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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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Denaturing gradient gel electrophoresis of thaumarchaeal 16S rRNA genes from spatially distinct locations within freshwater biofilters F5 and F6 during spatial test.For detailed characteristics of the samples, refer to Table 1.
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pone-0113515-g006: Denaturing gradient gel electrophoresis of thaumarchaeal 16S rRNA genes from spatially distinct locations within freshwater biofilters F5 and F6 during spatial test.For detailed characteristics of the samples, refer to Table 1.

Mentions: Three-media biofilters of aquaria F5 and F6 were examined to assess the effect of media type on AOA abundance and diversity. In F5, no AOB could be detected, as observed throughout the temporal test period. For F6, a new biofilter was inoculated with biomass originating from the previous F6 biofilter, which had a low AOB abundance. After a start-up and stabilization period of 6 months, AOA had fully outcompeted the AOB community (Table S1). The observed thaumarchaeal amoA gene abundances were distinct for the three compartments within each of the two filters, and these trends were consistent over all three sampling time points (Figure 5). For F5, relative AOA abundance was highest in the middle compartment (sponge), followed by the bottom (ceramic) and top (glass) compartments. For F6, relative AOA concentrations peaked in the top compartment (fine sponge), followed by the middle (rough sponge) and bottom (ceramic) compartments. Both filters had a bottom-to-top flow pattern, but the trends in F5 suggest that AOA copy number was not influenced by the position with respect to the water flow. The highest AOA copy numbers were detected in (fine) sponge carrier material for both F5 and F6, suggesting a preferential AOA growth or biofilm attachment to this medium. DGGE profiles for thaumarchaeal 16S rRNA genes revealed low diversity and high spatial stability among different compartments of F5 and F6 aquaria (Figure 6). The community composition of the top, middle and bottom compartment in both F5 and F6 was highly similar with the presence of two or three intense bands. This indicated that although AOA had preferential growth on fine sponge materials, the community composition across the biofilter media types was stable.


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)

Denaturing gradient gel electrophoresis of thaumarchaeal 16S rRNA genes from spatially distinct locations within freshwater biofilters F5 and F6 during spatial test.For detailed characteristics of the samples, refer to Table 1.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0113515-g006: Denaturing gradient gel electrophoresis of thaumarchaeal 16S rRNA genes from spatially distinct locations within freshwater biofilters F5 and F6 during spatial test.For detailed characteristics of the samples, refer to Table 1.
Mentions: Three-media biofilters of aquaria F5 and F6 were examined to assess the effect of media type on AOA abundance and diversity. In F5, no AOB could be detected, as observed throughout the temporal test period. For F6, a new biofilter was inoculated with biomass originating from the previous F6 biofilter, which had a low AOB abundance. After a start-up and stabilization period of 6 months, AOA had fully outcompeted the AOB community (Table S1). The observed thaumarchaeal amoA gene abundances were distinct for the three compartments within each of the two filters, and these trends were consistent over all three sampling time points (Figure 5). For F5, relative AOA abundance was highest in the middle compartment (sponge), followed by the bottom (ceramic) and top (glass) compartments. For F6, relative AOA concentrations peaked in the top compartment (fine sponge), followed by the middle (rough sponge) and bottom (ceramic) compartments. Both filters had a bottom-to-top flow pattern, but the trends in F5 suggest that AOA copy number was not influenced by the position with respect to the water flow. The highest AOA copy numbers were detected in (fine) sponge carrier material for both F5 and F6, suggesting a preferential AOA growth or biofilm attachment to this medium. DGGE profiles for thaumarchaeal 16S rRNA genes revealed low diversity and high spatial stability among different compartments of F5 and F6 aquaria (Figure 6). The community composition of the top, middle and bottom compartment in both F5 and F6 was highly similar with the presence of two or three intense bands. This indicated that although AOA had preferential growth on fine sponge materials, the community composition across the biofilter media types was stable.

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