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Deep Sequencing of Myxilla (Ectyomyxilla) methanophila, an Epibiotic Sponge on Cold-Seep Tubeworms, Reveals Methylotrophic, Thiotrophic, and Putative Hydrocarbon-Degrading Microbial Associations

  • Invertebrate Microbiology
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Abstract

The encrusting sponge Myxilla (Ectyomyxilla) methanophila (Poecilosclerida: Myxillidae) is an epibiont on vestimentiferan tubeworms at hydrocarbon seeps on the upper Louisiana slope of the Gulf of Mexico. It has long been suggested that this sponge harbors methylotrophic bacteria due to its low δ 13C value and high methanol dehydrogenase activity, yet the full community of microbial associations in M. methanophila remained uncharacterized. In this study, we sequenced 16S rRNA genes representing the microbial community in M. methanophila collected from two hydrocarbon-seep sites (GC234 and Bush Hill) using both Sanger sequencing and next-generation 454 pyrosequencing technologies. Additionally, we compared the microbial community in M. methanophila to that of the biofilm collected from the associated tubeworm. Our results revealed that the microbial diversity in the sponges from both sites was low but the community structure was largely similar, showing a high proportion of methylotrophic bacteria of the genus Methylohalomonas and polycyclic aromatic hydrocarbon (PAH)-degrading bacteria of the genera Cycloclasticus and Neptunomonas. Furthermore, the sponge microbial clone library revealed the dominance of thioautotrophic gammaproteobacterial symbionts in M. methanophila. In contrast, the biofilm communities on the tubeworms were more diverse and dominated by the chemoorganotrophic Moritella at GC234 and methylotrophic Methylomonas and Methylohalomonas at Bush Hill. Overall, our study provides evidence to support previous suggestion that M. methanophila harbors methylotrophic symbionts and also reveals the association of PAH-degrading and thioautotrophic microbes in the sponge.

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Acknowledgments

We gratefully acknowledge Mr. Rick Webb, at the Centre for Microscopy and Microanalysis (University of Queensland), who performed the TEM. We also thank Dr. Salim Bougouffa (Hong Kong University of Science and Technology) for the useful advice in bioinformatics and data analysis. Ship time and submersible dives were funded by grant number OCE-0527139 from the National Science Foundation to CMY. This research was supported by the National Basic Research Program of China (973 Program, No. 2012CB417304) and an award (SA-C0040/UK-C0016) made by the King Abdullah University of Science and Technology to PYQ. SMA was supported by a Woods Hole Oceanographic Institution postdoctoral scholarship during manuscript preparation.

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  1. Shawn M. Arellano

    Present address: Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, 02536, USA

Authors and Affiliations

  1. KAUST Global Collaborative Research Program, Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China

    Shawn M. Arellano, On On Lee, Jiangke Yang, Yong Wang & Pei-Yuan Qian

  2. Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955-6900, Kingdom of Saudi Arabia

    Feras F. Lafi

  3. Oregon Institute of Marine Biology, University of Oregon, P.O. Box 5389, Charleston, OR, 97420, USA

    Craig M. Young

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Shawn M. Arellano and On On Lee equally contributed in this manuscript.

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Fig. S1

Proportion of classified pyrosequencing reads at different taxonomic levels. Classification was performed with the RDP classifier at a confidence threshold of 50 % (GIF 63 kb)

High Resolution (EPS 4432 kb)

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Arellano, S.M., Lee, O.O., Lafi, F.F. et al. Deep Sequencing of Myxilla (Ectyomyxilla) methanophila, an Epibiotic Sponge on Cold-Seep Tubeworms, Reveals Methylotrophic, Thiotrophic, and Putative Hydrocarbon-Degrading Microbial Associations. Microb Ecol 65, 450–461 (2013). https://doi.org/10.1007/s00248-012-0130-y

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