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Bergey?s Manual of Systematics of Archaea and Bacteria Pullulanibacillus Journal: Bergey’s Manual of Systematics of Archaea and Bacteria Manuscript ID Draft Wiley - Manuscript type: Genus Paper Date Submitted by the Forn/a Peer Review Author: Complete List of Authors: Albuquerque, Luciana; Center for Neuroscience and Cell Biology, University of Coimbra, Biotechnology Tiago, Igor; Centre for Functional Ecology, Life Sciences Department, University of Coimbra Veríssimo, António; Centre for Functional Ecology, Life Sciences Department, University of Coimbra da Costa, Milton; Center for Neuroscience and Cell Biology, University of Coimbra, Biotechnology Firmicutes, Sporolactobacillaceae, Mesophilic, Moderately acidophilic, Keywords: Aerobic John Wiley & Sons Page 1 of 34 Bergey?s Manual of Systematics of Archaea and Bacteria 1 2 3 1 Firmicutes / Bacilli or Firmibacteria / Bacillales / Sporolactobacillaceae 4 5 6 2 7 8 3 gbm014445 9 10 4 11 12 13 5 Pullulanibacillus 14 15 6 16 17 7 Hatayama, Shoun, Ueda, and Nakamura 2006, 2549VP. Emend Pereira, Albuquerque, 18 19 VP 20 8 Nobre, Tiago, Veríssimo, Pereira and da Costa 2013, 161 . 21 For Peer Review 22 9 23 24 10 Luciana Albuquerque, Center for Neuroscience and Cell Biology, University of Coimbra, 25 26 27 11 Coimbra, Portugal 28 29 12 Igor Tiago, Centre for Functional Ecology, Department of Life Sciences, University of 30 31 13 Coimbra, Coimbra, Portugal 32 33 António Verissimo, Centre for Functional Ecology, Department of Life Sciences, 34 14 35 36 15 University of Coimbra, Coimbra, Portugal 37 38 16 Milton S. da Costa, Department of Life Sciences, University of Coimbra, Coimbra, 39 40 17 Portugal 41 42 43 18 44 45 19 Pul.lu.la.ni.ba.cil’lus. N.L. n. pullulanum pullulan; L. masc. n. bacillus a small staff; N.L. 46 47 20 masc. n. Pullulanibacillus a small staff hydrolyzing pullulan. 48 49 50 21 51 52 22 The species of the genus Pullulanibacillus produce rod-shaped cells, 0.5–4.0 µm in width 53 54 23 and 2.1–60.0 µm in length that stain Gram-positive. The endospores are oval, sub- 55 56 terminal to terminal in swollen sporangia. Some species possess flagella and motility is 57 24 58 59 25 observed. Colonies are nonpigmented or yellow-pigmented. The species of the genus 60 1 John Wiley & Sons Bergey?s Manual of Systematics of Archaea and Bacteria Page 2 of 34 1 2 3 26 Pullulanibacillus are mesophilic and are moderately acidophilic. The species are strictly 4 5 6 27 aerobic, cytochrome c oxidase is negative, and catalase is positive. The species of the 7 8 28 genus are chemoorganotrophic utilizing carbohydrates, polyols, amino acids and organic 9 10 29 acids as single carbon sources. Yeast extract is not necessary for growth in minimal 11 12 30 defined medium. The peptidoglycan contains meso-diaminopimelic acid (meso-Dpm) 13 14 15 31 plus alanine and glutamic acid and is of type A1γ. Menaquinone 7 (MK-7) is the major 16 17 32 respiratory quinone. Polar lipids consist of phosphatidylglycerol (PG), 18 19 33 diphosphatidylglycerol (DPG), unidentified phospholipids, unidentified aminolipids and 20 21 For Peer Review 22 34 unidentified glycolipids; in some species DPG and glycolipids are not detected. The 23 24 35 predominant fatty acids are saturated branched- and straight-chain; some species contains 25 26 36 large amounts of unsaturated fatty acids. DNA G+C content is 39.3–45.0 (%) (HPLC) 27 28 The members of the genus Pullulanibacillus have been isolated from soil, tea and a 29 37 30 31 38 uranium mill tailling effluent. 