Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling

Martin T. Jahn, Sebastian M. Markert, Tae Woo Ryu, Timothy Ravasi, Christian Stigloher, Ute Hentschel, Lucas Moitinho-Silva

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20 Scopus citations


Assigning functions to uncultivated environmental microorganisms continues to be a challenging endeavour. Here, we present a new microscopy protocol for fluorescence in situ hybridisation-correlative light and electron microscopy (FISH-CLEM) that enabled, to our knowledge for the first time, the identification of single cells within their complex microenvironment at electron microscopy resolution. Members of the candidate phylum Poribacteria, common and uncultivated symbionts of marine sponges, were used towards this goal. Cellular 3D reconstructions revealed bipolar, spherical granules of low electron density, which likely represent carbon reserves. Poribacterial activity profiles were retrieved from prokaryotic enriched sponge metatranscriptomes using simulation-based optimised mapping. We observed high transcriptional activity for proteins related to bacterial microcompartments (BMC) and we resolved their subcellular localisation by combining FISH-CLEM with immunohistochemistry (IHC) on ultra-thin sponge tissue sections. In terms of functional relevance, we propose that the BMC-A region may be involved in 1,2-propanediol degradation. The FISH-IHC-CLEM approach was proven an effective toolkit to combine -omics approaches with functional studies and it should be widely applicable in environmental microbiology.
Original languageEnglish (US)
JournalScientific Reports
Issue number1
StatePublished - Oct 31 2016

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We thank the KAUST Coastal and Marine Resources Core Lab for support with sample collection and the KAUST Biosciences Core Laboratory for support with sequencing. We further acknowledge the expert advice of Uriel Koziol for valuable suggestions on the IHC protocol (University of Würzburg). Harald Engelhardt provided helpful insights into the interpretation of the intracellular granules. SMM was supported by the German National Academic Foundation. This work was supported by the Deutsche Forschungsgemeinschaft (CRC 1182, project B1). MTJ and LMS were each supported by grants of the German Excellence Initiative to the Graduate School of Life Sciences, University of Würzburg.


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