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Lau MML, Kho CJY, Chung HH, Zulkharnain A. Isolation, identification and characterisation of Pseudomonas koreensis CM-01 isolated from diseased Malaysian mahseer (Tor tambroides). FISH & SHELLFISH IMMUNOLOGY 2024; 148:109518. [PMID: 38513913 DOI: 10.1016/j.fsi.2024.109518] [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: 01/09/2024] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Pseudomonas species are one of the most threatening fish pathogens which reside a wide range of environments. In this study, the dominant bacteria were isolated from diseased Malaysian mahseer (Tor tambroides) and tentatively named CM-01. It was identified as Pseudomonas koreensis based on its biochemical, morphological, genetic and physiological information. Its pathogenicity was found to be correlated with twelve virulence genes identified including iron uptake, protease, acylhomoserine lactone synthase gacS/gacA component regulation system, type IV secretion system, hydrogen cyanide production, exolysin, alginate biosynthesis, flagella and pili. The median lethal dose (LD50) for the CM-01 isolate on Malaysian mahseer was documented at 5.01 × 107 CFU/mL. The experimental infection revealed that CM-01 led to significant histological lesions in the fish, ultimately resulting in death. These lesions comprise necrosis, tissue thickening and aggregation. Drug sensitivity tests had shown its susceptibility to beta-lactam combination agents and further suggest its drug of choice. Its growing features had shown its growth at optimal temperature and pH. To the best of our knowledge, this is the first report of P. koreensis linked to diseased T. tambroides. STATEMENT OF RELEVANCE: In this research, a novel strain of Pseudomonas koreensis, CM-01 was isolated from diseased T. tambroides for the first time. The antimicrobial susceptibility, pathogenicity, virulence genes and growth characteristics of CM-01 were studied. These findings established a scientific foundation for the recognition of P. koreensis and the management of fish infections caused by this pathogen.
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Affiliation(s)
- Melinda Mei Lin Lau
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Cindy Jia Yung Kho
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Hung Hui Chung
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Azham Zulkharnain
- Department of Bioscience and Engineering, College of system Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma-ku, Saitama, 337-8570, Japan.
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El Fakhouri K, Ramdani C, Aasfar A, Boulamtat R, Sijilmassi B, El Bouhssini M, Kadmiri IM. Isolation, identification and pathogenicity of local entomopathogenic bacteria as biological control agents against the wild cochineal Dactylopius opuntiae (Cockerell) on cactus pear in Morocco. Sci Rep 2023; 13:21647. [PMID: 38062128 PMCID: PMC10703873 DOI: 10.1038/s41598-023-48976-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
The Opuntia ficus-indica (L.) cactus, a crucial crop in Morocco, is threatened by the wild cochineal, Dactylopius opuntiae (Cockerell). The aim of this research was to investigate the efficacy of nine bacterial strains against both D. opuntiae nymphs and adults females applied individually or after black soap in the laboratory, greenhouse, and field conditions. Using the partial 16S ribosomal DNA, the bacterial isolates were identified as Pseudomonas koreensis, Pseudomonas sp., Burkholderia sp. and Bacillus sp. Under laboratory conditions, the insecticidal activity of P. koreensis strain 66Ms.04 showed the level mortality (88%) of adult females' at 108 CFU/mL, 7 days after application. At a concentration of 108 CFU/mL, P. koreensis strain 66Ms.04 and Pseudomonas sp. (strains 37 and 5) caused 100% nymphs mortality rate three days after application. Under greenhouse conditions, the use of P. koreensis strain 66Ms.04 at 108 CFU/mL following the application of black soap (60 g/L) demonstrated the maximum levels of females and nymphs' mortalities with 80 and 91.25%, respectively, after 8 days of treatment. In field conditions, the combined application of the P. koreensis strain 66Ms.04 at 108 CFU/mL with black soap at 60 g/L, for an interval of 7 days, significantly increased the mortality of adult females to 93.33% at 7 days after the second application. These findings showed that the combined treatment of P. koreensis strain 66Ms.04 with black soap can be a potent and eco-friendly pesticide against D. opuntiae.
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Affiliation(s)
- Karim El Fakhouri
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco.
| | - Chaimae Ramdani
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Abderrahim Aasfar
- Plant and Microbial Biotechnology center, Moroccan Foundation for Advanced Science, Innovation and Rescarch (MAScIR), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Rachid Boulamtat
- Entomology Laboratory, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, P.O. Box 6299, Rabat, Morocco
| | - Badreddine Sijilmassi
- Rhizobium Laboratory, Genetic Resources Section, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Institutes, P.O. Box 6299, Rabat, Morocco
| | - Mustapha El Bouhssini
- AgroBioSciences Program, College of Agriculture and Environmental Science, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
| | - Issam Meftah Kadmiri
- Plant and Microbial Biotechnology center, Moroccan Foundation for Advanced Science, Innovation and Rescarch (MAScIR), Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, 43150, Benguerir, Morocco
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Sanow S, Kuang W, Schaaf G, Huesgen P, Schurr U, Roessner U, Watt M, Arsova B. Molecular Mechanisms of Pseudomonas-Assisted Plant Nitrogen Uptake: Opportunities for Modern Agriculture. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:536-548. [PMID: 36989040 DOI: 10.1094/mpmi-10-22-0223-cr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Pseudomonas spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including Azotobacter vinelandii AvOP, Pseudomonas stutzeri A1501, Pseudomonas stutzeri DSM4166, Pseudomonas szotifigens 6HT33bT, and Pseudomonas sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from Klebsiella pneumoniae, Pseudomonas stutzeri, and Azotobacter vinelandii. Today, this island is conserved in Pseudomonas spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind Pseudomonas-driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe Pseudomonas-plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind Pseudomonas-driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Stefan Sanow
- Institute for Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Germany
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Weiqi Kuang
- College of life and Environmental Sciences, Hunan University of Arts and Science, China
| | - Gabriel Schaaf
- Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany
| | - Pitter Huesgen
- Central institute for Engineering, Electronics and Analytics (ZEA-3), Forschungszentrum Juelich GmbH, Germany
| | - Ulrich Schurr
- Institute for Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Germany
| | - Ute Roessner
- Research School of Biology, The Australian National University, Acton, 2601 Australian Capital Territory, Australia
| | - Michelle Watt
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Borjana Arsova
- Institute for Bio- and Geosciences, Plant Sciences (IBG-2), Forschungszentrum Juelich GmbH, Germany
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Kho CJY, Lau MML, Chung HH, Chew IYY, Gan HM. Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides. Curr Microbiol 2023; 80:255. [PMID: 37356021 DOI: 10.1007/s00284-023-03354-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/28/2023] [Indexed: 06/27/2023]
Abstract
Unlike environmental P. koreensis isolated from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis isolated from fish has been rarely reported. Therefore, we investigated and isolated the possible pathogen that is responsible for the diseased state of Tor tambroides. Herein, we reported the morphological and biochemical characteristics, as well as whole-genome sequences of a newly identified P. koreensis strain. We assembled a high-quality draft genome of P. koreensis CM-01 with a contig N50 value of 233,601 bp and 99.5% BUSCO completeness. The genome assembly of P. koreensis CM-01 is consists of 6,171,880 bp with a G+C content of 60.5%. Annotation of the genome identified 5538 protein-coding genes, 3 rRNA genes, 54 tRNAs, and no plasmids were found. Besides these, 39 interspersed repeat and 141 tandem repeat sequences, 6 prophages, 51 genomic islands, 94 insertion sequences, 4 clustered regularly interspaced short palindromic repeats, 5 antibiotic-resistant genes, and 150 virulence genes were also predicted in the P. koreensis CM-01 genome. Culture-based approach showed that CM-01 strain exhibited resistance against ampicillin, aztreonam, clindamycin, and cefoxitin with a calculated multiple antibiotic resistance (MAR) index value of 0.4. In addition, the assembled CM-01 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genome pathway database. A comparative analysis of CM-01 with three representative strains of P. koreensis revealed that 92% of orthologous clusters were conserved among these four genomes, and only the CM-01 strain possesses unique elements related to pathogenicity and virulence. This study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain.
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Affiliation(s)
- Cindy Jia Yung Kho
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Melinda Mei Lin Lau
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Hung Hui Chung
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Ivy Yee Yen Chew
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Han Ming Gan
- Department of Biological Sciences, Sunway University, Bandar Sunway, 47500, Petaling Jaya, Malaysia
- Patriot Biotech Sdn. Bhd., 47500, Bandar Sunway, Selangor, Malaysia
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Ali S, Rehman A, Hussain SZ, Bukhari DA. Characterization of plastic degrading bacteria isolated from sewage wastewater. Saudi J Biol Sci 2023; 30:103628. [PMID: 37064755 PMCID: PMC10090700 DOI: 10.1016/j.sjbs.2023.103628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 04/18/2023] Open
Abstract
Plastic is a fundamental polymer used in routine life and disposed of in sewage. It leads to microplastic pollution in aquatic organisms, introducing it into the food chain and affecting human health. In the present study, samples were collected from sewage wastewater to isolate the bacteria that could potentially reduce plastic. The six samples were incubated with plastic pieces in minimal salt media for 120 days. After 120 days, the weight loss experiment showed that samples SH5B and SH6B degraded 25% plastic. After chemical and molecular characterization, these strains were identified as Pseudomonas sp. SH5B and Pseudomonas aeruginosa SH6B. The Fourier-transform infrared spectroscopy (FTIR) analysis showed peaks shifting, indicating bond stretching, bond bending, and new bond formation. The Gas Chromatography-Mass Spectrometry (GC-MS) analysis revealed various new compounds produced during plastic degradation by these bacterial strains. The plastic biodegradation potential makes these bacteria an impending foundation for green chemistry to eradicate tough pollutants from the environment.
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Affiliation(s)
- Shakir Ali
- Department of Zoology, Government College University, Lahore, Pakistan
| | - Abdul Rehman
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Syed Zajif Hussain
- Department of Chemistry, SBA School of Science and Engineering (SBASSE), Lahore University of Management Sciences (LUMS), DHA, Lahore Cantt 54792, Pakistan
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Oh S, Cho K, Park S, Kwon MJ, Chung J, Lee S. Denitrification dynamics in unsaturated soils with different porous structures and water saturation degrees: A focus on the shift in microbial community structures. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130413. [PMID: 36436452 DOI: 10.1016/j.jhazmat.2022.130413] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
Despite its environmental significance, little is known about denitrification in vadose zones owing to the complexity of such environments. Here, we investigated denitrification in unsaturated soils with different pore distributions. To this end, we performed batch-type denitrification experiments and analyzed microbial community shifts before and after possible reactions with nitrates to clarify the relevant denitrifying mechanism in the microcosms. For quantitative comparison, pore distribution in the test soil samples was characterized based on the uniformity coefficient (Cu) and water saturation degree (SD). Micro-CT analysis of the soil pore distribution confirmed that the proportion of bigger-sized pores increased with decreasing Cu. However, oxygen diffusion into the system was controlled by SD rather than Cu. Within a certain SD range (51-67%), the pore condition changed abruptly from an oxic to an anoxic state. Consequently, denitrification occurred even under unsaturated soil conditions when the SD increased beyond 51-67%. High throughput sequencing revealed that the same microbial species were potentially responsible for denitrification under both partially (SD 67%), and fully saturated (SD of 100%) conditions, implying that the mechanism of denitrification in a vadose zone, if it exists, might be possibly similar under varying conditions.
