Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Feb 20;4(1):e00043-19.
doi: 10.1128/mSphere.00043-19.

Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria

Holly M Bik  1 , Alexandra Alexiev  1 , Sabreen K Aulakh  1 , Lakshmi Bharadwaj  1 , Jennifer Flanagan  1 , John M Haggerty  2 , Sarah M Hird  1   3 , Guillaume Jospin  1 , Jenna M Lang  1 , Laura A Sauder  4 , Josh D Neufeld  4 , Andrew Shaver  1 , Akshay Sethi  1 , Jonathan A Eisen  5   6 , David A Coil  1
Affiliations

Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria

Holly M Bik et al. mSphere. .

Abstract

Although aquaria are common features of homes and other buildings, little is known about how environmental perturbations (i.e., tank cleaning, water changes, addition of habitat features) impact the diversity and succession of aquarium microbial communities. In this study, we sought to evaluate the hypotheses that newly established aquaria show clear microbial successional patterns over time and that common marine aquarium-conditioning practices, such as the addition of ocean-derived "live rocks" (defined as any "dead coral skeleton covered with crustose coralline algae" transferred into an aquarium from open ocean habitats) impact the diversity of microbial populations as well as nitrogen cycling in aquaria. We collected water chemistry data alongside water and sediment samples from two independent and newly established saltwater aquaria over a 3-month period. Microbial communities in samples were assessed by DNA extraction, amplification of the 16S rRNA gene, and Illumina MiSeq sequencing. Our results showed clear and replicable patterns of community succession in both aquaria, with the existence of multiple stable states for aquarium microbial assemblages. Notably, our results show that changes in aquarium microbial communities do not always correlate with water chemistry measurements and that operational taxonomic unit (OTU)-level patterns relevant to nitrogen cycling were not reported as statistically significant. Overall, our results demonstrate that aquarium perturbations have a substantial impact on microbial community profiles of aquarium water and sediment and that the addition of live rocks improves nutrient cycling by shifting aquarium communities toward a more typical saltwater assemblage of microbial taxa.IMPORTANCE Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed view of ecological succession and changes in microbial community assemblages in two saltwater aquaria which were sampled over a 3-month period, from initial tank setup and conditioning with "live rocks" through subsequent tank cleanings and water replacement. Our results showed that microbial succession appeared to be consistent and replicable across both aquaria. However, changes in microbial communities did not always correlate with water chemistry measurements, and aquarium microbial communities appear to have shifted among multiple stable states without any obvious buildup of undesirable nitrogen compounds in the tank environment.

Keywords: 16S rRNA gene; bacteria; community succession; metabarcoding; saltwater aquarium; water chemistry.

