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Pelletier DA, Alexander W, Burdick LH, Rush TA, Tannous J, Webb AB, Morrell-Falvey JL. Complete genome of Pseudomonas putida strain WBB028 isolated from leaf litter. Microbiol Resour Announc 2024; 13:e0023424. [PMID: 38860815 PMCID: PMC11256791 DOI: 10.1128/mra.00234-24] [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: 03/13/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
We report the complete genome of Pseudomonas putida strain WBB028, which exhibits broad-spectrum antifungal activity. This strain was isolated from leaf litter collected at Walker Branch Watershed located on the Oak Ridge Reservation in eastern Tennessee (35.9614 N 84.2864 W). The genome is 6.3 Mbp with a 62.5% GC content.
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Affiliation(s)
- D. A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - W. Alexander
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - L. H. Burdick
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - T. A. Rush
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - J. Tannous
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - A. B. Webb
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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2
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Guo Y, Cheng S, Fang H, Yang Y, Li Y, Shi F, Zhou Y. Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121724. [PMID: 37105465 DOI: 10.1016/j.envpol.2023.121724] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.
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Affiliation(s)
- Yifan Guo
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shulan Cheng
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huajun Fang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; The Zhongke-Ji'an Institute for Eco-Environmental Sciences, Ji'an, 343000, China; Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, 810001, China.
| | - Yan Yang
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuna Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangying Shi
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Zhou
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Guzmán-Moreno J, García-Ortega LF, Torres-Saucedo L, Rivas-Noriega P, Ramírez-Santoyo RM, Sánchez-Calderón L, Quiroz-Serrano IN, Vidales-Rodríguez LE. Bacillus megaterium HgT21: a Promising Metal Multiresistant Plant Growth-Promoting Bacteria for Soil Biorestoration. Microbiol Spectr 2022; 10:e0065622. [PMID: 35980185 PMCID: PMC9604106 DOI: 10.1128/spectrum.00656-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/26/2022] [Indexed: 12/30/2022] Open
Abstract
The environmental deterioration produced by heavy metals derived from anthropogenic activities has gradually increased. The worldwide dissemination of toxic metals in crop soils represents a threat for sustainability and biosafety in agriculture and requires strategies for the recovery of metal-polluted crop soils. The biorestoration of metal-polluted soils using technologies that combine plants and microorganisms has gained attention in recent decades due to the beneficial and synergistic effects produced by its biotic interactions. In this context, native and heavy metal-resistant plant growth-promoting bacteria (PGPB) play a crucial role in the development of strategies for sustainable biorestoration of metal-contaminated soils. In this study, we present a genomic analysis and characterization of the rhizospheric bacterium Bacillus megaterium HgT21 isolated from metal-polluted soil from Zacatecas, Mexico. The results reveal that this autochthonous bacterium contains an important set of genes related to a variety of operons associated with mercury, arsenic, copper, cobalt, cadmium, zinc and aluminum resistance. Additionally, halotolerance-, beta-lactam resistance-, phosphate solubilization-, and plant growth-promotion-related genes were identified. The analysis of resistance to metal ions revealed resistance to mercury (HgII+), arsenate [AsO4]³-, cobalt (Co2+), zinc (Zn2+), and copper (Cu2+). Moreover, the ability of the HgT21 strain to produce indole acetic acid (a phytohormone) and promote the growth of Arabidopsis thaliana seedlings in vitro was also demonstrated. The genotype and phenotype of Bacillus megaterium HgT21 reveal its potential to be used as a model of both plant growth-promoting and metal multiresistant bacteria. IMPORTANCE Metal-polluted environments are natural sources of a wide variety of PGPB adapted to cope with toxic metal concentrations. In this work, the bacterial strain Bacillus megaterium HgT21 was isolated from metal-contaminated soil and is proposed as a model for the study of metal multiresistance in spore-forming Gram-positive bacteria due to the presence of a variety of metal resistance-associated genes similar to those encountered in the metal multiresistant Gram-negative Cupriavidus metallidurans CH34. The ability of B. megaterium HgT21 to promote the growth of plants also makes it suitable for the study of plant-bacteria interactions in metal-polluted environments, which is key for the development of techniques for the biorestoration of metal-contaminated soils used for agriculture.
