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Zheng B, Xu Z, Yang L, Jiang G, Chen J, Yang Y, Tian Y. Leucobacter edaphi sp. nov., a highly chromate-tolerant bacterium isolated from chromium containing chemical plant soil. Antonie Van Leeuwenhoek 2023; 116:1433-1445. [PMID: 37874522 DOI: 10.1007/s10482-023-01895-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
A Gram-positive, aerobic, rod-shaped non-motile, non-sporulating bacterium, designated CSA2T, was isolated from chromium-containing soils collected from a chemical plant. The 16S rRNA gene sequence of strain CSA2T showed the highest homology with Leucobacter chromiireducens subsp. solipictus (97.85%), Leucobacter chromiireducens subsp. chromiireducens (97.85%). The digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and the amino acid identity (AAI) values among strains CSA2T and the selected Leucobacter species were 20.6-23.4% (dDDH), 72.67-78.03% (ANI) and 66.39-76.16% (AAI), falling below the recommended thresholds for species delimitation. The principal fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The major menaquinones detected were MK-10 and MK-11. The cell-wall amino acids included 2,4-diaminobutyric acid, threonine, glutamic acid, alanine and glycine. Based on molecular feature, phenotypic and chemotaxonomic, strain CSA2T was considered to be a novel species of the genus Leucobacter., and the name Leucobacter edaphi sp. nov. is proposed. The type strain is CSA2T (= JCM 34360T = CGMCC 1.18747T).
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Affiliation(s)
- Bijun Zheng
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China
| | - Zhe Xu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China
| | - Li Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China
| | - Guangyang Jiang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China
| | - Jia Chen
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China
| | - Yichen Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China
| | - Yongqiang Tian
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, People's Republic of China.
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu, 610065, People's Republic of China.
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2
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Ying Y, Yuan B, Liu T, Bai X, Zhao H. Leucobacter tenebrionis sp. nov., isolated from the gut of Tenebrio molitor. Int J Syst Evol Microbiol 2023; 73. [PMID: 37823785 DOI: 10.1099/ijsem.0.006081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Abstract
A novel Gram-stain-positive bacterium, designated NB10T, was isolated from the gut of Tenebrio molitor. The isolate was rod-shaped, aerobic, non-motile and non-spore-forming. Colonies of strain NB10T were light yellow, circular and smooth. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that the isolate was related to the genus Leucobacter. Its closest relatives were Leucobacter holotrichiae T14T (97.8 % 16S rRNA gene sequence similarity), Leucobacter zeae CC-MF41T (97.0%) and Leucobacter salsicius M1-8T (96.4%). The DNA G+C content of strain NB10T was 68.8 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization values among strain NB10T and the selected Leucobacter species were ≤83.8 % (ANI-blast), 87.6 % (ANI-MUMmer) and 29.6%, which were below the recommended cutoff values for species delineation. The predominant cellular fatty acids were anteiso-C15 : 0 (39.0%), anteiso-C17 : 0 (35.5%) and iso-C16 : 0 (17.0%). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and glycolipids. The predominant respiratory quinones were MK-11 and MK-10. The cell wall amino acids were Gly, Glu, Tr, Ala, and DAB. Based on these phylogenetic and phenotypic results, strain NB10T can be clearly distinguished from all of the recognized species of the genus Leucobacter and is considered to represent a novel species of that genus. The name Leucobacter tenebrionis sp. nov. is proposed, with the type strain NB10T (=MCCC 1K07072T=KCTC 49728T).
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Affiliation(s)
- Yu Ying
- Qingdao Institute for Food and Drug Control 266071, Qingdao, PR China
| | - Bo Yuan
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, 010022, Inner Mongolia, PR China
| | - Tingting Liu
- Qingdao Institute for Food and Drug Control 266071, Qingdao, PR China
| | - Xiaoshuan Bai
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, 010022, Inner Mongolia, PR China
| | - Haifeng Zhao
- Qingdao Institute for Food and Drug Control 266071, Qingdao, PR China
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Zhu J, Che J, Jiang X, Ma M, Guan D, Li L, Cao F, Zhao B, Kang Y, Zhao J, Kong D, Zhou Y, Ruan Z, Li J. Leucobacter chinensis sp. nov., with plant growth-promoting potential isolated from field soil after seven-years continuous maize cropping. Int J Syst Evol Microbiol 2022; 72. [PMID: 35939329 DOI: 10.1099/ijsem.0.005417] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A novel Gram-stain-positive, aerobic, non-motile and rod-shaped bacterium, designated strain NC76-1T, was isolated from soil from a field that had undergone seven years continuous maize cropping from Liuba town located in Zhangye city, Gansu province, PR China. Colonies of strain NC76-1T were white, opaque and circular with a convex shape. The isolate was found to be able to grow at 10-40 °C (optimum 30 °C), pH 6.0 to 12.0 (optimum 7.0-8.0) and with 0-5.0 % (w/v) NaCl (optimum 0%). On the basis of the results of 16S rRNA gene sequence analysis, the strain fell within the clade of the genus Leucobacter, showing the highest sequence similarities with Leucobacter iarius 40T (97.4%), Leucobacter aridicollis CIP 108388T (97.0%), Leucobacter chromiireducens subsp. solipictus TAN 31504T (96.7%) and Leucobacter denitrificans M1T8B10T (96.7%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between NC76-1T and its closest relatives, L. iarius 40T, L. aridicollis CIP 108388T, L. chromiireducens subsp. solipictus TAN 31504T and L. denitrificans M1T8B10T were ≤73.5 % and 20.3%, respectively. The genomic DNA G+C content of NC76-1T was 61.5 mol%. It presented MK-11 as the predominant menaquinone. The major cellular fatty acids were anteiso-C15 : 0 (49.2 %) and iso-C16 : 0 (35.7%). The major polar lipids were found to be diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminoglycolipid, five glycolipid and one unidentified lipids. The cell wall amino acids were 2,4-diaminobutyric acid, alanine, glutamic acid, glycine and threonine. On the basis of the phylogenetic, phenotypic and chemotaxonomic characteristics, strain NC76-1T is concluded to represent a novel species within the genus Leucobacter, for which the name Leucobacter chinensis sp. nov. is proposed. The type strain is NC76-1T (GDMCC 1.2286T= JCM 34651T).
