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Roman EKB, Ramos MA, Tomazetto G, Foltran BB, Galvão MH, Ciancaglini I, Tramontina R, de Almeida Rodrigues F, da Silva LS, Sandano ALH, Fernandes DGDS, Almeida DV, Baldo DA, de Oliveira Junior JM, Garcia W, Damasio A, Squina FM. Plastic-degrading microbial communities reveal novel microorganisms, pathways, and biocatalysts for polymer degradation and bioplastic production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174876. [PMID: 39067601 DOI: 10.1016/j.scitotenv.2024.174876] [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: 05/15/2024] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
Plastics derived from fossil fuels are used ubiquitously owing to their exceptional physicochemical characteristics. However, the extensive and short-term use of plastics has caused environmental challenges. The biotechnological plastic conversion can help address the challenges related to plastic pollution, offering sustainable alternatives that can operate using bioeconomic concepts and promote socioeconomic benefits. In this context, using soil from a plastic-contaminated landfill, two consortia were established (ConsPlastic-A and -B) displaying versatility in developing and consuming polyethylene or polyethylene terephthalate as the carbon source of nutrition. The ConsPlastic-A and -B metagenomic sequencing, taxonomic profiling, and the reconstruction of 79 draft bacterial genomes significantly expanded the knowledge of plastic-degrading microorganisms and enzymes, disclosing novel taxonomic groups associated with polymer degradation. The microbial consortium was utilized to obtain a novel Pseudomonas putida strain (BR4), presenting a striking metabolic arsenal for aromatic compound degradation and assimilation, confirmed by genomic analyses. The BR4 displays the inherent capacity to degrade polyethylene terephthalate (PET) and produce polyhydroxybutyrate (PHB) containing hydroxyvalerate (HV) units that contribute to enhanced copolymer properties, such as increased flexibility and resistance to breakage, compared with pure PHB. Therefore, BR4 is a promising strain for developing a bioconsolidated plastic depolymerization and upcycling process. Collectively, our study provides insights that may extend beyond the artificial ecosystems established during our experiments and supports future strategies for effectively decomposing and valorizing plastic waste. Furthermore, the functional genomic analysis described herein serves as a valuable guide for elucidating the genetic potential of microbial communities and microorganisms in plastic deconstruction and upcycling.
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Affiliation(s)
- Ellen Karen Barreto Roman
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Murilo Antonio Ramos
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Programa de Processos Tecnológicos e Ambientais, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Geizecler Tomazetto
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Bruno Botega Foltran
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | | | - Iara Ciancaglini
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil; Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Robson Tramontina
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil; Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | | | | | | | - Diógenes G da S Fernandes
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Dnane Vieira Almeida
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Denicezar Angelo Baldo
- Laboratory of Applied Nuclear Physics, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | | | - Wanius Garcia
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Fabio Marcio Squina
- Laboratory of Molecular Sciences, University of Sorocaba (UNISO), Sorocaba, SP, Brazil; Programa de Processos Tecnológicos e Ambientais, University of Sorocaba (UNISO), Sorocaba, SP, Brazil.
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Wang J, Pan J, Ma X, Li S, Chen X, Liu T, Wang Q, Wang JJ, Wei D, Zhang Z, Li R. Solid digestate biochar amendment on pig manure composting: Nitrogen cycle and balance. BIORESOURCE TECHNOLOGY 2022; 349:126848. [PMID: 35158036 DOI: 10.1016/j.biortech.2022.126848] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Effect of solid digestate biochar (DB) on nitrogen cycle and balance was evaluated during composting by adding DB into mixtures of pig manure and Lycium chinensis branch filings. Results indicated that DB addition improved composting microenvironment and increased the total N content of the final product. Furthermore, N balance calculation indicated that the NH3 and N2O emissions accounted for 72.14%-81.39% and 0.49%-2.37% of the total N loss without DB addition, respectively. After using DB, the N reductions in the form of NH3 and N2O reduced from 10.78% to < 5.73% and from 0.34% to < 0.041% of total N, respectively. Addition of DB affected N fixation with 92.32%-93.67% of total N fixed in the compost than that of the T1 treatment (85.63%). DB amendment enhanced the aerobic bacterial communities and hindered anaerobic bacterial growth, thus benefiting the NH3 and N2O emission mitigation and N conservation.