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Affiliation(s)
- Jesús Guzmán-Moreno
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Luis Fernando García-Ortega
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - Lilia Torres-Saucedo
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Paulina Rivas-Noriega
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Rosa María Ramírez-Santoyo
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Lenin Sánchez-Calderón
- Laboratorio de Genómica Evolutiva, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Iliana Noemi Quiroz-Serrano
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
| | - Luz Elena Vidales-Rodríguez
- Laboratorio de Biología de Bacterias y Hongos Filamentosos, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Zacatecas, Zacatecas, Mexico
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4
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Lo KH, Lu CW, Liu FG, Kao CM, Chen SC. Draft genome sequence of Pseudomonas sp. A46 isolated from mercury-contaminated wastewater. J Basic Microbiol 2022; 62:1193-1201. [PMID: 35849092 DOI: 10.1002/jobm.202200106] [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: 02/21/2022] [Revised: 06/07/2022] [Accepted: 06/30/2022] [Indexed: 11/08/2022]
Abstract
Pseudomonas sp. A46 was first isolated from mercury-contaminated groundwater in Taiwan. This study is the first to report the draft whole-genome sequence of Pseudomonas sp. A46. Its genome consists of 126 contigs, with a total length of 6,782,516 bp and a GC content of 64.7%. Phylogenetic analysis based on 16 S rRNA gene sequences revealed that Pseudomonas sp. A46 is closely related to Pseudomonas citronellolis. Assessment of the draft genome sequence revealed that Pseudomonas sp. A46 harbors sets of genes conferring resistance to heavy metals, such as mercury, zinc, lead, copper, cadmium, chromate, and arsenate. These identified genes enable this bacterium to tolerate heavy metal stress.
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Affiliation(s)
- Kai-Hung Lo
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Che-Wei Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan, Taiwan
| | - Fu-Guo Liu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan, Taiwan
| | - Chih-Ming Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ssu Ching Chen
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan, Taiwan
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Virieux-Petit M, Hammer-Dedet F, Aujoulat F, Jumas-Bilak E, Romano-Bertrand S. From Copper Tolerance to Resistance in Pseudomonas aeruginosa towards Patho-Adaptation and Hospital Success. Genes (Basel) 2022; 13:genes13020301. [PMID: 35205346 PMCID: PMC8872213 DOI: 10.3390/genes13020301] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
The hospital environment constitutes a reservoir of opportunistic pathogens responsible for healthcare-associated infections (HCAI) such as Pseudomonas aeruginosa (Pa). Pa persistence within technological niches, the increasing emergence of epidemic high-risk clones in HCAI, the epidemiological link between plumbing strains and clinical strains, make it a major nosocomial pathogen. Therefore, understanding the mechanisms of Pa adaptation to hospital water systems would be useful in preventing HCAI. This review deciphers how copper resistance contributes to Pa adaptation and persistence in a hospital environment, especially within copper water systems, and ultimately to its success as a causative agent of HCAI. Numerous factors are involved in copper homeostasis in Pa, among which active efflux conferring copper tolerance, and copper-binding proteins regulating the copper compartmentalization between periplasm and cytoplasm. The functional harmony of copper homeostasis is regulated by several transcriptional regulators. The genomic island GI-7 appeared as especially responsible for the copper resistance in Pa. Mechanisms of copper and antibiotic cross-resistance and co-resistance are also identified, with potential co-regulation processes between them. Finally, copper resistance of Pa confers selective advantages in colonizing and persisting in hospital environments but also appears as an asset at the host/pathogen interface that helps in HCAI occurrence.
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Affiliation(s)
- Maxine Virieux-Petit
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Florence Hammer-Dedet
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Fabien Aujoulat
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
| | - Estelle Jumas-Bilak
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
- Hospital Hygiene and Infection Control Team, University Hospital of Montpellier, 34093 Montpellier, France
| | - Sara Romano-Bertrand
- HydroSciences Montpellier, IRD, CNRS, Montpellier University, 34093 Montpellier, France; (M.V.-P.); (F.H.-D.); (F.A.); (E.J.-B.)
- Hospital Hygiene and Infection Control Team, University Hospital of Montpellier, 34093 Montpellier, France
- UMR 5151 HSM, Equipe Pathogènes Hydriques Santé et Environnements, U.F.R. des Sciences Pharmaceutiques et Biologiques, Université Montpellier, 15, Avenue Charles Flahault, BP 14491, CEDEX 5, 34093 Montpellier, France
- Correspondence: ; Tel.: +33-4-11-75-94-30
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6
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Ali M, Walait S, Farhan Ul Haque M, Mukhtar S. Antimicrobial activity of bacteria associated with the rhizosphere and phyllosphere of Avena fatua and Brachiaria reptans. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68846-68861. [PMID: 34282546 DOI: 10.1007/s11356-021-15436-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Environmental pollution especially heavy metal-contaminated soils adversely affects the microbial communities associated with the rhizosphere and phyllosphere of plants growing in these areas. In the current study, we identified and characterized the rhizospheric and phyllospheric bacterial strains from Avena fatua and Brachiaria reptans with the potential for antimicrobial activity and heavy metal resistance. A total of 18 bacterial strains from the rhizosphere and phyllosphere of A. fatua and 19 bacterial strains from the rhizosphere and phyllosphere of B. reptans were identified based on 16S rRNA sequence analysis. Bacterial genera, including Bacillus, Staphylococcus, Pseudomonas, and Enterobacter were dominant in the rhizosphere and phyllosphere of A. fatua and Bacillus, Marinobacter, Pseudomonas, Enterobacter, and Kocuria, were the dominating bacterial genera from the rhizosphere and phyllosphere of B. reptans. Most of the bacterial strains were resistant to heavy metals (Cd, Pb, and Cr) and showed antimicrobial activity against different pathogenic bacterial strains. The whole-genome sequence analysis of Pseudomonas putida BR-PH17, a strain isolated from the phyllosphere of B. reptans, was performed by using the Illumina sequencing approach. The BR-PH17 genome contained a chromosome with a size of 5774330 bp and a plasmid DNA with 80360 bp. In this genome, about 5368 predicted protein-coding sequences with 5539 total genes, 22 rRNAs, and 75 tRNA genes were identified. Functional analysis of chromosomal and plasmid DNA revealed a variety of enzymes and proteins involved in antibiotic resistance and biodegradation of complex organic pollutants. These results indicated that bacterial strains identified in this study could be utilized for bioremediation of heavy metal-contaminated soils and as a novel source of antimicrobial drugs.