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Affiliation(s)
- Jie Zhu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Juan Che
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,College of Life Science, Xinjiang Normal University, Urumqi, 830046, PR China
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Li Li
- Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Baisuo Zhao
- Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
| | - Yaowei Kang
- Life Sciences Collage of Zhaoqing University, Zhaoqing 526061, PR China
| | - Ji Zhao
- School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Delong Kong
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yiqing Zhou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Zhiyong Ruan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Laboratory of Quality and Safety Risk Assessment for Microbial Products (Beijing), Ministry of Agriculture, Beijing 100081, PR China
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Liu J, Song M, Wei X, Zhang H, Bai Z, Zhuang X. Responses of Phyllosphere Microbiome to Ozone Stress: Abundance, Community Compositions and Functions. Microorganisms 2022; 10:microorganisms10040680. [PMID: 35456732 PMCID: PMC9024792 DOI: 10.3390/microorganisms10040680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Ozone is a typical hazardous pollutant in Earth’s lower atmosphere, but the phyllosphere and its microbiome are promising for air pollution remediation. Despite research to explore the efficiency and mechanism of ozone phylloremediation, the response and role of the phyllosphere microbiome remains untouched. In this study, we exposed Euonymus japonicus to different ozone levels and revealed microbial successions and roles of the phyllosphere microbiome during the exposure. The low-level exposure (156 ± 20 ppb) induced limited response compared to other environmental factors. Fungi failed to sustain the community richness and diversity, despite the stable ITS concentration, while bacteria witnessed an abundance loss. We subsequently elevated the exposure level to 5000~10,000 ppb, which considerably deteriorated the bacterial and fungal diversity. Our results identified extremely tolerant species, including bacterial genera (Curtobacterium, Marmoricola, and Microbacterium) and fungal genera (Cladosporium and Alternaria). Compositional differences suggested that most core fungal taxa were related to plant diseases and biocontrol, and ozone exposure might intensify such antagonism, thus possibly influencing plant health and ozone remediation. This assumption was further evidenced in the functional predictions via a pathogen predominance. This study shed light on microbial responses to ozone exposure in the phyllosphere and enlightened the augmentation of ozone phylloremediation through the microbial role.
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Affiliation(s)
- Jiayu Liu
- Beijing Key Laboratory of Water Resources and Environment Engineering, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China; (J.L.); (H.Z.)
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
| | - Manjiao Song
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyuan Wei
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
| | - Huanzhen Zhang
- Beijing Key Laboratory of Water Resources and Environment Engineering, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China; (J.L.); (H.Z.)
| | - Zhihui Bai
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Xiongan Institute of Innovation, Xiongan New Area 071000, China
- Correspondence: (Z.B.); (X.Z.); Tel.: +86-10-6284-9156 (Z.B.); +86-10-6284-9193 (X.Z.)
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; (M.S.); (X.W.)
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Z.B.); (X.Z.); Tel.: +86-10-6284-9156 (Z.B.); +86-10-6284-9193 (X.Z.)
