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García-García R, Bocanegra-García V, Vital-López L, García-Mena J, Zamora-Antuñano MA, Cruz-Hernández MA, Rodríguez-Reséndiz J, Mendoza-Herrera A. Assessment of the Microbial Communities in Soil Contaminated with Petroleum Using Next-Generation Sequencing Tools. APPLIED SCIENCES 2023; 13:6922. [DOI: 10.3390/app13126922] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Microbial communities are known to play a principal role in petroleum degradation. This study tries to determine the composition of bacteria in selected crude oil-contaminated soil from Tabasco and Tamaulipas states, Mexico. We determined the microbial populations living under these conditions. We evaluated the structure and diversity of bacterial communities in the contaminated soil samples. The most abundant phylum is proteobacteria. Next Generation Sequencing (NGS) analysis of the sampled soils from both states revealed that this phylum has the most relative abundance among the identified bacteria phyla. The heatmap represented the relative percentage of each genus within each sample and clustered the four samples into two groups. Moreover, this allowed us to identify many genera in alkaline soil from Tamaulipas, such as Skermanella sp., Azospirillum sp. and Unclassified species from the Rhodospirillaceae family in higher abundance. Meanwhile, in acidic soil from Tabasco, we identified Thalassospira, Unclassified members of the Sphingomonadaceae family and Unclassified members of the Alphaproteobacteria class with higher abundance. Alpha diversity analysis showed a low diversity (Shannon and Simpson index); Chao observed species in both Regions. These results suggest that the bacteria identified in these genera may possess the ability to degrade petroleum, and further studies in the future should elucidate their role in petroleum degradation.
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Affiliation(s)
- Raul García-García
- Division of Chemistry and Renewable Energy, Universidad Tecnologica de San Juan del Rio (UTSJR), San Juan del Rio 76900, Queretaro, Mexico
| | - Virgilio Bocanegra-García
- Laboratorio Interacción Ambiente-Microorganismo, Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa 88710, Tamaulipas, Mexico
| | - Lourdes Vital-López
- Carrera de Mantenimiento Industrial, Universidad Tecnológica de Tamaulipas Norte, Reynosa 88680, Tamaulipas, Mexico
| | - Jaime García-Mena
- Department of Genetics and Molecular Biology, Cinvestav, Av. IPN# 2508, Col. Zacatenco, Mexico City 07360, Mexico
| | - Marco Antonio Zamora-Antuñano
- Engineering Area and Centro de Investigación, Innovación y Desarrollo Tecnológico de UVM (CIIDETEC-UVM), Universidad del Valle de Mexico (UVM), Santiago de Queretaro 76230, Queretaro, Mexico
| | - María Antonia Cruz-Hernández
- Laboratorio Interacción Ambiente-Microorganismo, Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa 88710, Tamaulipas, Mexico
| | | | - Alberto Mendoza-Herrera
- Laboratorio Interacción Ambiente-Microorganismo, Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Reynosa 88710, Tamaulipas, Mexico
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2
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Semenzato G, Faddetta T, Falsini S, Del Duca S, Esposito A, Padula A, Greco C, Mucci N, Zaccaroni M, Puglia AM, Papini A, Fani R. Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds. Microorganisms 2022; 10:microorganisms10102086. [PMID: 36296360 PMCID: PMC9612275 DOI: 10.3390/microorganisms10102086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic plants could use the seeds as vectors to vertically transfer beneficial endophytes, providing plants with metabolic pathways that could influence phytochemicals production. Here, we investigated the localization, the structure and the composition of the bacterial endophytic population that resides in Origanum heracleoticum L. seeds. Endocellular bacteria, surrounded by a wall, were localized close to the aleurone layer when using light and transmission electron microscopy. From surface-sterilized seeds, cultivable endophytes were isolated and characterized through RAPD analysis and 16S RNA gene sequencing, which revealed the existence of a high degree of biodiversity at the strain level and the predominance of the genus Pseudomonas. Most of the isolates grew in the presence of six selected antibiotics and were able to inhibit the growth of clinical and environmental strains that belong to the Burkholderia cepacia complex. The endophytes production of antimicrobial compounds could suggest their involvement in plant secondary metabolites production and might pave the way to endophytes exploitation in the pharmaceutical field.
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Affiliation(s)
- Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Sara Falsini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Antonia Esposito
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Anna Padula
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Claudia Greco
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Institute for Environmental Protection and Research, Via Ca’ Fornacetta, 9, Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Marco Zaccaroni
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies-STEBICEF, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Alessio Papini
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
- Correspondence:
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3
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Mancini A, Rodriguez MC, Zago M, Cologna N, Goss A, Carafa I, Tuohy K, Merz A, Franciosi E. Massive Survey on Bacterial-Bacteriophages Biodiversity and Quality of Natural Whey Starter Cultures in Trentingrana Cheese Production. Front Microbiol 2021; 12:678012. [PMID: 34194413 PMCID: PMC8236940 DOI: 10.3389/fmicb.2021.678012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/29/2021] [Indexed: 01/04/2023] Open
Abstract
This study focused on the microbial and bacteriophages identification and characterization in cheese-production facilities that use natural whey starter (NWS) cultures for Trentingrana production. Bacterial and phage screening was carried out on cooked not acidified whey and NWS samples isolated from six dairy factories, for 4 consecutive days in four different months. By means of a combined approach, using plate counts, bacterial isolation, and metataxonomic analysis Lactobacillus helveticus was found occurring as the dominant species in NWS cultures and Levilactobacillus brevis as codominant in the cheese factories where the temperature of NWS production was mainly lower than 40°C, suggesting that the variability in the parameters of the NWS culture preparation could differently modulate the bacterial species in NWS cultures. Using turbidity test approach on 303 bacterial isolates from the NWS cultures, 120 distinct phages were identified. L. helveticus phage contamination of NWS cultures was revealed in most of the analyzed samples, but despite the great recovery of bacteriophage contamination cases, the microbial quality of NWS cultures was high. Our results support the presence of natural bacteriophage resistance mechanisms in L. helveticus. The use of NWS cultures probably creates an ideal environment for the proliferation of different L. helveticus strains balanced with their phages without a clear dominance. It is evident, from this study, that the presence of a high biodiversity of NWS bacterial strains is relevant to avoid phages dominance in NWS cultures and consequently to keep a good acidification ability.
