Abstract
The biological nitrogen cycle is driven by a plethora of reactions transforming nitrogen compounds between various redox states. Here, we investigated the metagenomic potential for nitrogen cycle of the in situ microbial community in an oligotrophic, brackish environment of the Bothnian Sea sediment. Total DNA from three sediment depths was isolated and sequenced. The characterization of the total community was performed based on 16S rRNA gene inventory using SILVA database as reference. The diversity of diagnostic functional genes coding for nitrate reductases (napA;narG), nitrite:nitrate oxidoreductase (nxrA), nitrite reductases (nirK;nirS;nrfA), nitric oxide reductase (nor), nitrous oxide reductase (nosZ), hydrazine synthase (hzsA), ammonia monooxygenase (amoA), hydroxylamine oxidoreductase (hao), and nitrogenase (nifH) was analyzed by blastx against curated reference databases. In addition, Polymerase chain reaction (PCR)‐based amplification was performed on the hzsA gene of anammox bacteria. Our results reveal high genomic potential for full denitrification to N2, but minor importance of anaerobic ammonium oxidation and dissimilatory nitrite reduction to ammonium. Genomic potential for aerobic ammonia oxidation was dominated by Thaumarchaeota. A higher diversity of anammox bacteria was detected in metagenomes than with PCR‐based technique. The results reveal the importance of various N‐cycle driving processes and highlight the advantage of metagenomics in detection of novel microbial key players.
Highlights
Baltic Sea is a brackish basin which has been heavily impacted by eutrophication in the past decades (Jäntti & Hietanen, 2012)
The latest study on in situ N-cycle activities in brackish sediments of the Bothnian Bay and Bothnian Sea showed that total rates of denitrification were lower than in eutrophic sediments of the southern Baltic Sea basin with anammox contributing at some sites up to 26% in N- oxide reduction (Bonaglia et al, 2016)
The majority was assigned to bacteria (80% in oxic/anoxic interface zone (OAZ), 93% in sulfate methane transition zone (SMTZ), and 80% in methanic zone (MZ)) with archaea contributing 4% in OAZ, 5% in SMTZ, and 18% in MZ
Summary
Baltic Sea is a brackish basin which has been heavily impacted by eutrophication in the past decades (Jäntti & Hietanen, 2012). The latest study on in situ N-cycle activities in brackish sediments of the Bothnian Bay and Bothnian Sea showed that total rates of denitrification were lower than in eutrophic sediments of the southern Baltic Sea basin with anammox contributing at some sites up to 26% in N- oxide reduction (Bonaglia et al, 2016). Most of the molecular analyses have, focused on eutrophic areas of the Baltic Sea and very little is known about the microbial community composition in oligotrophic sediments of the Bothnian Sea. despite the existing activity studies, the underlying functional N-cycle potential of these sediments remains unknown and comparisons to other parts of the Baltic Sea are not possible. Curated datasets of the diagnostic N-cycle proteins (Figure 1) were used to estimate the abundance and diversity of the various reactions with specific emphasis on the anammox process
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