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Affiliation(s)
- Sungjik Oh
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea
| | - Kyungjin Cho
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea
| | - Saerom Park
- Urban Water Circulation Research Center, Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology (KICT), Gyeonggi-do 10223, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Jaeshik Chung
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea.
| | - Seunghak Lee
- Water Cycle Research Center, Climate and Environment Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea; Division of Energy & Environment Technology, Korea University of Science & Technology (UST), Daejeon 34113, South Korea; Graduate School of Energy and Environment (KU-KIST Green School), Korea University, Seoul 02841, South Korea.
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7
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Deniaud M, Tee E. Susceptibility pattern of bacterial isolates in equine ulcerative keratitis: Implications for empirical treatment at a university teaching hospital in Sydney. Aust Vet J 2023; 101:115-120. [PMID: 36433648 DOI: 10.1111/avj.13221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/03/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022]
Abstract
Corneal ulceration is a common ophthalmic condition in horses. It is frequently caused by trauma to the corneal surface, followed by secondary infection by commensal or pathogenic organisms including Streptococcus equi subspecies zooepidemicus, Pseudomonas aeruginosa and Staphylococcus spp. Emerging antimicrobial resistance amongst these organisms has raised the need for appropriate antimicrobial therapy selection, to optimise treatment efficacy while minimising further antimicrobial resistance. Medical records of 38 horses presented at the University Veterinary Teaching Hospital Camden for ulcerative keratitis between 2010 and 2020 were reviewed to identify those with positive bacterial cultures and antimicrobial susceptibility profiles (13/38). Common susceptibility patterns were identified and used to guide the empirical treatment of equine bacterial corneal ulcers. Pseudomonas spp. (64.3%), Streptococcus equi subspecies zooepidemicus (14.3%) and Actinobacillus spp. (14.3%) were most commonly identified. Susceptibility to amikacin, gentamicin and ciprofloxacin was observed in 100%, 66.7% and 85.7% Pseudomonas spp. isolates respectively. Resistance to polymyxin B and neomycin occurred in 85.7% and 71.4% of Pseudomonas spp., respectively. All Streptococcus equi subspecies zooepidemicus organisms in this study were susceptible to ceftiofur, cephalexin, penicillin and ampicillin, while they were all resistant to gentamicin, neomycin, enrofloxacin and marbofloxacin. Predominating in this study, Pseudomonas spp. maintained overall aminoglycoside susceptibility despite some emerging resistance, and good fluoroquinolone susceptibility. High resistance to Polymyxin B could have arisen from its common use as first-line therapy for bacterial corneal ulcers. Although further research is required, these new findings about predominant bacteria in equine corneal ulceration in the Camden region and their antimicrobial susceptibility patterns can be used to guide the empirical treatment of bacterial corneal ulcers in horses.
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Affiliation(s)
- M Deniaud
- School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - E Tee
- School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
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Huo Q, Li R, Chen C, Wang C, Long T, Liu X. Study on potential microbial community to the waste water treatment from bauxite desilication process. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:15438-15453. [PMID: 36169826 DOI: 10.1007/s11356-022-23150-1] [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: 01/19/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Discharging waste water from the bauxite desilication process will bring potential environmental risk from the residual ions and organic compounds, especially hydrolyzed polyacrylamide. Characterization of the microbial community diversity in waste water plays an important role in the biological treatment of waste water. In this study, eight waste water samples from five flotation plants in China were investigated. The microbial community and functional profiles within the waste water were analyzed by a metagenomic sequencing method and associated with geochemical properties. The results revealed that Proteobacteria and Firmicutes were the dominant bacterial phyla. Both phylogenetical and clusters of orthologous groups' analyses indicated that Tepidicella, Paracoccus, Pseudomonas, and Exiguobacterium could be the dominant bacterial genera in the waste water from bauxite desilication process for their abilities to biodegrade complex organic compounds. The results of the microbial community diversity and functional gene compositions analyses provided a beneficial orientation for the biotreatment of waste water, as well as regenerative using of water resources. Besides, this study revealed that waste water from bauxite desilication process was an ideal ecosystem to find novel microorganisms, such as efficient strains for bio-desilication and bio-desulfurization of bauxite.
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Affiliation(s)
- Qiang Huo
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Ruoyang Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Chunqiang Chen
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Chenquan Wang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Tengfa Long
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
- College of Environment and Resources, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China
| | - Xi Liu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, No. 1, Yanzhong Road, Guilin, 541006, China.
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, No. 1, Yanzhong Road, Guilin, 541006, China.
- School of Economics and Management, Guangxi Normal University, Guilin, 541006, China.
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Hwang S, Yang JH, Sim HS, Choi SH, Lee B, Bang WY, Moon KH. Characterization of Pseudomonas sp. NIBR-H-19, an Antimicrobial Secondary Metabolite Producer Isolated from the Gut of Korean Native Sea Roach, Ligia exotica. J Microbiol Biotechnol 2022; 32:1416-1426. [PMID: 36310358 PMCID: PMC9720083 DOI: 10.4014/jmb.2208.08043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/29/2022]
Abstract
The need to discover new types of antimicrobial agents has grown since the emergence of antibiotic-resistant pathogens that threaten human health. The world's oceans, comprising complex niches of biodiversity, are a promising environment from which to extract new antibiotics-like compounds. In this study, we newly isolated Pseudomonas sp. NIBR-H-19 from the gut of the sea roach Ligia exotica and present both phenotypes and genomic information consisting of 6,184,379 bp in a single chromosome possessing a total of 5,644 protein-coding genes. Genomic analysis of the isolated species revealed that numerous genes involved in antimicrobial secondary metabolites are predicted throughout the whole genome. Moreover, our analysis showed that among twenty-five pathogenic bacteria, the growth of three pathogens, including Staphylococcus aureus, Streptococcus hominis and Rhodococcus equi, was significantly inhibited by the culture of Pseudomonas sp. NIBR-H-19. The characterization of marine microorganisms with biochemical assays and genomics tools will help uncover the biosynthesis and action mechanism of antimicrobial metabolites for development as antagonistic probiotics against fish pathogens in an aquatic culture system.
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Affiliation(s)
- Sungmin Hwang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Jun Hyeok Yang
- Laboratory of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
- Department of Marine Bioscience and Environment, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
| | - Ho Seok Sim
- Laboratory of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Sung Ho Choi
- National Institute of Biological Resources, Environmental Research Complex, Incheon 22689, Republic of Korea
| | - Byounghee Lee
- National Institute of Biological Resources, Environmental Research Complex, Incheon 22689, Republic of Korea
| | - Woo Young Bang
- National Institute of Biological Resources, Environmental Research Complex, Incheon 22689, Republic of Korea
| | - Ki Hwan Moon
- Laboratory of Marine Microbiology, Division of Convergence on Marine Science, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
- Department of Marine Bioscience and Environment, Korea Maritime & Ocean University, Busan 49112, Republic of Korea
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10
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Peddinti G, Hotti H, Teeri TH, Rischer H. De novo transcriptome assembly of Conium maculatum L. to identify candidate genes for coniine biosynthesis. Sci Rep 2022; 12:17562. [PMID: 36266299 PMCID: PMC9584964 DOI: 10.1038/s41598-022-21728-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/30/2022] [Indexed: 01/13/2023] Open
Abstract
Poison hemlock (Conium maculatum L.) is a notorious weed containing the potent alkaloid coniine. Only some of the enzymes in the coniine biosynthesis have so far been characterized. Here, we utilize the next-generation RNA sequencing approach to report the first-ever transcriptome sequencing of five organs of poison hemlock: developing fruit, flower, root, leaf, and stem. Using a de novo assembly approach, we derived a transcriptome assembly containing 123,240 transcripts. The assembly is deemed high quality, representing over 88% of the near-universal ortholog genes of the Eudicots clade. Nearly 80% of the transcripts were functionally annotated using a combination of three approaches. The current study focuses on describing the coniine pathway by identifying in silico transcript candidates for polyketide reductase, L-alanine:5-keto-octanal aminotransferase, γ-coniceine reductase, and S-adenosyl-L-methionine:coniine methyltransferase. In vitro testing will be needed to confirm the assigned functions of the selected candidates.
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Affiliation(s)
- Gopal Peddinti
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, 02044, Espoo, Finland
| | - Hannu Hotti
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, 02044, Espoo, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014, Helsinki, Finland
| | - Teemu H Teeri
- Viikki Plant Science Centre, Department of Agricultural Sciences, University of Helsinki, PO Box 27, 00014, Helsinki, Finland
| | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, 02044, Espoo, Finland.
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Atanasov KE, Galbis DM, Cornadó D, Serpico A, Sánchez G, Bosch M, Ferrer A, Altabella T. Pseudomonas fitomaticsae sp. nov., isolated at Marimurtra Botanical Garden in Blanes, Catalonia, Spain. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
In the framework of the research project called fitomatics, we have isolated and characterized a bacterial plant-endophyte from the rhizomes of Iris germanica, hereafter referred to as strain FIT81T. The bacterium is Gram negative, rod-shaped with lophotrichous flagella, and catalase- and oxidase-positive. The optimal growth temperature of strain FIT81T is 28 °C, although it can grow within a temperature range of 4–32 °C. The pH growth tolerance ranges between pH 5 and 10, and it tolerates 4% (w/v) NaCl. A 16S rRNA phylogenetic analysis positioned strain FIT81T within the genus
Pseudomonas
, and multilocus sequence analysis revealed that
Pseudomonas gozinkensis
IzPS32dT,
Pseudomonas glycinae
MS586T,
Pseudomonas allokribbensis
IzPS23T, 'Pseudomonas kribbensis' 46–2 and
Pseudomonas koreensis
PS9-14T are the top five most closely related species, which were selected for further genome-to-genome comparisons, as well as for physiological and chemotaxonomic characterization. The genome size of strain FIT81T is 6 492 796 base-pairs long, with 60.6 mol% of G+C content. Average nucleotide identity and digital DNA–DNA hybridization analyses yielded values of 93.6 and 56.1%, respectively, when the FIT81T genome was compared to that of the closest type strain
P. gozinkensis
IzPS32dT. Taken together, the obtained genomic, physiologic and chemotaxonomic data indicate that strain FIT81T is different from its closest relative species, which lead us to suggest that it is a novel species to be included in the list of type strains with the name Pseudomonas fitomaticsae sp. nov. (FIT81T=CECT 30374T=DSM 112699T).