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Affiliation(s)
- Andrea Mancini
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Maria Cid Rodriguez
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Miriam Zago
- Centro di ricerca Zootecnia e Acquacoltura (CREA-ZA), Lodi, Italy
| | - Nicola Cologna
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Andrea Goss
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Ilaria Carafa
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Kieran Tuohy
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Andrea Merz
- Trentingrana Consorzio dei Caseifici Sociali Trentini s.c.a., Trento, Italy
| | - Elena Franciosi
- Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
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4
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Toffoli LM, Martínez-Zamora MG, Medrano NN, Fontana CA, Lovaisa NC, Delaporte-Quintana P, Elias JM, Salazar SM, Pedraza RO. Natural occurrence of Azospirillum brasilense in petunia with capacity to improve plant growth and flowering. J Basic Microbiol 2021; 61:662-673. [PMID: 34057226 DOI: 10.1002/jobm.202100064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/28/2021] [Accepted: 04/18/2021] [Indexed: 11/12/2022]
Abstract
To evaluate the natural occurrence of the plant growth-promoting bacterium Azospirillum brasilense and petunia plants, local strains were isolated and characterized by biochemical and molecular methods. Three strains were assessed in greenhouse conditions using Petunia × hybrida Ultra™. Treatments: Plants without bacterial inoculation or chemical fertilization; fertilized with NPK and KNO3 ; and independently inoculated with the strains 2A1, 2A2, and 2E1 by submerging their roots in a bacterial suspension (~106 CFU·ml-1 ). Root length, dry weight of roots and shoots, leaf area, leaf greenness, and nutrient content were evaluated. The number of days from transplanting to the opening of the first flower and the number of flowers per plant were also determined. As a result, five isolates were characterized as A. brasilense, showing the capacity to produce indoles and siderophores, to solubilize phosphate, nitrogenase activity, and nifH-PCR amplification. In general, all the parameters of the plant assay were improved in plants inoculated with A. brasilense, with variations among the strains, as well as the onset of flowering and the number of flowers per plant, compared with uninoculated or fertilized plants. This is the first report on the natural occurrence of A. brasilense in petunia with the capacity to improve plant growth and flowering.
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Affiliation(s)
- Lucía M Toffoli
- Estación Experimental Agropecuaria Famaillá, Instituto Nacional de Tecnología Agropecuaria, Tucumán, Argentina
| | - Martín G Martínez-Zamora
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Norma N Medrano
- Estación Experimental Agropecuaria Famaillá, Instituto Nacional de Tecnología Agropecuaria, Tucumán, Argentina
| | - Cecilia A Fontana
- Estación Experimental Agropecuaria Famaillá, Instituto Nacional de Tecnología Agropecuaria, Tucumán, Argentina
| | - Nadia C Lovaisa
- Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Paola Delaporte-Quintana
- Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Juliana M Elias
- Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Sergio M Salazar
- Estación Experimental Agropecuaria Famaillá, Instituto Nacional de Tecnología Agropecuaria, Tucumán, Argentina.,Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Raúl O Pedraza
- Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
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5
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Tedesco P, Palma Esposito F, Masino A, Vitale GA, Tortorella E, Poli A, Nicolaus B, van Zyl LJ, Trindade M, de Pascale D. Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier. Microorganisms 2021; 9:microorganisms9050890. [PMID: 33919419 PMCID: PMC8143284 DOI: 10.3390/microorganisms9050890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Extremophilic microorganisms represent a unique source of novel natural products. Among them, cold adapted bacteria and particularly alpine microorganisms are still underexplored. Here, we describe the isolation and characterization of a novel Gram-positive, aerobic rod-shaped alpine bacterium (KRL4), isolated from sediments from the Karuola glacier in Tibet, China. Complete phenotypic analysis was performed revealing the great adaptability of the strain to a wide range of temperatures (5-40 °C), pHs (5.5-8.5), and salinities (0-15% w/v NaCl). Genome sequencing identified KRL4 as a member of the placeholder genus Exiguobacterium_A and annotation revealed that only half of the protein-encoding genes (1522 of 3079) could be assigned a putative function. An analysis of the secondary metabolite clusters revealed the presence of two uncharacterized phytoene synthase containing pathways and a novel siderophore pathway. Biological assays confirmed that the strain produces molecules with antioxidant and siderophore activities. Furthermore, intracellular extracts showed nematocidal activity towards C. elegans, suggesting that strain KRL4 is a source of anthelmintic compounds.
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Affiliation(s)
- Pietro Tedesco
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Fortunato Palma Esposito
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Antonio Masino
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy
| | - Giovanni Andrea Vitale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Emiliana Tortorella
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
| | - Annarita Poli
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, 80078 Naples, Italy; (A.P.); (B.N.)
| | - Barbara Nicolaus
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, 80078 Naples, Italy; (A.P.); (B.N.)
