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Farkas D, Proctor K, Kim B, Avignone Rossa C, Kasprzyk-Hordern B, Di Lorenzo M. Assessing the impact of soil microbial fuel cells on atrazine removal in soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135473. [PMID: 39151358 DOI: 10.1016/j.jhazmat.2024.135473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/15/2024] [Accepted: 08/08/2024] [Indexed: 08/19/2024]
Abstract
Widespread pesticide use in agriculture is a major source of soil pollution, driving biodiversity loss and posing serious threads to human health. The recalcitrant nature of most of these pesticides demands for effective remediation strategies. In this study, we assess the ability of soil microbial fuel cell (SMFC) technology to bioremediate soil polluted by the model pesticide atrazine. To elucidate the degradation mechanism and consequently define effective implementation strategies, we provide the first comprehensive investigation of the SMFC performance, in which the monitoring of the electrochemical performance of the system is combined with Quadrupole Time-of-Flight (QTOF) mass spectrometry and microbial analyses. Our results show that, while both SMFC and natural attenuation lead to a reduction on atrazine levels, the SMFC modulates the activity of different microbial pathways. As a result, atrazine degradation by natural attenuation leads to high levels of deisoproylatrazine (DIPA), a very toxic degradation metabolite, while DIPA levels in soil treated by SMFC remain comparatively low. The beta diversity and differential abundance analyses revealed how the microbial community evolves over time in the SMFCs degrading atrazine, demonstrating the enrichment of electroactive taxa on the anode, and the enrichment of a mixture of electroactive and atrazine-degrading taxa at the cathode. The detection and taxonomic classification of peripheral atrazine degrading genes, atzA, atzB and atzC, was carried out in combination with the differential abundance analysis. Results revealed that these genes are likely harboured by members of the order Rhizobiales enriched at the cathode, thus promoting atrazine degradation via the conversion of hydroxyatrazine (HA) into N-isopropylammelide (NIPA), as confirmed by mass spectrometry data. Overall, the comprehensive approach adopted in this work, provides fundamental insights into the degradation pathways of atrazine in soil by SMFC technology, which is critical for practical applications, thus suggesting an effective approach to advance research in the field.
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Affiliation(s)
- Daniel Farkas
- Department of Microbial Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Kathryn Proctor
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK
| | - Bongkyu Kim
- Department of Chemical Engineering and Centre for Bioengineering and Biomedical Technologies (CBio), University of Bath, Bath BA2 7AY, UK; SELS Center, Division of Biotechnology, College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, Jeonbuk 54596, Republic of Korea
| | | | | | - Mirella Di Lorenzo
- Department of Chemical Engineering and Centre for Bioengineering and Biomedical Technologies (CBio), University of Bath, Bath BA2 7AY, UK.
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2
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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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3
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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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Zhang W, Yu C, Yin S, Chang X, Chen K, Xing Y, Yang Y. Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting. BIORESOURCE TECHNOLOGY 2023; 382:129190. [PMID: 37196739 DOI: 10.1016/j.biortech.2023.129190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/04/2023] [Accepted: 05/14/2023] [Indexed: 05/19/2023]
Abstract
Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM= 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.
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Affiliation(s)
- Wenming Zhang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Chenxu Yu
- Department of Agriculture and Biosystem Engineering, Iowa State University, Ames 50010, US
| | - Siqian Yin
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Xinyi Chang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Kaishan Chen
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Yanhong Xing
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Yingxiang Yang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, PR China
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5
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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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6
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Wessels AG. Influence of the Gut Microbiome on Feed Intake of Farm Animals. Microorganisms 2022; 10:microorganisms10071305. [PMID: 35889024 PMCID: PMC9315566 DOI: 10.3390/microorganisms10071305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/23/2022] [Accepted: 06/25/2022] [Indexed: 12/04/2022] Open
Abstract
With the advancement of microbiome research, the requirement to consider the intestinal microbiome as the “last organ” of an animal emerged. Through the production of metabolites and/or the stimulation of the host’s hormone and neurotransmitter synthesis, the gut microbiota can potentially affect the host’s eating behavior both long and short-term. Based on current evidence, the major mediators appear to be short-chain fatty acids (SCFA), peptide hormones such as peptide YY (PYY) and glucagon-like peptide-1 (GLP-1), as well as the amino acid tryptophan with the associated neurotransmitter serotonin, dopamine and γ-Aminobutyrate (GABA). The influence appears to extend into central neuronal networks and the expression of taste receptors. An interconnection of metabolic processes with mechanisms of taste sensation suggests that the gut microbiota may even influence the sensations of their host. This review provides a summary of the current status of microbiome research in farm animals with respect to general appetite regulation and microbiota-related observations made on the influence on feed intake. This is briefly contrasted with the existing findings from research with rodent models in order to identify future research needs. Increasing our understanding of appetite regulation could improve the management of feed intake, feed frustration and anorexia related to unhealthy conditions in farm animals.
