Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

Abstract

Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater Phylogenetic analyses showed that strain HM0024 T formed an independent phyletic line of descent within the family Flavobacteriaceae. The DNA G+C content of the strain was 29.6 mol% and its major cellular fatty acids (.10 %) were iso-C 15 : 0 , iso-C 17 : 0 3-OH, iso-C 17 : 1 v7c and summed feature 3 (C 16 : 1 v6c and/or C 16 : 1 v7c). The major isoprenoid quinone was MK-6 and the major polar lipids were phosphatidylethanolamine and several aminolipids. Strain HM0024 T was differentiated from phylogenetically related members of the family by having lower DNA G+C content, larger proportions of summed feature 3, anteiso-C 15 : 0 and iso-C 16 : 0 3-OH and particular phenotypic characteristics. On the basis of phenotypic and phylogenetic data, strain HM0024 T is classified as a representative of a novel genus and species, for which the name A seawater sample from the coastal surface of the Yellow Sea (Buan beach, Korea; 35 u 409 N 126 u 319 E) was serially diluted, spread onto nutrient agar (NA; BD Difco) and incubated aerobically at 30 u C. After 2 days of incubation, a yellow colony-forming strain, designated HM0024 T , was isolated and stored as a suspension in nutrient broth (NB; BD Difco) with 15 % (v/v) glycerol. For further taxonomic studies, the strain was maintained routinely at 30 u C on NA.The methods employed for DNA extraction, PCR amplification and sequencing of the 16S rRNA gene were essentially the same as described in a previous study (Cho & Giovannoni, 2003). The almost-complete 16S rRNA gene sequence (1449 bp) of strain HM0024T was aligned automatically using the PT server implemented in the ARB software package (Ludwig et al., 2004) and the alignment was checked manually. 16S rRNA gene sequence similarities were calculated from the sequence alignment in the ARB package and were confirmed by the EzTaxon server (Chun et al., 2007). Sequence comparisons showed that strain HM0024T was closely associated with several members of the genera Chryseobacterium and Elizabethkingia of the family Flavobacteriaceae. The strain was most closely related to Chryseobacterium balustinum LMG 8329 T (94.4 %), Chryseobacterium scophthalmum LMG 13028 T (94.4 %), Chryseobacterium piscium LMG 3These authors contributed equally to this work.The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain HM0024 T is FJ713810.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

“…Chryseobacterium (Vandamme et al, 1994; Kämpfer et al, 2009; Wu et al, 2013; Montero-Calasanz et al, 2014; Chen et al, 2015; Hahnke R. L. et al, 2016) appeared as paraphyletic in the GBDP tree (Figure 6) because Soonwooa buanensis (Joung et al, 2010) was placed within it. S. buanensis and S. purpurea (Sirra et al, 2017) were also clustered within Chryseobacterium in the 16S rRNA gene tree but with low support (Supplementary Data Sheet 1).…”

“…S. buanensis and S. purpurea (Sirra et al, 2017) were also clustered within Chryseobacterium in the 16S rRNA gene tree but with low support (Supplementary Data Sheet 1). When Soonwooa was proposed (Joung et al, 2010), many Chryseobacterium species were omitted from the 16S rRNA gene tree, which may have caused the two genera to appear as separate. Based on our comprehensive analysis we conclude that Soonwooa buanensis and S. purpurea should be classified in Chryseobacterium.…”

“…Based on our comprehensive analysis we conclude that Soonwooa buanensis and S. purpurea should be classified in Chryseobacterium. Soonwooa (Joung et al, 2010; Sirra et al, 2017) and Chryseobacterium (Vandamme et al, 1994; Kämpfer et al, 2009; Wu et al, 2013; Montero-Calasanz et al, 2014; Chen et al, 2015; Hahnke R. L. et al, 2016) cannot be differentiated based on their phenotypic characteristics (Supplementary Table 1) either. We are aware of the fact that even with this modification the taxonomic classification of Chryseobacterium remains unsatisfactory because its relationships to the most closely related genera are not fully resolved (Figure 6).…”

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual-family Immunophilin Chaperones

“…The linker of Soonwooa buanensis , a marine bacterium of the Flavobacteriaceae family, recently discovered in the Yellow Sea off the Korean coast, was placed in the Chrysobacterial group ( Fig. 2 ), but this is not an aberration, since 16S RNA sequencing revealed that S. buanensis is most closely related to several Chrysobacterium species (94.4% similarity in 16S RNA sequence) [ 32 ]. Thus, although named in memory of Soon-Woo Hong, a Korean microbiologist, this bacterium is essentially a Chrysobacterium sp.…”

Isolation and characterization of psychrotolerant endospore-forming Sporosarcina species associated with minced fish meat (surimi)

“…Carnobacterium species can cause spoilage of the surimi products, as they are tolerant to freezing and capable of growth at low temperatures (Leisner et al, 2007). However, all of the identified isolates from the raw surimi were inactivated by heat-treatment as they were all non-endospore-forming bacteria (Collins et al, 1983(Collins et al, , 1987O'Hara et al, 1989;Takeuchi et al, 1996;Kovacs et al, 1999;Collins et al, 2000;Mora et al, 2003;Romanenko et al, 2004;Irlinger et al, 2005;Liu et al, 2006;Yoon et al, 2006;Joung et al, 2010;Wirth et al, 2012;Kacagan et al, 2013).…”