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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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Relative amoA gene abundance of Thaumarchaea and Bacteria in sampled freshwater (F1–F6) and marine (M) aquaria, assuming 1 and 2.5 copies of amoA gene per thaumarchaeal and bacterial cell, respectively.
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pone-0113515-g001: Relative amoA gene abundance of Thaumarchaea and Bacteria in sampled freshwater (F1–F6) and marine (M) aquaria, assuming 1 and 2.5 copies of amoA gene per thaumarchaeal and bacterial cell, respectively.

Mentions: The qPCR results demonstrated that thaumarchaeal amoA genes were dominant in all freshwater biofilters (Figure 1, Table S1). Thaumarchaeal amoA genes represented the entire detected amoA signal for three out of the six freshwater aquaria (F2, F4 and F5) at all time points over the four-month period. Although AOB amoA genes were detected in the other three aquaria, their abundance was low and variable. In the case of F1, AOB contributed <20% of the total amoA genes detected. In aquarium F6, AOB accounted for <5% of the ammonia-oxidizing community (Figure 1). AOA outnumbered AOB by 200- to 400-fold in F6. The only exception was aquarium F3, in which AOB amoA genes were present in relatively high proportions (2.1–8.8×103 copies ng−1 DNA), outnumbering AOA by 7- to 30-fold during the initial period of one month, then remained undetectable for subsequent sampling, even after repeated qPCR analyses (Figure 1, Table S1).


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)

Relative amoA gene abundance of Thaumarchaea and Bacteria in sampled freshwater (F1–F6) and marine (M) aquaria, assuming 1 and 2.5 copies of amoA gene per thaumarchaeal and bacterial cell, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0113515-g001: Relative amoA gene abundance of Thaumarchaea and Bacteria in sampled freshwater (F1–F6) and marine (M) aquaria, assuming 1 and 2.5 copies of amoA gene per thaumarchaeal and bacterial cell, respectively.
Mentions: The qPCR results demonstrated that thaumarchaeal amoA genes were dominant in all freshwater biofilters (Figure 1, Table S1). Thaumarchaeal amoA genes represented the entire detected amoA signal for three out of the six freshwater aquaria (F2, F4 and F5) at all time points over the four-month period. Although AOB amoA genes were detected in the other three aquaria, their abundance was low and variable. In the case of F1, AOB contributed <20% of the total amoA genes detected. In aquarium F6, AOB accounted for <5% of the ammonia-oxidizing community (Figure 1). AOA outnumbered AOB by 200- to 400-fold in F6. The only exception was aquarium F3, in which AOB amoA genes were present in relatively high proportions (2.1–8.8×103 copies ng−1 DNA), outnumbering AOA by 7- to 30-fold during the initial period of one month, then remained undetectable for subsequent sampling, even after repeated qPCR analyses (Figure 1, Table S1).

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