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Affiliation(s)
- Anna Grete Wessels
- Institute of Animal Nutrition, Department of Veterinary Medicine, Freie Universität Berlin, 14195 Berlin, Germany
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7
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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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Hyun DW, Sung H, Kim PS, Yun JH, Bae JW. Leucobacter coleopterorum sp. nov., Leucobacter insecticola sp. nov., and Leucobacter viscericola sp. nov., isolated from the intestine of the diving beetles, Cybister brevis and Cybister lewisianus, and emended description of the genus Leucobacter. J Microbiol 2021; 59:360-368. [PMID: 33496938 DOI: 10.1007/s12275-021-0472-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 11/29/2022]
Abstract
Three novel bacterial strains, HDW9AT, HDW9BT, and HDW9CT, isolated from the intestine of the diving beetles Cybister lewisianus and Cybister brevis, were characterized as three novel species using a polyphasic approach. The isolates were Gram-staining-positive, strictly aerobic, non-motile, and rod-shaped. They grew optimally at 30°C (pH 7) in the presence of 0.5% (wt/vol) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that they belong to the genus Leucobacter and are closely related to L. denitrificans M1T8B10T (98.4-98.7% sequence similarity). Average nucleotide identity (ANI) values among the isolates were 76.4-84.1%. ANI values for the isolates and the closest taxonomic species, L. denitrificans KACC 14055T, were 72.3-73.1%. The isolates showed ANI values of < 76.5% with all analyzable Leucobacter strains in the EzBioCloud database. The genomic DNA G + C content of the isolates was 60.3-62.5%. The polar lipid components were phosphatidylglycerol, diphosphatidylglycerol, and other unidentified glycolipids, phospholipids, and lipids. The major cellular fatty acids were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. MK-10 was the major respiratory quinone, and MK-7 and MK-11 were the minor respiratory quinones. The whole-cell sugar components of the isolates were ribose, glucose, galactose, and mannose. The isolates harbored L-2,4-diaminobutyric acid, L-serine, L-lysine, L-aspartic acid, glycine, and D-glutamic acid within the cell wall peptidoglycan. Based on phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses, strains HDW9AT, HDW9BT, and HDW9CT represent three novel species within the genus Leucobacter. We propose the name Leucobacter coleopterorum sp. nov. for strain HDW9AT (= KACC 21331T = KCTC 49317T = JCM 33667T), the name Leucobacter insecticola sp. nov. for strain HDW9BT (= KACC 21332T = KCTC 49318T = JCM 33668T), and the name Leucobacter viscericola sp. nov. for strain HDW9CT (= KACC 21333T = KCTC 49319T = JCM 33669T).
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Affiliation(s)
- Dong-Wook Hyun
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hojun Sung
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Pil Soo Kim
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Ji-Hyun Yun
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Jin-Woo Bae
- Department of Biology and Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea.
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9
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Tu W, Zhang D, Wang H, Lin Z. Polyhydroxyalkanoates (PHA) production from fermented thermal-hydrolyzed sludge by PHA-storing denitrifiers integrating PHA accumulation with nitrate removal. BIORESOURCE TECHNOLOGY 2019; 292:121895. [PMID: 31398550 DOI: 10.1016/j.biortech.2019.121895] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
Polyhydroxyalkanoates (PHA) production from fermented thermal-hydrolyzed sludge was conducted by mixed microbial cultures (MMCs) in the study. An MMC enriched in the species Brachymonas_denitrificans (60.18%) was selected under an aerobic feast/famine regime, which is capable of denitrification and accumulating PHA. To take advantage of the PHA-storing denitrifiers, an aerobic-feast/anoxic-famine regime was applied to integrate culture selection with denitrification. The results showed that cultures enriched under the regime exhibited a PHA storage capacity with PHA yield on VFA of 0.47 gCOD/gCOD and well denitrification performance achieving nitrate removal of 98%. Moreover, the aerobic-feast/anoxic-famine regime could originate a comparable maximum PHA content to the complete aerobic feast/famine regime (49.7 wt% versus. 47.1 wt%, respectively), yet reduce aeration energy input by 79% in the culture selection process. Finally, this study investigated the accumulation of nitrite and nitrous oxide during PHA based denitrification and the feasibility of integrating the process with wastewater treatment.
