 DOI: 10.1128/jb.00058-13] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Phylogenetically diverse species of bacteria can catalyze the oxidation of ferrous iron [Fe(II)] coupled to nitrate (NO(3)(-)) reduction, often referred to as nitrate-dependent iron oxidation (NDFO). Very little is known about the biochemistry of NDFO, and though growth benefits have been observed, mineral encrustations and nitrite accumulation likely limit growth. Acidovorax ebreus, like other species in the Acidovorax genus, is proficient at catalyzing NDFO. Our results suggest that the induction of specific Fe(II) oxidoreductase proteins is not required for NDFO. No upregulated periplasmic or outer membrane redox-active proteins, like those involved in Fe(II) oxidation by acidophilic iron oxidizers or anaerobic photoferrotrophs, were observed in proteomic experiments. We demonstrate that while "abiotic" extracellular reactions between Fe(II) and biogenic NO(2)(-)/NO can be involved in NDFO, intracellular reactions between Fe(II) and periplasmic components are essential to initiate extensive NDFO. We present evidence that an organic cosubstrate inhibits NDFO, likely by keeping periplasmic enzymes in their reduced state, stimulating metal efflux pumping, or both, and that growth during NDFO relies on the capacity of a nitrate-reducing bacterium to overcome the toxicity of Fe(II) and reactive nitrogen species. On the basis of our data and evidence in the literature, we postulate that all respiratory nitrate-reducing bacteria are innately capable of catalyzing NDFO. Our findings have implications for a mechanistic understanding of NDFO, the biogeochemical controls on anaerobic Fe(II) oxidation, and the production of NO(2)(-), NO, and N(2)O in the environment.
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Adeolu M, Gupta RS. Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov. Antonie Van Leeuwenhoek 2013; 104:1-24. [PMID: 23575986 DOI: 10.1007/s10482-013-9920-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/01/2013] [Indexed: 11/29/2022]
Abstract
The species from the order Neisseriales are currently distinguished from other bacteria on the basis of branching in 16S rRNA gene trees. For this order containing a single family, Neisseriaceae, no distinctive molecular, biochemical, or phenotypic characters are presently known. We report here detailed phylogenetic and comparative analyses on the 27 genome sequenced species of the order Neisseriales. Our comparative genomic analyses have identified 54 conserved signature indels (CSIs) in widely distributed proteins that are specific for either all of the sequenced Neisseriales species or a number of clades within this order that are also supported by phylogenetic analyses. Of these CSIs, 11 are specifically present in all of the sequenced species from this order, but are not found in homologous proteins from any other bacteria. These CSIs provide novel molecular markers specific for, and delimiting, this order. Twenty-one CSIs in diverse proteins are specific for a group comprised of the genera Neisseria, Eikenella, Kingella, and Simonsiella (Clade I), which are obligate host-associated organisms, lacking flagella and exhibiting varied morphology. The species from these genera also formed a strongly supported clade in phylogenetic trees based upon concatenated protein sequences; a monophyletic grouping of these genera and other genera displaying similar morphological characteristics was also observed in the 16S rRNA gene tree. A second clade (Clade II), supported by seven of the identified CSIs and phylogenetic trees based upon concatenated protein sequences, grouped together species from the genera Chromobacterium, Laribacter, and Pseudogulbenkiania that are rod-shaped bacteria, which display flagella-based motility and are capable of free living. The remainder of the CSIs were uniquely shared by smaller groups within these two main clades. Our analyses also provide novel insights into the evolutionary history of the Neisseriales and suggest that the CSIs that are specific for the Clade I species may play an important role in the evolution of obligate host-association within this order. On the basis of phylogenetic analysis, the identified CSIs, and conserved phenotypic characteristics of different Neisseriales genera, we propose a division of this order into two families: an emended family Neisseriaceae (corresponding to Clade I) containing the genera Alysiella, Bergeriella, Conchiformibius, Eikenella, Kingella, Neisseria, Simonsiella, Stenoxybacter, Uruburuella and Vitreoscilla and a new family, Chromobacteriaceae fam. nov., harboring the remainder of the genera from this order (viz. Andreprevotia, Aquaspirillum, Aquitalea, Chitinibacter, Chitinilyticum, Chitiniphilus, Chromobacterium, Deefgea, Formivibrio, Gulbenkiania, Iodobacter, Jeongeupia, Laribacter, Leeia, Microvirgula, Paludibacterium, Pseudogulbenkiania, Silvimonas, and Vogesella).
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Affiliation(s)
- Mobolaji Adeolu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, March-April 2012. Stand Genomic Sci 2012. [PMCID: PMC3387800 DOI: 10.4056/sigs.2836114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
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Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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