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A Report of Nine Unrecorded Bacterial Species in the Phylum Bacteroidetes Collected from Freshwater Environments in Korea

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A Report of Nine Unrecorded Bacterial Species in the Phylum Bacteroidetes Collected from Freshwater Environments in Korea Journal of Species Research 7(3):187-192, 2018 A report of nine unrecorded bacterial species in the phylum Bacteroidetes collected from freshwater environments in Korea Sanghwa Park, Kiwoon Beak, Ji-Hye Han, Yoon-Jong Nam and Mi-Hwa Lee* Bacterial Resources Research Division, Freshwater Bioresources Research Bureau, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju, Gyengsangbuk-do 37242, Republic of Korea *Correspondent: [email protected] During a comprehensive study of indigenous prokaryotic species in South Korea, nine bacterial species in the phylum Bacteroidetes were isolated from freshwater environmental samples that were collected from three major rivers in the Republic of Korea. High 16S rRNA gene sequence similarity (≥98.7%) and robust phylogenetic clades with the closely related species suggest that each strain was correctly assigned to an independent and predefined bacterial species. There were no previous reports of these nine species in Korea. Within the phylum Bacteroidetes, four species were assigned to the genus Flavobacterium, order Flavobac- teriales, and five species to three genera of two families in the order Cytophagales. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section. Keywords: ‌16S rRNA gene, Bacteroidetes, Flavobacteriales, Cytophagales, unrecorded species Ⓒ 2018 National Institute of Biological Resources DOI:10.12651/JSR.2018.7.3.187 INTRODUCTION MATERIALS AND METHODS The phylum Bacteroidetes (Ludwig and Klenk, 2001), Samples of freshwater, brackish water, and sediment also known as the Bacteroides-Cytophaga-Flexibacter were collected from the Han River, Nakdong River, and group, are widely distributed over a diverse range of eco- Seomjin River. Each sample was processed separately, logical niches including soil, marine, freshwater, and the spread onto diverse culture media including R2A agar gastrointestinal tracts of animals (DeLong et al., 1993; and Marine Agar 2216 (Difco), and then incubated at 15- Bowman et al., 1997; Glöckner et al., 1999; O’Sullivan 30°C for 14 days. All strains were purified as single col- et al., 2002). This phylum consists of four classes, with onies and stored as 20% glycerol suspension at -80°C. most environmental Bacteroidetes belong to the Flavo- The designated strain IDs, sources, culture media, and bacteriia, Cytophagia, and Sphingobacteriia classes, incubation conditions are summarized in Table 1. while the gastrointestinal tract microbiota is primarily Colony morphology of the strains was observed on composed of members in the Bacteroidia. These bacteria agar plates with a magnifying glass after the cells grew to are Gram-stain-negative and rod-shaped that do not form stationary phase. Cellular morphology and cell size were endospores (Ludwig et al., 2010). examined by transmission electron microscopy (CM200, From 2015-2016, we collected freshwater environmen- Philips). Gram staining was performed using a Gram- tal samples from three major rivers, the Han River, Nak- staining kit (BD). Biochemical characteristics were tested dong River and Seomjin River in (Republic of) Korea, by using API 20NE (bioMérieux) according to the manu- and isolated novel and unrecorded bacterial species in facturer’s instructions. Korea. The isolates belonged to the phyla Proteobacte- The phylogenetic position of the strains assigned to the ria, Bacterioidetes, Firmicutes, Actinobacteria and Ver- phylum Bacteroidetes was investigated using 16S rRNA rucomicrobia. As a subset of this study, we report nine gene analysis. The 16S rRNA genes were amplified by unrecorded bacterial species belonging to the orders Fla- PCR and sequenced. The 16S rRNA gene sequences of vobacteriales and Cytophagales in the phylum Bacteroi- the strains assigned to the phylum Bacteroidetes were detes. analyzed using the EzTaxon-e server (Kim et al., 2012) 188 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 3 d d d d d d d d d and confirmed using GenBank database (http://ncbi.nlm. nih.gov). For phylogenetic analyses, the16S rRNA gene 25°C, 3 30°C, 3 25°C, 3 25°C, 2 25°C, 3 25°C, 2 30°C, 3 20°C, 2 25°C, 3 sequences were aligned using EzEditor (Jeon et al., 2014). Incubation condition A phylogenetic tree was constructed using the neighbor- joining (NJ) (Saitou and Nei, 1987), maximum-parsimony (MP) (Fitch, 1971) and maximum-likelihood (ML) (Fel- MA R2A R2A R2A MA MA R2A R2A R2A Medium senstein, 1981) methods in MEGA version 6 (Tamura et al., 2013). The topology of the phylogenetic tree was evaluated via a bootstrap analysis (Felsenstein, 1985), based on 1,000 replications. source