Nitrogen Metabolism of an Anoxygenic Filamentous Phototrophic Bacterium Oscillocholris trichoides Strain DG-6

Abstract

Abstract— The possible nitrogen sources for Osc. trichoides DG6, a typical strain of the Oscillochloridaceae family, are ammonium, N2, glutamate, asparagine, glycine, and glutamine. The assimilation of molecular nitrogen occurs with the participation of nitrogenase, the structural gene of which, nifH, is located in the gene cluster which also includes the genes of the nifD and nifK nitrogenase subunits and the auxiliary nifB gene. Considering that nifHBDK clusters have been also annotated in the genomes of other members of the Oscillochloridaceae family, including uncultured and candidate taxa, it can be assumed that the ability to fix nitrogen is a property immanent for this entire family. The pathways for assimilating ammonium in the cells grown using different nitrogen sources may differ. Osc. trichoides DG6 growing in a medium containing ammonium assimilated it with the participation of glutamate dehydrogenase, which is determined by a single gene. The expression product of this gene has dual functionality and can be used to implement the reaction with both NAD and NADP. With the growth of Osc. trichoides DG6 on a medium with glutamate as the only nitrogen source all the enzymes necessary for the implementation of the GS‑GOGAT pathway were found in the cells. However, for the glutamine synthetase reaction, ammonium, which was absent in the growth medium, was required. The source of ammonium may be glutamate metabolized through glutamate dehydrogenase.

Origin and Evolution of Nitrogen Fixation in Prokaryotes

“…Moreover, several studies found that only bacteria can use Group IV-Nfa NifHDKB to fix nitrogen ( Zheng, Dietrich, et al 2016 ; Méheust et al 2020 ; North et al 2020 ; Koirala and Brözel 2021 ). Note further that Oscillocholris trichoides has also been shown experimentally to fix nitrogen ( Ivanovsky et al 2021 ). As O. trichoides belongs to Group III (Chloroflexota) while E. proavitum belongs to Group IV, there might be other species with the four- nif -gene set ( nifHDKB ) that can fix nitrogen.…”

“…Although various sets of nif genes have been used as criteria to identify Nif species ( Dos Santos et al 2012 ; Poudel et al 2018 ; Albright et al 2019 ; Koirala and Brözel 2021 ), the entire set of the above six nif genes (i.e., nifHDKENB ) has been proposed to be the definition of Nif species ( Dos Santos et al 2012 ; Mus et al 2019 ). However, nifN or both nifE and nifN may not be essential because this gene is absent in the genomes of some Nif Chloroflexota (bacteria) ( Ivanovsky et al 2021 ), Firmicutes_A (bacteria) ( Chen et al 2021 ), Elusimicrobiota (bacteria) ( Zheng, Dietrich, et al 2016 ), and Nif methanogens (archaea) ( Mehta and Baross 2006 ). We therefore will also consider the criterion of “the five- nif- gene set” ( nifHDKEB ), which includes no nifN , and that of “the four- nif- gene set” ( nifHDKB ), which includes no nifEN .…”

Mapping Geological Events and Nitrogen Fixation Evolution Onto the Timetree of the Evolution of Nitrogen-Fixation Genes

“…We assumed that the common ancestor of all groups (node 0 in Fig. 1 ) was 3,700 MYA (Timetree 1), because all groups contain species that are known to be able to fix nitrogen ( Zheng et al 2016 ; Chen et al 2021 ; Ivanovsky et al 2021 ; Koirala and Brözel 2021 ). Figure 2 is based on these three calibration points (Timetrees 3 and 4 in Table 1 ).…”

“…Nif genes are usually present in a cluster in a genome ( Dos Santos et al 2012 ). The set of all six nif genes ( nifHDKENB ) was used to identify nitrogen-fixing species ( Dos Santos et al 2012 ) but some species with the five-gene set nifHDKEB or even the four-gene set nifHDKB have been found to be able to fix nitrogen ( Zheng et al 2016 ; Chen et al 2021 ; Ivanovsky et al 2021 ).…”