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Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat.

Fan H, Bolhuis H, Stal LJ - Front Microbiol (2015)

Bottom Line: In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes.The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate.We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats.

View Article: PubMed Central - PubMed

Affiliation: Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands.

ABSTRACT
The first step of nitrification, the oxidation of ammonia to nitrite, can be performed by ammonia-oxidizing archaea (AOA) or ammonium-oxidizing bacteria (AOB). We investigated the presence of these two groups in three structurally different types of coastal microbial mats that develop along the tidal gradient on the North Sea beach of the Dutch barrier island Schiermonnikoog. The abundance and transcription of amoA, a gene encoding for the alpha subunit of ammonia monooxygenase that is present in both AOA and AOB, were assessed and the potential nitrification rates in these mats were measured. The potential nitrification rates in the three mat types were highest in autumn and lowest in summer. AOB and AOA amoA genes were present in all three mat types. The composition of the AOA and AOB communities in the mats of the tidal and intertidal stations, based on the diversity of amoA, were similar and clustered separately from the supratidal microbial mat. In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes. The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate. The composition and abundance of amoA genes seemed to be partly driven by salinity, ammonium, temperature, and the nitrate/nitrite concentration. We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats.

No MeSH data available.


Relative abundance of (A) probes affiliated with the major bacterial amoA clusters suggested by Purkhold et al. (2003) and Francis et al. (2003) in the analyzed microbial mats; (B) probes affiliated with the major archaeal amoA clusters suggested by Pester et al. (2012) in the analyzed microbial mats.
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Figure 1: Relative abundance of (A) probes affiliated with the major bacterial amoA clusters suggested by Purkhold et al. (2003) and Francis et al. (2003) in the analyzed microbial mats; (B) probes affiliated with the major archaeal amoA clusters suggested by Pester et al. (2012) in the analyzed microbial mats.

Mentions: In all microbial mats, AOB amoA genes were detected belonging to Beta- and Gammaproteobacteria (Figure 1A). The majority (>98% signal intensities) AOB amoA sequences retrieved from the GeoChip hybridizations belonged to Betaproteobacteria (β-AOB). Among the Betaproteobacteria, the sequences clustered with Nitrosospira and Nitrosomonas. The sequences belonging to Nitrosospira can be subdivided into three major clusters (Table 3). Several cultivated species, such as Nitrosospira multiformis (AAC25057), Nitrosospira briensis and Nitrosospira sp. REGAU (AAV34189) were detected. 8.0% of the sequences obtained from the GeoChip belong to Nitrosospira cluster C. Nitrosovibrio sp. FJ182 (ABB69924) and some uncultured clones were detected that grouped in cluster C. The sequences belonging to Nitrosomonas can be sub-divided into four major clusters (Table 3). The nomenclature suggested by Purkhold et al. (2003) and Francis et al. (2003) was used. At all stations, the shifts between different groups were minor. Phylogenetic analysis revealed a broad distribution of archaeal amoA genes (Figure 1B). The nomenclature suggested by Pester et al. (2012) was used. 41.1, 14.7, 37.9, and 6.3% of the total number of sequences obtained from the GeoChip fell into Nitrosopumilus, Nitrosotalea, Nitrososphaera, and others, respectively (Table 3). Based on the GeoChip signal intensities, Nitrosopumilus and Nitrososphaera were predominant and accounted for respectively 39.6–45.5% and 28.7–34.3% of total AOA amoA gene signal intensities. Nitrosotalea accounted for 16.5–20.3% of the total AOA amoA gene signal intensities. Other groups accounted for the remaining 6.9–9.3% of the total AOA amoA gene signal intensities. In none of the stations shifts between different groups were observed.


Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat.

