Journal ArticleDOI
Cell biology and molecular basis of denitrification.
TLDR
Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1.Abstract:
Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.read more
Citations
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Journal ArticleDOI
The microbial nitrogen-cycling network
TL;DR: This Review summarizes the current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications.
Journal ArticleDOI
Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms
Alan Richardson,José Miguel Barea,Ann McNeill,Claire Prigent-Combaret,Claire Prigent-Combaret +4 more
TL;DR: Features of the rhizosphere that are important for nutrient acquisition from soil are reviewed, with specific emphasis on the characteristics of roots that influence the availability and uptake of phosphorus and nitrogen.
Journal ArticleDOI
Nitrite-driven anaerobic methane oxidation by oxygenic bacteria
Katharina F. Ettwig,Margaret K. Butler,Margaret K. Butler,Denis Le Paslier,Denis Le Paslier,Eric Pelletier,Eric Pelletier,Sophie Mangenot,Marcel M. M. Kuypers,Frank Schreiber,Bas E. Dutilh,Johannes Zedelius,Dirk de Beer,Jolein Gloerich,Hans J. C. T. Wessels,Theo A. van Alen,Francisca A. Luesken,Ming L. Wu,Katinka T. van de Pas-Schoonen,Huub J. M. Op den Camp,Eva M. Janssen-Megens,Kees-Jan Francoijs,Henk Stunnenberg,Jean Weissenbach,Jean Weissenbach,Mike S. M. Jetten,Marc Strous,Marc Strous +27 more
TL;DR: Evidence for a fourth pathway to produce oxygen is presented, possibly of considerable geochemical and evolutionary importance, and opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis.
Journal ArticleDOI
Complete nitrification by a single microorganism
Maartje A. H. J. van Kessel,Daan R. Speth,Mads Albertsen,Per Halkjær Nielsen,Huub J. M. Op den Camp,Boran Kartal,Boran Kartal,Mike S. M. Jetten,Mike S. M. Jetten,Sebastian Lücker +9 more
TL;DR: The enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrates to conserve energy are reported.
Journal ArticleDOI
Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE.
TL;DR: It was demonstrated that agricultural soil harbours a substantial diversity of nirS denitrifiers by use of the new nIRS primers, which acted as broad range primers for each of the three genes.
References
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