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Kämpfer P, McInroy JA, Clermont D, Neumann-Schaal M, Criscuolo A, Busse HJ, Glaeser SP. Leucobacter soli sp. nov., from soil amended with humic acid. Int J Syst Evol Microbiol 2021; 71. [PMID: 34904944 DOI: 10.1099/ijsem.0.005156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A Gram-positive, non-spore-forming actinobacterium (IMT-300T) was isolated from soil amended with humic acid in Malvern, AL, USA. This soil has been used for 50+years for the cultivation of earthworms for use as fish bait. Based on 16S rRNA gene sequence similarity studies, strain IMT-300T was shown to belong to the genus Leucobacter and was closely related to the type strain of 'Leucobacter margaritiformis' L1T (97.8%). Similarity to all other type strains of Leucobacter species was lower than 97.2 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the IMT-300T genome assembly and those of the closest relative Leucobacter type strain were 81.4 and 23.3 % (Leucobacter chironomi), respectively. The peptidoglycan of strain IMT-300T contained l-2,4-diaminobutyric acid as the diagnostic diamino acid. In addition, glycine, d- and l-alanine and d-glutamic acid were found. The peptidoglycan type represents a variant of B2δ (B11). The major quinones were menaquinones MK-10 and MK-11. The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and moderate to minor amounts of two unidentified phospholipids, two unidentified glycolipids and an unidentified aminophospholipid. The polyamine pattern contained major amounts of spermidine and spermine. Strain IMT-300T contained the major fatty acids C15 : 0 anteiso, C16 : 0 iso and C17 : 0 anteiso, like other members of the genus Leucobacter. The results of ANI and dDDH analyses and physiological and biochemical tests allowed a genotypic and phenotypic differentiation of strain IMT-300T from the most closely related Leucobacter species. Strain IMT-300T represents a novel Leucobacter species, for which we propose the name Leucobacter soli sp. nov., with the type strain IMT-300T (CIP 111803T=DSM 110505T=CCM 9020T=LMG 31600T).
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Affiliation(s)
- Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - John A McInroy
- Department of Entomology and Plant Pathology, Auburn University, AL 36849, USA
| | - Dominique Clermont
- Institut Pasteur, Université de Paris, CIP-Collection de l´Institut Pasteur, F-75015 Paris, France
| | - Meina Neumann-Schaal
- Deutsche Sammlung von Mikroorganismen und Zellkulturen, D-38124 Braunschweig, Germany
| | - Alexis Criscuolo
- Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, 75015 Paris, France
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, A-1210 Wien, Austria
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Xu Z, Li X, Tian J, Gan L, Tian Y. Leucobacter chromiisoli sp. nov., isolated from chromium-containing chemical plant soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 34319867 DOI: 10.1099/ijsem.0.004923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, aerobic, non-motile, non-sporulating bacterial strain, designated CSA1T, was isolated from chromium-containing soil sampled at a chemical plant. Growth of strain CSA1T occurred at pH 6-10 (optimum, pH 7), 15-45 °C (optimum, 30 °C) and in the presence of 0.5-6.5 % (w/v) NaCl (optimum, 2 %). The 16S rRNA gene sequence of strain CSA1T revealed the highest similarity to Leucobacter ruminantium A2T (97.5 %), Leucobacter tardus K 70/01T (97.3 %), Leucobacter humi Re6T (96.6 %), Leucobacter kyeonggiensis F3-P9T (96.2 %), Leucobacter zeae CC-MF41T (96.1 %) and Leucobacter weissii S27T (96.0 %). The draft genome of CSA1T was approximately 3 350 931 bp in size with a G+C content of 70.6 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among strain CSA1T and the selected Leucobacter species were 74.0-79.2 % (ANIb), 84.3-87.1 % (ANIm) and 21.5-25.4 % (dDDH), which are below the recommended cutoff values for species delineation. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The predominant menaquinones were MK-11, MK-8 and MK-6. The cell-wall amino acids were 2,4-diaminobutyric acid, alanine, glycine, glutamic acid and threonine. From the phenotypic, chemotaxonomic and molecular features, strain CSA1T was considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiisoli sp. nov. is proposed. The type strain is CSA1T (=JCM 34359T=CGMCC 1.18746T).
