TY  - JOUR
A1  - Jahn, Martin T.
A1  - Markert, Sebastian M.
A1  - Ryu, Taewoo
A1  - Ravasi, Timothy
A1  - Stigloher, Christian
A1  - Hentschel, Ute
A1  - Moitinho-Silva, Lucas
T1  - Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling
JF  - Scientific Reports
N2  - 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.
KW  - high resolution visualisation
KW  - transcriptional profiling
KW  - FISH-CLEM
KW  - cell compartmentation
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-167513
VL  - 6
IS  - 35860
ER  - 
TY  - JOUR
A1  - Horn, Hannes
A1  - Keller, Alexander
A1  - Hildebrandt, Ulrich
A1  - Kämpfer, Peter
A1  - Riederer, Markus
A1  - Hentschel, Ute
T1  - Draft genome of the \(Arabidopsis\) \(thaliana\) phyllosphere bacterium, \(Williamsia\) sp. ARP1
JF  - Standards in Genomic Sciences
N2  - The Gram-positive actinomycete \(Williamsia\) sp. ARP1 was originally isolated from the \(Arabidopsis\) \(thaliana\) phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus \(Williamsia\) and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.
KW  - arabidopsis thaliana
KW  - whole genome sequencing
KW  - adaption
KW  - Williamsia sp. ARP1
KW  - phyllosphere
KW  - draft genome
KW  - next generation sequencing
KW  - assembly
KW  - annotation
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-146008
VL  - 11
IS  - 8
ER  -