Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications View Full Text


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Article Info

DATE

2008-12-11

AUTHORS

Jorge Valdés, Inti Pedroso, Raquel Quatrini, Robert J Dodson, Herve Tettelin, Robert Blake, Jonathan A Eisen, David S Holmes

ABSTRACT

BackgroundAcidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism.ResultsThe genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes.ConclusionBioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential. More... »

PAGES

597

References to SciGraph publications

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  • Identifiers

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    DOI

    http://dx.doi.org/10.1186/1471-2164-9-597

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/19077236


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    30 schema:description BackgroundAcidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, γ-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1–2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism.ResultsThe genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes.ConclusionBioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.
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    36 schema:keywords A. ferrooxidans
    37 A. ferrooxidans ATCC 23270
    38 ATCC 23270
    39 DNA repair
    40 acid environment
    41 acid metabolism
    42 acidic environment
    43 activity
    44 amino acid metabolism
    45 anaerobic metabolism
    46 analysis
    47 applications
    48 atmosphere
    49 biofilm formation
    50 biogeochemical cycling
    51 bioleaching
    52 carbon
    53 carbon metabolism
    54 central carbon metabolism
    55 coherent view
    56 compound fluxes
    57 confusion
    58 consortium
    59 consortium of microorganisms
    60 content
    61 copper
    62 cycling
    63 discovery
    64 earlier models
    65 energy
    66 environment
    67 examination
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    69 features
    70 ferrooxidans
    71 fixes
    72 flux
    73 formation
    74 framework
    75 functional prediction
    76 gene content
    77 gene discovery
    78 general features
    79 genetic manipulation
    80 genome
    81 genome sequence
    82 growth
    83 important role
    84 industrial applications
    85 industrial bioleaching
    86 industrial recovery
    87 initial model
    88 inorganic ion uptake
    89 ion uptake
    90 iron
    91 lack
    92 major participants
    93 manipulation
    94 metabolic models
    95 metabolic potential
    96 metabolic reconstruction
    97 metabolism
    98 metals
    99 microorganisms
    100 minerals
    101 model
    102 nitrogen
    103 nutrients
    104 oxidation
    105 oxidation of iron
    106 participants
    107 physiology
    108 platform
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    111 primary producers
    112 producers
    113 quorum sensing
    114 reconstruction
    115 recovery
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    117 response
    118 rocks
    119 role
    120 sensing
    121 sequence
    122 silico metabolic reconstruction
    123 strains
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    125 sulfur oxidation
    126 sulfur-containing minerals
    127 system
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    131 valuable platform
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    134 schema:name Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications
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