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Affiliation(s)
- Kostadin Evgeniev Atanasov
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - David Miñana Galbis
- Department of Biology, Healthcare and the Environment, Microbiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Deborah Cornadó
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Annabel Serpico
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Guiomar Sánchez
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Montserrat Bosch
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Albert Ferrer
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Teresa Altabella
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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12
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Chung JH, Lee JY, Choi GH, Won M, Yeon J, Yoon Y, An SH, Kim DY, Park I, Kim YE, Ahn JH. Horticoccus luteus gen. nov., sp. nov., A Novel Member of the Phylum Verrucomicrobia Isolated from a Dichlorodiphenyltrichloroethane (DDT)-Contaminated Orchard Soil. Curr Microbiol 2022; 79:340. [PMID: 36209171 DOI: 10.1007/s00284-022-03036-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/06/2022] [Indexed: 11/03/2022]
Abstract
Strain KSB-15 T was isolated from an orchard soil that had been contaminated with the insecticide dichlorodiphenyltrichloroethane for about 60 years. The 16S rRNA gene sequence of this strain showed the highest sequence similarities with those of Oleiharenicola alkalitolerans NVTT (95.3%), Opitutus terrae PB90-1 T (94.8%), and Oleiharenicola lentus TWA-58 T (94.7%) among type strains, which are members of the family Opitutaceae within the phylum Verrucomicrobia. Strain KSB-15 T was an obligate aerobe, Gram-negative, non-motile, coccoid or short rod with the cellular dimensions of 0.37-0.62 μm width and 0.43-0.72 μm length. The strain grew at temperatures between 15-37 °C (optimum, 25 °C), at a pH range of 5.0-11.0 (optimum, pH 6.0), and at a NaCl concentration of 0-3% (w/v) (optimum, 0%). It contained menaquinone-7 (MK-7) as the major isoprenoid quinone (94.1%), and iso-C15:0 (34.9%) and anteiso-C15:0 (29.0%) as the two major fatty acids. The genome of strain KSB-15 T was composed of one chromosome with a total size of 4,320,198 bp, a G + C content of 64.3%, 3,393 coding genes (CDS), 14 pseudogenes, and 52 RNA genes. The OrthoANIu values, In silico DDH values and average amino acid identities between strain KSB-15 T and the members of the family Opitutaceae were 71.6 ~ 73.0%, 19.0 ~ 19.9%, and 55.9 ~ 62.0%, respectively. On the basis of our polyphasic taxonomic study, we conclude that strain KSB-15 T should be classified as a novel genus of the family Opitutaceae, for which the name Horticcoccus luteus gen. nov., sp. nov. is proposed.The type strain is KSB-15 T (= KACC 22271 T = DSM 113638 T).
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Affiliation(s)
- Joon-Hui Chung
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Ja-Yeon Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Geun-Hyung Choi
- Residual Chemical Assessment Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Jehyeong Yeon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Younggun Yoon
- College of Environmental and Bioresource Sciences, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Si-Hyun An
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Da-Yeon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - InCheol Park
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Ye-Eun Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Jae-Hyung Ahn
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
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13
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Fiedler G, Gieschler S, Kabisch J, Grimmler C, Brinks E, Wagner N, Hetzer B, Franz CMAP, Böhnlein C. Pseudomonas rustica sp. nov., isolated from bulk tank raw milk at a German dairy farm. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005288] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we present the description of a novel
Pseudomonas
species, designated Pseudomonas rustica sp. nov., which was isolated from raw milk samples obtained from Germany. Results of initial 16S rRNA gene sequence analysis assigned the strain into the genus
Pseudomonas
and showed
Pseudomonas helmanticensis
,
Pseudomonas neuropathica
and
Pseudomonas atagonensis
to be its closest relatives. Further studies including sequence analysis of the rpoB gene, multi-gene phylogenetic tree reconstruction, whole-genome sequence comparisons, cellular fatty acid analysis and chemotaxonomic characterization showed a clear separation from the known
Pseudomonas
species. Isolate MBT-4T was closely related to
Pseudomonas helmanticensis
, 'Pseudomonas crudilactis' and
Pseudomonas neuropathica
with average nucleotide identities based on blast values of 88.8, 88.8 and 88.6%, respectively. Therefore, the strain can be classified into the
Pseudomonas koreensis
subgroup of the
Pseudomonas fluorescens
group. The G+C content of strain MBT-4T was 58.9 mol%. The strain was catalase- and oxidase-positive, while the β-galactosidase reaction was negative. Growth occurred between 4 and 30 °C and at pH values from pH 6.0 to 8.0. In conclusion, strain MBT-4T belongs to a novel species, for which the name Pseudomonas rustica sp. nov. is proposed. The type strain is MBT-4T (=DSM 112348T=LMG 32241T) and strain MBT-17 is also a representative of this species.
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Affiliation(s)
- Gregor Fiedler
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Stefanie Gieschler
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Jan Kabisch
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Christina Grimmler
- Department of Safety and Quality of Meat, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, E.-C.-Baumann-Straße 20, 95326 Kulmbach, Germany
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Natalia Wagner
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Birgit Hetzer
- Department of Food Technology and Bioprocess Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Straße 9, 76131 Karlsruhe, Germany
| | - Charles M. A. P. Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
| | - Christina Böhnlein
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany
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14
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Atanasov KE, Galbis DM, Gallego J, Serpico A, Bosch M, Altabella T, Ferrer A. Pseudomonas germanica sp. nov., isolated from Iris germanica rhizomes. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Through bacterial plant–endophyte extraction from rhizomes of Iris germanica plant, a Gram-stain-negative, aerobic, catalase- and oxidase-positive gammaproteobacterial strain, referred to as FIT28T, was isolated. FIT28T shows vigorous growth on nutrient rich media within the temperature range of 4–35 °C, with optimal growth at 28 °C, a wide pH tolerance from pH 5 to 11, and salt tolerance up to 6 % (w/v) NaCl. Colonies are white-yellow and quickly become mucoid. The results of analysis of the 16S rRNA gene sequence placed the strain within the genus
Pseudomonas
, and multilocus sequence analysis (MLSA) using 16S rRNA, rpoB, gyrB and rpoD concatenated sequences revealed that the closest relatives of FIT28T are
Pseudomonas zeae
OE48.2T, '
Pseudomonas crudilactis
' UCMA 17988,
Pseudomonas tensinigenes
ZA5.3T,
Pseudomonas helmanticensis
OHA11T,
Pseudomonas baetica
a390T,
Pseudomonas iridis
P42T,
Pseudomonas atagonensis
PS14T and
Pseudomonas koreensis
Ps 9-14T, within the
Pseudomonas koreensis
subgroup of the
Pseudomonas fluorescens
lineage. The genome size of FIT28T is about 6.7 Mb with 59.09 mol% DNA G+C content. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values calculated from the genomic sequences of FIT28T, and the closely related
P. zeae
OE48.2T are 95.23 and 63.4 %, respectively. Biochemical, metabolic and chemotaxonomic studies further support our proposal that Pseudomonas germanica sp. nov., should be considered a novel species of the genus
Pseudomonas
. Hence, the type strain FIT28T (=LMG 32353T=DSM 112698T) has been deposited in public cell-type culture centres.
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Affiliation(s)
- Kostadin Evgeniev Atanasov
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - David Miñana Galbis
- Department of Biology, Healthcare and the Environment, Microbiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Julia Gallego
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Annabel Serpico
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Montserrat Bosch
- Applied Microbiology and Biotechnology Unit, LEITAT Technological Center, Terrassa, Spain
| | - Teresa Altabella
- Department of Biology, Healthcare and the Environment, Plant Physiology Section, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
| | - Albert Ferrer
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Bellaterra, Barcelona, Spain
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15
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Changes in Metabolic Regulation and the Microbiota Composition after Supplementation with Different Fatty Acids in db/db Mice. INTERNATIONAL JOURNAL OF FOOD SCIENCE 2022; 2022:3336941. [PMID: 35036426 PMCID: PMC8759926 DOI: 10.1155/2022/3336941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 12/15/2021] [Indexed: 12/20/2022]
Abstract
Introduction The effects of fatty acids on health vary and depend on the type, amount, and route of consumption. EPA and DHA have a defined role in health, unlike coconut oil. Objective The aim was to investigate the changes in metabolic regulation and the composition of the culture-dependent microbiota after supplementation with different fatty acids in db/db mice. Material and Methods. We were using 32 8-week-old db/db mice, supplemented for eight weeks with EPA/DHA derived from microalgae as well as coconut oil. The lipid, hormonal profiles, and composition of the culture-dependent microbiota and the phylogenetic analysis based on the 16S rRNA gene sequencing were determined for identification of the intestinal microbiota. Results Enriched diet with EPA/DHA reduced TNF-α, C-peptide, insulin resistance, resistin, and the plasma atherogenic index, but increased TC, LDL-c, VLDL-c, and TG without changes in HDL-c. Coconut oil raised the HDL-c, GIP, and TNF-α, with TG, insulin resistance, adiponectin, and C-peptide reduced. Conclusion The most abundant microbial populations were Firmicutes and the least Proteobacteria. EPA/DHA derived from microalgae contributes to improving the systemic inflammatory status, but depressed the diversity of the small intestine microbiota. Coconut oil only decreased the C-peptide, raising TNF-α, with an unfavorable hormonal and lipid profile.
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16
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Potgieter N, van der Loo C, Barnard TG. Co-Existence of Free-Living Amoebae and Potential Human Pathogenic Bacteria Isolated from Rural Household Water Storage Containers. BIOLOGY 2021; 10:biology10121228. [PMID: 34943143 PMCID: PMC8698325 DOI: 10.3390/biology10121228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 12/24/2022]
Abstract
Simple Summary In many households in rural communities, water needed for drinking and cooking is fetched from rivers, fountains, or boreholes shared by the community. The water is then stored in various storage containers for several days without treatment and exposed to several conditions that could potentially contaminate the water and cause diseases. If the storage containers are not regularly and properly cleaned, biofilms can form inside the containers. Several microorganisms can be found inside the biofilm that can potentially cause diseases in humans. One such group of organisms is called free-living amoebae, which graze on the bacteria found inside the biofilm. Several of these potentially harmful bacteria have adapted and can survive inside these free-living amoebae and potentially cause diseases when ingested by humans. Abstract This study investigated the co-existence of potential human pathogenic bacteria and free-living amoebae in samples collected from stored water in rural households in South Africa using borehole water as a primary water source. Over a period of 5 months, a total of 398 stored water and 392 biofilm samples were collected and assessed. Free-living amoebae were identified microscopically in 92.0% of the water samples and 89.8% of the biofilm samples. A further molecular identification using 18S rRNA sequencing identified Vermamoeba vermiformis, Entamoeba spp., Stenamoeba spp., Flamella spp., and Acanthamoeba spp. including Acanthamoeba genotype T4, which is known to be potentially harmful to humans. Targeted potential pathogenic bacteria were isolated from the water samples using standard culture methods and identified using 16S rRNA sequencing. Mycobacterium spp., Pseudomonas spp., Enterobacter spp., and other emerging opportunistic pathogens such as Stenotrophomonas maltophilia were identified. The results showed the importance of further studies to assess the health risk of free-living amoebae and potential human pathogenic bacteria to people living in rural communities who have no other option than to store water in their homes due to water shortages.