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Affiliation(s)
- Jingwen Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Junting Pan
- Key Laboratory of Non-point Source Pollution of Ministry of Agricultural and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuzhe Ma
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Songling Li
- Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Qinghai 810016, China
| | - Xing Chen
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Quan Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Jim J Wang
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, 104 Sturgis Hall, Baton Rouge, LA 70803, USA
| | - Dan Wei
- Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China
| | - Ronghua Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling 712100, Shaanxi, China.
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3
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Lee J, Mahandra H, Hein GA, Ramsay J, Ghahreman A. Toward Sustainable Solution for Biooxidation of Waste and Refractory Materials Using Neutrophilic and Alkaliphilic Microorganisms—A Review. ACS APPLIED BIO MATERIALS 2021; 4:2274-2292. [DOI: 10.1021/acsabm.0c01582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Jung Lee
- Hydrometallurgy and Environment Laboratory, Robert M. Buchan Department of Mining, Queen’s University, 25 Union Street, Kingston, Ontario K7L 3N6, Canada
| | - Harshit Mahandra
- Hydrometallurgy and Environment Laboratory, Robert M. Buchan Department of Mining, Queen’s University, 25 Union Street, Kingston, Ontario K7L 3N6, Canada
| | - Guillermo Alvial Hein
- Hydrometallurgy and Environment Laboratory, Robert M. Buchan Department of Mining, Queen’s University, 25 Union Street, Kingston, Ontario K7L 3N6, Canada
| | - Juliana Ramsay
- Department of Chemical Engineering, Queen’s University, 19 Division Street, Kingston, Ontario K7L 3N6, Canada
| | - Ahmad Ghahreman
- Hydrometallurgy and Environment Laboratory, Robert M. Buchan Department of Mining, Queen’s University, 25 Union Street, Kingston, Ontario K7L 3N6, Canada
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Nagar S, Talwar C, Haider S, Puri A, Ponnusamy K, Gupta M, Sood U, Bajaj A, Lal R, Kumar R. Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae. Front Microbiol 2020; 11:1725. [PMID: 33013721 PMCID: PMC7500135 DOI: 10.3389/fmicb.2020.01725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/30/2020] [Indexed: 11/28/2022] Open
Abstract
The genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter, with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities. Therefore, we hypothesized whether these substantial differences at the 16S rRNA gene level depict the true phylogeny or that these genomes have actually diverged. Thus, we performed genomic analysis of the four available genomes of Parapedobacter to better understand their phylogenomic position within family Sphingobacteriaceae. Our results demonstrated that Parapedobacter is more closely related to species of Olivibacter, as opposed to the genus Pedobacter. Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes of Parapedobacter luteus DSM 22899T and Parapedobacter composti DSM 22900T. These enzymes, specifically pectinesterases and pectate lyases, are presumed to have largely different catalytic activities based on very low sequence similarities to already known enzymes and thus may be exploited for industrial applications. We also determined the complete Bacteroides aerotolerance (Bat) operon (batA, batB, batC, batD, batE, hypothetical protein, moxR, and pa3071) within the genome of Parapedobacter indicus RK1T. This expands the definition of genus Parapedobacter to containing members that are able to tolerate oxygen stress using encoded oxidative stress responsive systems. By conducting a signal propagation network analysis, we determined that BatD, BatE, and hypothetical proteins are the major controlling hubs that drive the expression of Bat operon. As a key metabolic difference, we also annotated the complete iol operon within the P. indicus RK1T genome for utilization of all three stereoisomers of inositol, namely myo-inositol, scyllo-inositol, and 1D-chiro-inositol, which are abundant sources of organic phosphate found in soils. The results suggest that the genus Parapedobacter holds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.