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Affiliation(s)
- Muskan Ali
- Lahore College for Women University, Near Wapda Flats, Jail Rd, Jubilee Town, Lahore, Punjab, 54000, Pakistan
| | - Sadia Walait
- Riphah International University, Faisalabad, Adjacent Fish Farm, Satayana Rd, Faisalabad, Punjab, 44000, Pakistan
| | | | - Salma Mukhtar
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan.
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Mukhtar S, Farooq M, Baig DN, Amin I, Lazarovits G, Malik KA, Yuan ZC, Mehnaz S. Whole genome analysis of Gluconacetobacter azotocaptans DS1 and its beneficial effects on plant growth. 3 Biotech 2021; 11:450. [PMID: 34631351 DOI: 10.1007/s13205-021-02996-1] [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: 05/06/2021] [Accepted: 09/16/2021] [Indexed: 12/01/2022] Open
Abstract
Plant-associated bacteria play an important role in the enhancement of plant growth and productivity. Gluconacetobacter azotocaptans is an exceptional bacterium considering that till today it has been isolated and reported only from Mexico and Canada. It is a plant growth-promoting bacterium and can be used as biofertilizer for different crops and vegetables. The objective of the current study was to evaluate the inoculation effect of Gluconacetobacter azotocaptans DS1, Pseudomonas putida CQ179, Azosprillium zeae N7, Azosprillium brasilense N8, and Azosprillium canadense DS2, on the growth of vegetables including cucumber, sweet pepper, radish, and tomato. All strains increased the vegetables' growth; however, G. azotocaptans DS1 showed better results as compared to other inoculated and control plants and significantly increased the plant biomass of all vegetables. Therefore, the whole genome sequence of G. azotocaptans DS1 was analyzed to predict genes involved in plant growth promotion, secondary metabolism, antibiotics resistance, and bioremediation of heavy metals. Results of genome analysis revealed that G. azotocaptans DS1 has a circular chromosome with a size of 4.3 Mbp and total 3898 protein-coding sequences. Based on functional analysis, genes for nitrogen fixation, phosphate solubilization, indole acetic acid, phenazine, siderophore production, antibiotic resistance, and bioremediation of heavy metals including copper, zinc, cobalt, and cadmium were identified. Collectively, our findings indicated that G. azotocaptans DS1 can be used as a biofertilizer and biocontrol agent for growth enhancement of different crops and vegetables. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02996-1.
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Affiliation(s)
- Salma Mukhtar
- KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Muhammad Farooq
- Division of Agricultural Biotechnology, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - Deeba Noreen Baig
- KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Imran Amin
- Division of Agricultural Biotechnology, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
| | - George Lazarovits
- A & L Biologicals, Agroecology Research Services Centre, London, ON N5V 3P5 Canada
| | - Kauser Abdulla Malik
- KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Ze-Chun Yuan
- Agriculture and Agri Food Canada, London, ON Canada
| | - Samina Mehnaz
- KAM School of Life Sciences, Forman Christian College (A Chartered University), Lahore, Pakistan
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Montes-Osuna N, Gómez-Lama Cabanás C, Valverde-Corredor A, Berendsen RL, Prieto P, Mercado-Blanco J. Assessing the Involvement of Selected Phenotypes of Pseudomonas simiae PICF7 in Olive Root Colonization and Biological Control of Verticillium dahliae. PLANTS 2021; 10:plants10020412. [PMID: 33672351 PMCID: PMC7926765 DOI: 10.3390/plants10020412] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 12/19/2022]
Abstract
Pseudomonas simiae PICF7 is an indigenous inhabitant of the olive (Olea europaea L.) rhizosphere/root endosphere and an effective biocontrol agent against Verticillium wilt of olive (VWO), caused by the soil-borne fungus Verticillium dahliae. This study aimed to evaluate the potential involvement of selected phenotypes of strain PICF7 in root colonization ability and VWO biocontrol. Therefore, a random transposon-insertion mutant bank of P. simiae PICF7 was screened for the loss of phenotypes likely involved in rhizosphere/soil persistence (copper resistance), root colonization (biofilm formation) and plant growth promotion (phytase activity). Transposon insertions in genes putatively coding for the transcriptional regulator CusR or the chemotaxis protein CheV were found to affect copper resistance, whereas an insertion in fleQ gene putatively encoding a flagellar regulatory protein hampered the ability to form a biofilm. However, these mutants displayed the same antagonistic effect against V. dahliae as the parental strain. Remarkably, two mutants impaired in biofilm formation were never found inside olive roots, whereas their ability to colonize the root exterior and to control VWO remained unaffected. Endophytic colonization of olive roots was unaltered in mutants impaired in copper resistance and phytase production. Results demonstrated that the phenotypes studied were irrelevant for VWO biocontrol.