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Affiliation(s)
- Natasha Potgieter
- One Health Research Group, Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, Limpopo Province, South Africa
- Correspondence:
| | - Clarissa van der Loo
- Water and Health Research Centre, Doornfontein Campus, University of Johannesburg, Johannesburg 2112, Gauteng, South Africa; (T.G.B.); (C.v.d.L.)
| | - Tobias George Barnard
- Water and Health Research Centre, Doornfontein Campus, University of Johannesburg, Johannesburg 2112, Gauteng, South Africa; (T.G.B.); (C.v.d.L.)
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17
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Andriūnaitė E, Tamošiūnė I, Aleksandravičiūtė M, Gelvonauskienė D, Vinskienė J, Rugienius R, Baniulis D. Stimulation of Nicotiana tabacum L. In Vitro Shoot Growth by Endophytic Bacillus cereus Group Bacteria. Microorganisms 2021; 9:1893. [PMID: 34576789 PMCID: PMC8470653 DOI: 10.3390/microorganisms9091893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
In vitro plant tissue cultures face various unfavorable conditions, such as mechanical damage, osmotic shock, and phytohormone imbalance, which can be detrimental to culture viability, growth efficiency, and genetic stability. Recent studies have revealed a presence of diverse endophytic bacteria, suggesting that engineering of the endophytic microbiome of in vitro plant tissues has the potential to improve their acclimatization and growth. Therefore, the aim of this study was to identify cultivated tobacco (Nicotiana tabacum L.) endophytic bacteria isolates that are capable of promoting the biomass accumulation of in vitro tobacco shoots. Forty-five endophytic bacteria isolates were obtained from greenhouse-grown tobacco plant leaves and were assigned to seven Bacillus spp. and one Pseudomonas sp. based on 16S rRNA or genome sequence data. To evaluate the bacterial effect on in vitro plant growth, tobacco shoots were inoculated with 22 isolates selected from distinct taxonomic groups. Four isolates of Bacillus cereus group species B. toyonensis, B. wiedmannii and B. mycoides promoted shoot growth by 11-21%. Furthermore, a contrasting effect on shoot growth was found among several isolates of the same species, suggesting the presence of strain-specific interaction with the plant host. Comparative analysis of genome assemblies was performed on the two closely related B. toyonensis isolates with contrasting plant growth-modulating properties. This revealed distinct structures of the genomic regions, including a putative enzyme cluster involved in the biosynthesis of linear azol(in)e-containing peptides and polysaccharides. However, the function of these clusters and their significance in plant-promoting activity remains elusive, and the observed contrasting effects on shoot growth are more likely to result from genomic sequence variations leading to differences in metabolic or gene expression activity. The Bacillus spp. isolates with shoot-growth-promoting properties have a potential application in improving the growth of plant tissue cultures in vitro.
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Affiliation(s)
| | | | | | | | | | | | - Danas Baniulis
- Institute of Horticulture, Lithuanian Research Centre for Agriculture and Forestry, Kaunas str. 30, Babtai, 54333 Kaunas reg., Lithuania; (E.A.); (I.T.); (M.A.); (D.G.); (J.V.); (R.R.)
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18
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Breitkreuz C, Reitz T, Schulz E, Tarkka MT. Drought and Plant Community Composition Affect the Metabolic and Genotypic Diversity of Pseudomonas Strains in Grassland Soils. Microorganisms 2021; 9:microorganisms9081677. [PMID: 34442756 PMCID: PMC8399733 DOI: 10.3390/microorganisms9081677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/23/2022] Open
Abstract
Climate and plant community composition (PCC) modulate the structure and function of microbial communities. In order to characterize how the functional traits of bacteria are affected, important plant growth-promoting rhizobacteria of grassland soil communities, pseudomonads, were isolated from a grassland experiment and phylogenetically and functionally characterized. The Miniplot experiment was implemented to examine the mechanisms underlying grassland ecosystem changes due to climate change, and it investigates the sole or combined impact of drought and PCC (plant species with their main distribution either in SW or NE Europe, and a mixture of these species). We observed that the proportion and phylogenetic composition of nutrient-releasing populations of the Pseudomonas community are affected by prolonged drought periods, and to a minor extent by changes in plant community composition, and that these changes underlie seasonality effects. Our data also partly showed concordance between the metabolic activities and 16S phylogeny. The drought-induced shifts in functional Pseudomonas community traits, phosphate and potassium solubilization and siderophore production did not follow a unique pattern. Whereas decreased soil moisture induced a highly active phosphate-solubilizing community, the siderophore-producing community showed the opposite response. In spite of this, no effect on potassium solubilization was detected. These results suggest that the Pseudomonas community quickly responds to drought in terms of structure and function, the direction of the functional response is trait-specific, and the extent of the response is affected by plant community composition.
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Affiliation(s)
- Claudia Breitkreuz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH-UFZ, Theodor-Lieser-Str. 4, 06120 Halle, Germany; (T.R.); (E.S.); (M.T.T.)
- Correspondence: ; Tel.: +49-345-558-5416
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH-UFZ, Theodor-Lieser-Str. 4, 06120 Halle, Germany; (T.R.); (E.S.); (M.T.T.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Elke Schulz
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH-UFZ, Theodor-Lieser-Str. 4, 06120 Halle, Germany; (T.R.); (E.S.); (M.T.T.)
| | - Mika Tapio Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research GmbH-UFZ, Theodor-Lieser-Str. 4, 06120 Halle, Germany; (T.R.); (E.S.); (M.T.T.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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19
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Aigle A, Colin Y, Bouchali R, Bourgeois E, Marti R, Ribun S, Marjolet L, Pozzi ACM, Misery B, Colinon C, Bernardin-Souibgui C, Wiest L, Blaha D, Galia W, Cournoyer B. Spatio-temporal variations in chemical pollutants found among urban deposits match changes in thiopurine S-methyltransferase-harboring bacteria tracked by the tpm metabarcoding approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 767:145425. [PMID: 33636795 DOI: 10.1016/j.scitotenv.2021.145425] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
The bTPMT (bacterial thiopurine S-methyltransferase), encoded by the tpm gene, can detoxify metalloid-containing oxyanions and xenobiotics. The hypothesis of significant relationships between tpm distribution patterns and chemical pollutants found in urban deposits was investigated. The tpm gene was found conserved among eight bacterial phyla with no sign of horizontal gene transfers but a predominance among gammaproteobacteria. A DNA metabarcoding approach was designed for tracking tpm-harboring bacteria among polluted urban deposits and sediments recovered for more than six years in a detention basin (DB). This DB recovers runoff waters and sediments from a zone of high commercial activities. The PCR products from DB samples led to more than 540,000 tpm reads after DADA2 or MOTHUR bio-informatic manipulations that were allocated to more than 88 and less than 634 sequence variants per sample. The tpm community patterns were significantly different between the recent urban deposits and those that had accumulated for more than 2 years in the DB, and between those of the DB surface and the DB settling pit. These groups of samples had distinct mixture of priority pollutants. Significant relationships between tpm ordination patterns, sediment accumulation time periods and location, and concentrations in PAH, chlorpyrifos, and 4-nonylphenols (NP) were observed. These correlations matched the higher occurrences of, among others, Aeromonas, Pseudomonas, and Xanthomonas tpm-harboring bacteria in recent urban DB deposits more contaminated with chrysene and alkylphenol ethoxylates. Highly significant drops in tpm reads allocated to Aeromonas species were recorded in the oldest DB sediments accumulating naphthalene and metallic pollutants. Degraders of urban pollutants such as P. aeruginosa and P. putida showed conserved distribution patterns over time but P. syringae phytopathogens were more abundant in the oldest sediments. TPMT-harboring bacteria can be used to assess the incidence of high risk priority pollutants on environmental systems.
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Affiliation(s)
- Axel Aigle
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Yannick Colin
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Rayan Bouchali
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Emilie Bourgeois
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Romain Marti
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Sébastien Ribun
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Laurence Marjolet
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Adrien C M Pozzi
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Boris Misery
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Céline Colinon
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Claire Bernardin-Souibgui
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Laure Wiest
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS 5280, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Didier Blaha
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Wessam Galia
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France
| | - Benoit Cournoyer
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne, CNRS 5557, INRA 1418, Research team "Bacterial Opportunistic Pathogens and Environment", 69280 Marcy L'Etoile, France.
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Kim EJ, Park S, Adil S, Lee S, Cho K. Biogeochemical Alteration of an Aquifer Soil during In Situ Chemical Oxidation by Hydrogen Peroxide and Peroxymonosulfate. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5301-5311. [PMID: 33755424 DOI: 10.1021/acs.est.0c06206] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In this study, the effects of in situ chemical oxidation (ISCO) on the biogeochemical properties of an aquifer soil were evaluated. Microcosms packed with an aquifer soil were investigated for 4 months in two phases including oxidant exposure (phase I) and biostimulation involving acetate addition (phase II). The geochemical and microbial alterations from different concentrations (0.2 and 50 mM) of hydrogen peroxide (HP) and peroxymonosulfate (PMS) were assessed. The 50 mM PMS-treated sample exhibited the most significant geochemical changes, characterized by the decrease in pH and the presence of more crystalline phases. Microbial activity decreased for all ISCO-treated microcosms compared to the controls; particularly, the activity was severely inhibited at high PMS concentration exposure. The soil microbial community structures were shifted after the ISCO treatment, with the high PMS causing the most distinct changes. Microbes such as the Azotobacter chroococcum and Gerobacter spp. increased during phase II of the ISCO treatment, indicating these bacterial communities can promote organic degradation despite the oxidants exposure. The HP (low and high concentrations) and low concentration PMS exposure temporarily impacted the microbial activity, with recovery after some duration, whereas the microbial activity was less recovered after the high concentration PMS exposure. These results suggest that the use of HP and low concentration PMS are suitable ISCO strategies for aquifer soil bioattenuation.
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Affiliation(s)
- Eun-Ju Kim
- Water Cycle Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Saerom Park
- Urban Water Circulation Research Center, Department of Land, Water and Environment Research, Korea Institute of Civil Engineering and Building Technology, Gyeonggi-do 10223, Republic of Korea
| | - Sawaira Adil
- Water Cycle Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Seunghak Lee
- Water Cycle Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Kyungjin Cho
- Water Cycle Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Division of Energy and Environment Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
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21
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van der Loo C, Bartie C, Barnard TG, Potgieter N. Detection of Free-Living Amoebae and Their Intracellular Bacteria in Borehole Water before and after a Ceramic Pot Filter Point-of-Use Intervention in Rural Communities in South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:3912. [PMID: 33917870 PMCID: PMC8068299 DOI: 10.3390/ijerph18083912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 11/21/2022]
Abstract
Free-living amoebae (FLA) are ubiquitous in nature, whereas amoeba-resistant bacteria (ARB) have evolved virulent mechanisms that allow them to resist FLA digestion mechanisms and survive inside the amoeba during hostile environmental conditions. This study assessed the prevalence of FLA and ARB species in borehole water before and after a ceramic point-of-use intervention in rural households. A total of 529 water samples were collected over a five-month period from 82 households. All water samples were subjected to amoebal enrichment, bacterial isolation on selective media, and molecular identification using 16S PCR/sequencing to determine ARB species and 18S rRNA PCR/sequencing to determine FLA species present in the water samples before and after the ceramic pot intervention. Several FLA species including Acanthamoeba spp. and Mycobacterium spp. were isolated. The ceramic pot filter removed many of these microorganisms from the borehole water. However, design flaws could have been responsible for some FLA and ARB detected in the filtered water. FLA and their associated ARB are ubiquitous in borehole water, and some of these species might be potentially harmful and a health risk to vulnerable individuals. There is a need to do more investigations into the health risk of these organisms after point-of-use treatment.
