Fastidiosibacter lacustris gen. nov., sp. nov., isolated from a lake water sample, and proposal of Fastidiosibacteraceae fam. nov. within the order Thiotrichales

Abstract

AFrancisella-like bacterium, designated strain SYSU HZH-2, was isolated from a water sample collected from Haizhu Lake, Guangzhou, China. The bacterium was fastidious, and required an exogenous source of l-cysteine for its growth on artificial media. Cells were Gram-stain-negative, coccobacilli, non-motile and non-spore-forming. The strain shared highest 16S rRNA gene sequence similarities with Cysteiniphilum litorale SYSU D3-2 (94.6 % identity), Fangia hongkongensis UST040201-002 (93.2 %) and Caedibacter taeniospiralis 51 (91.6 %). This strain possessed ubiquinone-8 as the respiratory quinone; diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as the known polar lipids, and anteiso-C15 : 0 and C18 : 0 as the major fatty acids (>10 % of total fatty acids). The dendrograms based on 16S rRNA gene sequence analysis showed that it formed a separate cluster along with Cysteiniphilum litorale SYSU D3-2, Caedibactertaeiniospiralis 51 and Fangia hongkongensis UST040201-002. Based on the 16S rRNA gene sequence identity and differences in other phenotypic characteristics, the strain is considered to represent a novel species of a novel genus, for which the name Fastidiosibacter lacustris gen. nov., sp. nov. is proposed. The type strain of the type species Fastidiosibacter lacustris is SYSU HZH-2 (=NBRC 112274 = CGMCC 1.15950). Additionally, the new taxon along with the genera Caedibacter, Cysteiniphilum and Fangia (family unassigned) were distinctly separated from the related families Francisellaceae, Piscirickettsiaceae and Thiotrichaeae in the phylogenetic trees. Therefore, we proposed a new family Fastidiosibacteraceae fam. nov. within the order Thiotrichales to accommodate these four genera.

At the threshold of symbiosis: the genome of obligately endosymbiotic ‘Candidatus Nebulobacter yamunensis’ is almost indistinguishable from that of a cultivable strain

“…To replicate the conditions described by Xiao et al . [13] in cultivating F. lacustris , the lysate was then centrifuged (7000 g , 10 min) and the pellet resuspended in HCl-KCl buffer solution (1 : 9 v/v, pH ~2) for at least 5 min, prior to its inoculation on the BCYE agar medium under sterile conditions.…”

“…We sequenced the genome of the host-restricted ‘ Ca . Nebulobacter yamunensis’ and compared it with that of the free-living Fastidiosibacter lacustris [13] to see if key differences related to the transition to endosymbiosis could be observed. Instead, we found the two genomes to show extreme molecular and functional similarities, despite their apparently contrasting lifestyles, which we confirmed with a new attempt to cultivate both organisms in parallel.…”

The gammaproteobacterium Achromatium forms intracellular amorphous calcium carbonate and not (crystalline) calcite

“…A total of 350 bootstrap replicates automatically determined by the MRE‐based bootstopping criterion were conducted using the rapid bootstrapping algorithm, among which 100 were sampled to generate proportional support values. In this phylogeny, members of the Francisellaceae and Fastidiosibacteraceae families were used to root the tree based on previous phylogenies of the Thiotrichales order (Xiao et al., 2018).…”

Reclassification of Francisella noatunensis subsp. orientalis Ottem et al. 2009 as Francisella orientalis sp. nov., Francisella noatunensis subsp. chilensis subsp. nov. and emended description of Francisella noatunensis

“…In the last decade there has been a steady increase in the number of species and genera effectively and validly described, both cultured and uncultured, within the bacterial family Francisellaceae [1][2][3][4][5][6][7][8][9][10][11][12][13]. Although many of these studies have provided valuable insights into the population structure of the family as a whole, the lack of consistent clear criteria Table 1.…”

“…In the last decade there has been a steady increase in the number of species and genera effectively and validly described, both cultured and uncultured, within the bacterial family Francisellaceae [1–13]. Although many of these studies have provided valuable insights into the population structure of the family as a whole, the lack of consistent clear criteria and cut-off values for delineation of closely related taxa has made fine-scale taxonomy imprecise and led to numerous controversies including the initial description of Francisella endociliophora as ‘ Candidatus Francisella noatunensis endociliophora’, the reclassification of Francisella novicida as a subspecies of Francisella tularensis and the initial description of Francisella noatunensis as a subspecies of Francisella philomiragia [5, 14–21].…”