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

Handle URI:
http://hdl.handle.net/10754/621834
Title:
Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling
Authors:
Jahn, Martin T.; Markert, Sebastian M.; Ryu, Tae Woo; Ravasi, Timothy ( 0000-0002-9950-465X ) ; Stigloher, Christian; Hentschel, Ute; Moitinho-Silva, Lucas
Abstract:
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Jahn MT, Markert SM, Ryu T, Ravasi T, Stigloher C, et al. (2016) Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling. Scientific Reports 6: 35860. Available: http://dx.doi.org/10.1038/srep35860.
Publisher:
Springer Nature
Journal:
Scientific Reports
Issue Date:
31-Oct-2016
DOI:
10.1038/srep35860
Type:
Article
ISSN:
2045-2322
Sponsors:
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.
Is Supplemented By:
Jahn, M. T., Markert, S. M., Ryu, T., Ravasi, T., Stigloher, C., Hentschel, U., & Moitinho-Silva, L. (2016). Accession data for analysed Xestospongia testudinaria metatranscriptomes, supplement to: Jahn, Martin T; Markert, Sebastian M; Ryu, Taewoo; Ravasi, Timothy; Stigloher, Christian; Hentschel, Ute; Moitinho-Silva, Lucas (2016): Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling. Scientific Reports, 6, 35860 [Data set]. PANGAEA - Data Publisher for Earth & Environmental Science. https://doi.org/10.1594/pangaea.868922; DOI:10.1594/PANGAEA.868922; HANDLE:http://hdl.handle.net/10754/624162
Additional Links:
http://www.nature.com/articles/srep35860
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorJahn, Martin T.en
dc.contributor.authorMarkert, Sebastian M.en
dc.contributor.authorRyu, Tae Wooen
dc.contributor.authorRavasi, Timothyen
dc.contributor.authorStigloher, Christianen
dc.contributor.authorHentschel, Uteen
dc.contributor.authorMoitinho-Silva, Lucasen
dc.date.accessioned2016-11-17T09:00:09Z-
dc.date.available2016-11-17T09:00:09Z-
dc.date.issued2016-10-31en
dc.identifier.citationJahn MT, Markert SM, Ryu T, Ravasi T, Stigloher C, et al. (2016) Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling. Scientific Reports 6: 35860. Available: http://dx.doi.org/10.1038/srep35860.en
dc.identifier.issn2045-2322en
dc.identifier.doi10.1038/srep35860en
dc.identifier.urihttp://hdl.handle.net/10754/621834-
dc.description.abstractAssigning 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.en
dc.description.sponsorshipWe 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.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.nature.com/articles/srep35860en
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectEnvironmental microbiologyen
dc.subjectMarine biologyen
dc.titleShedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profilingen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalScientific Reportsen
dc.contributor.institutionJulius-von-Sachs Institute for Biological Sciences, University of Würzburg, Würzburg, 97082, Germanyen
dc.contributor.institutionMarine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germanyen
dc.contributor.institutionDivision of Electron Microscopy, Biocenter, University of Würzburg, 97074, Würzburg, Germanyen
dc.contributor.institutionSchool of Biotechnology and Biomolecular Sciences & Centre for Marine Bio-Innovation, University of New South Wales, Sydney, 2052, Australiaen
kaust.authorRyu, Tae Wooen
kaust.authorRavasi, Timothyen
dc.relation.isSupplementedByJahn, M. T., Markert, S. M., Ryu, T., Ravasi, T., Stigloher, C., Hentschel, U., & Moitinho-Silva, L. (2016). Accession data for analysed Xestospongia testudinaria metatranscriptomes, supplement to: Jahn, Martin T; Markert, Sebastian M; Ryu, Taewoo; Ravasi, Timothy; Stigloher, Christian; Hentschel, Ute; Moitinho-Silva, Lucas (2016): Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling. Scientific Reports, 6, 35860 [Data set]. PANGAEA - Data Publisher for Earth & Environmental Science. https://doi.org/10.1594/pangaea.868922en
dc.relation.isSupplementedByDOI:10.1594/PANGAEA.868922en
dc.relation.isSupplementedByHANDLE:http://hdl.handle.net/10754/624162en
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