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Affiliation(s)
- Clarissa van der Loo
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2094, South Africa; (C.v.d.L.); (T.G.B.)
| | | | - Tobias George Barnard
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2094, South Africa; (C.v.d.L.); (T.G.B.)
| | - Natasha Potgieter
- Environmental Health, Domestic Hygiene and Microbial Pathogens Research Group, Department of Microbiology, University of Venda, Thohoyandou 1950, South Africa
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22
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Schlusselhuber M, Girard L, Cousin FJ, Lood C, De Mot R, Goux D, Desmasures N. Pseudomonas crudilactis sp. nov., isolated from raw milk in France. Antonie van Leeuwenhoek 2021; 114:719-730. [PMID: 33715105 DOI: 10.1007/s10482-021-01552-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/22/2021] [Indexed: 12/20/2022]
Abstract
Strains belonging to the Pseudomonas genus have been isolated worldwide from various biotic (humans, animals and plant tissues) and abiotic (food, soil, water and air) environments. Raw milk provides a favorable environment for the growth of a broad spectrum of microorganisms, including Pseudomonas. Here we present the description of Pseudomonas sp. UCMA 17988 isolated from raw milk, which was previously reported to produce new antimicrobial lipopeptides. MultiLocus Sequence Analysis of four housekeeping genes (16S rRNA, gyrB, rpoD and rpoB), whole genome sequence comparison (orthoANI value, original ANI value and dDDH value), microscopy, FAME analysis, and biochemical tests were performed. Digital DNA-DNA hybridization and average nucleotide identity values between strain UCMA 17988 and its closest relatives, P. helmanticensis CECT 8548T (46.9%, 92.07%) and P. baetica CECT 7720T (26.8%, 88.50%), rate well below the designed threshold for assigning prokaryotic strains to the same species. In conclusion, strain UCMA 17988 belongs to a novel species, for which the name Pseudomonas crudilactis sp. nov (type strain UCMA 17988T = DSM 109949T = LMG 31804T) is proposed.
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Affiliation(s)
| | - Léa Girard
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | - Fabien J Cousin
- UNICAEN, UNIROUEN, ABTE, Normandie Univ, 14000, Caen, France
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium.,Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Leuven, Belgium
| | - René De Mot
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, Box 2460, 3001, Leuven, Belgium
| | - Didier Goux
- UNICAEN, Centre de Microscopie Appliquée á la Biologie, SF 4206 Interaction Cellule-Organisme-Environnement (ICORE), Normandie Univ, 14000, Caen, France.,ENSICAEN, UNICAEN, CNRS, CRISMAT, Normandie Univ, 14000, Caen, France
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23
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Eskandari S, Etemadifar Z. Melanin biopolymers from newly isolated Pseudomonas koreensis strain UIS 19 with potential for cosmetics application, and optimization on molasses waste medium. J Appl Microbiol 2021; 131:1331-1343. [PMID: 33609007 DOI: 10.1111/jam.15046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/22/2021] [Accepted: 02/17/2021] [Indexed: 11/28/2022]
Abstract
AIMS Bacterial melanins are UV-absorber biopolymers with potential applications in cosmetics and pharmaceutical industries. However, the cost concern of these pigments remains a limiting factor for their commercial production. Hence, the present study was aimed to isolate a bacterium with high yield of melanin by optimization of an inexpensive waste sources. METHODS AND RESULTS Pseudomonas koreensis UIS 19 (accession number: MG548583), which displayed significant bioproduction of melanin along with high tyrosinase enzyme activity was isolated from soil and introduced as a melanin-producing bacterium. Scanning and transmission electron microscope studies revealed that melanin pigments accumulated inside as well as the extracellular space of the cells. Melanin was extracted from the isolated strain and its detection was investigated using NMR and HPLC analyses. Here, we showed that the DPPH radical scavenging activity of 20 mg ml-1 melanin extracted from the isolated strain was >92·42% and its sun protection factor (SPF) value was 61·55. Melanin production by the UIS 19 in molasses medium showed sugar consumption (32 g l-1 ) for biomass production (5·4 g dry wt) and melanin yield of 0·44 g dry wt g-1 biomass from l-tyrosine. Some critical intermediated such tyramine, l-dopa, dopamine and dopaquinone related to the melanin Raper Mason pathway were detected by H-NMR. Furthermore, to achieve high bioproduction of melanin in inexpensive media include 5% molasses 5 Brix as an industrial waste, nutritional and environmental parameters were screened using response surface methodology by Box-Behnken design in which, maximum melanin yield of 5·5 g dry wt l-1 was obtained. CONCLUSIONS The bioproduction of melanin as valuable compound from P. koreensis was performed using an optimized waste medium. The purified melanin showed high radical scavenging activity and high SPF value. SIGNIFICANCE AND IMPACT OF THE STUDY Pseudomonas koreensis UIS 19 is a promising candidate for industrial production of melanin as cosmetic skin-care product.
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Affiliation(s)
- S Eskandari
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Z Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Fluit AC, Rogers MRC, Díez-Aguilar M, Cantón R, Benaissa-Trouw BJ, Bayjanov JR, Ekkelenkamp MB. Draft genome sequence of the strain 16-537536, isolated from a patient with bronchiectasis and its relationship to the Pseudomonas koreensis group of the Pseudomonas fluorescens complex. BMC Res Notes 2020; 13:10. [PMID: 31907003 PMCID: PMC6945793 DOI: 10.1186/s13104-019-4863-2] [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: 10/18/2019] [Accepted: 12/16/2019] [Indexed: 11/10/2022] Open
Abstract
Abstract
Objective
The Pseudomonas koreensis group bacteria are usually found in soil and are associated with plants. Currently they are poorly described. Here we report on the whole genome sequence of a bacterial isolate from a patient with bronchiectasis that was first identified as P. koreensis, and on its position in the P. koreensis group.
Results
Strain 16-537536 was isolated from a patient with bronchiectasis from Spain and initially identified by MALDI-TOF as P. koreensis, a member of the Pseudomonas fluorescens complex. However, the average nucleotide identity analysis (ANIb) and whole genome alignments of the draft genome sequence of this strain showed it to be a member of the P. koreensis group of the P. fluorescens complex, but belonging to an undescribed species. In addition, based on ANIb analysis, the P. koreensis group contains several other unnamed species. Several genes for putative virulence factors were identified. The only antibiotic resistance gene present in strain 16-537536 was a class C β-lactamase. The correct identification of bacterial species from patients is of utmost importance in order to understand their pathogenesis and to track the potential spread of pathogens between patients. Whole genome sequence data should be included for the description of new species.
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Nguyen HT, Kim Y, Choi JW, Cho K, Jeong S. Assimilable organic carbon removal strategy for aquifer storage and recovery applications. ENVIRONMENTAL RESEARCH 2020; 191:110033. [PMID: 32810494 DOI: 10.1016/j.envres.2020.110033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Aquifer storage and recovery (ASR) technology has been adopted as a strategic water management tool. However, during the injection of oxic and organic carbon-containing water to the underground aquifers, severe phenomena such as clogging and groundwater deterioration have been reported. To prevent these severe phenomena, assimilable organic carbon (AOC) concentration has been controlled in the ASR applications by supporting bacteria growth potential. In this study, the AOC removal strategy was investigated in a simulated ASR system using an indigenous bacterium, Pseudomonas jinjuensis. AOC removal was evaluated under three different experimental conditions: (i) 30 °C and aerobic, (ii) 15 °C and aerobic, and (iii) 15 °C and anoxic. The effects of contact media such as sand and granular activated carbon on AOC removal efficiency were also investigated. Results show that under the 30 °C aerobic condition, P. jinjuensis could remove 99.8% (13 μg L-1) of AOC with soil. The variations in the organic fractions determined by liquid chromatography with organic carbon detector analysis were observed and showed trends similar to those of AOC determined by the flow cytometry method. The indirect injection method in ASR application was recommended due to the AOC removal benefit by soil indigenous bacterium.
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Affiliation(s)
- Hien Thi Nguyen
- Division of Energy & Environment Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea; Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Youngjae Kim
- Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jae-Woo Choi
- Division of Energy & Environment Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea; Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Kyungjin Cho
- Division of Energy & Environment Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea; Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea.
| | - Seongpil Jeong
- Division of Energy & Environment Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, Republic of Korea; Water Cycle Research Center, National Agenda Research Division, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea.
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Orlando M, Pucciarelli S, Lotti M. Endolysins from Antarctic Pseudomonas Display Lysozyme Activity at Low Temperature. Mar Drugs 2020; 18:E579. [PMID: 33233712 PMCID: PMC7699920 DOI: 10.3390/md18110579] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Organisms specialized to thrive in cold environments (so-called psychrophiles) produce enzymes with the remarkable ability to catalyze chemical reactions at low temperature. Cold activity relies on adaptive changes in the proteins' sequence and structural organization that result in high conformational flexibility. As a consequence of flexibility, several such enzymes are inherently heat sensitive. Cold-active enzymes are of interest for application in a number of bioprocesses, where cold activity coupled with easy thermal inactivation can be of advantage. We describe the biochemical and functional properties of two glycosyl hydrolases (named LYS177 and LYS188) of family 19 (GH19), identified in the genome of an Antarctic marine Pseudomonas. Molecular evolutionary analysis placed them in a group of characterized GH19 endolysins active on lysozyme substrates, such as peptidoglycan. Enzyme activity peaks at about 25-35 °C and 40% residual activity is retained at 5 °C. LYS177 and LYS188 are thermolabile, with Tm of 52 and 45 °C and half-lives of 48 and 12 h at 37 °C, respectively. Bioinformatics analyses suggest that low heat stability may be associated to temperature-driven increases in local flexibility occurring mainly in a specific region of the polypeptide that is predicted to contain hot spots for aggregation.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, 20126 Milano, Italy;
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, 20126 Milano, Italy;
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Khoo LW, Srinivasan SS, Henriquez FL, Bal AM. A Rare Case of Mixed Infectious Keratitis Caused by <b><i>Pseudomonas koreensis</i></b> and <b><i>Aspergillus fumigatus</i></b>. Case Rep Ophthalmol 2020; 11:600-605. [PMID: 33437234 PMCID: PMC7747071 DOI: 10.1159/000510571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 07/29/2020] [Indexed: 11/19/2022] Open
Abstract
We report the clinical and microbiological features of contact lens-related mixed infectious keratitis caused by a spore-forming filamentous fungus and a rare gram-negative bacterial infection. A 66-year-old Caucasian female presented with right eye (OD) pain after sleeping in her 2-weekly contact lenses for 3 days. On presentation, corrected distance visual acuity was 0.46 LogMAR OD and 0.20 in the left eye. Slit lamp biomicroscopy revealed a 1.9 mm by 1.9 mm area of dense stromal infiltrate with epithelial defect. Corneal scrapes grew Aspergillus fumigatus and Pseudomonas koreensis, and culture-directed microbial therapy with oral and topical voriconazole and topical fortified gentamicin along with regular debridement resulted in slow resolution of the infection, leaving a dense stromal scar in the visual axis requiring penetrating keratoplasty. Mixed infectious keratitis caused by filamentous fungi and gram-negative bacteria is rare. Pseudomonas koreensis infection has not been previously reported as a cause of infectious keratitis in humans. In our experience, these mixed infections require prolonged systemic and topical therapy and the secondary scarring may require surgical intervention for vision rehabilitation.
