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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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Nonmetric multidimensional scaling (NMDS) ordination of thaumarchaeal 16S rRNA gene DGGE fingerprint.The two-dimensional stress value for the NMDS was 0.107 based on Bray Curtis distance. Coefficients of determination (R2) on each axis represent correlations between ordination distances and the corresponding distance matrix.
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pone-0113515-g003: Nonmetric multidimensional scaling (NMDS) ordination of thaumarchaeal 16S rRNA gene DGGE fingerprint.The two-dimensional stress value for the NMDS was 0.107 based on Bray Curtis distance. Coefficients of determination (R2) on each axis represent correlations between ordination distances and the corresponding distance matrix.

Mentions: To characterize AOA community composition over time, DGGE fingerprinting for thaumarchaeal 16S rRNA genes was performed. DGGE profiles for thaumarchaeal 16S rRNA genes revealed simple patterns and low diversity among different freshwater and marine aquaria (Figure 2). The community composition of the sampled freshwater biofilters was highly similar, with the presence of two or three intense bands shared between different aquaria. The thaumarchaeal 16S rRNA gene patterns associated with the marine aquarium also contained few bands but were distinct from their freshwater counterparts. Dendrograms based on Pearson correlations of DGGE fingerprint densitometric curves placed marine fingerprints in a distinct cluster (Figure 2). NMDS generated from DGGE fingerprints revealed that freshwater and marine aquaria were separated in a two-dimensional space (Figure 3). Consistently, MRPP based on DGGE fingerprints showed significant separation (T = −10.83) between freshwater and marine fingerprints. Quantitatively, the distance between different aquaria was assessed by pair-wise ANOSIM. The average distance from the marine aquarium to the freshwater aquaria was significantly higher (0.9, p<0.01 as determined by Student's t test) than between freshwater aquaria, indicating that the AOA community in the marine aquarium was distinct from their freshwater counterparts.


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)

Nonmetric multidimensional scaling (NMDS) ordination of thaumarchaeal 16S rRNA gene DGGE fingerprint.The two-dimensional stress value for the NMDS was 0.107 based on Bray Curtis distance. Coefficients of determination (R2) on each axis represent correlations between ordination distances and the corresponding distance matrix.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0113515-g003: Nonmetric multidimensional scaling (NMDS) ordination of thaumarchaeal 16S rRNA gene DGGE fingerprint.The two-dimensional stress value for the NMDS was 0.107 based on Bray Curtis distance. Coefficients of determination (R2) on each axis represent correlations between ordination distances and the corresponding distance matrix.
Mentions: To characterize AOA community composition over time, DGGE fingerprinting for thaumarchaeal 16S rRNA genes was performed. DGGE profiles for thaumarchaeal 16S rRNA genes revealed simple patterns and low diversity among different freshwater and marine aquaria (Figure 2). The community composition of the sampled freshwater biofilters was highly similar, with the presence of two or three intense bands shared between different aquaria. The thaumarchaeal 16S rRNA gene patterns associated with the marine aquarium also contained few bands but were distinct from their freshwater counterparts. Dendrograms based on Pearson correlations of DGGE fingerprint densitometric curves placed marine fingerprints in a distinct cluster (Figure 2). NMDS generated from DGGE fingerprints revealed that freshwater and marine aquaria were separated in a two-dimensional space (Figure 3). Consistently, MRPP based on DGGE fingerprints showed significant separation (T = −10.83) between freshwater and marine fingerprints. Quantitatively, the distance between different aquaria was assessed by pair-wise ANOSIM. The average distance from the marine aquarium to the freshwater aquaria was significantly higher (0.9, p<0.01 as determined by Student's t test) than between freshwater aquaria, indicating that the AOA community in the marine aquarium was distinct from their freshwater counterparts.

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