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Affiliation(s)
- Nuria Montes-Osuna
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus “Alameda del Obispo”, 14004 Córdoba, Spain; (N.M.-O.); (C.G.-L.C.); (A.V.-C.)
| | - Carmen Gómez-Lama Cabanás
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus “Alameda del Obispo”, 14004 Córdoba, Spain; (N.M.-O.); (C.G.-L.C.); (A.V.-C.)
| | - Antonio Valverde-Corredor
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus “Alameda del Obispo”, 14004 Córdoba, Spain; (N.M.-O.); (C.G.-L.C.); (A.V.-C.)
| | - Roeland L. Berendsen
- Plant–Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Pilar Prieto
- Departamento de Mejora Genética Vegetal, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus “Alameda del Obispo”, 14004 Córdoba, Spain;
| | - Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avenida Menéndez Pidal s/n, Campus “Alameda del Obispo”, 14004 Córdoba, Spain; (N.M.-O.); (C.G.-L.C.); (A.V.-C.)
- Correspondence:
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9
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Gallardo-Benavente C, Campo-Giraldo JL, Castro-Severyn J, Quiroz A, Pérez-Donoso JM. Genomics Insights into Pseudomonas sp. CG01: An Antarctic Cadmium-Resistant Strain Capable of Biosynthesizing CdS Nanoparticles Using Methionine as S-Source. Genes (Basel) 2021; 12:187. [PMID: 33514061 PMCID: PMC7912247 DOI: 10.3390/genes12020187] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/23/2022] Open
Abstract
Here, we present the draft genome sequence of Pseudomonas sp. GC01, a cadmium-resistant Antarctic bacterium capable of biosynthesizing CdS fluorescent nanoparticles (quantum dots, QDs) employing a unique mechanism involving the production of methanethiol (MeSH) from methionine (Met). To explore the molecular/metabolic components involved in QDs biosynthesis, we conducted a comparative genomic analysis, searching for the genes related to cadmium resistance and sulfur metabolic pathways. The genome of Pseudomonas sp. GC01 has a 4,706,645 bp size with a 58.61% G+C content. Pseudomonas sp. GC01 possesses five genes related to cadmium transport/resistance, with three P-type ATPases (cadA, zntA, and pbrA) involved in Cd-secretion that could contribute to the extracellular biosynthesis of CdS QDs. Furthermore, it exhibits genes involved in sulfate assimilation, cysteine/methionine synthesis, and volatile sulfur compounds catabolic pathways. Regarding MeSH production from Met, Pseudomonas sp. GC01 lacks the genes E4.4.1.11 and megL for MeSH generation. Interestingly, despite the absence of these genes, Pseudomonas sp. GC01 produces high levels of MeSH. This is probably associated with the metC gene that also produces MeSH from Met in bacteria. This work is the first report of the potential genes involved in Cd resistance, sulfur metabolism, and the process of MeSH-dependent CdS QDs bioproduction in Pseudomonas spp. strains.
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Affiliation(s)
- Carla Gallardo-Benavente
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, 4780000 Temuco, Chile;
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
| | - Jessica L. Campo-Giraldo
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8320000 Santiago, Chile;
| | - Juan Castro-Severyn
- Laboratorio de Microbiología Aplicada y Extremófilos, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, 1240000 Antofagasta, Chile;
| | - Andrés Quiroz
- Centro de Excelencia en Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, 4780000 Temuco, Chile
| | - José M. Pérez-Donoso
- BioNanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, 8320000 Santiago, Chile;
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Isolation and genomic characterization of a pathogenic Providencia rettgeri strain G0519 in turtle Trachemys scripta. Antonie van Leeuwenhoek 2020; 113:1633-1662. [PMID: 32951105 DOI: 10.1007/s10482-020-01469-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
Providencia rettgeri infection has occurred occasionally in aquaculture, but is rare in turtles. Here, a pathogenic P. rettgeri strain G0519 was isolated from a diseased slider turtle (Trachemys scripta) in China, and qPCR assay was established for the RTX toxin (rtxD) gene. Histopathological examination showed that many inflammatory cells were infiltrated into heart, liver and intestine, as well as the necrosis of liver, kidney and spleen. The genome consisted of one circular chromosome (4.493 Mb) and one plasmid (18.8 kb), and predicted to contain 4170 and 19 protein-coding genes, respectively. Multiple pathogenic and virulence factors (e.g., fimbria, adhesion, invasion, toxin, hemolysin, chemotaxis, secretion system), multidrug-resistant genes (e.g., ampC, per-1, oxa-1, sul1, tetR) and a novel genomic resistance island PRI519 were identified. Comparative genome analysis revealed the closest relationship was with P. rettgeri, and with P. heimbachae closer than with other Providencia spp. To our knowledge, this was first report on genomic characterization of multidrug-resistant pathogenic P. rettgeri in cultured turtles.