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Affiliation(s)
- Lin Wei Khoo
- Department of Ophthalmology, University Hospital Ayr, Ayr, United Kingdom
- School of Health and Life Sciences, University of West of Scotland, Paisley, United Kingdom
| | - Sathish S. Srinivasan
- Department of Ophthalmology, University Hospital Ayr, Ayr, United Kingdom
- School of Health and Life Sciences, University of West of Scotland, Paisley, United Kingdom
- *Sathish Srinivasan, Department of Ophthalmology, 3rd Floor, University Hospital Ayr, Dalmellington Road, Ayr KA6 6DX (UK),
| | - Fiona L. Henriquez
- School of Health and Life Sciences, University of West of Scotland, Paisley, United Kingdom
| | - Abhijit M. Bal
- Department of Medical Microbiology, University Hospital Crosshouse, Crosshouse, United Kingdom
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Yao Y, Hu L, Li S, Zeng Q, Zhong H, He Z. Exploration on the bioreduction mechanisms of Cr(VI) and Hg(II) by a newly isolated bacterial strain Pseudomonas umsongensis CY-1. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110850. [PMID: 32531571 DOI: 10.1016/j.ecoenv.2020.110850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/24/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Despite of significant progress in remediation of Cr(VI) or Hg(II) pollution by microorganisms, study on the reduction of both Cr(VI) and Hg(II) by the same microbial strain was not reported so far, which is actually important for bioremediation of contaminated sites with multiple heavy metals. In this study, Pseudomonas umsongensis CY-1 was newly isolated from chromium-contaminated soil and showed remediation potentials for both Cr(VI) and Hg(II) pollution. The highest Cr(VI) (93.9%) and Hg(II) (82.8%) reduction rates were obtained at the initial concentration of 5 mg/L. Comparison between removal by resting cells and heat-treated resting cells demonstrated that P. umsongensis CY-1 removed Cr(VI) and Hg(II) from Tris-HCl buffer (pH 7.0) mainly through reduction instead of adsorption. By comparing the Cr(VI) and Hg(II) reduction rates of different cellular fractions, it was found that Cr(VI) and Hg(II) reductions mainly happened in the cytoplasm of P. umsongensis CY-1, which were further demonstrated by Transmission electron microscopy (TEM) analysis. Furthermore, analysis of X-ray photoelectron spectroscopy demonstrated that the reduction products of Cr(VI) and Hg(II) were mainly in the form of Cr(III) and Hg (0), respectively. The findings in this study will provide a guide for further insights in the bioremediation of contaminated sites with multiple heavy metals.
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Affiliation(s)
- Yang Yao
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Liang Hu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Shuzhen Li
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Qiang Zeng
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China
| | - Hui Zhong
- School of Life Science, Central South University, Changsha, 410012, China.
| | - Zhiguo He
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha, 410083, China; Faculty of Materials Metallurgy & Chemistry, Jiangxi University of Science & Technology, Ganzhou, Jiangxi, 341000, China.
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29
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Gu Y, Ma Y, Wang J, Xia Z, Wei H. Genomic insights into a plant growth-promoting Pseudomonas koreensis strain with cyclic lipopeptide-mediated antifungal activity. Microbiologyopen 2020; 9:e1092. [PMID: 32537904 PMCID: PMC7520995 DOI: 10.1002/mbo3.1092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 11/06/2022] Open
Abstract
Strain S150 was isolated from the tobacco rhizosphere as a plant growth-promoting rhizobacterium. It increased plant fresh weight significantly and lateral root development, and it antagonized plant pathogenic fungi but not phytobacteria. Further tests showed that strain S150 solubilized organic phosphate and produced ammonia, siderophore, protease, amylase, and cellulase, but it did not produce indole-3-acetic acid. Using morphology, physiological characteristics, and multi-locus sequence analysis, strain S150 was identified as Pseudomonas koreensis. The complete genome of strain S150 was sequenced, and it showed a single circular chromosome of 6,304,843 bp with a 61.09% G + C content. The bacterial genome contained 5,454 predicted genes that occupied 87.7% of the genome. Venn diagrams of the identified orthologous clusters of P. koreensis S150 with the other three sequenced P. koreensis strains revealed up to 4,167 homologous gene clusters that were shared among them, and 21 orthologous clusters were only present in the genome of strain S150. Genome mining of the bacterium P. koreensis S150 showed that the strain possessed 10 biosynthetic gene clusters for secondary metabolites, which included four clusters of non-ribosomal peptide synthetases (NRPSs) involved in the biosynthesis of cyclic lipopeptides (CLPs). One of the NRPSs possibly encoded lokisin, a cyclic lipopeptide produced by fluorescent Pseudomonas. Genomic mutation of the lokA gene, which is one of the three structural NRPS genes for lokisin in strain S150, led to a deficiency in fungal antagonism that could be restored fully by gene complementation. The results suggested that P. koreensis S150 is a novel plant growth-promoting agent with specific cyclic lipopeptides and contains a lokisin-encoding gene cluster that is dominant against plant fungal pathogens.
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Affiliation(s)
- Yilin Gu
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesKey Laboratory of Microbial Resources Collection and PreservationMinistry of Agriculture and Rural AffairsBeijingChina
| | - Yi‐Nan Ma
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesKey Laboratory of Microbial Resources Collection and PreservationMinistry of Agriculture and Rural AffairsBeijingChina
| | - Jing Wang
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesKey Laboratory of Microbial Resources Collection and PreservationMinistry of Agriculture and Rural AffairsBeijingChina
| | - Zhenyuan Xia
- Yunnan Academy of Tobacco Agricultural ScienceKunmingChina
| | - Hai‐Lei Wei
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesKey Laboratory of Microbial Resources Collection and PreservationMinistry of Agriculture and Rural AffairsBeijingChina
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Benedek T, Szentgyörgyi F, Szabó I, Farkas M, Duran R, Kriszt B, Táncsics A. Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm. Appl Microbiol Biotechnol 2020; 104:6023-6043. [PMID: 32415320 PMCID: PMC7306034 DOI: 10.1007/s00253-020-10668-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/20/2022]
Abstract
In this study, we aimed at determining the impact of naphthalene and different oxygen levels on a biofilm bacterial community originated from a petroleum hydrocarbon-contaminated groundwater. By using cultivation-dependent and cultivation-independent approaches, the enrichment, identification, and isolation of aerobic and oxygen-limited naphthalene degraders was possible. Results indicated that, regardless of the oxygenation conditions, Pseudomonas spp. became the most dominant in the naphthalene-amended selective enrichment cultures. Under low-oxygen conditions, P. veronii/P. extremaustralis lineage affiliating bacteria, and under full aerobic conditions P. laurentiana-related isolates were most probably capable of naphthalene biodegradation. A molecular biological tool has been developed for the detection of naphthalene 1,2-dioxygenase-related 2Fe-2S reductase genes of Gram-negative bacteria. The newly developed COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP-PCR) technique may be used in the monitoring of the natural attenuation capacity of PAH-contaminated sites. A bacterial strain collection with prolific biofilm-producing and effective naphthalene-degrading organisms was established. The obtained strain collection may be applicable in the future for the development of biofilm-based bioremediation systems for the elimination of PAHs from groundwater (e.g., biofilm-based biobarriers).
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Affiliation(s)
- Tibor Benedek
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary.
| | - Flóra Szentgyörgyi
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - István Szabó
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Milán Farkas
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - Robert Duran
- IPREM UMR CNRS 5254, Equipe Environnement et Microbiologie, MELODY Group, Université de Pau et des Pays de l'Adour, Pau, France
| | - Balázs Kriszt
- Department of Environmental Protection and Safety, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
| | - András Táncsics
- Regional University Centre of Excellence in Environmental Industry, Szent István University, Páter K. u. 1, Gödöllő, H-2100, Hungary
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Soares R, Trejo J, Lorite MJ, Figueira E, Sanjuán J, Videira e Castro I. Diversity, Phylogeny and Plant Growth Promotion Traits of Nodule Associated Bacteria Isolated from Lotus parviflorus. Microorganisms 2020; 8:microorganisms8040499. [PMID: 32244524 PMCID: PMC7232477 DOI: 10.3390/microorganisms8040499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/18/2020] [Accepted: 03/30/2020] [Indexed: 11/18/2022] Open
Abstract
Lotus spp. are widely used as a forage to improve pastures, and inoculation with elite rhizobial strains is a common practice in many countries. However, only a few Lotus species have been studied in the context of plant-rhizobia interactions. In this study, forty highly diverse bacterial strains were isolated from root nodules of wild Lotus parviflorus plants growing in two field locations in Portugal. However, only 10% of these isolates could nodulate one or more legume hosts tested, whereas 90% were thought to be opportunistic nodule associated bacteria. Phylogenetic studies place the nodulating isolates within the Bradyrhizobium genus, which is closely related to B. canariense and other Bradyrhizobium sp. strains isolated from genistoid legumes and Ornithopus spp. Symbiotic nodC and nifH gene phylogenies were fully consistent with the taxonomic assignment and host range. The non-nodulating bacteria isolated were alpha- (Rhizobium/Agrobacterium), beta- (Massilia) and gamma-proteobacteria (Pseudomonas, Lysobacter, Luteibacter, Stenotrophomonas and Rahnella), as well as some bacteroidetes from genera Sphingobacterium and Mucilaginibacter. Some of these nodule-associated bacteria expressed plant growth promotion (PGP) traits, such as production of lytic enzymes, antagonistic activity against phytopathogens, phosphate solubilization, or siderophore production. This argues for a potential beneficial role of these L. parviflorus nodule-associated bacteria.