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Affiliation(s)
- Weiming Tu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Dandan Zhang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Hui Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Ziyu Lin
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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10
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Anandham R, Heo J, Krishnamoorthy R, SenthilKumar M, Gopal NO, Kim SJ, Kwon SW. Azospirillum ramasamyi sp. nov., a novel diazotrophic bacterium isolated from fermented bovine products. Int J Syst Evol Microbiol 2019; 69:1369-1375. [DOI: 10.1099/ijsem.0.003320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Rangasamy Anandham
- 1Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
| | - Jun Heo
- 2Agricultural Microbiology Division, National Institute of Agricultural Sciences, 166 Nongsaengmyeong-ro, Jeollabuk-do 55365, Republic of Korea
| | - Ramasamy Krishnamoorthy
- 1Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
| | - Murugaiyan SenthilKumar
- 1Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
| | | | - Soo-Jin Kim
- 2Agricultural Microbiology Division, National Institute of Agricultural Sciences, 166 Nongsaengmyeong-ro, Jeollabuk-do 55365, Republic of Korea
| | - Soon-Wo Kwon
- 2Agricultural Microbiology Division, National Institute of Agricultural Sciences, 166 Nongsaengmyeong-ro, Jeollabuk-do 55365, Republic of Korea
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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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Myer PR, Freetly HC, Wells JE, Smith TPL, Kuehn LA. Analysis of the gut bacterial communities in beef cattle and their association with feed intake, growth, and efficiency. J Anim Sci 2018; 95:3215-3224. [PMID: 28727105 DOI: 10.2527/jas.2016.1059] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The impetus behind the global food security challenge is direct, with the necessity to feed almost 10 billion people by 2050. Developing a food-secure world, where people have access to a safe and sustainable food supply, is the principal goal of this challenge. To achieve this end, beef production enterprises must develop methods to produce more pounds of animal protein with less. Selection for feed-efficient beef cattle using genetic improvement technologies has helped to understand and improve the stayability and longevity of such traits within the herd. Yet genetic contributions to feed efficiency have been difficult to identify, and differing genetics, feed regimens, and environments among studies contribute to great variation and interpretation of results. With increasing evidence that hosts and their microbiomes interact in complex associations and networks, examining the gut microbial population variation in feed efficiency may lead to partially clarifying the considerable variation in the efficiency of feed utilization. The use of metagenomics and high-throughput sequencing has greatly impacted the study of the ruminant gut. The ability to interrogate these systems at great depth has permitted a greater understanding of the microbiological and molecular mechanisms involved in ruminant nutrition and health. Although the microbial communities of the reticulorumen have been well documented to date, our understanding of the populations within the gastrointestinal tract as a whole is limited. The composition and phylogenetic diversity of the gut microbial community are critical to the overall well-being of the host and must be determined to fully understand the relationship between the microbiomes within segments of the cattle gastrointestinal tract and feed efficiency, ADG, and ADFI. This review addresses recent research regarding the bacterial communities along the gastrointestinal tract of beef cattle; their association with ADG, ADFI, and feed efficiency; and the potential implications for beef production.
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13
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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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Borsodi AK, Szili-Kovács T, Schumann P, Spröer C, Márialigeti K, Tóth E. Nesterenkonia pannonica sp. nov., a novel alkaliphilic and moderately halophilic actinobacterium. Int J Syst Evol Microbiol 2017; 67:4116-4120. [PMID: 28905704 DOI: 10.1099/ijsem.0.002263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An alkaliphilic and moderately halophilic bacterial strain characterized by optimal growth at pH 9.0-10.0 and with 5-7 % (w/v) NaCl, designated BV-35T, was isolated from water of a soda pan located in Kiskunság National Park, Hungary. Cells of the orange-pigmented colony were Gram-stain-positive, non-motile and non-endospore-forming coccoid rods. The isolate was strictly aerobic, catalase-positive and oxidase-negative. Strain BV-35T displayed a peptidoglycan similar to type A4α, l-Lys-l-Glu (A11.54 according to www.peptidoglycan-types.info) but containing additionally 4-aminobutyric acid. Menaquinone-7 (MK-7) was the predominant isoprenoid quinone, and anteiso-C15 : 0 and anteiso-C17 : 0 were its major cellular fatty acids. The DNA G+C content of strain BV-35T was 65.4 mol%. Based on 16S rRNA gene sequence similarities, the novel isolate showed the closest relationship to Nesterenkonia populi GP 10-3T (97.9 %). The DNA-DNA relatedness between BV-35T and N. populi was 46.7 %. The distinguishing phenotypic and genetic results of this polyphasic study revealed that strain BV-35T represents a novel member of the genus Nesterenkonia, for which the name Nesterenkonia pannonica sp. nov. is proposed. The type strain is BV-35T (=DSM 29786T=NCAIM B 02606T).