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, 7535 Cape Town, South Africa; (L.J.v.Z.); (M.T.)
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, 7535 Cape Town, South Africa; (L.J.v.Z.); (M.T.)
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
- Correspondence:
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6
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Carafa I, Navarro IC, Bittante G, Tagliapietra F, Gallo L, Tuohy K, Franciosi E. Shift in the cow milk microbiota during alpine pasture as analyzed by culture dependent and high-throughput sequencing techniques. Food Microbiol 2020; 91:103504. [PMID: 32539948 DOI: 10.1016/j.fm.2020.103504] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/19/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022]
Abstract
In the present study, two groups of cows from a permanent lowland farm (PF) were divided during summer and reared in the PF or in a temporary alpine farm (ALP), respectively. Microbiological analyses were performed with the objective to investigate the microbial evolution of milk before, during, and after summer transhumance comparing, in particular, the two groups of cows to determine whether the alpine pasture could directly influence the milk microbiota. A significant increase of all microbial groups was registered in milk samples collected in the ALP. Interestingly, many strains belonging to species with well reported technological and probiotic activities were isolated from Alpine milk (20% Lactococcus lactis subsp. lactis/cremoris, 18% Lactobacillus paracasei, 14% Bifidobacterium crudilactis and 18% Propionibacterium sp.), whereas only 16% of strains isolated from the permanent farm milk belonged to the species Lactococcus lactis subsp. lactis/cremoris, 6% to Lactobacillus paracasei, 2% to Bifidobacterium crudilactis and 5% to Propionibacterium sp. The MiSeq Illumina data showed that Alpine milk presented a significant reduction of Pseudomonas and an increase of Lactococcus, Bifidobacterium and Lactobacillus genera. These data confirmed the practice of Alpine pasture as one of the main drivers affecting the milk microbiota. All the microbial changes disappeared when cows were delivered back from Alpine pasture to the indoor farm.
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Affiliation(s)
- Ilaria Carafa
- Research and Innovation Centre, Food Quality and Nutrition Department, Fondazione Edmund Mach (FEM), San Michele all' Adige, TN, Italy
| | - Irma Castro Navarro
- Research and Innovation Centre, Food Quality and Nutrition Department, Fondazione Edmund Mach (FEM), San Michele all' Adige, TN, Italy
| | - Giovanni Bittante
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD, Italy
| | - Franco Tagliapietra
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD, Italy
| | - Luigi Gallo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Legnaro, PD, Italy
| | - Kieran Tuohy
- Research and Innovation Centre, Food Quality and Nutrition Department, Fondazione Edmund Mach (FEM), San Michele all' Adige, TN, Italy
| | - Elena Franciosi
- Research and Innovation Centre, Food Quality and Nutrition Department, Fondazione Edmund Mach (FEM), San Michele all' Adige, TN, Italy.
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7
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Ganuza M, Pastor N, Boccolini M, Erazo J, Palacios S, Oddino C, Reynoso MM, Rovera M, Torres AM. Evaluating the impact of the biocontrol agent Trichoderma harzianum ITEM 3636 on indigenous microbial communities from field soils. J Appl Microbiol 2018; 126:608-623. [PMID: 30382616 DOI: 10.1111/jam.14147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
AIM To investigate the impact of inoculating peanut seeds with the biocontrol agent Trichoderma harzianum ITEM 3636 on the structure of bacterial and fungal communities from agricultural soils. METHODS AND RESULTS Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing (NGS) of amplicons (or marker gene amplification metagenomics) were performed to investigate potential changes in the structure of microbial communities from fields located in a peanut-producing area in the province of Córdoba, Argentina. Fields had history of peanut smut (caused by Thecaphora frezii) incidence. The Shannon indexes (H'), which estimate diversity, obtained from the PCR-DGGE assays did not show significant differences neither for bacterial nor for fungal communities between control and inoculation treatments. On the other hand, the number of operational taxonomic units obtained after NGS was similar between all the analysed samples. Moreover, results of alpha and beta diversity showed that there were no significant variations between the relative abundances of the most representative bacterial and fungal phyla and genera, in both fields. CONCLUSIONS Trichoderma harzianum ITEM 3636 decreases the incidence and severity of agriculturally relevant diseases without causing significant changes in the microbial communities of agricultural soils. SIGNIFICANCE AND IMPACT OF THE STUDY Our investigations provide information on the structure of bacterial and fungal communities in peanut-producing fields after inoculation of seeds with a biocontrol agent.
