Advanced search
1 file | 881.12 KB Add to list

Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis

Yi-hua Sun (UGent) , Paul De Vos (UGent) and Kim Heylen (UGent)
Author
Organization
Abstract
Background: Firmicutes have the capacity to remove excess nitrate from the environment via either denitrification, dissimilatory nitrate reduction to ammonium or both. The recent renewed interest in their nitrogen metabolism has revealed many interesting features, the most striking being their wide variety of dissimilatory nitrate reduction pathways. In the present study, nitrous oxide production from Bacillus licheniformis, a ubiquitous Gram-positive, spore-forming species with many industrial applications, is investigated. Results: B. licheniformis has long been considered a denitrifier but physiological experiments on three different strains demonstrated that nitrous oxide is not produced from nitrate in stoichiometric amounts, rather ammonium is the most important end-product, produced during fermentation. Significant strain dependency in end-product ratios, attributed to nitrite and ammonium, and medium dependency in nitrous oxide production were also observed. Genome analyses confirmed the lack of a nitrite reductase to nitric oxide, the key enzyme of denitrification. Based on the gene inventory and building on knowledge from other non-denitrifying nitrous oxide emitters, hypothetical pathways for nitrous oxide production, involving NarG, NirB, qNor and Hmp, are proposed. In addition, all publically available genomes of B. licheniformis demonstrated similar gene inventories, with specific duplications of the nar operon, narK and hmp genes as well as NarG phylogeny supporting the evolutionary separation of previously described distinct BALI1 and BALI2 lineages. Conclusions: Using physiological and genomic data we have demonstrated that the common soil bacterium B. licheniformis does not denitrify but is capable of fermentative dissimilatory nitrate/nitrite reduction to ammonium (DNRA) with concomitant production of N2O. Considering its ubiquitous nature and non-fastidious growth in the lab, B. licheniformis is a suitable candidate for further exploration of the actual mechanism of N2O production in DNRA bacteria and its relevance in situ.
Keywords
Dissimilatory nitrate/nitrite reduction to ammonium (DNRA), Fermentation, Nitrate respiration, Denitrification, Ammonification, Nitrite detoxification, COLI FLAVOHAEMOGLOBIN HMP, COMPLETE GENOME SEQUENCE, C NITRITE REDUCTASE, ESCHERICHIA-COLI, SPECIES DEFINITION, NORB GENE, DENITRIFICATION, BACTERIA, STRAINS, FLAVOHEMOGLOBIN

Downloads

  • Yihua sun.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 881.12 KB

Citation

Please use this url to cite or link to this publication:

MLA
Sun, Yi-hua, Paul De Vos, and Kim Heylen. “Nitrous Oxide Emission by the Non-denitrifying, Nitrate Ammonifier Bacillus Licheniformis.” BMC GENOMICS 17 (2016): n. pag. Print.
APA
Sun, Yi-hua, De Vos, P., & Heylen, K. (2016). Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis. BMC GENOMICS, 17.
Chicago author-date
Sun, Yi-hua, Paul De Vos, and Kim Heylen. 2016. “Nitrous Oxide Emission by the Non-denitrifying, Nitrate Ammonifier Bacillus Licheniformis.” Bmc Genomics 17.
Chicago author-date (all authors)
Sun, Yi-hua, Paul De Vos, and Kim Heylen. 2016. “Nitrous Oxide Emission by the Non-denitrifying, Nitrate Ammonifier Bacillus Licheniformis.” Bmc Genomics 17.
Vancouver
1.
Sun Y, De Vos P, Heylen K. Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis. BMC GENOMICS. 2016;17.
IEEE
[1]
Y. Sun, P. De Vos, and K. Heylen, “Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis,” BMC GENOMICS, vol. 17, 2016.
@article{8508037,
  abstract     = {Background: Firmicutes have the capacity to remove excess nitrate from the environment via either denitrification, dissimilatory nitrate reduction to ammonium or both. The recent renewed interest in their nitrogen metabolism has revealed many interesting features, the most striking being their wide variety of dissimilatory nitrate reduction pathways. In the present study, nitrous oxide production from Bacillus licheniformis, a ubiquitous Gram-positive, spore-forming species with many industrial applications, is investigated. 
Results: B. licheniformis has long been considered a denitrifier but physiological experiments on three different strains demonstrated that nitrous oxide is not produced from nitrate in stoichiometric amounts, rather ammonium is the most important end-product, produced during fermentation. Significant strain dependency in end-product ratios, attributed to nitrite and ammonium, and medium dependency in nitrous oxide production were also observed. Genome analyses confirmed the lack of a nitrite reductase to nitric oxide, the key enzyme of denitrification. Based on the gene inventory and building on knowledge from other non-denitrifying nitrous oxide emitters, hypothetical pathways for nitrous oxide production, involving NarG, NirB, qNor and Hmp, are proposed. In addition, all publically available genomes of B. licheniformis demonstrated similar gene inventories, with specific duplications of the nar operon, narK and hmp genes as well as NarG phylogeny supporting the evolutionary separation of previously described distinct BALI1 and BALI2 lineages. 
Conclusions: Using physiological and genomic data we have demonstrated that the common soil bacterium B. licheniformis does not denitrify but is capable of fermentative dissimilatory nitrate/nitrite reduction to ammonium (DNRA) with concomitant production of N2O. Considering its ubiquitous nature and non-fastidious growth in the lab, B. licheniformis is a suitable candidate for further exploration of the actual mechanism of N2O production in DNRA bacteria and its relevance in situ.},
  articleno    = {68},
  author       = {Sun, Yi-hua and De Vos, Paul and Heylen, Kim},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keywords     = {Dissimilatory nitrate/nitrite reduction to ammonium (DNRA),Fermentation,Nitrate respiration,Denitrification,Ammonification,Nitrite detoxification,COLI FLAVOHAEMOGLOBIN HMP,COMPLETE GENOME SEQUENCE,C NITRITE REDUCTASE,ESCHERICHIA-COLI,SPECIES DEFINITION,NORB GENE,DENITRIFICATION,BACTERIA,STRAINS,FLAVOHEMOGLOBIN},
  language     = {eng},
  pages        = {11},
  title        = {Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis},
  url          = {http://dx.doi.org/10.1186/s12864-016-2382-2},
  volume       = {17},
  year         = {2016},
}

Altmetric
View in Altmetric
Web of Science
Times cited: