Limits...
Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria.

Kozlowski JA, Kits KD, Stein LY - Front Microbiol (2016)

Bottom Line: Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene.Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions.This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Biological Sciences Building, University of Alberta, Edmonton, AB Canada.

ABSTRACT
Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity.

No MeSH data available.


Related in: MedlinePlus

Rooted maximum likelihood phylogeny of 14 publically available genomes of ammonia oxidizing bacteria based on 400 broadly conserved amino-acid sequences. PhyloPhlAn (Segata et al., 2013) was used to identify and align the amino-acid sequences in all input genomes. The tree was constructed using PhyML 3.0 (Guindon et al., 2010) with the Gammaproteobacteria as the root. Bootstrap values (as a proportion of 500 replicates) are denoted above the branches and branch lengths correspond to sequence differences as indicated by the scale bar at the bottom.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4940428&req=5

Figure 1: Rooted maximum likelihood phylogeny of 14 publically available genomes of ammonia oxidizing bacteria based on 400 broadly conserved amino-acid sequences. PhyloPhlAn (Segata et al., 2013) was used to identify and align the amino-acid sequences in all input genomes. The tree was constructed using PhyML 3.0 (Guindon et al., 2010) with the Gammaproteobacteria as the root. Bootstrap values (as a proportion of 500 replicates) are denoted above the branches and branch lengths correspond to sequence differences as indicated by the scale bar at the bottom.

Mentions: A whole-genome analysis utilizing PhyloPhlAn showed that each of the 5 Betaproteobacteria AOB chosen for physiological analysis in the present study separated into individual clades (Figure 1). The separation of each AOB into a unique branch, using 400 core protein markers from available complete genome sequences to form a high-resolution tree, shows a clearer and greater separation than currently available 16S rRNA or amoA single gene sequence phylogenies (Norton, 2011). The results of this multiple-marker, genome-wide, comparison highlight a need to reevaluate and perhaps reclassify some members of Nitrosomonas into different genera.


Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria.

Kozlowski JA, Kits KD, Stein LY - Front Microbiol (2016)

Rooted maximum likelihood phylogeny of 14 publically available genomes of ammonia oxidizing bacteria based on 400 broadly conserved amino-acid sequences. PhyloPhlAn (Segata et al., 2013) was used to identify and align the amino-acid sequences in all input genomes. The tree was constructed using PhyML 3.0 (Guindon et al., 2010) with the Gammaproteobacteria as the root. Bootstrap values (as a proportion of 500 replicates) are denoted above the branches and branch lengths correspond to sequence differences as indicated by the scale bar at the bottom.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940428&req=5

Figure 1: Rooted maximum likelihood phylogeny of 14 publically available genomes of ammonia oxidizing bacteria based on 400 broadly conserved amino-acid sequences. PhyloPhlAn (Segata et al., 2013) was used to identify and align the amino-acid sequences in all input genomes. The tree was constructed using PhyML 3.0 (Guindon et al., 2010) with the Gammaproteobacteria as the root. Bootstrap values (as a proportion of 500 replicates) are denoted above the branches and branch lengths correspond to sequence differences as indicated by the scale bar at the bottom.
Mentions: A whole-genome analysis utilizing PhyloPhlAn showed that each of the 5 Betaproteobacteria AOB chosen for physiological analysis in the present study separated into individual clades (Figure 1). The separation of each AOB into a unique branch, using 400 core protein markers from available complete genome sequences to form a high-resolution tree, shows a clearer and greater separation than currently available 16S rRNA or amoA single gene sequence phylogenies (Norton, 2011). The results of this multiple-marker, genome-wide, comparison highlight a need to reevaluate and perhaps reclassify some members of Nitrosomonas into different genera.

Bottom Line: Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene.Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions.This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, Biological Sciences Building, University of Alberta, Edmonton, AB Canada.

ABSTRACT
Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity.

No MeSH data available.


Related in: MedlinePlus