32 33 39 Type species: Pullulanibacillus naganoensis Hatayama, Shoun, Ueda, and 34 35 40 Nakamura 2006, 2549VP. 36 37 38 41 39 40 41 42 Keywords: Firmicutes, Sporolactobacillaceae, mesophilic, moderately acidophilic, 42 43 43 aerobic 44 45 44 46 47 48 45 Rod-shaped cells, 0.5–4.0 µm in width and 2.1–60.0 µm in length. Endospores are oval, 49 50 51 46 sub-terminal to terminal in a swollen sporangium. Stain Gram-positive. Some species are 52 53 47 motile. Colonies are nonpigmented or yellow-pigmented. Mesophilic and moderately 54 55 48 acidophilic. Strictly aerobic. Cytochrome c oxidase negative and catalase positive. 56 57 49 Chemoorganotrophic. Yeast extract is not necessary for growth in minimal medium. 58 59 60 50 Carbohydrates, polyols, amino acids and organic acids serve as single carbon sources. 2 John Wiley & Sons Page 3 of 34 Bergey?s Manual of Systematics of Archaea and Bacteria 1 2 3 51 The peptidoglycan contains meso-diaminopimelic acid (meso-Dpm) plus alanine and 4 5 6 52 glutamic acid and is of type A1γ. Menaquinone 7 (MK-7) is the major respiratory 7 8 53 quinone. Polar lipids consist of phosphatidylglycerol (PG), diphosphatidylglycerol 9 10 54 (DPG), unidentified phospholipids, unidentified aminolipids and unidentified 11 12 55 glycolipids; in some species DPG and glycolipids are not detected. Major fatty acids are 13 14 15 56 saturated branched- and straight-chain; some species contains large amounts of 16 17 57 unsaturated fatty acids. Isolated from soil, tea and a uranium mill tailling effluent. 18 19 58 DNA G+C content (%): 39.3–45.0 (HPLC). 20 21 For Peer Review 22 59 Type species: Pullulanibacillus naganoensis Hatayama, Shoun, Ueda, and Nakamura 23 24 60 2006, 2549VP 25 26 61 Number of species with validated names: 4. 27 28 Family classification: The genus Pullulanibacillus is classified within the family 29 62 30 31 63 Sporolactobacillaceae (fbm00117). 32 33 64 34 35 36 65 Further descriptive information 37 38 66 39 40 67 Cell morphology and colony characteristics 41 42 43 68 The species of Pullulanibacillus produces Gram-positive rod-shaped cells, 0.5–1.0 µm in 44 45 69 width and 1.0–60.0 µm in length and form terminal to subterminal spores within a swollen 46 47 70 sporangium. With the exceptions of the type strain of P. pueri, which is motile by means 48 49 50 71 of peritrichous flagella, motility has not been observed in other strains of this genus. The 51 52 72 colonies of species P. naganoensis and P. uraniitolerans are nonpigmented; P. camelliae 53 54 73 and P. pueri are yellow to pale-yellow pigmented. Colonies of these organisms are 55 56 circular and convex with 1 to 3 mm in diameter after 48h of growth. Colonies of P. 57 74 58 59 60 3 John Wiley & Sons Bergey?s Manual of Systematics of Archaea and Bacteria Page 4 of 34 1 2 3 75 naganoensis have entire margins but P. uraniitolerans have undulate margins (Niu et al., 4 5 6 76 2016; Niu et al., 2015, Pereira et al., 2013; Tomimura et al., 1990). 7 8 77 9 10 78 Nutrition and growth conditions 11 12 79 The species of the genus Pullulanibacillus are mesophile; they have an optimum growth 13 14 15 80 temperature of about 28–37ºC and the temperature range for growth is between 15 to 16 17 81 50ºC. The species are moderately acidophilic, the optimum pH for growth is in the range 18 19 82 of 4.0–6.0 for P. naganoensis, P. pueri and P. uraniitolerans, but the optimum pH of P. 20 21 For Peer Review 22 83 camelliae is higher, between 6.5–7.5. The organisms do not grow below pH 3.0 or above 23 24 84 pH 8.0. The species of this genus do not require NaCl for growth; growth occurs in media 25 26 85 with NaCl up to 5.0% (w/v) for species P. naganoensis and P. camelliae, 6.0% (w/v) for 27 28 species P. uraniitolerans and 9.0% (w/v) for species P. pueri (Table 1). 29 86 30 31 87 The strains of Pullulanibacillus can utilize carbohydrates, polyols, amino acids and 32 33 88 organic acids as single carbon sources. Only lactate and fumarate were tested as possible 34 35 89 single carbon sources for P. camelliae but this organism did not use them for growth. 