Fan H, Bolhuis H, Stal LJ - Front Microbiol (2015)

Relative abundance of (A) probes affiliated with the major bacterial amoA clusters suggested by Purkhold et al. (2003) and Francis et al. (2003) in the analyzed microbial mats; (B) probes affiliated with the major archaeal amoA clusters suggested by Pester et al. (2012) in the analyzed microbial mats.
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Related In: Results  -  Collection

License
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Figure 1: Relative abundance of (A) probes affiliated with the major bacterial amoA clusters suggested by Purkhold et al. (2003) and Francis et al. (2003) in the analyzed microbial mats; (B) probes affiliated with the major archaeal amoA clusters suggested by Pester et al. (2012) in the analyzed microbial mats.
Mentions: In all microbial mats, AOB amoA genes were detected belonging to Beta- and Gammaproteobacteria (Figure 1A). The majority (>98% signal intensities) AOB amoA sequences retrieved from the GeoChip hybridizations belonged to Betaproteobacteria (β-AOB). Among the Betaproteobacteria, the sequences clustered with Nitrosospira and Nitrosomonas. The sequences belonging to Nitrosospira can be subdivided into three major clusters (Table 3). Several cultivated species, such as Nitrosospira multiformis (AAC25057), Nitrosospira briensis and Nitrosospira sp. REGAU (AAV34189) were detected. 8.0% of the sequences obtained from the GeoChip belong to Nitrosospira cluster C. Nitrosovibrio sp. FJ182 (ABB69924) and some uncultured clones were detected that grouped in cluster C. The sequences belonging to Nitrosomonas can be sub-divided into four major clusters (Table 3). The nomenclature suggested by Purkhold et al. (2003) and Francis et al. (2003) was used. At all stations, the shifts between different groups were minor. Phylogenetic analysis revealed a broad distribution of archaeal amoA genes (Figure 1B). The nomenclature suggested by Pester et al. (2012) was used. 41.1, 14.7, 37.9, and 6.3% of the total number of sequences obtained from the GeoChip fell into Nitrosopumilus, Nitrosotalea, Nitrososphaera, and others, respectively (Table 3). Based on the GeoChip signal intensities, Nitrosopumilus and Nitrososphaera were predominant and accounted for respectively 39.6–45.5% and 28.7–34.3% of total AOA amoA gene signal intensities. Nitrosotalea accounted for 16.5–20.3% of the total AOA amoA gene signal intensities. Other groups accounted for the remaining 6.9–9.3% of the total AOA amoA gene signal intensities. In none of the stations shifts between different groups were observed.

Bottom Line: In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes.The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate.We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats.

View Article: PubMed Central - PubMed

Affiliation: Department of Marine Microbiology, Royal Netherlands Institute for Sea Research Yerseke, Netherlands.

ABSTRACT
The first step of nitrification, the oxidation of ammonia to nitrite, can be performed by ammonia-oxidizing archaea (AOA) or ammonium-oxidizing bacteria (AOB). We investigated the presence of these two groups in three structurally different types of coastal microbial mats that develop along the tidal gradient on the North Sea beach of the Dutch barrier island Schiermonnikoog. The abundance and transcription of amoA, a gene encoding for the alpha subunit of ammonia monooxygenase that is present in both AOA and AOB, were assessed and the potential nitrification rates in these mats were measured. The potential nitrification rates in the three mat types were highest in autumn and lowest in summer. AOB and AOA amoA genes were present in all three mat types. The composition of the AOA and AOB communities in the mats of the tidal and intertidal stations, based on the diversity of amoA, were similar and clustered separately from the supratidal microbial mat. In all three mats AOB amoA genes were significantly more abundant than AOA amoA genes. The abundance of neither AOB nor AOA amoA genes correlated with the potential nitrification rates, but AOB amoA transcripts were positively correlated with the potential nitrification rate. The composition and abundance of amoA genes seemed to be partly driven by salinity, ammonium, temperature, and the nitrate/nitrite concentration. We conclude that AOB are responsible for the bulk of the ammonium oxidation in these coastal microbial mats.

No MeSH data available.