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. 2022 Mar 1;12(1):3356.
doi: 10.1038/s41598-022-07292-3.

Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges

Karin Steffen #  1 , Anak Agung Gede Indraningrat #  2   3 , Ida Erngren  4 , Jakob Haglöf  4 , Leontine E Becking  5 , Hauke Smidt  3 , Igor Yashayaev  6 , Ellen Kenchington  6 , Curt Pettersson  4 , Paco Cárdenas #  7 , Detmer Sipkema #  3
Affiliations

Oceanographic setting influences the prokaryotic community and metabolome in deep-sea sponges

Karin Steffen et al. Sci Rep. .

Abstract

Marine sponges (phylum Porifera) are leading organisms for the discovery of bioactive compounds from nature. Their often rich and species-specific microbiota is hypothesised to be producing many of these compounds. Yet, environmental influences on the sponge-associated microbiota and bioactive compound production remain elusive. Here, we investigated the changes of microbiota and metabolomes in sponges along a depth range of 1232 m. Using 16S rRNA gene amplicon sequencing and untargeted metabolomics, we assessed prokaryotic and chemical diversities in three deep-sea sponge species: Geodia barretti, Stryphnus fortis, and Weberella bursa. Both prokaryotic communities and metabolome varied significantly with depth, which we hypothesized to be the effect of different water masses. Up to 35.5% of microbial ASVs (amplicon sequence variants) showed significant changes with depth while phylum-level composition of host microbiome remained unchanged. The metabolome varied with depth, with relative quantities of known bioactive compounds increasing or decreasing strongly. Other metabolites varying with depth were compatible solutes regulating osmolarity of the cells. Correlations between prokaryotic community and the bioactive compounds in G. barretti suggested members of Acidobacteria, Proteobacteria, Chloroflexi, or an unclassified prokaryote as potential producers.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Map of the slope in the Davis Strait in the North Atlantic, where the samples were collected. The insert shows the geographic location of the sampling area (black box) between Canada and Greenland. Samples were collected at depths ranging from 244 to 1476 m. Figure made with R v3.5.1 (https://www.r-project.org) with packages marmap and ggplot2.
Figure 2
Figure 2
Temperature-salinity diagram showing the superimposed water masses at different depths in the Davis Strait. Shelf Water (ShW) and Slope Water (SW) are shallower than the samples in this study and display a range of salinities. We detect the core of the Irminger current (IC) at approx. 600 m depth, the core of the Labrador Sea Water (LSW) at approx. 1200 m depth, and the Icelandic Slope Water at approx. 1600 m and below. The abbreviations for the water masses were placed to approximate the cores of the water masses. Samples were attributed to the water masses based on their sample depth (see Table S1).
Figure 3
Figure 3
Prokaryotic community composition based on relative abundance of 16S rRNA gene sequences, aggregated at the phylum level. Specimens were grouped by sponge species and ordered by increasing depth from left to right, Geodia barretti (Gb, 407–1462 m), Stryphnus fortis (Sf, 483–1476 m) and Weberella bursa (Wb, 244–1271 m).
Figure 4
Figure 4
ASVs in G. barretti, S. fortis and W. bursa for which average relative abundance correlated with depth. The left panel shows ASVs increasing with depth, the right panel shows ASVs decreasing with depth in the three sponge respectively. ASV relative abundance is scaled from 0 to 1 for visualisation purposes. ASV labels coloured in red are sponge-enriched ASVs.
Figure 5
Figure 5
Overlain are the chromatograms acquired on a HILIC column (positive ESI) of (a) G. barretti, (b) S. fortis, and (c) W. bursa. Black lines indicate chromatograms from shallow specimens (< 1000 m), red lines indicate chromatograms from deep specimens (> 1000 m). For G. barretti, the green area highlights the peak of barettin (E- and Z-form), the blue area highlights the peak of 8,9-dihydrobarettin.
Figure 6
Figure 6
Signal intensities of annotated VIP compounds plotted against sample depth. Correlation tests and t-tests were performed to assess all compounds variation with depth. Significant results (pFDR < 0.05) were annotated in the plot, correlation (ρ and pFDR) on top, and t-test (pFDR) below.
Figure 7
Figure 7
Signal intensities of previously known bioactive compounds plotted against sample depth. Correlation tests and t-tests were performed to assess all compounds variation with depth. Significant results (pFDR < 0.05) were annotated in the plot, correlation (ρ and pFDR) on top, and t-test (pFDR) below. Compounds associated with G. barretti: top panel (1–6) are diketopiperazines, middle panel (7–10) are indole derivatives, bottom left are peptides. Compounds associated with S. fortis: bottom right panel (11, 12).
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References

    1. Taylor MW, Radax R, Steger D, Wagner M. Sponge-associated microorganisms: Evolution, ecology, and biotechnological potential. Microbiol. Mol. Biol. Rev. 2007;71:295–347. - PMC - PubMed
    1. Thomas T, et al. Diversity, structure and convergent evolution of the global sponge microbiome. Nat. Commun. 2016;7:11870. - PMC - PubMed
    1. Webster NS, et al. Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ. Microbiol. 2010;12:2070–2082. - PMC - PubMed
    1. Sipkema D, et al. Similar sponge-associated bacteria can be acquired via both vertical and horizontal transmission: Microbial transmission in Petrosia ficiformis. Environ. Microbiol. 2015;17:3807–3821. - PubMed
    1. Cleary, D. F. R. et al. The sponge microbiome within the greater coral reef microbial metacommunity. Nat. Commun.10, 1644 (2019). - PMC - PubMed

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