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Affiliation(s)
- Zhe Xu
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Xiaoguang Li
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Jiewei Tian
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Longzhan Gan
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
| | - Yongqiang Tian
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, PR China
- Key Laboratory of Leather Chemistry and Engineering (Sichuan University), Ministry of Education, Chengdu 610065, PR China
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Teheran-Sierra LG, Funnicelli MIG, de Carvalho LAL, Ferro MIT, Soares MA, Pinheiro DG. Bacterial communities associated with sugarcane under different agricultural management exhibit a diversity of plant growth-promoting traits and evidence of synergistic effect. Microbiol Res 2021; 247:126729. [PMID: 33667983 DOI: 10.1016/j.micres.2021.126729] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 02/08/2021] [Accepted: 02/13/2021] [Indexed: 01/04/2023]
Abstract
Plant-associated microbiomes have been a target of interest for the prospection of microorganisms, which may be acting as effectors to increase agricultural productivity. For years, the search for beneficial microorganisms has been carried out from the characterization of functional traits of growth-promotion using tests with a few isolates. However, eventually, the expectations with positive results may not be realized when the evaluation is performed in association with plants. In our study, we accessed the cultivable sugarcane microbiome under two conditions of agronomic management: organic and conventional. From the use of a new customized culture medium, we recovered 944 endophytic and epiphytic bacterial communities derived from plant roots, stalks, leaves, and rhizospheric soil. This could be accomplished by using a large-scale approach, initially performing an in planta (Cynodon dactylon) screening process of inoculation to avoid early incompatibility. The inoculation was performed using the bacterial communities, considering that in this way, they could act synergistically. This process resulted in 38 candidate communities, 17 of which had higher Indole-3-acetic acid (IAA) production and phosphate solubilization activity and, were submitted to a new in planta test using Brachiaria ruziziensis and quantification of functional traits for growth-promotion and physiological tests. Enrichment analysis of selected communities has shown that they derived mainly from epiphytic populations of sugarcane stalks under conventional management. The sequencing of the V3-V4 region of the 16S rRNA gene revealed 34 genera and 24 species distributed among the phylum Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. We also observed a network of genera in these communities where the genus Chryseobacterium stands out with a greater degree of interaction, indicating a possible direct or indirect role as a keystone taxon in communities with plant-growth promotion capacities. From the results achieved, we can conclude that the approach is useful in the recovery of a set of sugarcane bacterial communities and that there is, evidence of synergistic action providing benefits to plants, and that they are compatible with plants of the same family (Poaceae). Thus, we are reporting the beneficial bacterial communities identified as suitable candidates with rated potential to be exploited as bioinoculants for crops.
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Affiliation(s)
- Luis Guillermo Teheran-Sierra
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884- 900, SP, Brazil; Programa de Pós-Graduação em Microbiologia Agropecuária, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884-900, SP, Brazil
| | - Michelli Inácio Gonçalves Funnicelli
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884- 900, SP, Brazil; Programa de Pós-Graduação em Microbiologia Agropecuária, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884-900, SP, Brazil
| | - Lucas Amoroso Lopes de Carvalho
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884- 900, SP, Brazil; Programa de Pós-Graduação em Microbiologia Agropecuária, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884-900, SP, Brazil
| | - Maria Inês Tiraboschi Ferro
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884- 900, SP, Brazil
| | - Marcos Antônio Soares
- Universidade Federal de Mato Grosso, Instituto de Biociências, Av. Fernando Corrêa, Nº 2367, Cuiabá, MT, Brazil
| | - Daniel Guariz Pinheiro
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Câmpus Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, 14884- 900, SP, Brazil.
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8
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Miller C, Bates ST, Gielda LM, Creighton JC. The role of parental care in the establishment of the offspring digestive tract microbiome in Nicrophorus defodiens. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2020.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Benga L, Spröer C, Schumann P, Verbarg S, Bunk B, Engelhardt E, Benten WPM, Sager M. Leucobacter muris sp. nov., isolated from the nose of a laboratory mouse. Int J Syst Evol Microbiol 2019; 69:2095-2100. [PMID: 31099739 DOI: 10.1099/ijsem.0.003446] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, rod-shaped, aerobic, non-motile, white, opaque bacterial isolate, designated 924/12T, was isolated from the nose of a laboratory mouse in Düsseldorf, Germany. The 16S rRNA gene sequence analyses indicated the phylogenetic position of the strain within the genus Leucobacter. Similarity levels over 97 % were recorded between the 16S rRNA gene sequence of strain 924/12T and the type strains of the species Leucobacter chironomi DSM 19883T (99.5 %), followed by Leucobacter celersubsp. astrifaciens CBX151T (97.6 %), Leucobacter celersubsp. celer NAL101T (97.5 %), 'Leucobacter kyeonggiensis' F3-P9 (97.5 %), Leucobacter zeae CC-MF41T (97.3 %), Leucobacter chromiiresistens JG31T (97.1 %), Leucobacter triazinivorans JW-1T (97.1 %), Leucobacter corticis 2 C-7T (97.0 %) and Leucobacter aridicolis CIP108388T (97.0 %). DNA-DNA hybridization and whole genomic comparison, mandatory to taxonomically separate strain 924/12T from the type strain of L. chironomi, revealed similarity values of 40.4 and 30.8 %, respectively, thus below the threshold of 70 % recommended differentiating between species. The cell-wall amino acids of the novel isolate were diaminobutyric acid, alanine, glycine, threonine and glutamic acid. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unknown lipid, whereas the predominant menaquinones were MK-11 and MK-10. The genomic DNA G+C content of strain 924/12T was 70.6 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences and the phenotypical differences between strain 924/12T and the other closely related type strains of the genus Leucobacter indicated that strain 924/12T represents a novel species within the genus Leucobacter, family Microbacteriaceae, for which the name Leucobacter muris sp. nov. is proposed. The type strain is 924/12T (=DSM 101948T=CCM 8761T).