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Affiliation(s)
- Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi, India
| | - Chandni Talwar
- Department of Zoology, University of Delhi, Delhi, India
| | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Akshita Puri
- Department of Zoology, University of Delhi, Delhi, India.,P.G.T.D, Zoology, R.T.M Nagpur University, Nagpur, India
| | | | - Madhuri Gupta
- Department of Zoology, University of Delhi, Delhi, India
| | - Utkarsh Sood
- Department of Zoology, University of Delhi, Delhi, India.,The Energy and Resources Institute, New Delhi, India
| | - Abhay Bajaj
- Department of Zoology, University of Delhi, Delhi, India.,Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India.,The Energy and Resources Institute, New Delhi, India
| | - Roshan Kumar
- Department of Zoology, University of Delhi, Delhi, India.,P.G. Department of Zoology, Magadh University, Bodh Gaya, India
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Wu M, Guo X, Wu J, Chen K. Effect of compost amendment and bioaugmentation on PAH degradation and microbial community shifting in petroleum-contaminated soil. CHEMOSPHERE 2020; 256:126998. [PMID: 32470727 DOI: 10.1016/j.chemosphere.2020.126998] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 05/15/2023]
Abstract
Efficient degradation of polycyclic aromatic hydrocarbons (PAHs) in a petroleum-contaminated soil was challenging which requires ample PAH-degrading flora and nutrients. In this study, we investigated the effects of 'natural attenuation', 'bioaugmentation', 'compost only (raw materials of compost included pig manure and rice husk mixed at a 1:2 proportion, supplemented with 2.5% charcoal)', and 'compost with bioaugmentation' treatments on degradation of polycyclic aromatic hydrocarbons (PAHs) and microbial community shifts during the remediation of petroleum-contaminated soil. After sixteen weeks of incubation, the removal efficiencies of PAHs were 0.52 ± 0.04%, 6.92 ± 0. 32%, 9.53 ± 0.29%, and 18.2 ± 0.64% in the four treatments, respectively. 'Compost with bioaugmentation' was the most effective for PAH removal among all the treatments. Illumina sequencing analysis suggested that both the 'compost only' and 'compost with bioaugmentation' treatments changed soil microbial community structures and enhanced microbial biodiversity. Some of the microorganisms affiliated with the compost including Azomonas, Luteimonas, Pseudosphingobacterium, and Parapedobacter were able to survive and become dominant in the contaminated soil. The 'bioaugmentation and 'natural attenuation' treatments had no significant effects on soil microbial community structure. Inoculation of the PAH degraders including Bacillus, Pseudomonas, and Acinetobacter directly into the contaminated soil led to lower biodiversity under natural conditions. This result suggested that compost addition increased the α-diversity of both the bacterial and fungal communities in petroleum-contaminated soil, leading to higher PAH degradation efficiency in petroleum-contaminated soil.
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Affiliation(s)
- Manli Wu
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China.
| | - Xiqian Guo
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Jialuo Wu
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
| | - Kaili Chen
- Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China; Key Laboratory of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, 710055, People's Republic of China
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Yang L, Wang YH, Zhu HZ, Muhadesi JB, Wang BJ, Liu SJ, Jiang CY. Parapedobacter defluvii sp. nov., isolated from the sewage treatment packing of a coking chemical plant. Int J Syst Evol Microbiol 2017; 67:4698-4703. [PMID: 28984570 DOI: 10.1099/ijsem.0.002360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain WY-1T, a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from the sewage treatment packing of a coking chemical plant. Strain WY-1T grew over a temperature range of 15-45 °C (optimum, 30-37 °C), a pH range of 5.5-11.0 (optimum, pH 6.5-7.0) and an NaCl concentration range of 0-3 % (w/v; optimum, 0 %). 16S rRNA gene sequence analysis showed that strain WY-1T was closely related to Parapedobacter indicus RK1T with the highest sequence similarity of 96.0 %. The predominant cellular fatty acids of the novel strain were iso-C15 : 0, summed feature 3(C16 : 1ω6c and/or C16 : 1ω7c), iso-C17 : 0 3-OH, iso-C17 : 1ω9c, iso-C15 : 0 3-OH and C16 : 0. The respiratory quinone of the cells was menaquinone 7 (MK-7). The main polar lipid was phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminolipids and two unknown lipids. The G+C content of the DNA was 47.1 mol%. Chemotaxonomic characteristics and phylogenetic analyses revealed that strain WY-1T belonged to the genus Parapedobacter. Strain WY-1T showed a range of phenotypic characteristics that differentiated it from species of the genus Parapedobacter with validly published names, including its assimilation from carbon sources, enzyme activities and having a wider pH range for growth. Based on these results, it is concluded that strain WY-1T represents a novel species of the genus Parapedobacter, for which the name Parapedobacter defluvii sp. nov. is proposed. The type strain is WY-1T (=NBRC 112611T=CGMCC 1.15342T).
