A Report of 37 Unrecorded Anaerobic Bacterial Species Isolated from the Geum River in South Korea
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Journal of Species Research 9(2):105-116, 2020 A report of 37 unrecorded anaerobic bacterial species isolated from the Geum River in South Korea Changsu Lee, Joon Yong Kim, Yeon Bee Kim, Juseok Kim, Seung Woo Ahn, Hye Seon Song and Seong Woon Roh* Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea *Correspondent: [email protected] A total of 37 anaerobic bacteria strains within the classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidia, Flavobacteriia, Bacilli, Clostridia, and Fusobacteriia were isolated from freshwater and sediment of the Geum River in Korea. The unreported species were related with Rhizobium and Oleomonas of the class Alphaproteobacteria; Acidovorax, Pseudogulbenkiania, and Aromatoleum of the class Betaproteobacteria; Tolumonas, Aeromonas, Cronobacter, Lonsdalea, and Phytobacter of the class Gammaproteobacteria; Bacteroides, Dysgonomonas, Macellibacteroides, and Parabacteroides of the class Bacteroidia; Flavobacterium of the class Flavobacteriia; Bacillus and Paenibacillus of the class Bacilli; Clostridium, Clostridioides, Paraclostridium, Romboutsia, Sporacetigenium, and Terrisporobacter of the class Clostridia; and Cetobacterium and Ilyobacter of the class Fusobacteriia. A total of 37 strains, with >98.7% 16S rRNA gene sequence similarity with validly published bacterial species, but not reported in Korea, were determined to be unrecorded anaerobic bacterial species in Korea. Keywords: 16S rRNA, anaerobic bacteria, bacterial diversity, taxonomy, unrecorded species Ⓒ 2020 National Institute of Biological Resources DOI:10.12651/JSR.2020.9.2.105 INTRODUCTION lated culture in Korea. In the present study, we attempted to isolate anaerobic Since the Nagoya Protocol and the Convention on Bi- microorganisms from freshwater and sediment in the ological Diversity, securing and managing of biological Geum River of Korea. Here, 37 unreported species be- resources have become more important (Buck & Ham- longing to the classes Alphaproteobacteria, Betaproteo ilton, 2011). In order to be competitive with national bi- bacteria, Gammaproteobacteria, Bacteroidia, Flavobac ological resources, various biological resources should teriia, Bacilli, Clostridia, and Fusobacteriia are reported be secured. However, to date, systematic research on and described. domestic freshwater biological resources is insufficient. Freshwater basins are expected to have high diversity due to their diverse environmental conditions. According to MATERIALS AND METHODS the Korean Society of Ecology, reported in 1994, it is es- timated that 100,000 native species inhabit Korea, while Freshwater and sediment samples were collected from 52,628 species have been reported (National species list urban streams and wetland of the Geum River watershed of Korea, 2019); so there is an urgent need to study un- in 2019. A total of 37 anaerobic bacteria were isolated reported species. In particular, prokaryotes are a resource using various agar plates made of Deutsche Sammlung of biological industry and have the highest industrial val- von Mikroorganismen und Zellkulturen (DSMZ) medi- ue, but reported species are less than 1% of the estimated um No. 311c, DSMZ medium No. 320, DSMZ medium species. Most aerobic prokaryotes are being investigated No. 1451, and reinforced clostridial medium. These agar among reported species. Although anaerobic prokaryotic plates were incubated at 15-25℃ under anaerobic con- microorganisms derived from freshwater environment are dition (BD GasPak EZ Anaerobe Pouch System) for 3-7 actively being studied globally due to their high novelty days. Isolated bacterial strains were purified by serial di- as biological resources, there are few cases of purely iso- lution spreading and the pure cells were preserved in 20% 106 JOURNAL OF SPECIES RESEARCH Vol. 9, No. 2 (v/v) glycerol suspension containing 10% skimmed milk um aurantibutyricum, Acidovorax wautersii, Bacteroides at -80℃ and as lyophilized ampoules. luti, Flavobacterium tyrosinilyticum (Du & Yi, 2016), Colony morphology of the strains was observed by eye Lonsdalea britannica (Brady et al., 2012), Macellibacte or a magnifying glass after the cells were cultivated to roides fermentans (Jabari et al., 2012), Paraclostridium their stationary phase on agar plates. Cellular morphology benzoelyticum (Tushar et al., 2015), Tolumonas auensis and cell size were examined by field emission transmis- (Chertkov et al., 2011), Aeromonas rivipollensis (Marti sion electron microscopy (JEM 2100F; Jeol). Growth in & Balcázar, 2015), Cronobacter dublinensis subsp. lau the presence of oxygen was tested by aerobic incubation sannensis (Grim et al., 2013), Cetobacterium