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Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea).

Lipsewers YA, Bale NJ, Hopmans EC, Schouten S, Sinninghe Damsté JS, Villanueva L - Front Microbiol (2014)

Bottom Line: Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments.We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea.In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments.

View Article: PubMed Central - PubMed

Affiliation: Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands.

ABSTRACT
Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria.

No MeSH data available.


Transcriptional activity given as RNA:DNA ratio of (A) AOA 16S rRNA gene; (B) AOA amoA gene; (C) AOB 16S rRNA gene, (D) AOB amoA; (E) Anammox 16S rRNA gene, and (F) Anammox bacteria hzsA gene with sediment depth (cm) below sea floor (bsf).
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Figure 3: Transcriptional activity given as RNA:DNA ratio of (A) AOA 16S rRNA gene; (B) AOA amoA gene; (C) AOB 16S rRNA gene, (D) AOB amoA; (E) Anammox 16S rRNA gene, and (F) Anammox bacteria hzsA gene with sediment depth (cm) below sea floor (bsf).

Mentions: The RNA:DNA ratios of the AOA and AOB 16S rRNA and amoA genes were calculated as an indicator of the potential transcriptional activity of the targeted microbial group (Figures 3A–D). In all three seasons, AOA 16S rRNA gene RNA:DNA ratio showed relatively stable values down core ranging between 0.9 and 5.0 and 1.2 and 3.4 in May and August but reached slightly higher values (2.2–8.2) in February (Figure 3A). AOB 16S rRNA gene RNA:DNA ratio was between 0.1 and 2.1 with a minimum of 0.1 between 4 and 5 cm bsf in February and 0.1 and 3.7 with a minimum between 2 and 3 cm bsf in May. The AOB 16S rRNA gene RNA:DNA ratio was slightly higher (1.2–4.1) in August (Figure 3C). Values were relatively stable with depth in August whereas in February and May values were more variable. Compared to the RNA:DNA ratio of the AOA 16S rRNA gene, the AOB 16S rRNA gene RNA:DNA ratio was lower (fivefold in February, 1.5-fold in May and 1.3-fold lower in August) in all seasons (Figures 3A,C). AOA amoA gene transcripts (Figure 3B) were only detected in February in the first 3 cm and in August throughout the core, and were under the detection limit in May. AOB amoA gene RNA:DNA ratio (Figure 3D) varied between 4 × 10-5 and 2 × 10-2 in all seasons with a slight decrease with depth and highest values in August.


Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea).

Lipsewers YA, Bale NJ, Hopmans EC, Schouten S, Sinninghe Damsté JS, Villanueva L - Front Microbiol (2014)

Transcriptional activity given as RNA:DNA ratio of (A) AOA 16S rRNA gene; (B) AOA amoA gene; (C) AOB 16S rRNA gene, (D) AOB amoA; (E) Anammox 16S rRNA gene, and (F) Anammox bacteria hzsA gene with sediment depth (cm) below sea floor (bsf).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4155873&req=5

Figure 3: Transcriptional activity given as RNA:DNA ratio of (A) AOA 16S rRNA gene; (B) AOA amoA gene; (C) AOB 16S rRNA gene, (D) AOB amoA; (E) Anammox 16S rRNA gene, and (F) Anammox bacteria hzsA gene with sediment depth (cm) below sea floor (bsf).
Mentions: The RNA:DNA ratios of the AOA and AOB 16S rRNA and amoA genes were calculated as an indicator of the potential transcriptional activity of the targeted microbial group (Figures 3A–D). In all three seasons, AOA 16S rRNA gene RNA:DNA ratio showed relatively stable values down core ranging between 0.9 and 5.0 and 1.2 and 3.4 in May and August but reached slightly higher values (2.2–8.2) in February (Figure 3A). AOB 16S rRNA gene RNA:DNA ratio was between 0.1 and 2.1 with a minimum of 0.1 between 4 and 5 cm bsf in February and 0.1 and 3.7 with a minimum between 2 and 3 cm bsf in May. The AOB 16S rRNA gene RNA:DNA ratio was slightly higher (1.2–4.1) in August (Figure 3C). Values were relatively stable with depth in August whereas in February and May values were more variable. Compared to the RNA:DNA ratio of the AOA 16S rRNA gene, the AOB 16S rRNA gene RNA:DNA ratio was lower (fivefold in February, 1.5-fold in May and 1.3-fold lower in August) in all seasons (Figures 3A,C). AOA amoA gene transcripts (Figure 3B) were only detected in February in the first 3 cm and in August throughout the core, and were under the detection limit in May. AOB amoA gene RNA:DNA ratio (Figure 3D) varied between 4 × 10-5 and 2 × 10-2 in all seasons with a slight decrease with depth and highest values in August.

Bottom Line: Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments.We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea.In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments.

View Article: PubMed Central - PubMed

Affiliation: Department of Marine Organic Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research Den Burg, Netherlands.

ABSTRACT
Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria.

No MeSH data available.