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Affiliation(s)
- M Ganuza
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - N Pastor
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - M Boccolini
- INTA EEA - Instituto Nacional de Tecnología Agropecuaria Estación Experimental Marcos Juárez, Marcos Juárez, Córdoba, Argentina
| | - J Erazo
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - S Palacios
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - C Oddino
- Facultad de Agronomía y Veterinaria, UNRC, Río Cuarto, Córdoba, Argentina
| | - M M Reynoso
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
| | - M Rovera
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
| | - A M Torres
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina.,UNRC-CONICET, Río Cuarto, Argentina
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8
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Chandar B, Poovitha S, Ilango K, MohanKumar R, Parani M. Inhibition of New Delhi Metallo-β-Lactamase 1 (NDM-1) Producing Escherichia coli IR-6 by Selected Plant Extracts and Their Synergistic Actions with Antibiotics. Front Microbiol 2017; 8:1580. [PMID: 28878746 PMCID: PMC5572277 DOI: 10.3389/fmicb.2017.01580] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/03/2017] [Indexed: 11/13/2022] Open
Abstract
Improper use of antibiotics has led to a great concern in the development of pathogenic microbial resistance. New Delhi metallo-β-lactamase 1 (NDM-1) producing bacteria are resistant to most of the β-lactam antibiotics, and so far, no new compounds have been clinically tested against these bacteria. In this study, ethanol extracts from the leaves of 240 medicinal plant species were screened for antibacterial activity against an NDM-1 Escherichia coli strain. The extracts that showed antibacterial activity were then tested for minimum inhibitory concentrations (MICs) and zones of inhibition. The extract from Combretum albidum G. Don, Hibiscus acetosella Welw. ex Hiern, Hibiscus cannabinus L., Hibiscus furcatus Willd., Punica granatum L., and Tamarindus indica L. showed bactericidal activity between 5 and 15 mg/ml and the MIC was between 2.56 and 5.12 mg/ml. All six plant extracts inhibited activity of the NDM-1 enzyme in vitro, and the IC50 value ranged between 0.50 and 1.2 ng/μl. Disruption of bacterial cell wall integrity by the plant extracts was clearly visible with scanning electron microscopy. Increases in membrane permeability caused 79.4–89.7% bacterial cell deaths as investigated by fluorescence-activated cell sorting. All the plant extracts showed synergistic effects when combined with colistin [fractional inhibitory concentration (ΣFIC) = 0.125–0.375], meropenem (ΣFIC = 0.09–0.313), and tetracycline (ΣFIC = 0.125–0.313). Thus, the plant extracts can be fractionated for the identification of active compounds, which could be used as new antibacterial compounds for the development of drugs against NDM-1 E. coli in addition to their use in combination therapy.
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Affiliation(s)
- Brinda Chandar
- Genomics Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM UniversityKattankulathur, India
| | - Sundar Poovitha
- Genomics Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM UniversityKattankulathur, India
| | - Kaliappan Ilango
- Interdisciplinary Institute of Indian System of Medicine, SRM UniversityKattankulathur, India
| | - Ramasamy MohanKumar
- Interdisciplinary Institute of Indian System of Medicine, SRM UniversityKattankulathur, India
| | - Madasamy Parani
- Genomics Laboratory, Department of Genetic Engineering, School of Bioengineering, SRM UniversityKattankulathur, India
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9
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Ivanović Ž, Perović T, Popović T, Blagojević J, Trkulja N, Hrnčić S. Characterization of Pseudomonas syringae pv. syringae, Causal Agent of Citrus Blast of Mandarin in Montenegro. THE PLANT PATHOLOGY JOURNAL 2017; 33:21-33. [PMID: 28167885 PMCID: PMC5291395 DOI: 10.5423/ppj.oa.08.2016.0161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/22/2016] [Accepted: 11/01/2016] [Indexed: 05/09/2023]
Abstract
Citrus blast caused by bacterium Pseudomonas syringae is a very important disease of citrus occuring in many areas of the world, but with few data about genetic structure of the pathogen involved. Considering the above fact, this study reports genetic characterization of 43 P. syringae isolates obtained from plant tissue displaying citrus blast symptoms on mandarin (Citrus reticulata) in Montenegro, using multilocus sequence analysis of gyrB, rpoD, and gap1 gene sequences. Gene sequences from a collection of 54 reference pathotype strains of P. syringae from the Plant Associated and Environmental Microbes Database (PAMDB) was used to establish a genetic relationship with our isolates obtained from mandarin. Phylogenetic analyses of gyrB, rpoD, and gap1 gene sequences showed that P. syringae pv. syringae causes citrus blast in mandarin in Montenegro, and belongs to genomospecies 1. Genetic homogeneity of isolates suggested that the Montenegrian population might be clonal which indicates a possible common source of infection. These findings may assist in further epidemiological studies of this pathogen and for determining mandarin breeding strategies for P. syringae control.
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Affiliation(s)
- Žarko Ivanović
- Institute for Plant Protection and Environment, Belgrade 11040,
Serbia
| | - Tatjana Perović
- Biotechnical Faculty, University of Podgorica, Podgorica 81000,
Montenegro
| | - Tatjana Popović
- Institute for Plant Protection and Environment, Belgrade 11040,
Serbia
| | - Jovana Blagojević
- Scholar of Ministry of Education, Science and Technological Development of the Republic of Serbia, Department of Plant Disease, Institute for Plant Protection and Environment, Belgrade 11040,
Serbia
| | - Nenad Trkulja
- Institute for Plant Protection and Environment, Belgrade 11040,
Serbia
| | - Snježana Hrnčić
- Biotechnical Faculty, University of Podgorica, Podgorica 81000,
Montenegro
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10
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Tripti K. pH modulates arsenic toxicity in Bacillus licheniformis DAS-2. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 130:240-247. [PMID: 27135959 DOI: 10.1016/j.ecoenv.2016.04.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/21/2016] [Accepted: 04/23/2016] [Indexed: 06/05/2023]
Abstract
The toxic characteristics of arsenic species, As(V) and As(III) result in ecological risks. Arsenic tolerant bacterium was isolated and identified as the Bacillus licheniformis DAS-2 through 16SrDNA sequencing. B. licheniformis DAS-2 was efficient to tolerate and remove both the As(V)[MIC 8mM] and As(III)[MIC 6mM] from the growth medium. The potential for the removal/uptake of arsenic from the 3, 5 and 7mM As(V) enriched growth media was 100%, 60% and 35% respectively and from the 1, 3 and 5mM As(III) enrichment it was 100%, 99% and 58% respectively at neutral pH. 80% of uptake As(V) was reduced to As(III) in 3mM As(V) enrichment which was gradually decreased to only 17% at 7mM As(V) enrichment at neutral pH. The arsenic toxicity in B. licheniformis DAS-2 was found modulated by pH and was examined through alteration in growth, uptake/removal, reduction and measurement of chemical toxicity.
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Affiliation(s)
- K Tripti
- Laboratory of Environment and Biotechnology, Department of Botany, Patna Science College, Patna University, Patna 800005, India
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11
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Tedesco P, Maida I, Palma Esposito F, Tortorella E, Subko K, Ezeofor CC, Zhang Y, Tabudravu J, Jaspars M, Fani R, de Pascale D. Antimicrobial Activity of Monoramnholipids Produced by Bacterial Strains Isolated from the Ross Sea (Antarctica). Mar Drugs 2016; 14:md14050083. [PMID: 27128927 PMCID: PMC4882557 DOI: 10.3390/md14050083] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 04/18/2016] [Accepted: 04/18/2016] [Indexed: 11/16/2022] Open
Abstract
Microorganisms living in extreme environments represent a huge reservoir of novel antimicrobial compounds and possibly of novel chemical families. Antarctica is one of the most extraordinary places on Earth and exhibits many distinctive features. Antarctic microorganisms are well known producers of valuable secondary metabolites. Specifically, several Antarctic strains have been reported to inhibit opportunistic human pathogens strains belonging to Burkholderia cepacia complex (Bcc). Herein, we applied a biodiscovery pipeline for the identification of anti-Bcc compounds. Antarctic sub-sea sediments were collected from the Ross Sea, and used to isolate 25 microorganisms, which were phylogenetically affiliated to three bacterial genera (Psychrobacter, Arthrobacter, and Pseudomonas) via sequencing and analysis of 16S rRNA genes. They were then subjected to a primary cell-based screening to determine their bioactivity against Bcc strains. Positive isolates were used to produce crude extracts from microbial spent culture media, to perform the secondary screening. Strain Pseudomonas BNT1 was then selected for bioassay-guided purification employing SPE and HPLC. Finally, LC-MS and NMR structurally resolved the purified bioactive compounds. With this strategy, we achieved the isolation of three rhamnolipids, two of which were new, endowed with high (MIC < 1 μg/mL) and unreported antimicrobial activity against Bcc strains.
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Affiliation(s)
- Pietro Tedesco
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino, 111, I-80131 Naples, Italy.
| | - Isabel Maida
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (FI), Italy.
| | - Fortunato Palma Esposito
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino, 111, I-80131 Naples, Italy.
| | - Emiliana Tortorella
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino, 111, I-80131 Naples, Italy.
| | - Karolina Subko
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE Scotland, UK.
| | - Chidinma Christiana Ezeofor
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE Scotland, UK.
| | - Ying Zhang
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE Scotland, UK.
| | - Jioji Tabudravu
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE Scotland, UK.
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen, AB24 3UE Scotland, UK.
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino (FI), Italy.
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, Via P. Castellino, 111, I-80131 Naples, Italy.
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12
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Perrin E, Fondi M, Maida I, Mengoni A, Chiellini C, Mocali S, Cocchi P, Campana S, Taccetti G, Vaneechoutte M, Fani R. Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers. J Microbiol Methods 2015; 117:108-12. [PMID: 26235543 DOI: 10.1016/j.mimet.2015.07.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 12/21/2022]
Abstract
The growing number of available microbial genomes offers the possibility to identify features that could be used for identification. In this work, the possibility to exploit overlapping genes to develop a simple PCR based method of identification, was explored. Using the Burkholderia cepacia complex as a model, genomic analyses were performed to check the phylogenetic distribution of an overlap between marC and hisH genes and then, a PCR specific for Burkholderia was designed, set up and tested on a panel of strains and on DNA extracted from the sputum of cystic fibrosis patients. Results obtained revealed the usefulness of this approach, which could then be used to develop PCR for the identification of specific bacteria species or genera.
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Affiliation(s)
- Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
| | - Isabel Maida
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
| | - Carolina Chiellini
- CRA-ABP Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'Agrobiologia e la Pedologia, Piazza M. D'Azeglio 30, 50121 Firenze, FI, Italy.
| | - Stefano Mocali
- CRA-ABP Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di ricerca per l'Agrobiologia e la Pedologia, Piazza M. D'Azeglio 30, 50121 Firenze, FI, Italy.
| | - Priscilla Cocchi
- Department of Paediatric Medicine, Anna Meyer Children's University Hospital, Viale G. Pieraccini, 24, 50141 Florence, Italy.
| | - Silvia Campana
- Department of Paediatric Medicine, Anna Meyer Children's University Hospital, Viale G. Pieraccini, 24, 50141 Florence, Italy.
| | - Giovanni Taccetti
- Department of Paediatric Medicine, Anna Meyer Children's University Hospital, Viale G. Pieraccini, 24, 50141 Florence, Italy.
| | - Mario Vaneechoutte
- Ghent University, Laboratory of Bacteriology Research, De Pintelaan 185 BA-3/4, 9000 Ghent, Belgium.
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto F.no, Florence, Italy.