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Havryliuk O, Hovorukha V, Patrauchan M, Youssef NH, Tashyrev O. Draft whole genome sequence for four highly copper resistant soil isolates Pseudomonas lactis strain UKR1, Pseudomonas panacis strain UKR2, and Pseudomonas veronii strains UKR3 and UKR4. CURRENT RESEARCH IN MICROBIAL SCIENCES 2020; 1:44-52. [PMID: 34841301 PMCID: PMC8610347 DOI: 10.1016/j.crmicr.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 01/22/2023] Open
Abstract
Four bacterial strains with record resistance to Cu(II) have been isolated. Genomic sequences are available for genome mining and studying the genetic determinants of bacterial resistance to Cu(II). Genomic sequences provide the foundation necessary for transcriptional and functional studies of genes encoding for Cu(II) resistance mechanisms in Pseudomonas spp. The data will be of interest for a broad community of biotechnologists and microbiologists and will aid in developing novel technologies for copper detoxification in contaminated soils and industrial wastewaters.
Environmental copper pollution causes major destruction to ecological systems, which require the development of environmentally friendly biotechnological, in particular, microbial methods for copper removal. These methods rely on the availability of microorganisms resistant to high levels of copper. Here we isolated four bacterial strains with record resistance to up to 1.0 M Cu(II). The strains were isolated from ecologically diverse soil samples, and their genomes were sequenced. A 16S rRNA sequence-based phylogenetic analysis identified that all four isolates belong to the genus Pseudomonas. Particularly, strains UKR1 and UKR2 isolated from Kyiv region in Ukraine were identified as P. lactis and P. panacis, respectively, and strains UKR3 and UKR4 isolated from Svalbard Island in the Arctic Ocean and Galindez Island in Antarctica, respectively, were identified as P. veronii. Initial in-silico screening for genes encoding copper resistance mechanisms showed that all four strains encode copper resistance proteins CopA, CopB, CopD, CopA3, CopZ, as well as two-component regulatory system CusRS, all known to be associated with metal resistance in Pseudomonas genus. Further detailed studies will aim to characterize the full genomic potential of the isolates to enable their application for copper bioremediation in contaminated soils and industrial wastewaters.
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Affiliation(s)
- Olesia Havryliuk
- Department of Extremophilic Microorganisms Biology, D. K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 154 Zabolotny St., Kyiv 03143, Ukraine
- Corresponding author.
| | - Vira Hovorukha
- Department of Extremophilic Microorganisms Biology, D. K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 154 Zabolotny St., Kyiv 03143, Ukraine
| | - Marianna Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 LSE, Stillwater, Oklahoma 74075, United States of America
| | - Noha H. Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 LSE, Stillwater, Oklahoma 74075, United States of America
| | - Oleksandr Tashyrev
- Department of Extremophilic Microorganisms Biology, D. K. Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 154 Zabolotny St., Kyiv 03143, Ukraine
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Chaudhari D, Rangappa K, Das A, Layek J, Basavaraj S, Kandpal BK, Shouche Y, Rahi P. Pea ( Pisum sativum l.) Plant Shapes Its Rhizosphere Microbiome for Nutrient Uptake and Stress Amelioration in Acidic Soils of the North-East Region of India. Front Microbiol 2020; 11:968. [PMID: 32582047 PMCID: PMC7283456 DOI: 10.3389/fmicb.2020.00968] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/22/2020] [Indexed: 12/26/2022] Open
Abstract
Rhizosphere microbiome significantly influences plant growth and productivity. Legume crops such as pea have often been used as a rotation crop along with rice cultivation in long-term conservation agriculture experiments in the acidic soils of the northeast region of India. It is essential to understand how the pea plant influences the soil communities and shapes its rhizosphere microbiome. It is also expected that the long-term application of nutrients and tillage practices may also have a lasting effect on the rhizosphere and soil communities. In this study, we estimated the bacterial communities by 16S rRNA gene amplicon sequencing of pea rhizosphere and bulk soils from a long-term experiment with multiple nutrient management practices and different tillage history. We also used Tax4Fun to predict the functions of bacterial communities. Quantitative polymerase chain reaction (qPCR) was used to estimate the abundance of total bacterial and members of Firmicutes in the rhizosphere and bulk soils. The results showed that bacterial diversity was significantly higher in the rhizosphere in comparison to bulk soils. A higher abundance of Proteobacteria was recorded in the rhizosphere, whereas the bulk soils have higher proportions of Firmicutes. At the genus level, proportions of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter, and Sphingomonas were significantly higher in the rhizosphere. At the same time, Massilia, Paenibacillus, and Planomicrobium were more abundant in the bulk soils. Higher abundance of genes reported for plant growth promotion and several other genes, including iron complex outer membrane receptor, cobalt-zinc-cadmium resistance, sigma-70 factor, and ribonuclease E, was predicted in the rhizosphere samples in comparison to bulk soils, indicating that the pea plants shape their rhizosphere microbiome, plausibly to meet its requirements for nutrient uptake and stress amelioration.
