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Fernandez HN, Kretsch AM, Kunakom S, Kadjo AE, Mitchell DA, Eustáquio AS. High-Yield Lasso Peptide Production in a Burkholderia Bacterial Host by Plasmid Copy Number Engineering. ACS Synth Biol 2024; 13:337-350. [PMID: 38194362 PMCID: PMC10947786 DOI: 10.1021/acssynbio.3c00597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The knotted configuration of lasso peptides confers thermal stability and proteolytic resistance, addressing two shortcomings of peptide-based drugs. However, low isolation yields hinder the discovery and development of lasso peptides. While testing Burkholderia sp. FERM BP-3421 as a bacterial host to produce the lasso peptide capistruin, an overproducer clone was previously identified. In this study, we show that an increase in the plasmid copy number partially contributed to the overproducer phenotype. Further, we modulated the plasmid copy number to recapitulate titers to an average of 160% relative to the overproducer, which is 1000-fold higher than previously reported with E. coli, reaching up to 240 mg/L. To probe the applicability of the developed tools for lasso peptide discovery, we targeted a new lasso peptide biosynthetic gene cluster from endosymbiont Mycetohabitans sp. B13, leading to the isolation of mycetolassin-15 and mycetolassin-18 in combined titers of 11 mg/L. These results validate Burkholderia sp. FERM BP-3421 as a production platform for lasso peptide discovery.
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Affiliation(s)
- Hannah N. Fernandez
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ashley M. Kretsch
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sylvia Kunakom
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Adjo E. Kadjo
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Douglas A. Mitchell
- Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alessandra S. Eustáquio
- Department of Pharmaceutical Sciences and Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
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2
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Li J, Liu L, Huang Y, Pan J, Li M. Zeimonas sediminis sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748486 DOI: 10.1099/ijsem.0.005673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium, FT117T, was isolated from mangrove sediment collected in Shenzhen, Guangdong, PR China. Growth occurred at 20-45 °C (optimum, 40 °C), pH 6-10 (optimum, 8) and in the presence of 0-5 % NaCl (optimum, 0 %). The results of 16S rRNA gene sequence analysis indicated that the identity between FT117T and Zeimonas arvi CC-CFT501T was the highest (98.7 %), followed by Quisquiliibacterium transsilvanicum JCM 31785T (93.6 %), Lautropia mirabilis CCUG 34794T (93.6 %) and Pandoraea eparura LMG 31012T (93.5 %). The main fatty acids (>10 %) were C16 : 0 (35.8 %), cyclo-C17 : 0 (18.5 %) and summed feature 3 (18.1 %). The polar lipids contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, two unidentified aminophospholipids and one unidentified lipid. The sole respiratory quinone was ubiquinone-8 (Q-8). Its DNA G+C content was 70.6 % (data from the genome sequence) and the estimated genome size was 3.860 Mb. The average nucleotide identity values between the FT117T genome and the genomes of Z. arvi CC-CFT501T, Q. transsilvanicum JCM 31785T, L. mirabilis CCUG 34794T and Paraburkholderia strydomiana LMG 31012T were 85.4 %, 76.4 %, 73.0 % and 71.3 %, and the digital DNA-DNA hybridization values were 29.1 %, 21.0 %, 20.3 % and 19.1 %, respectively. The phylogenetic, phenotypic and chemotaxonomic differences between FT117T and its phylogenetic relatives indicate that FT117T should be regarded as representing a novel species within the genus Zeimonas, for which the name Zeimonas sediminis sp. nov. is proposed. The type strain is FT117T (=KCTC 92314T = MCCC 1K07396T).
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Affiliation(s)
- Jiayi Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Lirui Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Yuhan Huang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China.,Shenzhen Xbiome Biotech Co. Ltd., Shenzhen, Guangdong 518058, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518057, PR China
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Celis AI, Relman DA, Huang KC. The impact of iron and heme availability on the healthy human gut microbiome in vivo and in vitro. Cell Chem Biol 2023; 30:110-126.e3. [PMID: 36603582 PMCID: PMC9913275 DOI: 10.1016/j.chembiol.2022.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 07/12/2022] [Accepted: 12/14/2022] [Indexed: 01/06/2023]
Abstract
Responses of the indigenous human gut commensal microbiota to iron are poorly understood because of an emphasis on in vitro studies of pathogen iron sensitivity. In a study of iron supplementation in healthy humans, we identified gradual microbiota shifts in some participants correlated with bacterial iron internalization. To identify direct effects due to taxon-specific iron sensitivity, we used participant stool samples to derive diverse in vitro communities. Iron supplementation of these communities caused small compositional shifts, mimicking those in vivo, whereas iron deprivation dramatically inhibited growth with irreversible, cumulative reduction in diversity and replacement of dominant species. Sensitivity of individual species to iron deprivation in axenic culture generally predicted iron dependency in a community. Finally, exogenous heme acted as a source of inorganic iron to prevent depletion of some species. Our results highlight the complementarity of in vivo and in vitro studies in understanding how environmental factors affect gut microbiotas.