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Affiliation(s)
- Ricardo Soares
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
- Laboratório de Bioquímica Inorgânica e RMN, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Jesús Trejo
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
| | - Maria J. Lorite
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, E-18160 Granada, Spain; (M.L.); (J.S.)
| | - Etelvina Figueira
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal;
| | - Juan Sanjuán
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, E-18160 Granada, Spain; (M.L.); (J.S.)
| | - Isabel Videira e Castro
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
- Correspondence:
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Comparison of Light Microscopy and Polymerase Chain Reaction for the Detection of Haemoparasites in Cattle in Nigeria. Acta Parasitol 2020; 65:44-56. [PMID: 31571143 DOI: 10.2478/s11686-019-00123-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/14/2019] [Indexed: 11/20/2022]
Abstract
PURPOSE Haemoparasitic diseases are among the important factors that threaten cattle health and productivity especially in the sub-Saharan region. In Nigeria, their detection using sensitive molecular techniques is scanty. This study was designed to investigate and to reevaluate the repertoire of haemoparasites of cattle in Ibadan, Nigeria with a comparative evaluation of light microscopy (LM) and polymerase chain reaction (PCR) methods. METHODS Blood samples from 100 cattle slaughtered at Ibadan abattoirs were examined using LM and PCR techniques for haemoparasite detection. The PCR reactions using three primer sets targeting the 16S rRNA genes for Hemoplasma spp. and Anaplasma/Ehrlichia spp. and 18S rRNA genes of Babesia/Theleiria spp. were done. A few randomly selected amplicons from each set were sequenced and analysed. RESULTS A total infection rate of 34% by LM including Hemoplasma spp. (17%), Anaplasma spp. (16%), microfilaria (5%) and Trypanosoma spp. (12%) was recorded. While, 86% positivity was recorded with PCR amplification as follows: Hemoplasma spp. (64%), Babesia/Theleiria spp. (46%) and Anaplasma/Ehrlichia spp. (5%). Comparison of LM and PCR findings showed that no LM Anaplasma spp.-positive samples and 7 out of the 17 LM hemoplasma-positive cattle were confirmed by PCR. In addition, LM led to misdiagnosis of 46 Babesia/Theleiria spp.-positive samples. Amplicon sequencing and phylogenetic analysis of Babesia/Theileria spp.-positive samples revealed Theileria velifera and Theileria annulata. In the Anaplasma/Ehrlichia spp.-positive samples, only Anaplasma marginale was characterized. Mycoplasma wenyonii, "Candidatus Mycoplasma haemobos" and Pseudomonas fluorescens like were characterized among the hemoplasma-infected cattle. CONCLUSIONS The first report of "Candidatus Mycoplasma haemobos" and Pseudomonas fluorescens like in Nigerian cattle is herewith documented. The alarming LM misdiagnosis of haemoparasites during this study confirms its limitations as it fails to identify many parasites and emphasizes the need for inclusion of molecular techniques to improve their detection. The study also shows for the first time the high prevalence of haemotropic mycoplasma in Nigerian cattle via molecular diagnostic methods, thus indicating a strong need for the investigation of their zoonotic implications.
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Eskandari S, Etemadifar Z. Isolation and Characterization of Melanin Producing Pseudomonas stutzeri Strain UIS2 in the Presence of l-tyrosine and Survey of Biological Properties of Its Melanin. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2020; 14:70-83. [DOI: 10.30699/ijmm.14.1.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
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Dobrovolskaya TG, Golovchenko AV, Yurchenko EN, Yakushev AV, Manucharova NA, Lysak LV, Kostina NV. Bacterial Communities of Regressive Spots in Ombrotrophic Bogs: Structure and Functions. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Dobrovolskaya TG, Golovchenko AV, Yurchenko EN, Yakushev AV, Manucharova NA, Glukhova TV. Abundance, Taxonomic Structure, and Functions of Bacterial Communities of Heather Plants in Ombrotrophic Bogs. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Piccirilli A, Pompilio A, Rossi L, Segatore B, Amicosante G, Rosatelli G, Perilli M, Di Bonaventura G. Identification of CTX-M-15 and CTX-M-27 in Antibiotic-Resistant Gram-Negative Bacteria Isolated from Three Rivers Running in Central Italy. Microb Drug Resist 2019; 25:1041-1049. [DOI: 10.1089/mdr.2019.0016] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Arianna Pompilio
- Department of Medical, Oral and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine (CeSI-MeT), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Laura Rossi
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Bernardetta Segatore
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Gianfranco Amicosante
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Gianluigi Rosatelli
- Department of Psychology, Health and Territory Sciences, “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanni Di Bonaventura
- Department of Medical, Oral and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine (CeSI-MeT), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
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Kaur M, Jangra M, Singh H, Tambat R, Singh N, Jachak SM, Mishra S, Sharma C, Nandanwar H, Pinnaka AK. Pseudomonas koreensis Recovered From Raw Yak Milk Synthesizes a β-Carboline Derivative With Antimicrobial Properties. Front Microbiol 2019; 10:1728. [PMID: 31417521 PMCID: PMC6681700 DOI: 10.3389/fmicb.2019.01728] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022] Open
Abstract
Natural evolution in microbes exposed to antibiotics causes inevitable selection of resistant mutants. This turns out to be a vicious cycle which requires the continuous discovery of new and effective antibiotics. For the last six decades, we have been relying on semisynthetic derivatives of natural products discovered in "Golden Era" from microbes, especially Streptomyces sp. Low success rates of rational drug-design sparked a resurgence in the invention of novel natural products or scaffolds from untapped or uncommon microbial niches. Therefore, in this study, we examined the microbial diversity inhabiting the yak milk for their ability to produce antimicrobial compounds. We prepared the crude fermentation extracts of fifty isolates from yak milk and screened them against indicator strains for the inhibitory activity. Later, with the aid of gel filtration chromatography followed by reversed-phase HPLC, we isolated one antimicrobial compound Y5-P1 from the strain Y5 (Pseudomonas koreensis) which showed bioactivity against Gram-positive and Gram-negative bacteria. The compound was chemically characterized using HRMS, FTIR, and NMR spectroscopy and identified as 1-acetyl-9H-β-carboline-3-carboxylic acid. It showed minimum inhibitory activity (MIC) in the range of 62.5-250 μg /ml. The cytotoxicity results revealed that IC50 against two mammalian cell lines i.e., HepG2 and HEK293T was 500 and 750 μg/ml, respectively. This is the first report on the production of this derivative of β-carboline by the microorganism. Also, the study enlightens the importance of microbes residing in uncommon environments or unexplored habitats in the discovery of a diverse array of natural products which could be designed further as drug candidates against highly resistant pathogens.
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Affiliation(s)
- Manpreet Kaur
- Clinical Microbiology and Bioactive Screening Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
- Council of Scientific and Industrial Research-Central Scientific Instruments Organisation, Chandigarh, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, New Delhi, India
| | - Manoj Jangra
- Clinical Microbiology and Bioactive Screening Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Harjodh Singh
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
- Council of Scientific and Industrial Research-Central Scientific Instruments Organisation, Chandigarh, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, New Delhi, India
| | - Rushikesh Tambat
- Clinical Microbiology and Bioactive Screening Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Nittu Singh
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Sanjay M. Jachak
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Sahibzada Ajit Singh Nagar, India
| | - Sunita Mishra
- Council of Scientific and Industrial Research-Central Scientific Instruments Organisation, Chandigarh, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, New Delhi, India
| | - Charu Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Hemraj Nandanwar
- Clinical Microbiology and Bioactive Screening Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, New Delhi, India
| | - Anil Kumar Pinnaka
- Microbial Type Culture Collection and Gene Bank, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research, Council of Scientific and Industrial Research, New Delhi, India
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Srivastava AK, Saxena P, Sharma A, Srivastava R, Jamali H, Bharati AP, Yadav J, Srivastava AK, Kumar M, Chakdar H, Kashyap PL, Saxena AK. Draft genome sequence of a cold-adapted phosphorous-solubilizing Pseudomonas koreensis P2 isolated from Sela Lake, India. 3 Biotech 2019; 9:256. [PMID: 31192081 DOI: 10.1007/s13205-019-1784-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 05/30/2019] [Indexed: 12/20/2022] Open
Abstract
The draft genome sequence of a cold-adapted phosphorus-solubilizing strain Pseudomonas koreensis P2 isolated from the Sela Lake contains 6,436,246 bp with G + C content of 59.8%. The genome sequence includes 5743 protein coding genes, 68 non-protein coding genes, 1007 putative proteins, 5 rRNA genes, 64 tRNAs and two prophage regions in 40 contigs. Besides these, genes involved in phosphate solubilization, siderophore production, iron uptake, heat shock and cold shock tolerance, multidrug resistance and glycine-betaine production were also identified.
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Schmid M, Frei D, Patrignani A, Schlapbach R, Frey JE, Remus-Emsermann MNP, Ahrens CH. Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats. Nucleic Acids Res 2019; 46:8953-8965. [PMID: 30137508 PMCID: PMC6158609 DOI: 10.1093/nar/gky726] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/15/2018] [Indexed: 12/16/2022] Open
Abstract
Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length, which contained several genes that may confer fitness advantages to the strain. Its complex genome, which also included a variable shufflon region, could not be de novo assembled with long reads produced by Pacific Biosciences’ technology, but required very long reads from Oxford Nanopore Technologies. Importantly, a repeat analysis, whose results we release for over 9600 prokaryotes, indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas. Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this ‘dark matter’ for de novo genome assembly of prokaryotes. Several of these ‘dark matter’ genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assembly algorithms capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.
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Affiliation(s)
- Michael Schmid
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Daniel Frei
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Andrea Patrignani
- Functional Genomics Center Zurich, University of Zurich & ETH Zurich, Zurich CH-8057, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich & ETH Zurich, Zurich CH-8057, Switzerland
| | - Jürg E Frey
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Mitja N P Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8140, New Zealand
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil CH-8820, Switzerland
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Lee CM, Kim SY, Yoon SH, Kim JB, Yeo YS, Sim JS, Hahn BS, Kim DG. Characterization of a novel antibacterial N-acyl amino acid synthase from soil metagenome. J Biotechnol 2019; 294:19-25. [DOI: 10.1016/j.jbiotec.2019.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 11/30/2022]
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Cho H, Park JY, Kim YK, Sohn SH, Park DS, Kwon YS, Kim CW, Back CG. Whole-Genome Sequence of Erwinia persicina B64, Which Causes Pink Soft Rot in Onions. Microbiol Resour Announc 2019; 8:e01302-18. [PMID: 30637383 PMCID: PMC6318354 DOI: 10.1128/mra.01302-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/16/2018] [Indexed: 11/30/2022] Open
Abstract
Erwinia persicina B64 was isolated from rotten onions in cold-storage facilities. Here, we report the complete genome sequence of E. persicina B64, which contains 5,070,450 bp with 55.17% GC content. The genome of this isolate is composed of one chromosome and two plasmids.
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Affiliation(s)
- Heejung Cho
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Ji Yeon Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Yong Ki Kim
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Seong-Han Sohn
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Dong Suk Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, Republic of Korea
| | - Young-Seok Kwon
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Cheol-Woo Kim
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Chang-Gi Back
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, Republic of Korea
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Pseudomonas humi sp. nov., isolated from leaf soil. Arch Microbiol 2018; 201:245-251. [PMID: 30478729 DOI: 10.1007/s00203-018-1588-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/24/2018] [Indexed: 10/27/2022]
Abstract
An aerobic, Gram-negative, non-sporulating, motile, rod-shaped and lignin-degrading bacterial strain, Pseudomonas sp. CCA1, was isolated from leaf soil collected in Japan. This strain grew at 20-45 °C (optimum 20 °C), at pH 5.0-10.0 (optimum pH 5.0), and in the presence of 2% NaCl. Its major cellular fatty acids were C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The predominant quinone system was ubiquinone-9. Comparative 16S rRNA gene sequence analysis showed that Pseudomonas sp. CCA1 was related most closely to P. citronellolis NBRC 103043T (98.9%), but multilocus sequence analysis based on fragments of the atpD, gyrA, gyrB and rpoB gene sequences showed strain CCA1 to branch separately from its most closely related Pseudomonas type strains. DNA-DNA hybridization values between Pseudomonas sp. CCA1 and type strains of closely related Pseudomonas species were less than 53%. Based on its phenotypic, chemotaxonomic and phylogenetic features, we propose that Pseudomonas sp. CCA1 represents a novel species within the genus Pseudomonas, for which the name Pseudomonas humi sp. nov. is proposed. The type strain is CCA1 (= HUT 8136T = TBRC 8616T).