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13
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Carafa I, Nardin T, Larcher R, Viola R, Tuohy K, Franciosi E. Identification and characterization of wild lactobacilli and pediococci from spontaneously fermented Mountain Cheese. Food Microbiol 2015; 48:123-32. [DOI: 10.1016/j.fm.2014.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 12/03/2014] [Accepted: 12/10/2014] [Indexed: 11/26/2022]
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14
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Biodiversity and γ-aminobutyric acid production by lactic acid bacteria isolated from traditional alpine raw cow's milk cheeses. BIOMED RESEARCH INTERNATIONAL 2015; 2015:625740. [PMID: 25802859 PMCID: PMC4352725 DOI: 10.1155/2015/625740] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/04/2014] [Accepted: 10/02/2014] [Indexed: 11/18/2022]
Abstract
“Nostrano-cheeses” are traditional alpine cheeses made from raw cow's milk in Trentino-Alto Adige, Italy. This study identified lactic acid bacteria (LAB) developing during maturation of “Nostrano-cheeses” and evaluated their potential to produce γ-aminobutyric acid (GABA), an immunologically active compound and neurotransmitter. Cheese samples were collected on six cheese-making days, in three dairy factories located in different areas of Trentino and at different stages of cheese ripening (24 h, 15 days, and 1, 2, 3, 6, and 8 months). A total of 1,059 LAB isolates were screened using Random Amplified Polymorphic DNA-PCR (RAPD-PCR) and differentiated into 583 clusters. LAB strains from dominant clusters (n = 97) were genetically identified to species level by partial 16S rRNA gene sequencing. LAB species most frequently isolated were Lactobacillus paracasei, Streptococcus thermophilus, and Leuconostoc mesenteroides. The 97 dominant clusters were also characterized for their ability in producing GABA by high-performance liquid chromatography (HPLC). About 71% of the dominant bacteria clusters evolving during cheeses ripening were able to produce GABA. Most GABA producers were Lactobacillus paracasei but other GABA producing species included Lactococcus lactis, Lactobacillus plantarum, Lactobacillus rhamnosus, Pediococcus pentosaceus, and Streptococcus thermophilus. No Enterococcus faecalis or Sc. macedonicus isolates produced GABA. The isolate producing the highest amount of GABA (80.0±2.7 mg/kg) was a Sc. thermophilus.
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15
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Bagheripoor-Fallah N, Mortazavian A, Hosseini H, Khoshgozaran-Abras S, Rad AH. Comparison of Molecular Techniques with other Methods for Identification and Enumeration of Probiotics in Fermented Milk Products. Crit Rev Food Sci Nutr 2014; 55:396-413. [DOI: 10.1080/10408398.2012.656771] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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16
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Bevivino A, Paganin P, Bacci G, Florio A, Pellicer MS, Papaleo MC, Mengoni A, Ledda L, Fani R, Benedetti A, Dalmastri C. Soil bacterial community response to differences in agricultural management along with seasonal changes in a Mediterranean region. PLoS One 2014; 9:e105515. [PMID: 25144665 PMCID: PMC4140800 DOI: 10.1371/journal.pone.0105515] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 07/23/2014] [Indexed: 11/18/2022] Open
Abstract
Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil health and sustainable productivity.
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Affiliation(s)
- Annamaria Bevivino
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy
- * E-mail:
| | - Patrizia Paganin
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy
| | - Giovanni Bacci
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Research Centre for the Soil-Plant System, Rome, Italy
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy
| | - Alessandro Florio
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Research Centre for the Soil-Plant System, Rome, Italy
| | - Maite Sampedro Pellicer
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy
| | - Maria Cristiana Papaleo
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy
| | - Alessio Mengoni
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy
| | - Luigi Ledda
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Renato Fani
- Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Florence, Italy
| | - Anna Benedetti
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura - Research Centre for the Soil-Plant System, Rome, Italy
| | - Claudia Dalmastri
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Economic Development) Casaccia Research Center, Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Rome, Italy
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17
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A new resource from traditional wines: characterisation of the microbiota of “Vino Santo” grapes as a biocontrol agent against Botrytis cinerea. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2195-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Baldi F, Gallo M, Marchetto D, Faleri C, Maida I, Fani R. Manila clams from Hg polluted sediments of Marano and Grado lagoons (Italy) harbor detoxifying Hg resistant bacteria in soft tissues. ENVIRONMENTAL RESEARCH 2013; 125:188-196. [PMID: 23398778 DOI: 10.1016/j.envres.2012.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 11/17/2012] [Accepted: 11/27/2012] [Indexed: 06/01/2023]
Abstract
A mechanism of mercury detoxification has been suggested by a previous study on Hg bioaccumulation in Manila clams (Ruditapes philippinarum) in the polluted Marano and Grado lagoons and in this study we demonstrate that this event could be partly related to the detoxifying activities of Hg-resistant bacteria (MRB) harbored in clam soft tissues. Therefore, natural clams were collected in six stations during two different periods (winter and spring) from Marano and Grado Lagoons. Siphons, gills and hepatopancreas from acclimatized clams were sterile dissected to isolate MRB. These anatomical parts were glass homogenized or used for whole, and they were lying on a solid medium containing 5mgl(-1) HgCl2 and incubated at 30°C. A total of fourteen bacterial strains were isolated and were identified by 16S rDNA sequencing and analysis, revealing that strains were representative of eight bacterial genera, four of which were Gram-positive (Enterococcus, Bacillus, Jeotgalicoccus and Staphylococcus) and other four were Gram-negative (Stenotrophomonas, Vibrio, Raoultella and Enterobacter). Plasmids and merA genes were found and their sequences determined. Fluorescence in situ hybridization (FISH) technique shows the presence of Firmicutes, Actinobacteria and Gammaproteobacteria by using different molecular probes in siphon and gills. Bacterial clumps inside clam flesh were observed and even a Gram-negative endosymbiont was disclosed by transmission electronic microscope inside clam cells. Bacteria harbored in cavities of soft tissue have mercury detoxifying activity. This feature was confirmed by the determination of mercuric reductase in glass-homogenized siphons and gills.
