Denitrification and Nitrate-Dependent Fe(II) Oxidation in Various Pseudogulbenkiania Strains

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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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Community structure and metabolism through reconstruction of microbial genomes from the environment.

Gene W. Tyson, Jarrod Chapman, Philip Hugenholtz … (2004)

Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.

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GenomeMatcher: A graphical user interface for DNA sequence comparison

Yoshiyuki Ohtsubo, Wakako Ikeda-Ohtsubo, Yuji Nagata … (2008)

Background The number of available genome sequences is increasing, and easy-to-use software that enables efficient comparative analysis is needed. Results We developed GenomeMatcher, a stand-alone software package for Mac OS X. GenomeMatcher executes BLAST and MUMmer, and the detected similarities are displayed in two-dimensional and parallel views with similarity values indicated by color. Selection and re-computation of any subregions is easily performed and allows flexible and in-depth analysis. Furthermore, symbols for annotation data are displayed along the views, and the user can relate the genomic differences with annotation data. While bl2seq allows sub-Giga base comparison, three alignment programs, bl2seq, MAFFT and ClustalW, together with a dotmatch program allow comparative analysis of single-nucleotide level resolution. GenomeMatcher images can be saved as PDF and TIFF files for presentation. As examples of graphical ability of GenomeMatcher to show similarity in colors, we show two cases in Burkholderia and Vivrio strains that the nucleotide sequence of the second largest chromosome changes more rapidly than the largest chromosome. Conclusion GenomeMatcher is efficient and easy-to-use stand-alone software for in-depth comparative analysis of two sequences. GenomeMatcher is useful for detecting similarities in DNA sequences ranging in size from a few to sub-Giga bases.

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Genetic identification of a respiratory arsenate reductase.

C. Saltikov, D K Newman (2011)

For more than a decade, it has been recognized that arsenate [H2AsO41-; As(V)] can be used by microorganisms as a terminal electron acceptor in anaerobic respiration. Given the toxicity of arsenic, the mechanistic basis of this process is intriguing, as is its evolutionary origin. Here we show that a two-gene cluster (arrAB; arsenate respiratory reduction) in the bacterium Shewanella sp. strain ANA-3 specifically confers respiratory As(V) reductase activity. Mutants with in-frame deletions of either arrA or arrB are incapable of growing on As(V), yet both are able to grow on a wide variety of other electron acceptors as efficiently as the wild-type. Complementation by the wild-type sequence rescues the mutants' ability to respire As(V). arrA is predicted to encode a 95.2-kDa protein with sequence motifs similar to the molybdenum containing enzymes of the dimethyl sulfoxide reductase family. arrB is predicted to encode a 25.7-kDa iron-sulfur protein. arrA and arrB comprise an operon that contains a twin arginine translocation (Tat) motif in ArrA (but not in ArrB) as well as a putative anaerobic transcription factor binding site upstream of arrA, suggesting that the respiratory As(V) reductase is exported to the periplasm via the Tat pathway and under anaerobic transcriptional control. These genes appear to define a new class of reductases that are specific for respiratory As(V) reduction.

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Author and article information

Journal

Journal ID (nlm-ta): Microbes Environ

Journal ID (iso-abbrev): Microbes Environ

Title: Microbes and Environments

ISSN (Print): 1342-6311

ISSN (Electronic): 1347-4405

Publication date (Print): September 2016

Publication date (Electronic): 15 July 2016

Volume: 31

Issue: 3

Pages: 293-298

Affiliations

[1 ]Department of Soil, Water, and Climate; BioTechnology Institute, University of Minnesota 140 Gortner Laboratory, 1479 Gortner Ave., St. Paul, MN 55108–6106USA

[2 ]Division of Environmental Engineering, Faculty of Engineering, Hokkaido University Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido 060–8628Japan

[3 ]Department of Applied Biological Chemistry, The University of Tokyo 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657Japan

Author notes

[* ]Corresponding author. E-mail: ishi0040@ 123456umn.edu ; Tel: +1–612–624–7902.

Article

Publisher ID: 31_293

DOI: 10.1264/jsme2.ME16001

PMC ID: 5017806

PubMed ID: 27431373

SO-VID: 3f294d31-7dd6-4717-ade8-a5960e3ded06

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This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Denitrification and Nitrate-Dependent Fe(II) Oxidation in Various Pseudogulbenkiania Strains

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Most cited references 41

Community structure and metabolism through reconstruction of microbial genomes from the environment.

GenomeMatcher: A graphical user interface for DNA sequence comparison

Genetic identification of a respiratory arsenate reductase.

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