title: Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling.
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.
authors: Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Würzburg, 97082, Germany.|Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany.
authors: Martin T
authors: MT
authors: Jahn
authors: Division of Electron Microscopy, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
authors: Sebastian M
authors: SM
authors: Markert
authors: Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors: Taewoo
authors: T
authors: Ryu
authors: Division of Biological and Environmental Sciences &Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors: Timothy
authors: T
authors: Ravasi
authors: Division of Electron Microscopy, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
authors: Christian
authors: C
authors: Stigloher
authors: Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany.|Christian-Albrechts-University of Kiel, Germany.
authors: Ute
authors: U
authors: Hentschel
authors: School of Biotechnology and Biomolecular Sciences &Centre for Marine Bio-Innovation, University of New South Wales, Sydney, 2052, Australia.
authors: Lucas
authors: L
authors: Moitinho-Silva
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000378:metabolism / Q000648:ultrastructure*; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002451:Cell Compartmentation; D020869:Gene Expression Profiling / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence; D008854:Microscopy, Electron; D011161:Porifera / Q000382:microbiology; D017423:Sequence Analysis, RNA
chemical_list: D001426:Bacterial Proteins