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Affiliation(s)
- Franco Baldi
- Dipartimento di Scienze Molecolari e Nanosistemi, Cà Foscari University of Venice, Dorsoduro 2137, 30123 Venice, Italy.
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Alteration of bacterial communities and organic matter in microbial fuel cells (MFCs) supplied with soil and organic fertilizer. Appl Microbiol Biotechnol 2013; 97:1299-315. [PMID: 22290652 DOI: 10.1007/s00253-012-3906-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/12/2012] [Accepted: 01/16/2012] [Indexed: 10/14/2022]
Abstract
The alteration of the organic matter (OM) and the composition of bacterial community in microbial fuel cells (MFCs) supplied with soil (S) and a composted organic fertilizer (A) was examined at the beginning and at the end of 3 weeks of incubation under current-producing as well as no-current-producing conditions. Denaturing gradient gel electrophoresis revealed a significant alteration of the microbial community structure in MFCs generating electricity as compared with no-current-producing MFCs. The genetic diversity of cultivable bacterial communities was assessed by random amplified polymorphic DNA (RAPD) analysis of 106 bacterial isolates obtained by using both generic and elective media. Sequencing of the 16S rRNA genes of the more representative RAPD groups indicated that over 50.4% of the isolates from MFCs fed with S were Proteobacteria, 25.1% Firmicutes, and 24.5% Actinobacteria, whereas in MFCs supplied with A 100% of the dominant species belonged to γ-Proteobacteria. The chemical analysis performed by fractioning the OM and using thermal analysis showed that the amount of total organic carbon contained in the soluble phase of the electrochemically active chambers significantly decreased as compared to the no-current-producing systems, whereas the OM of the solid phase became more humified and aromatic along with electricity generation, suggesting a significant stimulation of a humification process of the OM. These findings demonstrated that electroactive bacteria are commonly present in aerobic organic substrates such as soil or a fertilizer and that MFCs could represent a powerful tool for exploring the mineralization and humification processes of the soil OM.
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20
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Mehnaz S. Microbes - friends and foes of sugarcane. J Basic Microbiol 2013; 53:954-71. [PMID: 23322584 DOI: 10.1002/jobm.201200299] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 08/14/2012] [Indexed: 11/09/2022]
Abstract
Sugarcane is an important cash crop for many countries because it is a major source of several products including sugar and bioethanol. To obtain maximum yields there is a need to apply large quantities of chemical fertilizers.Worldwide yields are also severely affected by more than sixty diseases, mostly caused by fungi but viruses, phytoplasmas, nematodes and other pests can also damage this crop. For most of these diseases, chemical control is not available and breeders are struggling with the development of pest resistant varieties. Many members of the grass family Poaceae establish associations with beneficial microbes which promote their growth by direct and indirect mechanisms. They can be used as means to reduce the need for chemical fertilizer and to minimize the impacts of pathogen invasion. This review highlights the diversity of the microbes associated with sugarcane and the role of beneficial microbes for growth promotion and biocontrol. More extensive use of beneficial microbes will help the sugarcane grower not only to reduce the use of chemical fertilizers but also minimize the disease. In this paper, a brief description of both the non-pathogenic and pathogenic microbes associated with sugarcane is provided. Future prospects for the expanded use of beneficial microbes for sugarcane are also discussed and detailed herein.
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Affiliation(s)
- Samina Mehnaz
- Department of Biological Sciences, Forman Christian College University, Lahore, Pakistan
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21
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Virolainen N, Guglielmetti S, Arioli S, Karp M. Bioluminescence-based identification of nisin producers - a rapid and simple screening method for nisinogenic bacteria in food samples. Int J Food Microbiol 2012; 158:126-32. [PMID: 22831816 DOI: 10.1016/j.ijfoodmicro.2012.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 06/29/2012] [Accepted: 07/07/2012] [Indexed: 10/28/2022]
Abstract
We present a simple and rapid method for screening nisin producers that directly identifies nisinogenic bacteria by induction of bioluminescence within the Lactococcus lactis NZ9800lux biosensor strain (Immonen and Karp, 2007, Biosensors and Bioelectronics 22, 1982-7). An overlay of putative nisinogenic colonies with the biosensor strain gives identification results within 1h. Functionality and specificity of the method were verified by screening nisin producers among 144 raw milk colonies and a panel of 91 lactococcal strains. Studies performed on strains and colonies that did not induce bioluminescence but inhibited growth of the biosensor demonstrated that only nisinogenic bacteria can cause induction. Bacteria known to produce bacteriocins other than nisin failed to induce bioluminescence, further verifying the specificity of the assay. We discovered a non-inducing but inhibitory lactococcal strain harboring a modified nisin Z gene, and demonstrated that the source of the inhibitory action is not a non-inducing variant of nisin, but a bacteriocin of lower molecular weight. The concentration of nisin producers in a raw milk sample was 1.3 × 10(2)CFU/ml. We identified from raw milk a total of seven nisin Z producing L. lactis subsp. lactis colonies, which were shown by genetic fingerprinting to belong to three different groups. Among the panel of 91 lactococci, four strains were nisin A producers, and one strain harbored the modified nisin Z gene. The method presented here is robust, cost-effective and simple to perform, and avoids the pitfalls of traditional screening methods by directly specifying the identity of the inhibitory substance.