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Affiliation(s)
- Laurentiu Benga
- 1Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich - Heine - University, Geb. 22.22, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Cathrin Spröer
- 2Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Peter Schumann
- 2Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Susanne Verbarg
- 2Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Boyke Bunk
- 2Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Eva Engelhardt
- 1Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich - Heine - University, Geb. 22.22, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - W Peter M Benten
- 1Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich - Heine - University, Geb. 22.22, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Martin Sager
- 1Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich - Heine - University, Geb. 22.22, Universitätsstr. 1, 40225 Düsseldorf, Germany
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A novel pigmented and heavy metal biosorptive bacterium, Leucobacter epilobiisoli sp. nov., isolated from rhizosphere soil of Epilobium hirsutum L. Antonie van Leeuwenhoek 2018; 111:1825-1833. [DOI: 10.1007/s10482-018-1071-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/20/2018] [Indexed: 10/17/2022]
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11
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Sun LN, Pan DD, Wu XW, Yang ED, Hua RM, Li QX. Leucobacter triazinivorans sp. nov., a s-triazine herbicide prometryn-degrading bacterium isolated from sludge. Int J Syst Evol Microbiol 2018; 68:204-210. [PMID: 29139349 DOI: 10.1099/ijsem.0.002483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Le-Ni Sun
- School of Life Science, Anhui Agricultural University, Hefei 230036, PR China
| | - Dan-Dan Pan
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, PR China
| | - Xiang-Wei Wu
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, PR China
| | - En-Dong Yang
- School of Life Science, Anhui Agricultural University, Hefei 230036, PR China
| | - Ri-Mao Hua
- School of Resources and Environment, Anhui Agricultural University, Hefei 230036, PR China
| | - Qing X. Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East–West Road, Honolulu, HI 957822, USA
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Schumann P, Pukall R. Leucobacter weissii sp. nov., an isolate from activated sludge once described as first representative of the peptidoglycan variation B2δ, and emended description of the genus Leucobacter. Int J Syst Evol Microbiol 2017; 67:5244-5251. [PMID: 29087268 DOI: 10.1099/ijsem.0.002454] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain S27T is a Gram-stain-positive, regular rod-shaped, non-motile, non-spore-forming, yellow pigmented actinobacterium which was isolated from an aerated laboratory scale fermenter fed with wastes of a yeast factory. The strain was classified as Microbacterium sp. after the analysis of its peptidoglycan revealed a novel B-type structure established as variation B2δ by Hensel in 1984. As the combination of the peptidoglycan amino acids 2,4-diaminobutyric acid (Dab), threonine (Thr), glycine (Gly), alanine (Ala) and glutamic acid (Glu) is in disagreement with the current genus definition of Microbacterium but is typical of several Leucobacter species, the taxonomic status of strain S27T was re-examined by a polyphasic study. Comparative analyses of 16S rRNA gene sequences and the occurrence of l-Dab, d-Ala, l-Ala, Gly, l-Thr, d-Glu and lower amounts of l-Glu in the peptidoglycan in combination with the predominating menaquinones MK-11, MK-10 and MK-9, phosphatidylglycerol, and one unknown glycolipid as the major polar lipids (and trace amounts of diphosphatidylglycerol and an unknown phospholipid), a profile with anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and iso-C17 : 0 as major fatty acids and the G+C value of 70.1 mol% confirmed the affiliation to the genus Leucobacter and revealed that S27T (=DSM 20621T =CCM 8762T) is the type strain of a new species for which the name Leucobacter weissii sp. nov. is proposed. The availability of new data allows for an emended description of the genus Leucobacter.
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Affiliation(s)
- Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rüdiger Pukall
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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Chun BH, Lee HJ, Jeong SE, Schumann P, Jeon CO. Leucobacter ruminantium sp. nov., isolated from the bovine rumen. Int J Syst Evol Microbiol 2017; 67:2634-2639. [DOI: 10.1099/ijsem.0.002003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyo Jung Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
- Department of Biology, Kunsan National University, Gunsan 54150, Republic of Korea
| | - Sang Eun Jeong
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, D-38124 Braunschweig, Germany
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Lai WA, Lin SY, Hameed A, Hsu YH, Liu YC, Huang HR, Shen FT, Young CC. Leucobacter zeae sp. nov., isolated from the rhizosphere of maize (Zea mays L.). Int J Syst Evol Microbiol 2015; 65:4734-4742. [DOI: 10.1099/ijsem.0.000640] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel yellow-pigmented, aerobic, rod-shaped, non-motile bacterium, designated strain CC-MF41T, was isolated from rhizosphere soil of maize (Zea mays) collected in Wufeng District, Taichung, Taiwan. Strain CC-MF41T exhibited 16S rRNA gene sequence similarity of 97.5, 97.3, 97.2 and 97.1 % to Leucobacter chironomi MM2LBT (and ‘Leucobacter kyeonggiensis’ F3-P9 and ‘L. humi’ Re-6, the names of which have not been validly published), Leucobacter tardus K70/01T, L. komagatae IFO 15245T and ‘Leucobacter margaritiformis’ A23. However, CC-MF41T and ‘L. margaritiformis’ A23 formed a loosely bound phylogenetic lineage (with a low bootstrap value) associated with species of the genus Leucobacter. In DNA–DNA reassociation experiments, the relatedness of strain CC-MF41T to L. chironomi DSM 19883T was 57.1 % (reciprocal value 29.1 %). The DNA G+C content of strain CC-MF41T was 72.1 mol% and the cell-wall peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine, glutamic acid and threonine. The major menaquinone was MK-11 and the predominant fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipid profile of strain CC-MF41T contained major amounts of diphosphatidylglycerol followed by an unidentified glycolipid, phosphatidylglycerol and an unknown phospholipid. Based on its phylogenetic, phenotypic and chemotaxonomic distinctiveness, strain CC-MF41T represents a novel species of Leucobacter, for which the name Leucobacter zeae sp. nov. is proposed. The type strain is CC-MF41T ( = BCRC 80515T = LMG 27265T).