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Affiliation(s)
- Lan Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yun-Hao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jiang-Baota Muhadesi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China.,RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, PR China
| | - Cheng-Ying Jiang
- RCEECAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
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Kim JM, Lee SA, Cho H, Kim SJ, Joa JH, Kwon SW, Weon HY. Parapedobacter lycopersici sp. nov., isolated from the rhizosphere soil of tomato plants (Solanum lycopersicum L.). Int J Syst Evol Microbiol 2017; 67:3728-3732. [PMID: 28895519 DOI: 10.1099/ijsem.0.002162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative bacterial strain, designated T16R-256T, was isolated from the rhizosphere soil of tomato plants grown in a greenhouse in Yecheon-gun, Gyeongsangbuk-do, Republic of Korea and characterized using polyphasic taxonomy. Cells were aerobic, non-flagellated and rod-shaped. Colonies were light yellow, convex and round. The strain grew in the temperature range of 15-37 °C (optimally at 28-30 °C) and pH range of 7.0-9.0 (optimally at 7.0-8.0) and in 4 % NaCl (w/v). A comparison of 16S rRNA gene sequences showed that strain T16R-256T is a member of the genus Parapedobacter, exhibiting high sequence similarity with Parapedobacter pyrenivorans P-4T (94.2 %), Parapedobacter indicus RK1T (93.7 %), Parapedobacter koreensis Jip14T (93.7 %), Parapedobacter luteus 4M29T (93.6 %) and Parapedobacter soli DCY14T (93.4 %). The major polar lipids were phosphatidylethanolamine, sphingolipid, one aminophospholipid, two aminolipids and three unknown lipids. The major fatty acids (>10 % of the total fatty acids) were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 2-OH/C16 : 1ω7c. Strain T16R-256T contained MK-7 as the predominant respiratory quinone and homospermidine as the major polyamine. The genomic DNA G+C content of the type strain was 55.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain T16R-256T should be designated as representative of a novel species of the genus Parapedobacter, for which the name Parapedobacter lycopersici sp. nov. is proposed. The type strain is T16R-256T (=KACC 18788T=JCM 31602T).
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Affiliation(s)
- Jeong Myeong Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Hayoung Cho
- Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Jae-Ho Joa
- National Institute of Horticultural and Herbal Science (NIHHS), RDA, Jeju 63240, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration (RDA), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
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Liu L, Li L, Song Z, Wang S, Zhang J, Zhang X, Sun Q. Parapedobacter deserti sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems. Int J Syst Evol Microbiol 2017; 67:2148-2152. [PMID: 28699863 DOI: 10.1099/ijsem.0.001911] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain N5SSJ16T, a Gram-negative-staining, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from Haloxylon ammodendron stems. The strain grew in the presence of 0-4 % (w/v) NaCl (optimum growth in the absence of NaCl), at pH 7-9 (optimum: pH 8) and at 12-50 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain N5SSJ16T was related phylogenetically to Parapedobacter composti 4M40T (96.5 %) and Parapedobacter luteus 4M29T (95.9 %). The cellular fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), summed feature 9 (C16 : 0 10-methyl and/or iso-C17 : 1ω9c) and iso-C17 : 0 3-OH. MK-7 was the respiratory quinone. The main polar lipids were phosphatidylethanolamine, unidentified aminophospholipid and two unknown lipids. The G+C content of the DNA was 45.8 mol%. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain N5SSJ16T represents a novel species of the genus Parapedobacter, for which the name Parapedobacter deserti sp. nov. is proposed. The type strain is N5SSJ16T (=ACCC 19928T=KCTC 52416T).
