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Clostridium Liquoris Sp. Nov., Isolated from a Fermentation Pit Used for The International Journal of Systematic and Evolutionary Microbiology (2016), 66, 749–754 DOI 10.1099/ijsem.0.000787 Clostridium liquoris sp. nov., isolated from a fermentation pit used for the production of Chinese strong-flavoured liquor Qi Yin,1,2 Yong Tao,1 Xiaoye Zhu,1 Yan Zhou,3 Xiaohong He,1 Lei Cheng,4 Yan Huang4 and Daping Li1 Correspondence 1Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences & Yong Tao Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, [email protected] Chinese Academy of Sciences, Chengdu 610041, PR China Daping Li 2Chengdu Shishi High School, Chengdu 610041, PR China [email protected] 3College of Life Science, Sichuan University, Chengdu 610041, PR China 4Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu 610041, PR China Strain BEY10T was isolated from an old fermentation pit, which had been used for the production of Chinese strong-flavoured liquor for over 20 years. The strain was strictly anaerobic, Gram-stain positive, rod-shaped, non-motile and spore-forming. Strain BEY10T grew at temperatures of 22–47 8C (optimum 37 8C), at pH 5.5–9.0 (optimum pH 7.5–8.5) and with NaCl concentrations of 0–4 % (w/v) (optimum 0 %). The isolate was able to utilize glucose, mannitol, lactose, xylose, maltose, glycerol, cellobiose and trehalose as carbon sources for growth. The major end-products from glucose fermentation were ethanol and butyric acid. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phospholipids, a glycolipid and an aminolipid. The predominant fatty acids (.10 %) were C20 : 0,C18 : 0,C16 : 0, C12 : 0 and C14 : 0.The DNA G+C content was 34.4 mol%. Sequence analysis of the 16S rRNA gene indicated that strain BEY10T belongs to the genus Clostridium in the family Clostridiaceae. The closest phylogenetic neighbour is Clostridium lundense DSM 17049T, showing 97.6 % 16S rRNA gene sequence similarity with strain BEY10T. DNA–DNA relatedness values of strain BEY10T with Clostridium lundense DSM 17049T, Clostridium tetanomorphum DSM 4474T and Clostridium pascui DSM 10365T were 58.8 %, 57.9 % and 42.2 %, respectively. This characterization based on phylogenetic, phenotypic and chemotaxonomic evidence demonstrated that strain BEY10T represents a novel species of the genus Clostridium, for which the name Clostridium liquoris sp. nov. is proposed. The type strain is BEY10T (5ACCC 00785T5DSM 100320T). Clostridium is a genus of Gram-positive bacteria belong- as converting bio-waste into organic acids (focusing on ing to the phylum Firmicutes, and contains around 200 acetate, butyrate and caproate) (Mu¨ller, 2003; species (UK-Standards-for-Microbiology-Investigations, 2011; Tracy et al., 2012). There are many reports about pathways Wiegel et al., 2006), of which only a few are pathogenic and metabolism of Clostridium butyricum or Clostridium to humans. A majority of members of the genus Clostri- kluyveri to produce butyrate or caproate in anaerobic fer- dium possess value in commercial applications, such mentation (Cai et al., 2011; Colin et al., 2001; Papoutsakis, 2008; Seedorf et al., 2008). Abbreviation: CSFL, Chinese strong-flavoured liquor. Chinese strong-flavoured liquor (CSFL), also called The GenBank/EMBL/DDBJ accession number for the16S rRNA gene ‘Luzhou-flavor liquor’, accounts for more than 70 % of sequence of strain BEY10T is KC331197. 54 bacterial strains Chinese liquor production every year in China (Zhao (GenBank accession nos 5 KC331155–KC331208) are isolated in et al., 2012). The CSFL quality is to a large degree depen- this study and unpublished. dent on the flavour components (e.g. butyric acid, caproic Two supplementary figures are available with the online Supplementary acid, ethyl caproate and other microbial extracellular fatty Material. acids) produced by microbes in the pit mud of the Downloaded from www.microbiologyresearch.org by 000787 G 2015 IUMS Printed in Great Britain 749 IP: 130.132.173.170 On: Mon, 27 Jun 2016 13:30:03 Q. Yin and others fermentation pit (Xu et al., 2010). The genus Clostridium is ranging from 20 to 55 8C, at initial pH values of 4–10 one of the dominant taxa in the pit mud of fermentation (adjusted with 2.5 M NaOH or 2.5 M HCl) and in 0– pits for CSFL production, corresponding to the increase 8 % (w/v) NaCl for 7 days. All experiments were con- of caproic acid concentration and playing an important ducted in triplicate. Cell morphology and size were exam- role in the quality of CSFL (Shi et al., 2010; Tao et al., ined by scanning electron microscope (Quanta200; FEI). 