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Affiliation(s)
- Wei-An Lai
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan ROC
| | - Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Hsuan-Ru Huang
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Fo-Ting Shen
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan ROC
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan ROC
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Clark LC, Hodgkin J. Leucobacter musarum subsp. musarum sp. nov., subsp. nov., Leucobacter musarum subsp. japonicus subsp. nov., and Leucobacter celer subsp. astrifaciens subsp. nov., three nematopathogenic bacteria isolated from Caenorhabditis, with an emended description of Leucobacter celer. Int J Syst Evol Microbiol 2015; 65:3977-3984. [PMID: 26275616 PMCID: PMC4804768 DOI: 10.1099/ijsem.0.000523] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-positive, irregular-rod-shaped, non-motile, non-spore-forming bacteria were isolated from nematodes collected from Santa Antao, Cabo Verde (CBX151T, CBX152T) and Kakegawa, Japan (CBX130T). Based on 16S rRNA gene sequence similarity, strains CBX130T, CBX151T and CBX152T were shown to belong to the genus Leucobacter. This affiliation was supported by chemotaxonomic data (2,4-diaminobutyric acid in the cell wall; major respiratory quinones MK-10 and MK-11; major polar lipids phosphatidylglycerol and diphosphatidylglycerol; major fatty acids anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0). Strains CBX130T and CBX152T were found to share salient characteristics. Based on morphological, physiological, chemotaxonomic and biochemical analysis, strain CBX152T represents a novel species of the genus Leucobacter, for which the name Leucobacter musarum sp. nov. (type strain CBX152T = DSM 27160T = CIP 110721T) is proposed. Two subspecies of Leucobacter musarum sp. nov. are proposed: Leucobacter musarum sp. nov. subsp. musarum subsp. nov. (type strain CBX152T = DSM 27160T = CIP 110721T) and Leucobacter musarum sp. nov. subsp. japonicus subsp. nov. (type strain CBX130T = DSM 27158T = CIP 110719T). The third novel strain, CBX151T, showed genetic similarities with Leucobacter celer NAL101T indicating that these strains belong to the same species. Based on morphological, physiological, chemotaxonomic and biochemical differences it is proposed to split the species Leucobacter celer into two novel subspecies, Leucobacter celer subsp. celer subsp. nov. (type strain NAL101T = KACC 14220T = JCM 16465T) and Leucobacter celer subsp. astrifaciens subsp. nov. (type strain CBX151T = DSM 27159T = CIP 110720T), and to emend the description of Leucobacter celerShin et al. 2011.
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Affiliation(s)
- Laura C Clark
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jonathan Hodgkin
- Biochemistry Department, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Laviad S, Lapidus A, Copeland A, Reddy T, Huntemann M, Pati A, Ivanova NN, Markowitz VM, Pukall R, Klenk HP, Woyke T, Kyrpides NC, Halpern M. High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass. Stand Genomic Sci 2015. [PMID: 26203333 PMCID: PMC4511665 DOI: 10.1186/s40793-015-0003-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Leucobacter chironomi strain MM2LBT (Halpern et al., Int J
Syst Evol Microbiol 59:665-70 2009) is a Gram-positive, rod shaped, non-motile,
aerobic, chemoorganotroph bacterium. L. chironomi belongs to the family
Microbacteriaceae, a family within the class Actinobacteria.
Strain MM2LBT was isolated from a chironomid (Diptera;
Chironomidae) egg mass that was sampled from a waste stabilization pond in
northern Israel. In a phylogenetic tree based on 16S rRNA gene sequences, strain
MM2LBT formed a distinct branch within the radiation encompassing the
genus Leucobacter. Here we describe the features of this organism, together
with the complete genome sequence and annotation. The DNA GC content is 69.90%. The
chromosome length is 2,964,712 bp. It encodes 2,690 proteins and 61 RNA genes. L.
chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase
I: the one thousand microbial genomes (KMG) project.