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Affiliation(s)
- Arianna I Celis
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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4
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Lu CH, Zhang YY, Jiang N, Chen W, Shao X, Zhao ZM, Lu WL, Hu X, Xi YX, Zou SY, Wei QJ, Lin ZL, Gong L, Gai XT, Zhang LQ, Li JY, Jin Y, Xia ZY. Ralstonia chuxiongensis sp. nov., Ralstonia mojiangensis sp. nov., and Ralstonia soli sp. nov., isolated from tobacco fields, are three novel species in the family Burkholderiaceae. Front Microbiol 2023; 14:1179087. [PMID: 37213510 PMCID: PMC10196183 DOI: 10.3389/fmicb.2023.1179087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/14/2023] [Indexed: 05/23/2023] Open
Abstract
Eight Gram-negative, aerobic, motile with paired polar flagella and rod-shaped bacteria were isolated from six tobacco fields in Yunnan, PR China. 16S rRNA gene sequence analysis revealed that all the strains belonged to the genus Ralstonia. Among them, strain 22TCCZM03-6 had an identical 16S rRNA sequence to that of R. wenshanensis 56D2T, and the other strains were closely related to R. pickettii DSM 6297T (98.34–99.86%), R. wenshanensis 56D2T (98.70–99.64%), and R. insidiosa CCUG 46789T (97.34–98.56%). Genome sequencing yielded sizes ranging from 5.17 to 5.72 Mb, with overall G + C contents of 63.3–64.1%. Pairwise genome comparisons showed that strain 22TCCZM03-6 shared average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values above the species cut-off with R. wenshanensis 56D2T, suggesting that strain 22TCCZM03-6 is a special strain of the R. wenshanensis. Five strains, including 21MJYT02-10T, 21LDWP02-16, 22TCJT01-1, 22TCCZM01-4, and 22TCJT01-2, had ANI values >95% and dDDH values >70% when compared with each other. These five strains had ANI values of 73.32–94.17% and dDDH of 22.0–55.20% with the type strains of the genus Ralstonia individually, supporting these five strains as a novel species in the genus Ralstonia. In addition, strains 21YRMH01-3T and 21MJYT02-11T represent two independent species. They both had ANI and dDDH values below the thresholds for species delineation when compared with the type species of the genus Ralstonia. In strains 21YRMH01-3T and 21MJYT02-10T, the main fatty acids were summed features 3, 8, and C16:0; however, strain 21MJYT02-11T contained C16:0, cyclo-C17:0, and summed features 3 as major fatty acids. The main polar lipids, including diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine, were identified from strains 21YRMH01-3T, 21MJYT02-10T, and 21MJYT02-11T. The ubiquinones Q-7 and Q-8 were also detected in these strains, with Q-8 being the predominant quinone. Based on the above data, we propose that the eight strains represent one known species and three novel species in the genus Ralstonia, for which the names Ralstonia chuxiongensis sp. nov., Ralstonia mojiangensis sp. nov., and Ralstonia soli sp. nov. are proposed. The type strains are 21YRMH01-3T (=GDMCC 1.3534T = JCM 35818T), 21MJYT02-10T (=GDMCC 1.3531T = JCM 35816T), and 21MJYT02-11T (=GDMCC 1.3532T = JCM 35817T), respectively.
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Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
- *Correspondence: Zhen-Yuan Xia, ; Can-Hua Lu,
| | - Ying-Ying Zhang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Ning Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Wei Chen
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaoli Shao
- Puer Branch of Yunnan Tobacco Company, Puer, China
| | - Zhi-Ming Zhao
- Baoshan Branch of Yunnan Tobacco Company, Baoshan, China
| | - Wen-Lin Lu
- Zhaotong Branch of Yunnan Tobacco Company, Zhaoyang, China
| | - Xiaodong Hu
- Chuxiong Branch of Yunnan Tobacco Company, Chuxiong, China
| | - Yi-Xuan Xi
- Baoshan Branch of Yunnan Tobacco Company, Baoshan, China
| | - Si-Yuan Zou
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Qiu-Ju Wei
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Zhong-Long Lin
- China National Tobacco Corporation Yunnan Company, Kunming, China
| | - Li Gong
- Puer Branch of Yunnan Tobacco Company, Puer, China
| | - Xiao-Tong Gai
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Li-Qun Zhang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Jun-Ying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Yan Jin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, China
- *Correspondence: Zhen-Yuan Xia, ; Can-Hua Lu,
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5
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Ichikawa S, Abe R, Fujimoto H, Higashi K, Zang L, Nakayama H, Matsuoka I, Shimada Y. Paraburkholderia sabiae administration alters zebrafish anxiety-like behavior via gut microbial taurine metabolism. Front Microbiol 2023; 14:1079187. [PMID: 36876090 PMCID: PMC9977788 DOI: 10.3389/fmicb.2023.1079187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/09/2023] [Indexed: 02/18/2023] Open
Abstract
Interventions to the gut microbiome manipulate the gut-brain axis and could be useful in the treatment of anxiety and depression. In this study, we demonstrated that administration of the bacterium Paraburkholderia sabiae reduces anxiety-like behavior in adult zebrafish. P. sabiae administration increased the diversity of the zebrafish gut microbiome. Linear discriminant analysis Effect Size (LEfSe) analysis revealed that the populations of Actinomycetales including Nocardiaceae, Nocardia, Gordoniaceae, Gordonia, Nakamurellaceae, and Aeromonadaceae were reduced, whereas those of Rhizobiales including Xanthobacteraceae, Bradyrhizobiaceae, Rhodospirillaceae, and Pirellulaceae were increased in the gut microbiome. Functional analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) predicted that P. sabiae administration altered taurine metabolism in the zebrafish gut, and we demonstrated that P. sabiae administration increased the taurine concentration in the brain. Since taurine functions as an antidepressant neurotransmitter in vertebrates, our results suggest that P. sabiae could improve anxiety-like behavior in zebrafish via the gut-brain axis.