Isolation Brackish water Sediments Freshwater Sediment Brackish water Sediments Freshwater Sediments Brackish water RESULTS AND DISCUSSION On the basis of 16S rRNA gene sequence comparisons (%) 99.3 99.5 98.7 98.8 99.7 99.9 99.2 98.8 98.8 and phylogenetic analyses, allnine strains were assigned Similarity to the phylum Bacteroidetes. The nine strains were dis- tributed in two orders: four strains in the order Flavobac- T T T teriales and five strains in the order Cytophagales (Table T T T T 1). These strains were Gramstaining-negative, chemohet- T 12C11 erotrophic and rod-shaped bacteria except for strain SJ- T Txc1 WB 3.2-61 an-8 AC-74 153 and BK-168 showing a coccoid or oval shape (Fig. VUG-A23a 10Alg 130 GPTSA100-9 1). Cultural, morphological and physiological character- GFA-11 istics are also shown in the species description section. Based on 16S rRNA gene sequence similarity, nine Mostly related species strains were identified as unrecorded bacterial species in F. indicum F. macrobrachii F. reichenbachii F. A. zhangzhouensis roseus F. H. algoricola H. chitinivorans A. alkaliphilus F. ahnfeltiae F. Korea. A phylogenetic tree of bacterial strains assigned to the order Flavobacteriales and Cytophagales in the phylum Bacteroidetes are shown in Figs. 2 and 3 respec- tively. The four species that were assigned to the order NNIBR ID Flavobacteriales belonged to the genus Flavobacterium NNIBRBA 8 NNIBRBA 47 NNIBRBA 55 NNIBRBA 61 NNIBRBA 26 NNIBRBA 58 NNIBRBA 39 NNIBRBA NNIBRBA 40 NNIBRBA NNIBRBA 38 NNIBRBA in the family Flavobacteriaceae (Fig. 2). Another five species were assigned to the families Cyclobacteriaceae and Cytophagaceae in the order Cytophagales. Among these species, two species that were assigned to the fam- and their taxonomic affiliations. Strain ID SS1-37 BK-550 KS1-10 ES1-03 BK-168 04KS1-21 SJ-175 SJ-361 SJ-153 ily Cyclobacteriaceae which belongs to the genus Algori- phagus. Three species that were assigned to the family Cytophagaceae belonged to the genera Flectobacillus (1 Bacteroidetes species) and Hymenobacter (2 species) (Fig. 3). Genus There are no previous reports of these nine species in Korea. In this study, we propose that these species are Flavobacterium Flavobacterium Flavobacterium Algoriphagus Flectobacillus Hymenobacter Hymenobacter Algoriphagus Flavobacterium unrecorded bacterial species: Flavobacterium ahnfeltiae, F. indicum, F. macrobrachii, F. reichenbachii, Algoriph- agus alkaliphilus, A. zhangzhouensis, Flectobacillus ro- seus, Hymenobacter algoricola, and H. chitinivorans in Korea. Family Cytophagaceae Cyclobacteriaceae Flavobacteriaceae Description of Flavobacterium ahnfeltiae SJ-153 Cells are Gram-staining-negative, non-flagellated and coccus-shaped. Colonies are circular, convex with entire edge and yellow-colored after 3 days on MA at 25°C. Summary of strainsbelonging to the phylum Order Positive for esculin hydrolysis and indole production, but negative for nitrate reduction, glucose fermentation, argi- Cytophagales Table1. Flavobacteriales August 2018 Park et al. 9 unrecorded bacterial species affiliated with the phylumBacteroidetes 189 (A) (B) (C) (D) (E) (F) (G) (H) ( I ) Fig. 1. Transmission electron micrographs of the strains isolated in this study. Strains: A, SJ-153; B, SS1-37; C, BK-550; D, KS1-10; E, SJ- 361; F, ES1-03; G, BK-168; H, 04KS1-21; I, SJ-175. Bar: 0.2 μm (A-G), 0.5 μm (H and I). nine dihydrolase, urease, gelatinase and β-galactosidase. adipic acid, D-maltose, N-acetyl-glucosamine, potassium Does not utilize D-glucose, L-arabinose, D-mannose, D- gluconate, capric acid, trisodium citrate and phenylacetic mannitol, N-acetyl-glucosamine, D-maltose, potassium acid. The strain SS1-37 ( =NNIBRBA 8) was isolated gluconate, capric acid, adipic acid, malic acid, trisodium from a riverside sediment of Nakdong River, Gyeong- citrate and phenylacetic acid. The strain SJ-513 (=NNI cheon-island, Sangju, Korea. BRBA 38) was isolated from brackish water of Seomjin River, Gwangyang, Korea. Description of Flavobacterium macrobrachii BK-550 Cells are Gram-staining-negative, non-flagellated and Description of Flavobacterium indicum SS1-37 rod-shaped. Colonies are circular, convex, opaque with Cells are Gram-staining-negative, non-flagellated and entire edge and yellow-colored after 3 days on R2A agar rod-shaped. Colonies are circular, convex to umbonate at 25°C. Positive for nitrate reduction, esculin hydrolysis, with irregular margin and yellow-colored after 3 days on urease and β-galactosidase, but negative for indole pro- R2A agar at 30°C. Positive for esculin hydrolysis, gelati- duction, gelatinase, glucose fermentation, arginine dihy- nase and β-galactosidase, but negative for nitrate reduc- drolase. D-Glucose, D-mannitol and malic acid are uti- tion, indole production, urease, arginine dihydrolase and lized. Does not utilize L-arabinose, D-mannose, D-malt- glucose
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