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Affiliation(s)
- Sivan Laviad
- Dept. of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab. St. Petersburg Academic University, St. Petersburg, Russia
| | - Alex Copeland
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Tbk Reddy
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Marcel Huntemann
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Amrita Pati
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Natalia N Ivanova
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Victor M Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rüdiger Pukall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA
| | - Nikos C Kyrpides
- Dept. of Energy Joint Genome Institute, Genome Biology Program, Walnut Creek, CA, USA ; Dept. of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Malka Halpern
- Dept. of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa, Israel ; Dept. of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Kiryat Tivon, Israel
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Genome Sequence of Leucobacter sp. 4J7B1, a Plant-Osmoprotectant Soil Microorganism. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00398-15. [PMID: 25999566 PMCID: PMC4440946 DOI: 10.1128/genomea.00398-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We report the first genome sequence for Leucobacter sp. 4J7B1, a newly described desiccation-tolerant strain. The complete genome sequence of Leucobacter sp. 4J7B1 has been sequenced and is estimated to be around 3.5 Mb in size, with an average GC content of 62.18%. We predict 2,953 protein-coding sequences.
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Yun JH, Cho YJ, Chun J, Hyun DW, Bae JW. Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.). Stand Genomic Sci 2014; 9:495-504. [PMID: 25197435 PMCID: PMC4148977 DOI: 10.4056/sigs.4708537] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leucobacter salsicius M1-8(T) is a member of the Microbacteriaceae family within the class Actinomycetales. This strain is a Gram-positive, rod-shaped bacterium and was previously isolated from a Korean fermented food. Most members of the genus Leucobacter are chromate-resistant and this feature could be exploited in biotechnological applications. However, the genus Leucobacter is poorly characterized at the genome level, despite its potential importance. Thus, the present study determined the features of Leucobacter salsicius M1-8(T), as well as its genome sequence and annotation. The genome comprised 3,185,418 bp with a G+C content of 64.5%, which included 2,865 protein-coding genes and 68 RNA genes. This strain possessed two predicted genes associated with chromate resistance, which might facilitate its growth in heavy metal-rich environments.
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Affiliation(s)
- Ji-Hyun Yun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, South Korea
| | - Yong-Joon Cho
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Jongsik Chun
- ChunLab Inc., Seoul National University, Seoul, South Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, South Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, South Korea
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Weon HY, Anandham R, Tamura T, Hamada M, Kim SJ, Kim YS, Suzuki KI, Kwon SW. Leucobacter denitrificans sp. nov., isolated from cow dung. J Microbiol 2012; 50:161-5. [DOI: 10.1007/s12275-012-1324-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/29/2011] [Indexed: 11/28/2022]
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Leucobacter margaritiformis sp. nov., Isolated from Bamboo Extract. Curr Microbiol 2012; 64:441-8. [DOI: 10.1007/s00284-012-0089-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 01/13/2012] [Indexed: 10/28/2022]
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Kim HJ, Lee SS. Leucobacter kyeonggiensis sp. nov., a new species isolated from dye waste water. J Microbiol 2011; 49:1044-9. [DOI: 10.1007/s12275-011-1548-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 12/08/2011] [Indexed: 11/29/2022]
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Sturm G, Jacobs J, Spröer C, Schumann P, Gescher J. Leucobacter chromiiresistens sp. nov., a chromate-resistant strain. Int J Syst Evol Microbiol 2011; 61:956-960. [DOI: 10.1099/ijs.0.022780-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, irregular rod-shaped, non-motile, yellow-pigmented bacterium, strain JG 31T, was isolated in the course of identifying chromium-resistant soil bacteria. 16S rRNA gene sequence analysis of the isolated bacterium indicated its phylogenetic position within the genus Leucobacter. Binary 16S rRNA gene sequence alignments of the isolated bacterium with the 11 species of the genus recognized at the time of writing revealed sequence similarities of more than 97 % with Leucobacter alluvii (GenBank accession no: AM072820; 99.4 %), Leucobacter iarius (AM040493; 98.2 %), Leucobacter aridicollis (AJ781047; 97.8 %), Leucobacter komagatae (AB007419; 97.4 %), Leucobacter chironomi (EU346911; 97.1 %) and Leucobacter luti (AM072819; 97.1 %). In contrast, DNA–DNA hybridization experiments showed similarity values below 28 % for DNA samples from the most closely related type strains of L. alluvii, L. aridicollis and L. iarius. Protein analysis by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and automated RiboPrinting using the restriction enzyme PvuII differentiated strain JG 31T from all type strains of the genus Leucobacter. The dominant fatty acids of the novel isolate were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, while the quinone system consisted of menaquinones MK-11, MK-10, MK-9 and MK-8. In a B-type cross-linked peptidoglycan, the cell-wall amino acids were alanine, glycine, threonine, glutamic acid and 2,4-diaminobutyric acid. Strain JG 31T was able to grow in a medium containing up to 300 mM K2CrO4 and showed cellular aggregation in response to chromate stress. From biochemical and genomic analyses, the new strain is considered to represent a novel species of the genus Leucobacter, for which the name Leucobacter chromiiresistens sp. nov. is proposed. The type strain is strain JG 31T ( = DSM 22788T = CCOS 200T).