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Affiliation(s)
- Diptaraj Chaudhari
- National Center for Microbial Resource, National Center for Cell Science, Pune, India
| | | | - Anup Das
- ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - Jayanta Layek
- ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | - Savita Basavaraj
- ICAR Research Complex for North Eastern Hill Region, Umiam, India
| | | | - Yogesh Shouche
- National Center for Microbial Resource, National Center for Cell Science, Pune, India
| | - Praveen Rahi
- National Center for Microbial Resource, National Center for Cell Science, Pune, India
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Phenotypic and genomic analysis of multiple heavy metal–resistant Micrococcus luteus strain AS2 isolated from industrial waste water and its potential use in arsenic bioremediation. Appl Microbiol Biotechnol 2020; 104:2243-2254. [DOI: 10.1007/s00253-020-10351-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/23/2019] [Accepted: 01/05/2020] [Indexed: 12/23/2022]
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Yan Z, Li M, Wang J, Pan J. Genome Analysis Revealing the Potential Mechanisms for the Heavy Metal Resistance of Pseudomonas sp. P11, Isolated from Industrial Wastewater Sediment. Curr Microbiol 2019; 76:1361-1368. [PMID: 31471685 DOI: 10.1007/s00284-019-01728-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 06/25/2019] [Indexed: 11/29/2022]
Abstract
Pseudomonas sp. P11 was isolated from the industrial wastewater sediment nearby the Daye Non-ferrous Metals Company, China. This strain possesses the ability to resist various heavy metals and efficiently precipitate arsenic. We here present a summary classification and a set of features of Pseudomonas sp. P11, together with the description of the genomic sequencing and annotation. The genomic sequence is 6,644,817 bp with a G+C content of 62.20% and contains 6143 protein-coding genes, 250 pseudo genes, and 76 tRNAs/rRNAs genes. Operons and gene clusters responsible for multiple heavy metal tolerance or detoxification were identified and accounted for the observed resistance phenotypes. Phylogenetic analysis revealed that the paralogous arsenic resistant genes possess different evolutionary paths. This study provides important insights to illuminate the versatility and adaptation of this strain to the heavy metal-contaminated environment.
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Affiliation(s)
- Zhenjun Yan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization & College of Life Sciences, Hubei Normal University, Huangshi, 435002, Hubei, People's Republic of China
| | - Minglan Li
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization & College of Life Sciences, Hubei Normal University, Huangshi, 435002, Hubei, People's Republic of China
| | - Jingsong Wang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization & College of Life Sciences, Hubei Normal University, Huangshi, 435002, Hubei, People's Republic of China
| | - Jicheng Pan
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization & College of Life Sciences, Hubei Normal University, Huangshi, 435002, Hubei, People's Republic of China.
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Elabed H, González-Tortuero E, Ibacache-Quiroga C, Bakhrouf A, Johnston P, Gaddour K, Blázquez J, Rodríguez-Rojas A. Seawater salt-trapped Pseudomonas aeruginosa survives for years and gets primed for salinity tolerance. BMC Microbiol 2019; 19:142. [PMID: 31234794 PMCID: PMC6591848 DOI: 10.1186/s12866-019-1499-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/31/2019] [Indexed: 01/08/2023] Open
Abstract
Background In nature, microorganisms have to adapt to long-term stressful conditions often with growth limitations. However, little is known about the evolution of the adaptability of new bacteria to such environments. Pseudomonas aeruginosa, an opportunistic pathogen, after natural evaporation of seawater, was shown to be trapped in laboratory-grown halite crystals and to remain viable after entrapment for years. However, how this bacterium persists and survives in such hypersaline conditions is not understood. Results In this study, we aimed to understand the basis of survival, and to characterise the physiological changes required to develop salt tolerance using P. aeruginosa as a model. Several clones of P. aeruginosa were rescued after 14 years in naturally evaporated marine salt crystals. Incubation of samples in nutrient-rich broth allowed re-growth and subsequent plating yielded observable colonies. Whole genome sequencing of the P. aeruginosa isolates confirmed the recovery of the original strain. The re-grown strains, however, showed a new phenotype consisting of an enhanced growth in growing salt concentration compared to the ancestor strain. The intracellular accumulation of K+ was elicited by high concentration of Na+ in the external medium to maintain the homeostasis. Whole transcriptomic analysis by microarray indicated that 78 genes had differential expression between the parental strain and its derivative clones. Sixty-one transcripts were up-regulated, while 17 were down-regulated. Based on a collection of single-gene knockout mutants and gene ontology analysis, we suggest that the adaptive response in P. aeruginosa to hyper-salinity relies on multiple gene product interactions. Conclusions The individual gene contributions build up the observed phenotype, but do not ease the identification of salinity-related metabolic pathways. The long-term inclusion of P. aeruginosa in salt crystals primes the bacteria, mediating a readjustment of the bacterial physiology to growth in higher salt concentrations. Our findings provide a starting point to understand how P. aeruginosa, a relevant environmental and pathogenic bacterium, survives to long-term salt stress. Electronic supplementary material The online version of this article (10.1186/s12866-019-1499-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hamouda Elabed