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Affiliation(s)
- Shunsuke Ichikawa
- Faculty of Education, Mie University, Tsu, Mie, Japan.,Mie University Zebrafish Drug Screening Center, Tsu, Japan
| | - Reimi Abe
- Faculty of Education, Mie University, Tsu, Mie, Japan
| | | | | | - Liqing Zang
- Mie University Zebrafish Drug Screening Center, Tsu, Japan.,Graduate School of Regional Innovation Studies, Mie University, Tsu, Mie, Japan
| | - Hiroko Nakayama
- Mie University Zebrafish Drug Screening Center, Tsu, Japan.,Graduate School of Regional Innovation Studies, Mie University, Tsu, Mie, Japan
| | - Izumi Matsuoka
- Mie University Zebrafish Drug Screening Center, Tsu, Japan
| | - Yasuhito Shimada
- Mie University Zebrafish Drug Screening Center, Tsu, Japan.,Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Japan.,Department of Bioinformatics, Mie University Advanced Science Research Promotion Center, Tsu, Japan
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6
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Liu JY, Zhang JF, Wu HL, Chen Z, Li SY, Li HM, Zhang CP, Zhou YQ, Lu CH. Proposal to classify Ralstonia solanacearum phylotype I strains as Ralstonia nicotianae sp. nov., and a genomic comparison between members of the genus Ralstonia. Front Microbiol 2023; 14:1135872. [PMID: 37032877 PMCID: PMC10073495 DOI: 10.3389/fmicb.2023.1135872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/07/2023] [Indexed: 04/11/2023] Open
Abstract
A Gram-negative, aerobic, rod-shaped, motile bacterium with multi-flagella, strain RST, was isolated from bacterial wilt of tobacco in Yuxi city of Yunnan province, China. The strain contains the major fatty acids of C16:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The polar lipid profile of strain RST consists of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and unidentified aminophospholipid. Strain RST contains ubiquinones Q-7 and Q-8. 16S rRNA gene sequence (1,407 bp) analysis showed that strain RST is closely related to members of the genus Ralstonia and shares the highest sequence identities with R. pseudosolanacearum LMG 9673T (99.50%), R. syzygii subsp. indonesiensis LMG 27703T (99.50%), R. solanacearum LMG 2299T (99.28%), and R. syzygii subsp. celebesensis LMG 27706T (99.21%). The 16S rRNA gene sequence identities between strain RST and other members of the genus Ralstonia were below 98.00%. Genome sequencing yielded a genome size of 5.61 Mbp and a G + C content of 67.1 mol%. The genomic comparison showed average nucleotide identity (ANIb) values between strain RST and R. pseudosolanacearum LMG 9673T, R. solanacearum LMG 2299T, and R. syzygii subsp. indonesiensis UQRS 627T of 95.23, 89.43, and 91.41%, respectively, and the corresponding digital DNA-DNA hybridization (dDDH) values (yielded by formula 2) were 66.20, 44.80, and 47.50%, respectively. In addition, strains belonging to R. solanacearum phylotype I shared both ANIb and dDDH with strain RST above the species cut-off values of 96 and 70%, respectively. The ANIb and dDDH values between the genome sequences from 12 strains of R. solanacearum phylotype III (Current R. pseudosolanacearum) and those of strain RST were below the species cut-off values. Based on these data, we concluded that strains of phylotype I, including RST, represent a novel species of the genus Ralstonia, for which the name Ralstonia nicotianae sp. nov. is proposed. The type strain of Ralstonia nicotianae sp. nov. is RST (=GDMCC 1.3533T = JCM 35814T).