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Affiliation(s)
- Gunnar Sturm
- Institut für Biologie II, Mikrobiologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Johanna Jacobs
- Institut für Biologie II, Mikrobiologie, Universität Freiburg, 79104 Freiburg, Germany
| | - Cathrin Spröer
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Peter Schumann
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Johannes Gescher
- Institut für Biologie II, Mikrobiologie, Universität Freiburg, 79104 Freiburg, Germany
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Abstract
Strain M1-8T was isolated from jeotgal, a Korean salt-fermented food. Cells were aerobic, non-motile, Gram-reaction-positive and rod-shaped. Colonies were cream-coloured and circular with entire margins. Strain M1-8T exhibited optimal growth at 25–30 °C and pH 7.0–8.0 and in 0–4 % (w/v) NaCl. The strain tolerated up to 10.0 mM Cr(VI). Phylogenetic analyses of 16S rRNA gene sequences indicated that strain M1-8T represents a novel species in the genus Leucobacter. The 16S rRNA gene sequence of M1-8T exhibited 98.1 % similarity to that of Leucobacter chromiireducens subsp. chromiireducens L-1T. The new isolate was clustered with Leucobacter species on a 16S rRNA gene sequence-based phylogenetic tree. The chromosomal DNA G+C content of strain M1-8T was 62.8 mol%. Its cell-wall peptidoglycan contained 2,4-diaminobutyric acid, glutamic acid, alanine, glycine and γ-aminobutyric acid. The major menaquinone was MK-11 and the predominant fatty acids were anteiso-C15 : 0 (63.6 %), anteiso-C17 : 0 (16.7 %) and iso-C16 : 0 (14.2 %). The polar lipid profile of strain M1-8T contained diphosphatidylglycerol and one unknown glycolipid. Significant genotypic and phenotypic differences were found between strain M1-8T and other Leucobacter species. These differentiating characteristics indicate that strain M1-8T represents a novel species of the genus Leucobacter, for which the name Leucobacter salsicius sp. nov. is proposed. The type strain is M1-8T (=KACC 21127T =JCM 16362T).
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Ue H. Leucobacter exalbidus sp. nov., an actinobacterium isolated from a mixed culture from compost. J GEN APPL MICROBIOL 2011; 57:27-33. [DOI: 10.2323/jgam.57.27] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Martin E, Lodders N, Jäckel U, Schumann P, Kämpfer P. Leucobacter aerolatus sp. nov., from the air of a duck barn. Int J Syst Evol Microbiol 2010; 60:2838-2842. [DOI: 10.1099/ijs.0.021303-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, non-spore-forming actinobacterium (Sj 10T) was isolated on tryptone soy agar from the air of a duck barn after filter sampling. Based on 16S rRNA gene sequence similarity studies, strain Sj 10T was shown to belong to the genus Leucobacter and was closely related to Leucobacter chromiireducens subsp. chromiireducens L-1T (97.8 %), Leucobacter tardus DSM 19811T (97.3 %) and Leucobacter luti RF6T (97.3 %). The peptidoglycan of strain Sj 10T contained 2,4-diaminobutyric acid in combination with a lower amount of lysine as diagnostic diamino acids. In addition, threonine, glycine, alanine and glutamic acid were found. Menaquinone MK-11 was the major respiratory quinone; MK-12 and MK-10 were detected in minor amounts. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol and one unknown component each of a phospholipid, glycolipid and aminoglycolipid. Strain Sj 10T contained the major fatty acids anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, like other members of the genus Leucobacter. Results of DNA–DNA hybridization, physiological and biochemical tests enabled strain Sj 10T to be differentiated genotypically and phenotypically from the most closely related Leucobacter species. Strain Sj 10T represents a novel species of the genus Leucobacter, for which the name Leucobacter aerolatus sp. nov. is proposed, with Sj 10T (=DSM 22806T =CCM 7705T) as the type strain.
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Affiliation(s)
- E. Martin
- Bundesanstalt für Arbeitschutz und Arbeitsmedizin, D-10317 Berlin, Germany
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - N. Lodders
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - U. Jäckel
- Bundesanstalt für Arbeitschutz und Arbeitsmedizin, D-10317 Berlin, Germany
| | - P. Schumann
- Deutsche Sammlung von Mikroorganismen und Zellkulturen, D-38124 Braunschweig, Germany
| | - P. Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Halpern M, Shaked T, Pukall R, Schumann P. Leucobacter chironomi sp. nov., a chromate-resistant bacterium isolated from a chironomid egg mass. Int J Syst Evol Microbiol 2009; 59:665-70. [DOI: 10.1099/ijs.0.004663-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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