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Affiliation(s)
- Lei Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Lubin Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Zheng Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Shiyan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Jun Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoxia Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qiwu Sun
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
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Lin SY, Hameed A, Chiu KY, Liu YC, Hsu YH, Lai WA, Young CC. Olivibacter composti sp. nov., isolated from compost collected at a greenhouse. Int J Syst Evol Microbiol 2017; 67:148-152. [PMID: 28211312 DOI: 10.1099/ijsem.0.001593] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic approach was used to characterize a presumably novel bacterium, designated strain CC-KYC063T, isolated from a compost sample collected at a greenhouse facility within Taiwan. Strain CC-KYC063T was Gram-stain-negative and aerobic, able to grow at 15-37 °C (optimal 30 °C), at pH 7.0-9.0 (optimal pH 7.0) and with 0-2 % (w/v) NaCl. The 16S rRNA gene sequence of strain CC-KYC063T showed highest similarity to Olivibacter ginsengisoli Gsoil 060T (96.2 %) and Olivibacter terrae Jip13T (95.5 %). The DNA G+C content was 43.0 mol% and the predominant quinone system was menaquinone-7 (MK-7). The polyamine pattern showed a predominance of sym-homospermidine. The major fatty acids found in strain CC-KYC063T were iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω6c/C16 : 1ω7c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-KYC063T is considered to represent a novel species of the genus Olivibacter, for which the name Olivibacter composti sp. nov. is proposed. The type strain is CC-KYC063T (=BCRC 80939T=JCM 31198T).
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Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Kai-Yeh Chiu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- 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, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- 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, Taichung, Taiwan, ROC
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Xia J, Ling SK, Wang XQ, Chen GJ, Du ZJ. Aliifodinibius halophilus sp. nov., a moderately halophilic member of the genus Aliifodinibius, and proposal of Balneolaceae fam. nov. Int J Syst Evol Microbiol 2016; 66:2225-2233. [PMID: 26961808 DOI: 10.1099/ijsem.0.001012] [Citation(s) in RCA: 17] [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 Gram-stain-negative, rod-shaped, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated 2W32T, was isolated from a marine solar saltern on the coast of Weihai, Shandong Province, China. Strain 2W32T was tolerant to moderate salt conditions. Optimal growth occurred at 33-37 °C (range 20-45 °C) and pH 7.5-8.0 (range pH 7.0-8.5) with 6-10 % (w/v) NaCl (range 2-18 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2W32T shared highest similarity with Aliifodinibius sediminis YIM J21T (94.6 %), Aliifodinibius roseus YIM D15T (94.4 %), Fodinibius salinus YIM C003T (93.6 %), Gracilimonas tropica CL-CB462T (88.6 %) and Balneola vulgaris 13IX/A01/164T (86.4 %) and less than 83.0 % similarity with other species of the phylum Bacteroidetes. The isolate and closely related species formed a novel family-level clade in the phylum Bacteroidetes. The polar lipid profile of the novel isolate consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. The dominant cellular fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15 : 0 2-OH) and the sole respiratory quinone was menaquinone 7 (MK-7). The DNA G+C content of strain 2W32T was 47.5 mol %. Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain 2W32T represents a novel species within the genus Aliifodinibius, for which the name Aliifodinibius halophilus sp. nov. is proposed. The type strain is 2W32T (=KCTC 42497T=CICC 23869T). In addition, a novel family, Balneolaceae fam. nov., is proposed to accommodate the genera Fodinibius, Aliifodinibius, Gracilimonas and Balneola.
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Affiliation(s)
- Jun Xia
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Si-Kai Ling
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Xiao-Qun Wang
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China
| | - Guan-Jun Chen
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Zong-Jun Du
- College of Marine Science, Shandong University at Weihai, Weihai 264209, PR China.,State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
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High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates. Appl Environ Microbiol 2016; 82:2210-8. [PMID: 26850294 DOI: 10.1128/aem.03588-15] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/19/2016] [Indexed: 12/16/2022] Open
Abstract
This paper describes the microfluidic streak plate (MSP), a facile method for high-throughput microbial cell separation and cultivation in nanoliter sessile droplets. The MSP method builds upon the conventional streak plate technique by using microfluidic devices to generate nanoliter droplets that can be streaked manually or robotically onto petri dishes prefilled with carrier oil for cultivation of single cells. In addition, chemical gradients could be encoded in the droplet array for comprehensive dose-response analysis. The MSP method was validated by using single-cell isolation of Escherichia coli and antimicrobial susceptibility testing of Pseudomonas aeruginosa PAO1. The robustness of the MSP work flow was demonstrated by cultivating a soil community that degrades polycyclic aromatic hydrocarbons. Cultivation in droplets enabled detection of the richest species diversity with better coverage of rare species. Moreover, isolation and cultivation of bacterial strains by MSP led to the discovery of several species with high degradation efficiency, including four Mycobacterium isolates and a previously unknown fluoranthene-degrading Blastococcus species.