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Affiliation(s)
- Jun-Ying Liu
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
- Institute of Biology and Environmental Engineering, Yuxi Normal University, Yuxi, China
| | - Jian-Feng Zhang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Han-Lian Wu
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Zhen Chen
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Shu-Ying Li
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Hong-Mei Li
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Cui-Ping Zhang
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
| | - Yuan-Qing Zhou
- College of Chemistry Biology and Environment, Yuxi Normal University, Yuxi, China
- Yuan-Qing Zhou,
| | - Can-Hua Lu
- Institute of Biology and Environmental Engineering, Yuxi Normal University, Yuxi, China
- *Correspondence: Can-Hua Lu,
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Lu CH, Chen W, Yin HH, Lin ZL, Li JY, Ma JH, Gai XT, Jiang N, Cao ZH, Qian L, Zhang LQ, Jin Y, Xia ZY. Ralstonia wenshanensis sp. nov., a novel bacterium isolated from a tobacco field in Yunnan, China. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748420 DOI: 10.1099/ijsem.0.005622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A Gram-negative, aerobic, motile with paired polar flagella and rod-shaped bacterium strain (56D2T) was isolated from tobacco planting soil in Yunnan, PR China. Major fatty acids were C16 : 1 ω7c (summed feature 3), C16 : 0 and C18 : 1 ω7c (summed feature 8). The polar lipid profile of strain 56D2T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminophospholipid and one unidentified glycolipid. Moreover, strain 56D2T contained ubiquinone Q-8 as the sole respiratory quinone. 16S rRNA gene sequence analysis showed that strain 56D2T was closely related to members of the genus Ralstonia and the two type strains with the highest sequence identities were R. mannitolilytica LMG 6866T (98.36 %) and R. pickettii K-288T (98.22 %). The 16S rRNA gene sequence identities between strain 56D2T and other members of the genus Ralstonia were below 98.00 %. Genome sequencing revealed a genome size of 5.87 Mb and a G+C content of 63.7 mol%. The average nucleotide identity values between strain 56D2T and R. pickettii K-288T, R. mannitolilytica LMG 6866 T and R. insidiosa CCUG 46789T were less than 95 %, and the in silico DNA-DNA hybridization values (yielded by formula 2) were less than 70 %. Based on these data, we conclude that strain 56D2T represents a novel species of the genus Ralstonia, for which the name Ralstonia wenshanensis sp. nov. is proposed. The type strain of Ralstonia wenshanensis sp. nov. is 56D2T (=CCTCC AB 2021466T=GDMCC 1.2886T=JCM 35178T).
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Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Wei Chen
- Colledge of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Hong-Hui Yin
- Wenshan Branch of Yunnan Provincial Tobacco Company, Wenshan 663000, PR China
| | - Zhong-Long Lin
- China National Tobacco Corporation Yunnan Company, Kunming 650011, PR China
| | - Jun-Ying Li
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Jun-Hong Ma
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Xiao-Tong Gai
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Ning Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Zheng-Hua Cao
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Lei Qian
- Hongta Branch of Yuxi Tobacco Company, Yuxi 653100, PR China
| | - Li-Qun Zhang
- Colledge of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Yan Jin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
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8
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Vesamäki JS, Nissinen R, Kainz MJ, Pilecky M, Tiirola M, Taipale SJ. Decomposition rate and biochemical fate of carbon from natural polymers and microplastics in boreal lakes. Front Microbiol 2022; 13:1041242. [PMID: 36425032 PMCID: PMC9679218 DOI: 10.3389/fmicb.2022.1041242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/24/2022] [Indexed: 11/15/2023] Open
Abstract
Microbial mineralization of organic compounds is essential for carbon recycling in food webs. Microbes can decompose terrestrial recalcitrant and semi-recalcitrant polymers such as lignin and cellulose, which are precursors for humus formation. In addition to naturally occurring recalcitrant substrates, microplastics have been found in various aquatic environments. However, microbial utilization of lignin, hemicellulose, and microplastics as carbon sources in freshwaters and their biochemical fate and mineralization rate in freshwaters is poorly understood. To fill this knowledge gap, we investigated the biochemical fate and mineralization rates of several natural and synthetic polymer-derived carbon in clear and humic lake waters. We used stable isotope analysis to unravel the decomposition processes of different 13C-labeled substrates [polyethylene, polypropylene, polystyrene, lignin/hemicellulose, and leaves (Fagus sylvatica)]. We also used compound-specific isotope analysis and molecular biology to identify microbes associated with used substrates. Leaves and hemicellulose were rapidly decomposed compared to microplastics which were degraded slowly or below detection level. Furthermore, aromatic polystyrene was decomposed faster than aliphatic polyethylene and polypropylene. The major biochemical fate of decomposed substrate carbon was in microbial biomass. Bacteria were the main decomposers of all studied substrates, whereas fungal contribution was poor. Bacteria from the family Burkholderiaceae were identified as potential leaf and polystyrene decomposers, whereas polypropylene and polyethylene were not decomposed.