somerae for seven days. Gram staining was performed using a (Finegold et al., 2003), Aromatoleum toluolicum (Krieger Gram-staining kit (BD). Biochemical characteristics were et al., 1999), Parabacteroides chartae (Tan et al., 2012), evaluated by using API 20NE (bioMérieux) according to Dysgonomonas oryzarvi (Kodama et al., 2012), Clostrid the manufacturer’s instructions. ium amazonense (O’Neal et al., 2015), Clostridium chro Chromosomal DNA extraction, PCR amplification, miireducens (Inglett et al., 2011), Ilyobacter delafieldii, and 16S rRNA gene sequencing were performed using Phytobacter diazotrophicus (Zhang et al., 2008), and Ba standard procedures as described elsewhere (Kim et al., cillus endoradicis (Zhang et al., 2012). 2019). For the determination of 16S rRNA gene sequenc- Fourteen strains were isolated from freshwater and the es, primers 27F, 337F, 518R, 785F, and 1492R were used. others were isolated from sediment. Based on 16S rRNA Based on full 16S rRNA gene sequences, the closely re- gene sequences, phylogenetic position of 37 unrecorded lated type species were obtained using the EzBioCloud strains is shown in Fig. 2. Detailed physiological and server (Yoon et al., 2017). 16S rRNA gene sequences morphological characteristics of the 37 unrecorded bac- were aligned with the most closely related strains using terial strains determined in present study are given in the Clustal W (Thompson et al., 1994). The phylogenetic following strain descriptions. trees were constructed using neighbor-joining (Saitou & Nei, 1987), maximum likelihood (Felsenstein, 1981), and Description of Clostridioides mangenotii CBA7501 maximum parsimony methods (Fitch, 1971) in MEGA7 Cells are obligate anaerobic, Gram-stain-positive, non- (Kumar et al., 2016) with bootstrap values based on 1,000 pigmented, and cocci-shaped. Colonies are circular, con- randomly generated trees. vex, and entire after incubation for four days on DSMZ medium No. 311c at 25℃. Positive for esculin hydrolysis and gelatinase. Negative for nitrate reduction, indole pro- RESULTS AND DISCUSSION duction, glucose fermentation, arginine dihydrolase, ure- ase, and β-galactosidase activity. Does not utilize D-glu- The designation of strains, ID, similarity, and source cose, L-arabinose, D-mannose, D-mannitol, N-acetyl-glu- of isolation are described at Table 1. Thirty-seven strains cosamine, potassium gluconate, D-maltose, capric acid, were distributed into eight classes: two strains in Al adipic acid, malic acid, trisodium citrate, and phenylacetic phaproteobacteria, four strains in Bacilli, four strains acid. Strain CBA7501 (=NNIBR2019644BA4) was iso- in Bacteroidia, three strains in Betaproteobacteria, 16 lated from a sediment sample, Jinan-gun, Jeollabuk-do, strains in Clostridia, one strain in the Flavobacteriia, two Korea. strains in Fusobacteriia, and five strains in Gammapro teobacteria. Unrecorded anaerobic bacterial strains in Description of Clostridium botulinum CBA7502 the eight classes were identified as following species in the order of strain ID (Fig. 1): Clostridioides mangenotii, Cells are obligate anaerobic, Gram-stain-positive, non- Clostridium botulinum, Clostridium lundense (Cirne et pigmented, and rod-shaped. Colonies are irregular, raised, al., 2006), Pseudogulbenkiania subflava, Rhizobium alvei and entire after incubation for four days on DSMZ me- (Sheu et al., 2015), Sporacetigenium mesophilum (Chen dium No. 311c at 25℃. Positive for esculin hydrolysis. et al., 2006), Terrisporobacter glycolicus (Collins et al., Negative for nitrate reduction, indole production, glucose 1994), Clostridium huakuii (Ruan et al., 2014), Oleo fermentation, arginine dihydrolase, urease, gelatinase, monas sagaranensis, Clostridium algidicarnis, Clostridi and β-galactosidase activity. Does not utilize D-glucose, um intestinale (Collins et al., 1994), Paenibacillus sonchi L-arabinose, D-mannose, D-mannitol, N-acetyl-glucos- (Hong et al., 2009), Paenibacillus riograndensis, Clos amine, potassium gluconate, D-maltose, capric acid, adip- tridium sartagoforme (Stackebrandt et al., 1999), Clos ic acid, malic acid, trisodium citrate, and phenylacetic tridium gasigenes (Broda et al., 2000), Romboutsia sed acid. Strain CBA7502 (=NNIBR2019644BA41) was iso- imentorum (Wang et al., 2015), Bacillus benzoevorans, lated from a sediment sample, Jangsu-gun, Jeollabuk-do, Clostridium senegalense (Mishra et al., 2012), Clostridi Korea. May 2020 Table 1. Summary of strains isolated belonging to the classes Alphaproteobacteria, Bacilli, Bacteroidia, Betaproteobacteria, Clostridia, Flavobacteriia, Fusobacteriia, and Gammaproteobac teria and their taxonomic affiliations. Most closely related species Accession Similarity Isolation Class Order Family Genus Species Strain ID NNIBR ID number source Closest type