2014). Recently, we isolated 54 bacterial strains (GenBank Samples were coated with Au/Pt before scanning electron accession nos KC331155–KC331208 for 16S rRNA gene microscopy observation. Gram staining was performed by sequences) from the fermentation pit for the production using a Difco Gram stain set and cultures were grown in of CSFL. The most abundant microbes were members of medium A according to standard procedures (Gerhardt the family Clostridiaceae (accounting for 46 % of all iso- et al., 1994). lates), followed by members of the families Eubacteriaceae Genomic DNA was extracted by using the TIANamp Bac- (16.7 %), Lachnospiraceae (13 %) and Lactobacillaceae teria DNA kit (TIANGEN Biotech), and the 16S rRNA gene (11 %). was amplified using universal primers 27F and 1492R In this paper, a novel saccharolytic, butyrate-producing (Lane, 1991). The PCR product was purified using the bacterium, designated BEY10T, was isolated from an old TIANgel Midi Purification kit (TIANGEN Biotech), fermentation pit (located in Mianzhu, Sichuan, China) cloned to the pM18-T vector (TaKaRa) and sequenced which maintained brewing operation for over 20 years using an automated DNA sequencer (ABI 3730; Applied without interruption. Based on the phenotypic and phylo- BioSystems). An almost-complete 16S rRNA gene sequence T genetic characteristics, it is proposed that the isolate rep- (1474 bp) of strain BEY10 was submitted to the GenBank resents a novel species of the genus Clostridium. database, and the identification of phylogenetic neighbours and the calculation of pairwise 16S rRNA gene sequence The anaerobic cultivation technique was used throughout the similarities were achieved using the EzTaxon server course of this study. In brief, pit-mud samples collected from (http://www.ezbiocloud.net/; Kim et al., 2012). Sequences the fermentation pit were inoculated (5 %, v/v) into 100 ml were aligned using CLUSTAL X 1.8 (Thompson et al., serum bottles containing sterilized saline and mixed well. 1997). Phylogenetic trees were reconstructed using the Cultures were then serially diluted with sterilized saline, neighbour-joining (Saitou & Nei, 1987) and maximum- and spread on modified MCM agar (2 %, w/v) plates (the likelihood (Yang, 1997) methods implemented in the pro- 21 isolation medium) containing (l , distilled water): 1.1 g gram MEGA version 5 (Tamura et al., 2011). The topological KH2PO4,0.5g(NH4)2SO4, 1.8 g sodium acetate, 0.5 g Casa- robustness was evaluated by bootstrap analysis (Felsenstein, mino acids, 0.5 g Bacto-peptone, 0.5 g yeast extract, 1.5 g 1985) based on 1000 replicates. KCl, 4.0 g NaHCO3, 0.5 g L-cysteine hydrochloride, 20 ml alcohol, 0.001 g resazurin, 2 ml vitamin solution and 1 ml trace element solution (Atlas, 2010). Plates were incubated for 3–5 days at 30 8C under anaerobic conditions (90 % N2, 5 % CO, and 5 % H2; SHELLAB). Colonies on MCM agar plates were transferred to fresh MCM medium three consecu- tive times to get a pure organism. The liquid medium (denoted medium A) used as a base medium in physiological GL T tests for strain BEY10 , contained the basal salts (Markossian PL et al., 2000) supplemented with 0.1 % (w/v) yeast extract, PL 0.0025 % (w/v) resazurin and 120 mg L-cysteine hydrochlo- PL PL 2 ride l 1; to obtain a solid medium, 2 % agar was added. All PE media had a final pH of 6.8–7.2 after autoclaving. Liquid cul- PG tures were grown with shaking (180 r.p.m.) at 37 8C. The iso- PL late was characterized biochemically using conventional tests as described previously (Tindall et al., 2007) and utilization of various organic substrates as carbon and energy sources was determined by using the API 20A test system (bioMe´rieux) PL AL according to the manufacturer’s instructions. The metabolic PL products from glucose fermentation were determined by an Agilent 1260 Infinity liquid chromatography system (Agilent PL Technologies) equipped with a HPLC column Hi-Plex H (30066.5 mm) and a differential refraction detector (RID). Growth rates, optimum growth temperature and tolerance to pH and NaCl were determined in medium A containing Fig. 1. Polar lipid profile of the strain BEY10T after two-dimen- 1 % (w/v) yeast extract as the sole carbon and energy sional TLC. PG, phosphatidylglycerol; PE, phosphatidylethanola- source. For these studies, cells were grown at temperatures mine; PL, phospholipids; GL, glycolipid; AL, aminolipid. Downloaded from www.microbiologyresearch.org by 750 International Journal of Systematic and Evolutionary Microbiology 66 IP: 130.132.173.170 On: Mon, 27 Jun 2016 13:30:03 Clostridium liquoris sp. nov. Polar lipids were extracted using a chloroform/methanol/ constitutes a different clade. Furthermore, the isolate 0.3 % aqueous NaCl mixture (1 : 2 : 0.8, by vol.) (Bligh showed 97.6 %, 96.9 % and 95.3 % 16S rRNA gene sequence & Dyer, 1959) and then were detected by two-dimensional similarity with the type strains of C. lundense, C. tetanomor- silica gel thin-layer chromatography (Tindall et al., 2007). phum and C. pascui respectively, which were the phylogeneti- Strain BEY10T was found to possess a very characteristic cally closest related species. Strain BEY10T showed less than polar lipid pattern of the genus Clostridium, consisting of 95.0 % 16S rRNA gene sequence similarity with other related phosphatidylglycerol, phosphatidylethanolamine, phos- species of the genus Clostridium.
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