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Affiliation(s)
- Jussi S. Vesamäki
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Riitta Nissinen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Martin J. Kainz
- WasserCluster Lunz—Biological Station, Donau-Universität Krems, Lunz am See, Austria
| | - Matthias Pilecky
- WasserCluster Lunz—Biological Station, Donau-Universität Krems, Lunz am See, Austria
| | - Marja Tiirola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Sami J. Taipale
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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9
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Nakayasu M, Yamazaki S, Aoki Y, Yazaki K, Sugiyama A. Triterpenoid and Steroidal Saponins Differentially Influence Soil Bacterial Genera. Plants (Basel) 2021; 10:2189. [PMID: 34685998 PMCID: PMC8538258 DOI: 10.3390/plants10102189] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 11/23/2022]
Abstract
Plant specialized metabolites (PSMs) are secreted into the rhizosphere, i.e., the soil zone surrounding the roots of plants. They are often involved in root-associated microbiome assembly, but the association between PSMs and microbiota is not well characterized. Saponins are a group of PSMs widely distributed in angiosperms. In this study, we compared the bacterial communities in field soils treated with the pure compounds of four different saponins. All saponin treatments decreased bacterial α-diversity and caused significant differences in β-diversity when compared with the control. The bacterial taxa depleted by saponin treatments were higher than the ones enriched; two families, Burkholderiaceae and Methylophilaceae, were enriched, while eighteen families were depleted with all saponin treatments. Sphingomonadaceae, which is abundant in the rhizosphere of saponin-producing plants (tomato and soybean), was enriched in soil treated with α-solanine, dioscin, and soyasaponins. α-Solanine and dioscin had a steroid-type aglycone that was found to specifically enrich Geobacteraceae, Lachnospiraceae, and Moraxellaceae, while soyasaponins and glycyrrhizin with an oleanane-type aglycone did not specifically enrich any of the bacterial families. At the bacterial genus level, the steroidal-type and oleanane-type saponins differentially influenced the soil bacterial taxa. Together, these results indicate that there is a relationship between the identities of saponins and their effects on soil bacterial communities.
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Affiliation(s)
- Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan; (M.N.); (K.Y.)
| | - Shinichi Yamazaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; (S.Y.); (Y.A.)
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; (S.Y.); (Y.A.)
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan; (M.N.); (K.Y.)
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji 611-0011, Japan; (M.N.); (K.Y.)
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10
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Herpell JB, Vanwijnsberghe S, Peeters C, Schindler F, Fragner L, Bejtović M, Weckwerth W, Vandamme P. Paraburkholderia dioscoreae sp. nov., a novel plant associated growth promotor. Int J Syst Evol Microbiol 2021; 71:004969. [PMID: 34542391 PMCID: PMC8549267 DOI: 10.1099/ijsem.0.004969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022] Open
Abstract
A novel bacterium, designated strain Msb3T, was recently isolated from leaves of the yam family plant Dioscorea bulbifera (Dioscoreaceae). Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Paraburkholderia with Paraburkholderia xenovorans as nearest validly named neighbour taxon (99.3 % sequence similarity towards the P. xenovorans type strain). Earlier genome sequence analysis revealed a genome of 8.35 Mb in size with a G+C content of 62.5 mol%, which was distributed over two chromosomes and three plasmids. Here, we confirm that strain Msb3T represents a novel Paraburkholderia species. In silico DNA-DNA hybridization and average nucleotide identity (OrthoANIu) analyses towards P. xenovorans LB400T yielded 58.4 % dDDH and 94.5 % orthoANIu. Phenotypic and metabolic characterization revealed growth at 15 °C on tryptic soy agar, growth in the presence of 1 % NaCl and the lack of assimilation of phenylacetic acid as distinctive features. Together, these data demonstrate that strain Msb3T represents a novel species of the genus Paraburkholderia, for which we propose the name Paraburkholderia dioscoreae sp. nov. The type strain is Msb3T (=LMG 31881T, DSM 111632T, CECT 30342T).
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Affiliation(s)
- Johannes B. Herpell
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sarah Vanwijnsberghe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Florian Schindler
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Lena Fragner
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Mersad Bejtović
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology Division (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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11
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Galluzzo P, Capri FC, Vecchioni L, Realmuto S, Scalisi L, Cottone S, Nuzzo D, Alduina R. Comparison of the Intestinal Microbiome of Italian Patients with Multiple Sclerosis and Their Household Relatives. Life (Basel) 2021; 11:life11070620. [PMID: 34206853 PMCID: PMC8307959 DOI: 10.3390/life11070620] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system, caused by a combination of genetic and environmental factors. In recent years, a role in MS pathogenesis was assigned to the gut microbiota. However, different signatures of gut dysbiosis have been shown to depend on environmental factors, like diet and lifestyle. In this study, we compared the gut microbiome in MS patients and their household healthy relatives sharing lifestyle and environmental factors. Faecal metagenomic DNA was extracted and the V3–V4 regions of the conserved bacterial 16S ribosomal RNA gene were amplified and sequenced. While overall bacterial communities were similar, specific families differed between healthy and MS subjects. We observed an increase in Ruminococcaceae, Christensenellaceae, Desulfovibrionaceae, Clostridiales, and Family XIII in MS patients, while Bacteroidaceae, Tannerellaceae, Veillonellaceae, and Burkholderiaceae were more abundant in healthy controls. In addition, principle coordinate analysis showed that the gut microbiome of all MS patients formed a cluster being less diverse than the household relatives and that gut microbiota of MS patients with EDSS 4.5–7 formed a distinct cluster in respect to their controls. Overall, our study is consistent with the hypothesis that MS patients have gut microbial dysbiosis and evidenced the importance of environmental factors in shaping the gut microbiome.