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Selvakumar G, Shagol CC, Kim K, Han S, Sa T. Spore associated bacteria regulates maize root K +/Na + ion homeostasis to promote salinity tolerance during arbuscular mycorrhizal symbiosis. BMC PLANT BIOLOGY 2018; 18:109. [PMID: 29871605 PMCID: PMC5989414 DOI: 10.1186/s12870-018-1317-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/23/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND The interaction between arbuscular mycorrhizal fungi (AMF) and AMF spore associated bacteria (SAB) were previously found to improve mycorrhizal symbiotic efficiency under saline stress, however, the information about the molecular basis of this interaction remain unknown. Therefore, the present study aimed to investigate the response of maize plants to co-inoculation of AMF and SAB under salinity stress. RESULTS The co-inoculation of AMF and SAB significantly improved plant dry weight, nutrient content of shoot and root tissues under 25 or 50 mM NaCl. Importantly, co-inoculation significantly reduced the accumulation of proline in shoots and Na+ in roots. Co-inoculated maize plants also exhibited high K+/Na+ ratios in roots at 25 mM NaCl concentration. Mycorrhizal colonization significantly positively altered the expression of ZmAKT2, ZmSOS1, and ZmSKOR genes, to maintain K+ and Na+ ion homeostasis. Confocal laser scanning microscope (CLSM) view showed that SAB were able to move and localize into inter- and intracellular spaces of maize roots and were closely associated with the spore outer hyaline layer. CONCLUSION These new findings indicate that co-inoculation of AMF and SAB effectively alleviates the detrimental effects of salinity through regulation of SOS pathway gene expression and K+/Na+ homeostasis to improve maize plant growth.
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Affiliation(s)
- Gopal Selvakumar
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Wanju, South Korea
| | - Charlotte C. Shagol
- Department of Agronomy, Benguet State University, La Trinidad, 2601 Benguet, Philippines
| | - Kiyoon Kim
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
| | - Seunggab Han
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Wanju, South Korea
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763 Republic of Korea
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Hemalatha D, Prabhu S, Rani WB, Anandham R. Isolation and characterization of toxins from Xenorhabdus nematophilus against Ferrisia virgata (Ckll.) on tuberose, Polianthes tuberosa. Toxicon 2018; 146:42-49. [DOI: 10.1016/j.toxicon.2018.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 03/21/2018] [Accepted: 03/24/2018] [Indexed: 10/17/2022]
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Furmanczyk EM, Kaminski MA, Lipinski L, Dziembowski A, Sobczak A. Pseudomonas laurylsulfatovorans sp. nov., sodium dodecyl sulfate degrading bacteria, isolated from the peaty soil of a wastewater treatment plant. Syst Appl Microbiol 2018; 41:348-354. [PMID: 29752019 DOI: 10.1016/j.syapm.2018.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 03/26/2018] [Accepted: 03/30/2018] [Indexed: 10/17/2022]
Abstract
Pseudomonas are known from their flexible degradation capabilities and their engagement in xenobiotic biotransformation and bioremediation in habitats like soil, active sludge, plant surfaces, and freshwater or marine environments. Here we present taxonomic characterization of three efficient sodium dodecyl sulfate degrading strains: AP3_10, AP3_20 and AP3_22T belonging to the genus Pseudomonas, recently isolated from peaty soil used in a biological wastewater treatment plant. Sequence analyses of 16S rRNA and housekeeping genes: gyrB, rpoD and rpoB showed that the three closely related isolates classify within the Pseudomonas jessenii subgroup. ANIb or dDDH genomic comparisons of AP3_22T (type strain DSM 105098T=PCM 2904T) supported by biochemical tests showed that the isolates differ significantly from their closest relatives. The combined genotypic, phenotypic and chemotaxonomic data strongly support the classification of the three strains: AP3_10, AP3_20 and AP3_22T as a novel species of Pseudomonas, for which we propose the name Pseudomonas laurylsulfatovorans sp. nov. with AP3_22T as the type strain.
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Affiliation(s)
- Ewa M Furmanczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Michal A Kaminski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland.
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Mitsutomi S, Sekimizu K, Kaito C. Isolation of antibiotic-producing Pseudomonas species with low-temperature cultivation of temperate soil. Drug Discov Ther 2017; 11:267-275. [PMID: 29081439 DOI: 10.5582/ddt.2017.01053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We performed low-temperature cultivation of soil samples in Tokyo, Japan, and isolated 30 bacterial strains that formed colonies at 4°C. All the culture supernatants of these bacteria exhibited antibacterial activity against Escherichia coli. The 16S rDNA sequences of 29 strains showed similarity to that of the Pseudomonas genus, whereas the 16S rDNA sequence of one strain showed similarity to that of the Janthinobacterium genus. We classified the 29 strains into 10 groups according to the 16S rDNA sequence similarities, and performed two phylogenetic analyses using the 16S rDNA and rpoD gene sequences. Four groups formed a unique branch within Pseudomonas species in both phylogenetic analyses. Four other groups were closely related to the Pseudomonas species, but the most closely related species differed between the two phylogenic tree analyses. These results suggest that low-temperature cultivation of temperate soil is effective for isolating new bacterial sources for producing antibiotics.
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Affiliation(s)
- Shuhei Mitsutomi
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | | | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo
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Draft Genome Sequence of the Type Strain Pseudomonas umsongensis DSM 16611. GENOME ANNOUNCEMENTS 2017; 5:5/39/e01038-17. [PMID: 28963215 PMCID: PMC5624761 DOI: 10.1128/genomea.01038-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequence of Pseudomonas umsongensis type strain DSM 16611. The assembly consists of 14 contigs containing 6,701,403 bp with a GC content of 59.73%.
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Yeom JR, Yoon SU, Kim CG. Quantification of residual antibiotics in cow manure being spread over agricultural land and assessment of their behavioral effects on antibiotic resistant bacteria. CHEMOSPHERE 2017; 182:771-780. [PMID: 28535485 DOI: 10.1016/j.chemosphere.2017.05.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 05/09/2017] [Accepted: 05/13/2017] [Indexed: 06/07/2023]
Abstract
Antibiotic resistant bacteria (ARB) in livestock manure used as fertilizer and spread over agriculture land, may pose a threat to the health of humans. Considering this, the concentrations of tetracycline (TC), oxytetracycline (OTC), and sulfathiazole (STZ) in the surface soil were quantified using LC-MS. These antibiotics have been used in livestock and are found in fertilizer produced from livestock excretions. Species of ABR were identified using 16S rDNA. Soil samples were collected at depths of 0, 7, and 15 cm from farmland in Incheon (South Korea). In the surface soil, three compounds were detected: TC (17.74 μg/kg), OTC (0.78 μg/kg), and STZ (0.23 μg/kg). However, except for STZ, antibiotics were not detected in the deeper samples. Overall, TC can form a chelated complex with cations, which consequently enhances its adsorption to the organic matter and metals in soil. This property can significantly reduce the mobility of TC (to lower than that of STZ). The result of 16S rDNA gene analysis indicated that Pseudomonas spp., Arthrobacter spp., and Rhodococcus spp. showed persistent resistance to the three antibiotics tested. DNA quantification results revealed strong resistance of Pseudomonas spp. to STZ, whereas Arthrobacter spp. and Rhodococcus spp. had resistance to TC and OTC. Antibiotics biodegradation suggested ability of ARB to grow in soil samples in presence of residual antibiotics during 13 days incubation. The concentrations of STZ, TC, and OTC reduced as much as 23.53, 35.60 and 66.88%, respectively.
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Affiliation(s)
- Ji-Ran Yeom
- Department of Environment Engineering, INHA University, Incheon, South Korea
| | - Soon-Uk Yoon
- Department of Environment Engineering, INHA University, Incheon, South Korea
| | - Chang-Gyun Kim
- Department of Environment Engineering, INHA University, Incheon, South Korea.
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Vicente JG, Rothwell S, Holub EB, Studholme DJ. Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida. Int J Syst Evol Microbiol 2017; 67:3645-3654. [PMID: 28840805 DOI: 10.1099/ijsem.0.002189] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe two new species of the genus Xanthomonas, represented by yellow mucoid bacterial strains isolated from diseased leaves of watercress (Nasturtium officinale) produced in Florida, USA. One strain was pathogenic on watercress, but not in other species including a range of brassicas; other strains were not pathogenic in any of the tested plants. Data from Biolog carbon source utilization tests and nucleotide sequence data from 16S and gyrB loci suggested that both pathogenic and non-pathogenic strains were related to, yet distinct from, previously described Xanthomonas species. Multilocus sequence analysis and whole genome-wide comparisons of the average nucleotide identity (ANI) of genomes of two strains from watercress showed that these are distinct and share less than 95 % ANI with all other known species; the non-pathogenic strain WHRI 8848 is close to Xanthomonascassavae (ANI of 93.72 %) whilst the pathogenic strain WHRI 8853 is close to a large clade of species that includes Xanthomonasvesicatoria (ANI ≤90.25 %). Based on these results, we propose that both strains represent new Xanthomonas species named Xanthomonas floridensis sp. nov. (type strain WHRI 8848=ATCC TSD-60=ICMP 21312=LMG 29665=NCPPB 4601) and Xanthomonas nasturtii sp. nov. (type strain WHRI 8853=ATCC TSD-61=ICMP 21313=LMG 29666=NCPPB 4600), respectively. The presence of non-pathogenic Xanthomonas strains in watercress and their interaction with pathogenic strains needs to be further investigated. Although the importance of the new pathogenic species is yet to be determined, the bacterial disease that it causes constitutes a threat to watercress production and its distribution should be monitored.
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Affiliation(s)
- Joana G Vicente
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
| | - Steve Rothwell
- Vitacress Ltd, Lower Link Farm, St. Mary Bourne, Andover, Hampshire SP11 6DB, UK
| | - Eric B Holub
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
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Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus "Hitchhiker" from the Soybean Rhizosphere. GENOME ANNOUNCEMENTS 2017; 5:5/26/e00570-17. [PMID: 28663293 PMCID: PMC5638277 DOI: 10.1128/genomea.00570-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pseudomonas koreensis CI12 was coisolated with Bacillus cereus from a root of a soybean plant grown in a field in Arlington, WI. Here, we report the draft genome sequence of P. koreensis CI12 obtained by Illumina sequencing.
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