Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species exhibiting two variants

Abstract

Gemmata massiliana is a new Planctomycetes bacterium isolated from a hospital water network in France, using a new culture medium. It is an aerobic microorganism with optimal growth at pH 8, at 30 °C and salinity ≤ 1.25 % NaCl. G. massiliana is resistant to β-lactam antibiotics, due to lack of peptidoglycan in its cell wall.G. massiliana shares a 97 % 16S rRNA gene sequence similarity with the nearest species, Gemmata obscuriglobus; and 99 % similarity with unnamed soil isolates. Its 9,249,437-bp genome consists in one chromosome and no detectable plasmid and has a 64.07 % G + C content, 32.94 % of genes encoding for hypothetical proteins. The genome contains an incomplete 19.6-kb phage sequence, 26 CRISPRs, 3 CAS and 15 clusters of secondary metabolites. G. massiliana genome increases knowledge of a poorly known world of bacteria.

Keywords: Culture; Gemmata; Gemmata massiliana; Gemmata obscuriglobus; Genome; Hospital water network; Planctomycetes.

Fig. 1

Gemmata massiliana phylogenetic position amongst other Planctomycetes species. The following Phylogenetic tree shows G. massiliana strain CSUR P189^T position relatively to Gemmata obscuriglobus, to undescribed Gemmata species and to other Planctomycetes. Sequences were aligned using CLUSTALW [39], and phylogenetic inferences obtained using the neighbor-joining method within the MEGA software [40] only bootstrap values ≥95 % are indicated at nodes. T. maritima (M21774) was used as an outgroup. The scale bar represents a 5 % nucleotide sequence divergence

Fig. 2

Gram staining of G. massiliana strain CSUR P189^T. The bar scale reprensents 10 μm

Fig. 3

G. massiliana transmission electron microscopy. We observed two size-different populations of G. massiliana strain CSUR P189^T, using a Morgagni 268D (Philips) at an operating voltage of 60kV. The scale bar represents 500 nm

Fig. 4

G. massiliana two cell variants as demonstrated by flow cytometry. Representative histogram of the two cell variants in a G. massiliana sample shown in purple, was generated by a BD LSRFortessa (Le Pont de Claix, France) and FACSDiva software (version 6.2)

Fig. 5

Reference mass spectrum of G. Massiliana strain CSUR P189^T. This reference spectrum was generated from 10 spectra corresponding to 10 deposited colonies of G. massiliana

Fig. 6

Graphical circular map of the chromosome. From outside to the center: Genes on the forward strand colored by COG categories (only genes assigned to COG), genes on the reverse strand colored by COG categories (only gene assigned to COG), RNA genes (tRNAs green, rRNAs red), GC content and GC skew