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Affiliation(s)
- Paola Galluzzo
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, University of Palermo, 90133 Palermo, Italy; (P.G.); (F.C.C.); (L.V.)
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via G. Marinuzzi 3, 90129 Palermo, Italy
| | - Fanny Claire Capri
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, University of Palermo, 90133 Palermo, Italy; (P.G.); (F.C.C.); (L.V.)
| | - Luca Vecchioni
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, University of Palermo, 90133 Palermo, Italy; (P.G.); (F.C.C.); (L.V.)
| | - Sabrina Realmuto
- Centro Sclerosi Multipla, UOC Neurologia e Stroke Unit, AOOR Villa Sofia Cervello, 90146 Palermo, Italy;
| | - Luca Scalisi
- Centro Medico di Fisioterapia “Villa Sarina“, Via Porta Palermo 123, 91011 Alcamo, Italy;
| | - Salvatore Cottone
- U.O.C. Neurologia con Stroke Unit A.R.N.A.S. Civico, 90127 Palermo, Italy;
| | - Domenico Nuzzo
- Istituto per la Ricerca e l’Innovazione Biomedica, CNR, Via U. La Malfa 153, 90146 Palermo, Italy
- Correspondence: (D.N.); (R.A.); Tel.: +39-091-23897306 (R.A.)
| | - Rosa Alduina
- Dipartimento Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, University of Palermo, 90133 Palermo, Italy; (P.G.); (F.C.C.); (L.V.)
- Correspondence: (D.N.); (R.A.); Tel.: +39-091-23897306 (R.A.)
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12
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Venice F, Desirò A, Silva G, Salvioli A, Bonfante P. The Mosaic Architecture of NRPS-PKS in the Arbuscular Mycorrhizal Fungus Gigaspora margarita Shows a Domain With Bacterial Signature. Front Microbiol 2020; 11:581313. [PMID: 33329443 PMCID: PMC7732545 DOI: 10.3389/fmicb.2020.581313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/29/2020] [Indexed: 12/31/2022] Open
Abstract
As obligate biotrophic symbionts, arbuscular mycorrhizal fungi (AMF) live in association with most land plants. Among them, Gigaspora margarita has been deeply investigated because of its peculiar features, i.e., the presence of an intracellular microbiota with endobacteria and viruses. The genome sequencing of this fungus revealed the presence of some hybrid non-ribosomal peptide synthases-polyketide synthases (NRPS-PKS) that have been rarely identified in AMF. The aim of this study is to describe the architecture of these NRPS-PKS sequences and to understand whether they are present in other fungal taxa related to G. margarita. A phylogenetic analysis shows that the ketoacyl synthase (KS) domain of one G. margarita NRPS-PKS clusters with prokaryotic sequences. Since horizontal gene transfer (HGT) has often been advocated as a relevant evolutionary mechanism for the spread of secondary metabolite genes, we hypothesized that a similar event could have interested the KS domain of the PKS module. The bacterial endosymbiont of G. margarita, Candidatus Glomeribacter gigasporarum (CaGg), was the first candidate as a donor, since it possesses a large biosynthetic cluster involving an NRPS-PKS. However, bioinformatics analyses do not confirm the hypothesis of a direct HGT from the endobacterium to the fungal host: indeed, endobacterial and fungal sequences show a different evolution and potentially different donors. Lastly, by amplifying a NRPS-PKS conserved fragment and mining the sequenced AMF genomes, we demonstrate that, irrespective of the presence of CaGg, G. margarita, and some other related Gigasporaceae possess such a sequence.
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Affiliation(s)
- Francesco Venice
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Institute for Sustainable Plant Protection (IPSP)-SS Turin-National Research Council (CNR), Turin, Italy
| | - Alessandro Desirò
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Gladstone Silva
- Department of Mycology, Federal University of Pernambuco, Recife, Brazil
| | - Alessandra Salvioli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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13
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Wilhelm RC, Murphy SJL, Feriancek NM, Karasz DC, DeRito CM, Newman JD, Buckley DH. Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil. Int J Syst Evol Microbiol 2020; 70:2137-2146. [PMID: 32027304 DOI: 10.1099/ijsem.0.004029] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RP11T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3-4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr-1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as Paraburkholderia aspalathi LMG 27731T, Paraburkholderia fungorum LMG 16225T and Paraburkholderia caffeinilytica CF1T. Strain RP11T is genetically distinct from P. aspalathi, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA-DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11T from its closest relatives, including growth on phthalic acid. Strain RP11T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11T was Q-8, and the major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11T represents a novel species from the genus Paraburkholderia for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11T (=DSM 110123T=LMG 31517T).