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Effects of aeration strategy on the evolution of dissolved organic matter (DOM) and microbial community structure during sludge bio-drying. Appl Microbiol Biotechnol 2015; 99:7321-31. [DOI: 10.1007/s00253-015-6640-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/17/2015] [Accepted: 04/24/2015] [Indexed: 10/23/2022]
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Kumar R, Dwivedi V, Nayyar N, Verma H, Singh AK, Rani P, Rao DLN, Lal R. Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2014; 65:129-134. [PMID: 25298380 DOI: 10.1099/ijs.0.069104-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain RK1(T), a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium was isolated from a hexachlorocyclohexane (HCH) dumpsite, Lucknow, India. 16S rRNA gene sequence analysis revealed that strain RK1(T) belongs to the family Sphingobacteriaceae and showed highest sequence similarity to Parapedobacter koreensis Jip14(T) (95.63%). The major cellular fatty acids of strain RK1(T) were iso-C15:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C17:0 3-OH, summed feature 9 (10-methyl C16:0 and/or iso-C17:1ω9c), iso-C15:0 3-OH and C16 : 0. The major respiratory pigment and polyamine of RK1(T) were menaquinone (MK-7) and homospermidine, respectively. The main polar lipids were phosphatidylethanolamine and sphingolipid. The G+C content of the DNA was 44.5 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly demonstrated that strain RK1(T) represents a novel species of the genus Parapedobacter, for which the name Parapedobacter indicus sp. nov. is proposed. The type strain is RK1(T) ( = DSM 28470(T) =MCC 2546(T)).
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Affiliation(s)
- Roshan Kumar
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Vatsala Dwivedi
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Namita Nayyar
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Helianthous Verma
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Amit Kumar Singh
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - Pooja Rani
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
| | - D L N Rao
- ICAR-Indian Institute of Soil Science, Bhopal 462038, Madhya Pradesh, India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India
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Jiang S, Chen M, Su S, Yang M, Li A, Zhang C, Lin M, Zhang W, Luo X. Sphingobacterium arenae sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 2013; 64:248-253. [PMID: 24052628 DOI: 10.1099/ijs.0.051706-0] [Citation(s) in RCA: 22] [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 novel, Gram-stain-negative, non-motile, non-spore-forming, short rod-shaped, aerobic bacterium designated H-12(T) was isolated from a mixed sandy soil sample collected from Xinjiang, China. Strain H-12(T) grew at 20-37 °C (optimum, 30 °C), pH 7.0-11.0 (optimum, pH 8.5) on TGY medium with 0-5 % NaCl (w/v). 16S rRNA gene sequence analysis indicated that strain H-12(T) shared sequence similarities with Sphingobacterium composti DSM 18850(T) (90.0 %). Strain H-12(T) showed a low level of DNA-DNA relatedness to Sphingobacterium composti DSM 18850(T) (45.5 %). The predominant isoprenoid quinone of strain H-12(T) was MK-7 and the major polar lipid was phosphatidylethanolamine. The predominant cellular fatty acids were C16:1ω7c and/or C16 : 1ω6c, iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, C16 : 0 3-OH and iso-C15 : 0 3-OH. DNA G+C content of strain H-12(T) was 44.15 mol%. On the basis of phenotypic, genetic and phylogenetic data, strain H-12(T) is proposed to be a representative of a novel species of the genus Sphingobacterium, for which the name Sphingobacterium arenae sp. nov. is suggested and the type strain is H-12(T) ( = ACCC 05758(T) = KCTC 32294(T)).
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Affiliation(s)
- Shijie Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Life Science and Engineering College, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
| | - Ming Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shiyou Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mingkun Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Aihua Li
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, PR China
| | - Chen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xuegang Luo
- Life Science and Engineering College, Southwest University of Science and Technology, Mianyang, Sichuan 621010, PR China
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