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

Handle URI:
http://hdl.handle.net/10754/624162
Title:
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
Authors:
Jahn, Martin T ( 0000-0001-8322-9334 ) ; Markert, Sebastian M; Ryu, Tae Woo; Ravasi, Timothy ( 0000-0002-9950-465X ) ; Stigloher, Christian ( 0000-0001-6941-2669 ) ; Hentschel, Ute ( 0000-0003-0596-790X ) ; 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, 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
Publisher:
PANGAEA - Data Publisher for Earth & Environmental Science
Issue Date:
2016
DOI:
10.1594/PANGAEA.868922
Type:
Dataset
Is Supplement To:
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.; DOI:10.1038/srep35860; HANDLE:http://hdl.handle.net/10754/621834
Appears in Collections:
Datasets; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorJahn, Martin Ten
dc.contributor.authorMarkert, Sebastian Men
dc.contributor.authorRyu, Tae Wooen
dc.contributor.authorRavasi, Timothyen
dc.contributor.authorStigloher, Christianen
dc.contributor.authorHentschel, Uteen
dc.contributor.authorMoitinho-Silva, Lucasen
dc.coverage.spatialgeoLocationPoint: 22.383 39.05en
dc.date.accessioned2017-06-06T08:02:23Z-
dc.date.available2017-06-06T08:02:23Z-
dc.date.issued2016en
dc.identifier.citationJahn, 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.identifier.doi10.1594/PANGAEA.868922en
dc.identifier.urihttp://hdl.handle.net/10754/624162-
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.formattext/tab-separated-valuesen
dc.format.extent18 data pointsen
dc.language.isoengen
dc.publisherPANGAEA - Data Publisher for Earth & Environmental Scienceen
dc.rightsCreative Commons Attribution 3.0 Unported (CC-BY)en
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/en
dc.titleAccession 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, 35860en
dc.typeDataseten
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
kaust.authorRyu, Tae Wooen
kaust.authorRavasi, Timothyen
dc.type.resourceSupplementary Dataseten
dc.relation.isSupplementToJahn 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.relation.isSupplementToDOI:10.1038/srep35860en
dc.relation.isSupplementToHANDLE:http://hdl.handle.net/10754/621834en
dc.date.collected2010-11-02en
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