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. 2015 Jul 21;6:738.
doi: 10.3389/fmicb.2015.00738. eCollection 2015.

Drivers of the Dynamics of Diazotrophs and Denitrifiers in North Sea Bottom Waters and Sediments

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Free PMC article

Drivers of the Dynamics of Diazotrophs and Denitrifiers in North Sea Bottom Waters and Sediments

Haoxin Fan et al. Front Microbiol. .
Free PMC article

Abstract

The fixation of dinitrogen (N2) and denitrification are two opposite processes in the nitrogen cycle. The former transfers atmospheric dinitrogen gas into bound nitrogen in the biosphere, while the latter returns this bound nitrogen back to atmospheric dinitrogen. It is unclear whether or not these processes are intimately connected in any microbial ecosystem or that they are spatially and/or temporally separated. Here, we measured seafloor nitrogen fixation and denitrification as well as pelagic nitrogen fixation by using the stable isotope technique. Alongside, we measured the diversity, abundance, and activity of nitrogen-fixing and denitrifying microorganisms at three stations in the southern North Sea. Nitrogen fixation ranged from undetectable to 2.4 nmol N L(-1) d(-1) and from undetectable to 8.2 nmol N g(-1) d(-1) in the water column and seafloor, respectively. The highest rates were measured in August at Doggersbank, both for the water column and for the seafloor. Denitrification ranged from 1.7 to 208.8 μmol m(-2) d(-1) and the highest rates were measured in May at the Oyster Grounds. DNA sequence analysis showed sequences of nifH, a structural gene for nitrogenase, related to sequences from anaerobic sulfur/iron reducers and sulfate reducers. Sequences of the structural gene for nitrite reductase, nirS, were related to environmental clones from marine sediments. Quantitative polymerase chain reaction (qPCR) data revealed the highest abundance of nifH and nirS genes at the Oyster Grounds. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) data revealed the highest nifH expression at Doggersbank and the highest nirS expression at the Oyster Grounds. The distribution of the diazotrophic and denitrifying communities seems to be subject to different selecting factors, leading to spatial and temporal separation of nitrogen fixation and denitrification. These selecting factors include temperature, organic matter availability, and oxygen concentration.

Keywords: N2 fixation; North Sea; denitrification; nifH gene; nirS gene.

Figures

Figure 1
Figure 1
Map of the North Sea with the three sampling stations marked.
Figure 2
Figure 2
N2 fixation (nmol N L−1 d−1) in surface and deep water at the stations DB, OG, and DC in February, May and August.
Figure 3
Figure 3
N2 fixation in the bottom sediments at the stations DB, OG, and DC in February, May, and August. (A) potential nitrogen fixation rates (nmol N day−1 g−1 wet sediment). (B) nifH copy number (g−1 wet sediment). (C) nifH transcript number (g−1 wet sediment). n.d., no data.
Figure 4
Figure 4
Denitrification in the bottom sediments at the stations DB, OG, and DC in February, May, and August. (A) in situ denitrification (μmol m−2 day−1). (B) nirS copy number (g−1 wet sediment). (C) nirS transcript number (g−1 wet sediment). n.d., no data.
Figure 5
Figure 5
Phylogenetic tree of NifH based on the translated amino acid sequence, constructed by the neighbor-joining method in MEGA 6. The scale bar indicates the number of sequence substitution per sites. Sequences retrieved in this study fell into 22 groups (NS1-NS22) and are shown in bold. Table S1 gives all sequences in groups NS1–NS22. Groups that contain sequences from both genomic DNA and cDNA are marked by a solid circle. Asterisks indicate groups that contain sequences from the water column. nifH sequences that have been reported previously as potential contaminants in RT-PCR reagents are marked by a solid triangle.
Figure 6
Figure 6
Phylogenetic tree of NirS based on the translated amino acid sequence, constructed by the neighbor-joining method in MEGA 6. The scale bar indicates the number of sequence substitution per sites. Sequences retrieved in this study are shown in bold. The numbers in the parenthesis following the station name indicate the number of sequences within this cluster at that station.
Figure 7
Figure 7
Principal coordinate analyses of nifH (solid circle) and nirS (solid triangle) translated amino acid sequences at the 95% cutoff.

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