Draft Genome Sequence of Rheinheimera sp. F8, a Biofilm-Forming
Strain Which Produces Large Amounts of Extracellular DNA
Anna-Kathrin Schuster, Ulrich Szewzyk
Technische Universität Berlin, Berlin, Germany
Rheinheimera sp. strain F8 is a biofilm-forming gammaproteobacterium that has been found to produce large amounts of fila-
mentous extracellular DNA. Here, we announce the de novo assembly of its genome. It is estimated to be 4,464,511 bp in length,
with 3,970 protein-coding sequences and 92 RNA-coding sequences.
Received 21 January 2016 Accepted 28 January 2016 Published 10 March 2016
Citation Schuster A-K, Szewzyk U. 2016. Draft genome sequence of Rheinheimera sp. F8, a biofilm-forming strain which produces large amounts of extracellular DNA. Genome
Announc 4(2):e00082-16. doi:10.1128/genomeA.00082-16.
Copyright © 2016 Schuster and Szewzyk. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
Address correspondence to Anna-Kathrin Schuster, [email protected].
Rheinheimera sp. strain F8 is an aquatic biofilm-forming bacte-
rium, which was isolated from “river snow” of the South Sas-
katchewan River, Saskatoon, Saskatchewan, Canada (1). F8 is a
typical rod-shaped Gram-negative gammaproteobacterium about
2
m in length and 1
m in width, with nonpigmented to yellow-
ish colonies. It was shown that F8 forms stable filaments of extra-
cellular DNA, which have a width of 1.8 to 2.0 nm (2) and can be
stained by DNA-specific fluorescent dyes, like Syto9 or propidium
iodide (Molecular Probes, USA) (1).
An assessment of the metabolic profile of F8 using the com-
mercial multiwell system Biolog (Biolog, Hayward, CA) showed
that the strain is not fastidious. It was able to use the majority of
carbohydrates and carboxylic acids offered, as well as a wide range
of other substrates.
For the extraction of genomic DNA, F8 was grown on FBM
agar plates at room temperature and harvested after 7 days. FBM
medium contains 3.0 g of Na
2
SO
4
, 0.4 g of MgCl
2
·6H
2
O, 1.2 g of
NaCl, 0.3 g of NH
4
Cl, 0.3 g of KCl, and 0.15 g of CaCl
2
·2H
2
O
(pH 6,8) and was supplemented with yeast extract (75 mg/liter),
glucose (10
M), and a trace element (SL8) and vitamin solution.
Here, we report the de novo genome assembly of F8. It is the
latest of eight fully sequenced strains in the genus Rheinheimera.
The extraction and purification of genomic DNA were done with
the bacterial and yeast genomic DNA kit (Roboklon, Germany).
For library preparation, the TruSeq DNA LT library and Nextera
mate-pair library version 2 prep kits (Illumina, United States)
were used. Paired-end sequencing (2 ⫻300 bp) was performed
using the Illumina MiSeq sequencer with the MiSeq reagent kit
version 3. The resulting 7,192,490 reads were assembled with the
CLC Workbench 8 and SPAdes 3.5.0. In the final assembly of the
draft genome of F8, a 4,464,511-bp sequence with 3,970 protein-
coding sequences, 9 genes for rRNAs (including 3 versions for 16S
rRNA), and 83 genes for tRNAs was generated. The G⫹C content
is 51.8%.
The 16S rRNA genes of 16 Rheinheimera strains were aligned
with MEGA6, based on Clustal W, and phylogenetic analysis was
made using the maximum-likelihood neighbor-joining algo-
rithms. Those analyses suggest that Rheinheimera tilapiae (acces-
sion no. HQ111524 [3]) is the next relative of F8. Alignment with
the NCBI Nucleotide Basic Local Alignment Tool (BLAST) shows
an identity of 99% between the 16S rRNA genes of the two species.
Nucleotide sequence accession number. The draft genome se-
quence of Rheinheimera sp. F8 has been deposited at DDBJ/ENA/
GenBank under the accession no. CP013656. The version de-
scribed in this paper is the first version.
ACKNOWLEDGMENTS
We acknowledge Karsten Liere and Martin Meixner from Services in Mo-
lecular Biology (SMB, Berlin, Germany) for sequencing and assembly of
the Rheinheimera sp. F8 genome sequence.
FUNDING INFORMATION
This research received no specific grant from any funding agency in the
public, commercial, or nonprofit sectors.
REFERENCES
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2. Böckelmann U, Lünsdorf H, Szewzyk U. 2007. Ultrastructural and elec-
tron energy-loss spectroscopic analysis of an extracellular filamentous ma-
trix of an environmental bacterial isolate. Environ Microbiol 9:2137–2144.
http://dx.doi.org/10.1111/j.1462-2920.2007.01325.x.
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