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Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

Bagchi S, Vlaeminck SE, Sauder LA, Mosquera M, Neufeld JD, Boon N - PLoS ONE (2014)

Bottom Line: In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time.Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters.These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium.

ABSTRACT
Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.

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Maximum likelihood phylogenetic tree of thaumarchaeal 16S rRNA gene sequences and DGGE bands based on 500 bootstrap values.Only bootstrap values greater than 50% are indicated. The scale bar represents 5% nucleotide divergence.
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pone-0113515-g004: Maximum likelihood phylogenetic tree of thaumarchaeal 16S rRNA gene sequences and DGGE bands based on 500 bootstrap values.Only bootstrap values greater than 50% are indicated. The scale bar represents 5% nucleotide divergence.

Mentions: We further assessed the temporal dynamics among freshwater AOA communities to determine the stability of the community over time. Freshwater samples were dispersed in the NMDS ordination but there was no gradual succession away from the initial condition (Figure 3). MVDISP showed a higher dispersion for freshwater aquaria F1 and F3 (IMD of 1.37 and 1.24, respectively) by global MVDISP analysis, indicating a change in community from the initial condition of these aquaria. Despite dispersion, communities did not change significantly over time, but instead samples were clustered based by aquarium (A = 0.53), with separation (T = −11.55) between aquaria as calculated by MRPP. DGGE patterns also revealed similarity in community composition of the sampled freshwater biofilters (Figure 2). Thus, AOA communities in freshwater aquaria were temporally stable despite of their differences in pH (6–8), temperature (19–28°C), dissolved oxygen levels (6.5–9.0 mg O2 L−1) and housed fish and crustaceans. Representative DGGE bands from freshwater and marine aquaria were sequenced to identify the AOA taxa found within biofilters. Most marine 16S rRNA gene sequences clustered together and shared sequence homology with N. maritimus. The freshwater sequences were more diverse and clustered with archaeal sequences from a variety of environments, including saline soils and a wastewater treatment plant (Figure 4).


Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

Bagchi S, Vlaeminck SE, Sauder LA, Mosquera M, Neufeld JD, Boon N - PLoS ONE (2014)

Maximum likelihood phylogenetic tree of thaumarchaeal 16S rRNA gene sequences and DGGE bands based on 500 bootstrap values.Only bootstrap values greater than 50% are indicated. The scale bar represents 5% nucleotide divergence.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257543&req=5

pone-0113515-g004: Maximum likelihood phylogenetic tree of thaumarchaeal 16S rRNA gene sequences and DGGE bands based on 500 bootstrap values.Only bootstrap values greater than 50% are indicated. The scale bar represents 5% nucleotide divergence.
Mentions: We further assessed the temporal dynamics among freshwater AOA communities to determine the stability of the community over time. Freshwater samples were dispersed in the NMDS ordination but there was no gradual succession away from the initial condition (Figure 3). MVDISP showed a higher dispersion for freshwater aquaria F1 and F3 (IMD of 1.37 and 1.24, respectively) by global MVDISP analysis, indicating a change in community from the initial condition of these aquaria. Despite dispersion, communities did not change significantly over time, but instead samples were clustered based by aquarium (A = 0.53), with separation (T = −11.55) between aquaria as calculated by MRPP. DGGE patterns also revealed similarity in community composition of the sampled freshwater biofilters (Figure 2). Thus, AOA communities in freshwater aquaria were temporally stable despite of their differences in pH (6–8), temperature (19–28°C), dissolved oxygen levels (6.5–9.0 mg O2 L−1) and housed fish and crustaceans. Representative DGGE bands from freshwater and marine aquaria were sequenced to identify the AOA taxa found within biofilters. Most marine 16S rRNA gene sequences clustered together and shared sequence homology with N. maritimus. The freshwater sequences were more diverse and clustered with archaeal sequences from a variety of environments, including saline soils and a wastewater treatment plant (Figure 4).

Bottom Line: In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time.Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters.These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, 9000 Gent, Belgium.

ABSTRACT
Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium biofilters, and that AOA community composition within a given aquarium is stable over time and across biofilter support material types.

Show MeSH
Related in: MedlinePlus