- Laboratory of Contagious Diseases and Biologically Active Substances LR99-ES27 Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia.,Department of Microbial Biotechnology, Spanish National Center for Biotechnology (CNB), Madrid, Spain
| | - Enrique González-Tortuero
- Department of Veterinary and Animal Sciences, Center for non-coding RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Ibacache-Quiroga
- Department of Microbial Biotechnology, Spanish National Center for Biotechnology (CNB), Madrid, Spain.,Centro de Micro-Bioinnovación, Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile
| | - Amina Bakhrouf
- Laboratory of Analysis, Treatment and Valorization of Environmental Polluants and products, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Paul Johnston
- Institute of Biology, FreieUniversität Berlin, Berlin, Germany
| | - Kamel Gaddour
- Laboratory of Analysis, Treatment and Valorization of Environmental Polluants and products, Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Jesús Blázquez
- Department of Microbial Biotechnology, Spanish National Center for Biotechnology (CNB), Madrid, Spain
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Jeanvoine A, Meunier A, Puja H, Bertrand X, Valot B, Hocquet D. Contamination of a hospital plumbing system by persister cells of a copper-tolerant high-risk clone of Pseudomonas aeruginosa. WATER RESEARCH 2019; 157:579-586. [PMID: 30999256 DOI: 10.1016/j.watres.2019.04.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/30/2019] [Accepted: 04/06/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Pseudomonas aeruginosa (PA) is an important opportunistic pathogen that thrives best in the distal elements of plumbing and waste-water systems. Although nosocomial outbreaks of PA have been associated with water sources, the role of the plumbing system of healthcare premises as a reservoir for this pathogen is still unclear. MATERIALS AND METHODS We collected water samples from 12 technical areas, distant from any medical activity, in a teaching hospital in France once a week for 11 weeks. We used a method that resuscitates persister cells because of the nutrient-poor conditions and the presence of inhibitors (e.g. chlorine and copper ions). Briefly, water was sampled in sterile bottles containing 100 μM of the copper-ion chelating agent diethyldithiocarbamate (DDTC). A portion of the samples was immediately filtered through 0.45-μm membranes, deposited on R2A agar plates, and incubated seven days at 22 °C (following European recommendations). The remaining water was incubated 14 days at 22 °C and then filtered and cultured on R2A, blood-, or cetrimide-containing agar plates. PA isolates were identified by MS MALDI-TOF, genotyped by PFGE and WGS, and tested for survival in a 150 μg/L copper (II) sulphate solution. RESULTS Although the 12 water sampling points always tested negative with the recommended method, 67% were positive at least once for PA with the adapted method (i.e. with DDTC). The 14 PA persister isolates found throughout the plumbing system were clonal and belong to the high-risk clone ST308. Their genome harbours a 37-kb genomic island (GI-7) containing 13 genes linked to copper resistance. ST308 survived better in the copper solution than comparators that did not harbour GI-7 (P. aeruginosa strains PAO1, PA14, and ST235). The deletion of GI-7 in ST308 abrogated its tolerance to copper. The GI-7 nucleotide sequence shares 98% and 72% identity with sequences from the environmental species Pseudomonas putida and the phytopathogenic species Pseudomonas syringae, respectively. CONCLUSION We report the contamination of the plumbing system of a healthcare premises by persister cells of the high-risk clone P. aeruginosa ST308. New recommendations for the monitoring of water contamination should consider persister cells. The genomic island GI-7, which confers tolerance to copper, probably originates from Pseudomonas species found in copper-contaminated soils and plants. Agricultural practices may have an unexpected consequence, allowing copper-tolerant pathogens to survive in the hospital environment and contaminate fragile patients.
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Affiliation(s)
- Audrey Jeanvoine
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR CNRS 6249, Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Alexandre Meunier
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Hélène Puja
- UMR CNRS 6249, Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Xavier Bertrand
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR CNRS 6249, Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Benoît Valot
- UMR CNRS 6249, Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Didier Hocquet
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR CNRS 6249, Chrono-environnement, Université de Bourgogne Franche-Comté, Besançon, France; Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France.