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Affiliation(s)
- Roland C Wilhelm
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Sean J L Murphy
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Nicole M Feriancek
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - David C Karasz
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher M DeRito
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY, 14853, USA
| | | | - Daniel H Buckley
- School of Integrative Plant Sciences, Bradfield Hall, Cornell University, Ithaca, NY, 14853, USA
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14
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Gan HM. Commentary: Complete Genome Sequence of 3-Chlorobenzoate-Degrading Bacterium Cupriavidus necator NH9 and Reclassification of the Strains of the Genera Cupriavidus and Ralstonia Based on Phylogenetic and Whole-Genome Sequence Analyses. Front Microbiol 2019; 10:2011. [PMID: 31555242 PMCID: PMC6724576 DOI: 10.3389/fmicb.2019.02011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/16/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia.,School of Science, Monash University Malaysia, Petaling Jaya, Malaysia
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15
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Abstract
Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipartite genomes. Almost all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that interreplicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon's pangenome indicated a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also overrepresented on the chromosomes of the environmental genera (Paraburkholderia and Cupriavidus) compared with the pathogenic genera (Burkholderia and Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in replicons enriched in genes associated with adaptation to novel environments.
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Affiliation(s)
- George C diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Elena Perrin
- Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy
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16
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Kim H, Bae MJ, Yu SM, Oh J, Lee CS, Yeon Jo B, Chae JC, Kim JH. Ephemeroptericola cinctiostellae gen. nov., sp. nov., isolated from gut of an aquatic insect. Int J Syst Evol Microbiol 2019; 69:1546-1550. [PMID: 30932804 DOI: 10.1099/ijsem.0.003296] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, catalase- and oxidase-positive, non-motile bacterium, designated F02T, was isolated from of gut of Cincticostellalevanidovae (Tshernova). Growth occurred at a temperature range of 4-30 °C, at pH 6-9 and in the presence of 0-0.5 % (w/v) NaCl. Phylogenetic analysis demonstrated that the 16S rRNA gene sequence of strain F02T shared the highest similarity to that of the type strain of Hydromonas duriensis A2P5T (96.82 %). The major isoprenoid quinone was Q-8. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and iso-C13 : 0 3-OH. The polyamines were cadaverine and putrescine. Combined data from phylogenetic, phenotypic and chemotaxonomic analyses demonstrated that strain F02T represents a novel genus and species, for which the name Ephemeroptericolacinctiostellae gen. nov., sp. nov. is proposed. The type strain of Ephemeroptericola cinctiostellae gen. nov., sp. nov. is F02T (=FBCC 500047T=KCTC 62567T=JCM 32722T).
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Affiliation(s)
- Hyangmi Kim
- 2Division of Biotechnology, Chonbuk National University, Iksan 54596, Republic of Korea.,1Bioresources Culture Collection Division, NNIBR, Sangju 37242, Republic of Korea
| | - Mi-Jung Bae
- 3Biodiversity Conservation & Change Research Division, NNIBR, Sangju 37242, Republic of Korea
| | - Sang Mi Yu
- 4Freshwater Bioresources Utilization Division, NNIBR, Sangju 37242, Republic of Korea
| | - Jeongsu Oh
- 5Bioresource Information Research Division, NNIBR, Sangju 37242, Republic of Korea
| | - Chang Soo Lee
- 1Bioresources Culture Collection Division, NNIBR, Sangju 37242, Republic of Korea
| | - Bok Yeon Jo
- 1Bioresources Culture Collection Division, NNIBR, Sangju 37242, Republic of Korea
| | - Jong-Chan Chae
- 2Division of Biotechnology, Chonbuk National University, Iksan 54596, Republic of Korea
| | - Jee-Hwan Kim
- 1Bioresources Culture Collection Division, NNIBR, Sangju 37242, Republic of Korea
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17
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Kutralam-Muniasamy G, Marsch R, Pérez-Guevara F. Investigation on the Evolutionary Relation of Diverse Polyhydroxyalkanoate Gene Clusters in Betaproteobacteria. J Mol Evol 2018; 86:470-83. [PMID: 30062554 DOI: 10.1007/s00239-018-9859-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
Products of numerous genes (phaC, phaA, phaB, phaP, phaR, and phaZ) are involved in the synthesis and degradation processes of the ubiquitous prokaryotic polyhydroxyalkanoate (PHA) intracellular reserve storage system. In this study, we performed a bioinformatics analysis to identify PHA-related genes and proteins in the genome of 66 selected organisms (class: Betaproteobacteria) that occur in various habitats; besides, evolutionary trajectories of the PHA system are reported here. The identified PHA-related genes were organized into clusters, and the gene arrangement was highly diverse. The occurrence and distribution of PHA-related clusters revealed that a single cluster was primarily segmented into small gene groups among various genomes, which were further reorganized as novel clusters based on various functional genes. The individual phylogenies of gene and protein sequences supported that the clusters were assembled through the relocation of native orthologous genes that underwent insertion, deletion, and elongation events. Furthermore, the neighboring genes provided valuable evolutionary and functional cues regarding the conservation and maintenance of PHA-related genes in the genome. Overall, the aforementioned results strongly indicate the influence of horizontal gene transfer on the organization of PHA-related gene clusters. Therefore, our results reveal new insights into the organization, evolutionary history, and cluster conservation of the PHA-related gene inventories among Betaproteobacterial organisms.