PubMed Disclaimer

Figures

FIG 1
FIG 1
Water chemistry data, UniFrac results, and perturbations to coral pond 1 (CP1, dark blue) and coral pond 2 (CP2, light blue) experimental aquaria, displayed across time. The top panel displays UniFrac distances between sediment and water communities for each aquarium. The second panel shows UniFrac distances of microbial community 16S rRNA gene profiles between aquaria for a given substrate (sediment or water samples taken on the same date, regardless of when the aquarium was set up). The bottom 10 panels show water chemistry data over time for the two saltwater aquaria. Salinity is displayed as percent salt (refractometer) values. E coli, Escherichia coli.
FIG 2
FIG 2
Area chart of alpha taxonomy for water and sediment samples from coral pond 1 (CP1) and coral pond 2 (CP2) experimental aquaria, plotted across time. Results are from 97% open-reference OTU picking in QIIME (singletons discarded). Taxonomic assignments for 16S rRNA gene OTUs are summarized and plotted at the phylum level, with relative abundances displayed for the eight most abundant microbial phyla.
FIG 3
FIG 3
Changes in aquarium microbial community richness over time, including responses to introduced perturbations. Results from 97% open-reference OTU picking in QIIME are summarized according to genus-level taxonomy (L5, level 5 from the Greengenes taxonomic ranks). Graphs illustrate the number of bacterial/archaeal genera assigned to OTU sequences recovered across time for two independent saltwater aquaria (coral pond 1 [CP1] and coral pond 2 [CP2] water and sediment samples). Vertical lines indicate perturbations introduced during the sampling time series. On each line graph, solid colors represent overall community richness calculated from all OTUs with a minimum cluster size >2 (excluding singletons). Dashed lines represent community richness inferred for samples rarefied to 5,000 sequences per sample (with the samples with levels below that threshold discarded). Yellow stars on the far left display the genus-level OTU richness for laboratory seawater and commercial sand used for initial aquarium setup (sampled on day 0).
FIG 4
FIG 4
Aquarium perturbations spur large shifts in microbial beta-diversity patterns over time. Data represent results of principal-coordinate-analysis (PCoA) ordination based on unweighted UniFrac distances of microbial community 16S rRNA gene profiles, displaying sediment samples from the coral pond 1 (CP1) aquarium, with the gradient color scale illustrating sampling across time. Dotted lines on the left color legend indicate the three major perturbation events (LR = live rock addition, WC = walls cleaned, WR = water replacement). Following tank setup, microbial community assemblages showed closest similarity to those seen with the commercial sand sample used to set up the aquarium on day 0. Rocks and sediment were transferred from an established aquarium on day 12, at which point the microbial assemblage showed rapid change over the course of a few hours (CP.12.sed, collected in the morning before aquarium perturbation; CP12.sed.PM, collected in the afternoon immediately following perturbation). A second major shift in community changes occurred after the addition of live rocks (CP.45.sed onward; orange and red dots). Dotted gray arrows indicate general trends in community shifts over time. Data represent results from 97% open-reference OTU picking in QIIME (singletons discarded), rarefied at 1,000 sequences per sample.
FIG 5
FIG 5
Relative abundances of putative nitrogen-transforming OTUs in the coral pond 1 (CP1) experimental aquarium. Data represent relative abundances of OTUs belonging to six different microbial groups summarized and plotted over time for sediment (A) and water (B) microhabitats. The first two bars of each panel represent baseline microbial communities (displayed for comparison) from a separate established tropical saltwater aquarium (T.0.water and T.0.sed), commercial sand used to set up aquaria (CP.0.sand), and a laboratory seawater system (IW.0.water). Microbial taxa displayed include ammonia-oxidizing bacteria (AOB; Nitrosococcus, Nitrosomonadaceae), nitrite-oxidizing bacteria (NOB; Nitrospina, Nitrospira), anaerobic ammonia-oxidizing bacteria (anammox; Scalindua), and ammonia-oxidizing archaea (AOA; Thaumarchaeota).
FIG 6
FIG 6
Weighted and unweighted UniFrac PCoA ordination plots showing water, sediment, and perturbation/intake samples from the coral pond 1 (CP1) and coral pond 2 (CP2) experimental aquaria. Principal-coordinate-analysis (PCoA) ordination plots based on UniFrac distances of microbial community 16S rRNA gene profiles display differentiation of microbial communities in sediment (circles) and water samples (triangles) across two independent aquaria (panels A and B, CP1; panels C and D, CP2). Unweighted UniFrac (A and C) and weighted UniFrac (B and D) data are shown. For reference, plots include initial samples from laboratory seawater (“seawater” for CP1 setup and “intake” for CP2 setup) and commercial sand (“sand”) used to set up both aquaria. All plots additionally show sediment (“tropical_sed,” open circles) and water samples (“tropical_water,” open triangles) taken from an established tropical aquarium and used to inoculate CP1. All PCoA ordination plots display results from 97% open-reference OTU picking in QIIME v1.8 (singletons discarded), rarefied at 1,000 sequences per sample.
FIG 7
FIG 7
Changes in conditionally rare taxa (CRT) over time in the coral pond 1 (CP1) experimental aquarium. CRT were identified by computing the coefficient of bimodality to statistically detect “blooms” of rare OTUs which were otherwise present at low or zero abundances at most time points, following previously described methods (38). Each colored line represents sequence reads from a single OTU, plotted over time. Taxonomic annotations are indicated for a subset of CRT OTUs with the highest number of sequence reads, with all taxonomic names directly derived from the Greengenes database. Figure panels represent consecutive sample time points collected from sediment (A) and water (B) locations in the CP1 experimental aquarium.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Adams RI, Bateman AC, Bik HM, Meadow JF. 2015. Microbiota of the indoor environment: a meta-analysis. Microbiome 3:49. doi:10.1186/s40168-015-0108-3. - DOI - PMC - PubMed
    1. Lax S, Gilbert JA. 2015. Hospital-associated microbiota and implications for nosocomial infections. Trends Mol Med 21:427–432. doi:10.1016/j.molmed.2015.03.005. - DOI - PubMed
    1. Hewitt KM, Mannino FL, Gonzalez A, Chase JH, Caporaso JG, Knight R, Kelley ST. 2013. Bacterial diversity in two neonatal intensive care units (NICUs). PLoS One 8:e54703. doi:10.1371/journal.pone.0054703. - DOI - PMC - PubMed
    1. Oberauner L, Zachow C, Lackner S, Högenauer C, Smolle K-H, Berg G. 2013. The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing. Sci Rep 3:1413. doi:10.1038/srep01413. - DOI - PMC - PubMed
    1. Ross AA, Neufeld JD. 2015. Microbial biogeography of a university campus. Microbiome 3:66. doi:10.1186/s40168-015-0135-0. - DOI - PMC - PubMed

Publication types