Denitrifying bacteria

About: Denitrifying bacteria is a research topic. Over the lifetime, 7152 publications have been published within this topic receiving 197751 citations.

Cell biology and molecular basis of denitrification.

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.

Mineralization of organic matter in the sea bed—the role of sulphate reduction

Abstract: The bacterial reduction of sulphate to sulphide at the sea bed is a key process in the oceanic sulphur cycle, and is responsible for the oxidation of organic matter which becomes buried below the oxic and sub-oxic zones of the sea bed. The oxic surface layer of the sea bed varies in thickness from a few millimetres in sheltered coastal areas to ⩾1 m in pelagic sediments1,2. Below this layer, organic matter is mineralized mainly by fermenting, denitrifying, sulphate-reducing and methane-producing bacteria. Sulphate reduction is the predominant terminal step in the mineralization processes of sulphate-rich shelf sediments where the sulphate reducers inhibit the methanogens by competing with them for common substrates3–5. Sulphate reduction may therefore have a quantitatively important role in the overall oxidation of organic matter in the sea bed. Recently, concurrent measurements of oxygen uptake and sulphate reduction in a coastal sediment6 have demonstrated the importance of the sulphate-reducing bacteria in the mineralization of organic carbon. I present here the first comparative survey of aerobic and anaerobic mineralization in the sea bed based on direct rate measurements of the two processes. The results demonstrate a surprisingly high contribution from the sulphate-reducers. In coastal sediments, this specialized group of bacteria oxidized as much organic matter to CO2 as did all the aerobic organisms. Their relative contribution decreased three fold over the continental shelf from the shore to a depth of 200 m.

A Bacterial Method for the Nitrogen Isotopic Analysis of Nitrate in Seawater and Freshwater

Abstract: We report a new method for measurement of the isotopic composition of nitrate (NO3-) at the natural-abundance level in both seawater and freshwater. The method is based on the isotopic analysis of nitrous oxide (N2O) generated from nitrate by denitrifying bacteria that lack N2O-reductase activity. The isotopic composition of both nitrogen and oxygen from nitrate are accessible in this way. In this first of two companion manuscripts, we describe the basic protocol and results for the nitrogen isotopes. The precision of the method is better than 0.2‰ (1 SD) at concentrations of nitrate down to 1 μM, and the nitrogen isotopic differences among various standards and samples are accurately reproduced. For samples with 1 μM nitrate or more, the blank of the method is less than 10% of the signal size, and various approaches may reduce it further.