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Aslam F, Yasmin A, Thomas T. Essential Gene Clusters Identified in Stenotrophomonas MB339 for Multiple Metal/Antibiotic Resistance and Xenobiotic Degradation. Curr Microbiol 2018; 75:1484-1492. [DOI: 10.1007/s00284-018-1549-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 08/06/2018] [Indexed: 11/28/2022]
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Escribano-Viana R, López-Alfaro I, López R, Santamaría P, Gutiérrez AR, González-Arenzana L. Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity. Front Microbiol 2018; 9:59. [PMID: 29467723 PMCID: PMC5808214 DOI: 10.3389/fmicb.2018.00059] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022] Open
Abstract
This study was aimed to measure the impact of the application of a bio-fungicide against Botrytis cinerea on the microbiota involved in the alcoholic fermentation (AF) of Tempranillo Rioja wines. For this purpose, a bio-fungicide composed of the biological control bacterium Bacillus subtilis QST713 was applied to the vineyard. The microbial diversity was analyzed from grape biofilm to wine. Impact on microbial diversity was measured employing indexes assessed with the software PAST 3.10 P.D. Results were compared to non-treated samples and to samples treated with a chemical fungicide mainly composed by fenhexamid. Overall, the impact of the biological-fungicide (bio-fungicide) on the microbial diversity assessed for grape biofilm and for musts was not remarkable. Neither of the tested fungicides enhanced the growth of any species or acted against the development of any microbial groups. The bio-fungicide had no significant impact on the wine microbiota whereas the chemical fungicide caused a reduction of microbial community richness and diversity. Although environmental threats might generate a detriment of the microbial species richness, in this study the tested bio-fungicide did not modify the structure of the microbial community. Indeed, some of the Bacillus applied at the grape surface, were detected at the end of the AF showing its resilience to the harsh environment of the winemaking; in contrast, its impact on wine quality during aging is yet unknown.
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Affiliation(s)
- Rocío Escribano-Viana
- Instituto de Ciencias de la Vid y del Vino, ICVV (Gobierno de La Rioja, Centro Superior de Investigaciones Científicas and Universidad de La Rioja), Logroño, Spain
| | - Isabel López-Alfaro
- Instituto de Ciencias de la Vid y del Vino, ICVV (Gobierno de La Rioja, Centro Superior de Investigaciones Científicas and Universidad de La Rioja), Logroño, Spain
| | - Rosa López
- Instituto de Ciencias de la Vid y del Vino, ICVV (Gobierno de La Rioja, Centro Superior de Investigaciones Científicas and Universidad de La Rioja), Logroño, Spain
| | - Pilar Santamaría
- Instituto de Ciencias de la Vid y del Vino, ICVV (Gobierno de La Rioja, Centro Superior de Investigaciones Científicas and Universidad de La Rioja), Logroño, Spain
| | - Ana R Gutiérrez
- Instituto de Ciencias de la Vid y del Vino, ICVV (Gobierno de La Rioja, Centro Superior de Investigaciones Científicas and Universidad de La Rioja), Logroño, Spain
| | - Lucía González-Arenzana
- Instituto de Ciencias de la Vid y del Vino, ICVV (Gobierno de La Rioja, Centro Superior de Investigaciones Científicas and Universidad de La Rioja), Logroño, Spain
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Comparative genome analysis of the vineyard weed endophyte Pseudomonas viridiflava CDRTc14 showing selective herbicidal activity. Sci Rep 2017; 7:17336. [PMID: 29229911 PMCID: PMC5725424 DOI: 10.1038/s41598-017-16495-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/13/2017] [Indexed: 12/17/2022] Open
Abstract
Microbes produce a variety of secondary metabolites to be explored for herbicidal activities. We investigated an endophyte Pseudomonas viridiflava CDRTc14, which impacted growth of its host Lepidium draba L., to better understand the possible genetic determinants for herbicidal and host-interaction traits. Inoculation tests with a variety of target plants revealed that CDRTc14 shows plant-specific effects ranging from beneficial to negative. Its herbicidal effect appeared to be dose-dependent and resembled phenotypically the germination arrest factor of Pseudomonas fluorescens WH6. CDRTc14 shares 183 genes with the herbicidal strain WH6 but the formylaminooxyvinylglycine (FVG) biosynthetic genes responsible for germination arrest of WH6 was not detected. CDRTc14 showed phosphate solubilizing ability, indole acetic acid and siderophores production in vitro and harbors genes for these functions. Moreover, genes for quorum sensing, hydrogen cyanide and ACC deaminase production were also found in this strain. Although, CDRTc14 is related to plant pathogens, we neither found a complete pathogenicity island in the genome, nor pathogenicity symptoms on susceptible plant species upon CDRTc14 inoculation. Comparison with other related genomes showed several unique genes involved in abiotic stress tolerance in CDRTc14 like genes responsible for heavy metal and herbicide resistance indicating recent adaptation to plant protection measures applied in vineyards.
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Chong TM, Chen JW, See-Too WS, Yu CY, Ang GY, Lim YL, Yin WF, Grandclément C, Faure D, Dessaux Y, Chan KG. Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate. AMB Express 2017; 7:138. [PMID: 28655216 PMCID: PMC5484659 DOI: 10.1186/s13568-017-0437-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/19/2017] [Indexed: 12/30/2022] Open
Abstract
Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.
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Affiliation(s)
- Teik Min Chong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jian-Woon Chen
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Choo-Yee Yu
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Geik-Yong Ang
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Yan Lue Lim
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-Sur-Yvette, France
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- UM Omics Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia
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