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18
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Pitt A, Schmidt J, Lang E, Whitman WB, Woyke T, Hahn MW. Polynucleobacter meluiroseus sp. nov., a bacterium isolated from a lake located in the mountains of the Mediterranean island of Corsica. Int J Syst Evol Microbiol 2018; 68:1975-1985. [PMID: 29688164 DOI: 10.1099/ijsem.0.002777] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain AP-Melu-1000-B4 was isolated from a lake located in the mountains of the Mediterranean island of Corsica (France). Phenotypic, chemotaxonomic and genomic traits were investigated. Phylogenetic analyses based on 16S rRNA gene sequencing referred the strain to the cryptic species complex PnecC within the genus Polynucleobacter. The strain encoded genes for biosynthesis of proteorhodopsin and retinal. When pelleted by centrifugation the strain showed an intense rose colouring. Major fatty acids were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and summed feature 2 (C16 : 1 isoI and C14 : 0-3OH). The sequence of the 16S rRNA gene contained an indel which was not present in any previously described Polynucleobacter species. Genome sequencing revealed a genome size of 1.89 Mbp and a G+C content of 46.6 mol%. In order to resolve the phylogenetic position of the new strain within subcluster PnecC, its phylogeny was reconstructed from sequences of 319 shared genes. To represent all currently described Polynucleobacter species by whole genome sequences, three type strains were additionally sequenced. Our phylogenetic analysis revealed that strain AP-Melu-100-B4 occupied a basal position compared with previously described PnecC strains. Pairwise determined whole genome average nucleotide identity (gANI) values suggested that strain AP-Melu-1000-B4 represents a new species, for which we propose the name Polynucleobacter meluiroseus sp. nov. with the type strain AP-Melu-1000-B4T (=DSM 103591T=CIP 111329T).
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Elke Lang
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - William B Whitman
- Department of Microbiology, 527 Biological Sciences Building, University of Georgia, Athens, GA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
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19
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Sarkar P, Roy A, Pal S, Mohapatra B, Kazy SK, Maiti MK, Sar P. Enrichment and characterization of hydrocarbon-degrading bacteria from petroleum refinery waste as potent bioaugmentation agent for in situ bioremediation. Bioresour Technol 2017; 242:15-27. [PMID: 28533069 DOI: 10.1016/j.biortech.2017.05.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/30/2017] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Intrinsic biodegradation potential of bacteria from petroleum refinery waste was investigated through isolation of cultivable strains and their characterization. Pseudomonas and Bacillus spp. populated the normal cultivable taxa while prolonged enrichment with hydrocarbons and crude oil yielded hydrocarbonoclastic bacteria of genera Burkholderia, Enterobacter, Kocuria, Pandoraea, etc. Strains isolated through enrichment showed assemblages of superior metabolic properties: utilization of aliphatic (C6-C22) and polyaromatic compounds, anaerobic growth with multiple terminal electron acceptors and higher biosurfactant production. Biodegradation of dodecane was studied thoroughly by GC-MS along with detection of gene encoding alkane hydroxylase (alkB). Microcosms bioaugmented with Enterobacter, Pandoraea and Burkholderia strains showed efficient biodegradation (98% TPH removal) well fitted in first order kinetic model with low rate constants and decreased half-life. This study proves that catabolically efficient bacteria resides naturally in complex petroleum refinery wastes and those can be useful for bioaugmentation based bioremediation.
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Affiliation(s)
- Poulomi Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713209, India
| | - Siddhartha Pal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713209, India
| | - Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713209, India
| | - Mrinal K Maiti
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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Meincke L, Copeland A, Lapidus A, Lucas S, Berry KW, Del Rio TG, Hammon N, Dalin E, Tice H, Pitluck S, Richardson P, Bruce D, Goodwin L, Han C, Tapia R, Detter JC, Schmutz J, Brettin T, Larimer F, Land M, Hauser L, Kyrpides NC, Ivanova N, Göker M, Woyke T, Wu QL, Pöckl M, Hahn MW, Klenk HP. Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)). Stand Genomic Sci 2012; 6:74-83. [PMID: 22675600 PMCID: PMC3368402 DOI: 10.4056/sigs.2395367] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006.
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Affiliation(s)
- Linda Meincke
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Nancy Hammon
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Eileen Dalin
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Bruce
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jeremy Schmutz
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Thomas Brettin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank Larimer
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loren Hauser
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | | | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Qinglong L. Wu
- Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria
| | - Matthias Pöckl
- Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria
| | - Martin W. Hahn
- Austrian Academy of Sciences, Institute for Limnology, Mondsee, Austria
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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