36 37 38 90 Of the polyols tested, P. uraniitolerans only uses glycerol for growth (Table 1). Yeast 39 40 91 extract is not necessary for growth in a minimal medium (Niu et al., 2016; Niu et al., 41 42 92 2015). 43 44 45 93 There have been conflicting results related to the production of acid from the type 46 47 94 strains of the species of this genus using the API 50CH system. For example, the type 48 49 95 strain of the species of P. naganoensis appears not to produce acid from the carbon 50 51 sources using the API 50CH test strips (Pereira et al., 2013). However, Tomimura et al. 52 96 53 54 97 (1990) found that P. naganoensis, produced acid from L-arabinose, D-xylose, D-glucose, 55 56 98 D-mannitol and lactose, by measuring the decrease of the pH in a minimal medium using 57 58 99 the method of Gordon et al. (1973). Also using the API 50CH, Prasirtsak et al., 2016, Yao 59 60 4 John Wiley & Sons Page 5 of 34 Bergey?s Manual of Systematics of Archaea and Bacteria 1 2 3 100 et al., 2016 and Yan et al. 2018 found acid production from a large variety of carbon 4 5 6 101 sources by P. naganoensis. The type strains of the species P. camelliae and P. pueri 7 8 102 produce acid from several carbohydrates using the API 50CH (Yao et al., 2016; Yan et 9 10 103 al., 2018). However, the type strain of P. uraniitolerans does not appear to produce acid 11 12 104 from carbohydrates using the API 50CH (Pereira et al., 2013; Yan et al., 2018).
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  • A Sporolactobacillus-, Clostridium-, and Paenibacillus- Dominant Microbial Consortium Improved Anaerobic RDX Detoxification by Starch Addition

    A Sporolactobacillus-, Clostridium-, and Paenibacillus- Dominant Microbial Consortium Improved Anaerobic RDX Detoxification by Starch Addition

    J. Microbiol. Biotechnol. 2020. 30(6): 839–847 https://doi.org/10.4014/jmb.1910.10034 A Sporolactobacillus-, Clostridium-, and Paenibacillus- Dominant Microbial Consortium Improved Anaerobic RDX Detoxification by Starch Addition Muhammad Imran Khan1,2,4, Keunje Yoo1,5, Seonghoon Kim1, Sardar Alam Cheema3, Safdar Bashir2, and Joonhong Park1* 1Department of Civil and Environmental Engineering, College of Engineering, Yonsei University, Seoul 03722, Republic of Korea 2Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38040, Pakistan 3Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan 4Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research- UFZ, 04318 Leipzig, Germany 5Department of Environmental Engineering, College of Engineering, Korea Maritime and Ocean University, Busan 49112, Republic of Korea In the present study, an anaerobic microbial consortium for the degradation of hexahydro-1,3,5- trinitro-1,3,5-triazine (RDX) was selectively enriched with the co-addition of RDX and starch under nitrogen-deficient conditions. Microbial growth and anaerobic RDX biodegradation were effectively enhanced by the co-addition of RDX and starch, which resulted in increased RDX biotransformation to nitroso derivatives at a greater specific degradation rate than those for previously reported anaerobic RDX-degrading bacteria (isolates). The accumulation of the most toxic RDX degradation intermediate (MNX [hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine]) was significantly reduced by starch addition, suggesting improved RDX detoxification by the co-addition of RDX and starch. The subsequent MiSeq sequencing that targeted the bacterial 16S rRNA gene revealed that the Sporolactobacillus, Clostridium, and Paenibacillus populations were involved in the enhanced anaerobic RDX degradation.