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Affiliation(s)
- Andrea K Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Tibor Szili-Kovács
- Institute for Soil Sciences and Agricultural Chemistry, Agricultural Research Center, Hungarian Academy of Sciences, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7 B, 38124 Braunschweig, Germany
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, H-1117 Budapest, Hungary
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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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Strategies for efficiently selecting PHA producing mixed microbial cultures using complex feedstocks: Feast and famine regime and uncoupled carbon and nitrogen availabilities. N Biotechnol 2017; 37:69-79. [DOI: 10.1016/j.nbt.2016.10.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 09/10/2016] [Accepted: 10/23/2016] [Indexed: 11/21/2022]
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18
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Zhu D, Zhang P, Li P, Wu J, Xie C, Sun J, Niu L. Description of Leucobacter holotrichiae sp. nov., isolated from the gut of Holotrichia oblita larvae. Int J Syst Evol Microbiol 2016; 66:1857-1861. [PMID: 26869452 DOI: 10.1099/ijsem.0.000957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
A Gram-stain-positive bacterium, designated T14T, was isolated from the gut of Holotrichia oblita larvae and was subjected to a taxonomic study. The isolate was rod-shaped, aerobic, non-motile, non-spore-forming and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequence comparison indicated that the isolate is related to the genus Leucobacter. Its closest neighbours were the type strains 'Leucobacter kyeonggiensis' F3-P9 (96.8% 16S rRNA gene sequence similarity), Leucobacter celer NAL101T (96.2%) and Leucobacter chironomi DSM 19883T (95.5%). The DNA G+C content of strain T14T was 69.3 mol%, and DNA-DNA hybridization values with closely related strains were <32%. The predominant cellular fatty acids were anteiso-C15:0 (49.3%), iso-C16:0 (16.4%) and anteiso-C17:0 (16.8%). The major polar lipids were aminolipid, diphosphatidylglycerol, phosphatidylglycerol, phospholipid, phosphoglycolipid and unidentified glycolipids. The predominant respiratory quinone was MK-11. Based on these phylogenetic and phenotypic results, strain T14T can be clearly distinguished from all of the recognized species of the genus Leucobacter and is considered to represent a novel species of the genus Leucobacter. The name Leucobacter holotrichiae sp. nov. is proposed, with the type strain T14T (=DSM 28968T=JCM 30245T).
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Affiliation(s)
- Daochen Zhu
- School of Environmental Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PRChina
| | - Peipei Zhang
- School of Environmental Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PRChina
| | - Pingping Li
- Institute of Agricultural Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PRChina
| | - Jian Wu
- School of Environmental Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PRChina
| | - Changxiao Xie
- School of Environmental Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PRChina
| | - Jianzhong Sun
- School of Environmental Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, PRChina
| | - Lili Niu
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, PRChina
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19
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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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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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21
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Sun MZ, Zheng HC, Meng LC, Sun JS, Song H, Bao YJ, Pei HS, Yan Z, Zhang XQ, Zhang JS, Liu YH, Lu FP. Direct cloning, expression of a thermostable xylanase gene from the metagenomic DNA of cow dung compost and enzymatic production of xylooligosaccharides from corncob. Biotechnol Lett 2015; 37:1877-86. [DOI: 10.1007/s10529-015-1857-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
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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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Tan H, Deng Q, Cao L. Ruminant feces harbor diverse uncultured symbiotic actinobacteria. World J Microbiol Biotechnol 2013; 30:1093-100. [DOI: 10.1007/s11274-013-1529-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/15/2013] [Indexed: 11/29/2022]
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Draft Genome Sequence of Leucobacter sp. Strain UCD-THU (Phylum Actinobacteria). GENOME ANNOUNCEMENTS 2013; 1:1/3/e00325-13. [PMID: 23792744 PMCID: PMC3675516 DOI: 10.1128/genomea.00325-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here we present the draft genome of Leucobacter sp. strain UCD-THU. The genome contains 3,317,267 bp in 11 scaffolds. This strain was isolated from a residential toilet as part of an undergraduate project to sequence reference genomes of microbes from the built environment.
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25
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2012. [DOI: 10.1099/ijs.0.043240-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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