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Affiliation(s)
- Nina Virolainen
- Tampere University of Technology, Department of Chemistry and Bioengineering, Finland.
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22
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Zuno-Floriano FG, Miller MG, Aldana-Madrid ML, Hengel MJ, Gaikwad NW, Tolstikov V, Contreras-Cortés AG. Effect of Acinetobacter sp on metalaxyl degradation and metabolite profile of potato seedlings (Solanum tuberosum L.) alpha variety. PLoS One 2012; 7:e31221. [PMID: 22363586 PMCID: PMC3281949 DOI: 10.1371/journal.pone.0031221] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/04/2012] [Indexed: 11/19/2022] Open
Abstract
One of the most serious diseases in potato cultivars is caused by the pathogen Phytophthora infestans, which affects leaves, stems and tubers. Metalaxyl is a fungicide that protects potato plants from Phytophthora infestans. In Mexico, farmers apply metalaxyl 35 times during the cycle of potato production and the last application is typically 15 days before harvest. There are no records related to the presence of metalaxyl in potato tubers in Mexico. In the present study, we evaluated the effect of Acinetobacter sp on metalaxyl degradation in potato seedlings. The effect of bacteria and metalaxyl on the growth of potato seedlings was also evaluated. A metabolite profile analysis was conducted to determine potential molecular biomarkers produced by potato seedlings in the presence of Acinetobacter sp and metalaxyl. Metalaxyl did not affect the growth of potato seedlings. However, Acinetobacter sp strongly affected the growth of inoculated seedlings, as confirmed by plant length and plant fresh weights which were lower in inoculated potato seedlings (40% and 27%, respectively) compared to the controls. Acinetobacter sp also affected root formation. Inoculated potato seedlings showed a decrease in root formation compared to the controls. LC-MS/MS analysis of metalaxyl residues in potato seedlings suggests that Acinetobacter sp did not degrade metalaxyl. GC–TOF–MS platform was used in metabolic profiling studies. Statistical data analysis and metabolic pathway analysis allowed suggesting the alteration of metabolic pathways by both Acinetobacter sp infection and metalaxyl treatment. Several hundred metabolites were detected, 137 metabolites were identified and 15 metabolic markers were suggested based on statistical change significance found with PLS-DA analysis. These results are important for better understanding the interactions of putative endophytic bacteria and pesticides on plants and their possible effects on plant metabolism.
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Affiliation(s)
- Fabiola G Zuno-Floriano
- Department of Environmental Toxicology, University of California Davis, Davis, California, United States of America.
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Papaleo MC, Fondi M, Maida I, Perrin E, Lo Giudice A, Michaud L, Mangano S, Bartolucci G, Romoli R, Fani R. Sponge-associated microbial Antarctic communities exhibiting antimicrobial activity against Burkholderia cepacia complex bacteria. Biotechnol Adv 2012; 30:272-93. [DOI: 10.1016/j.biotechadv.2011.06.011] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 05/27/2011] [Accepted: 06/13/2011] [Indexed: 11/26/2022]
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Lal S, Romano S, Chiarini L, Signorini A, Tabacchioni S. The Paenibacillus polymyxa species is abundant among hydrogen-producing facultative anaerobic bacteria in Lake Averno sediment. Arch Microbiol 2011; 194:345-51. [PMID: 22038026 DOI: 10.1007/s00203-011-0763-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 09/27/2011] [Accepted: 10/11/2011] [Indexed: 11/30/2022]
Abstract
Lake Averno sediment was used to isolate the facultative anaerobic bacteria having the potential for H(2) production. Twenty-five out of 35 isolates recovered from the sediment sample produced hydrogen under anaerobic conditions from glucose with yields ranging from 0.1 to 0.49 mol H(2)/mol glucose. Identification based on 16S rRNA gene sequence analysis revealed that most of them belong to the Firmicutes group, with a prevalence of the Paenibacillus polymyxa species. Seven distinct genomic fingerprints among the 11 P. polymyxa isolates were obtained using the random amplified polymorphic DNA (RAPD) technique. Glucose fermentation by P. polymyxa isolates was investigated. Glucose was totally consumed after 3 days of fermentation. The fermentation products were hydrogen (0.18-0.47 mol H(2)/mol glucose), ethanol (0.1-0.5 mol ethanol/mol glucose), and 2,3-butanediol (0.1 mol 2,3-butanediol/mol glucose). Lower amounts of acetic, butyric, formic, lactic, and propionic acids were detected. All metabolic data concerning P. polymyxa isolates were analyzed by cluster analysis to reveal similarities and/or differences with clustering based on RAPD profiles. Despite the high metabolic similarity among almost all P. paenibacillus isolates, results of cluster analyses of metabolic and genetic data do not match completely.
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Affiliation(s)
- Sadhana Lal
- Technical Unit for Sustainable Development and Innovation of Agroindustrial System, S. Maria di Galeria, Rome, Italy
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Shime-Hattori A, Kobayashi S, Ikeda S, Asano R, Shime H, Shinano T. A rapid and simple PCR method for identifying isolates of the genus Azospirillum within populations of rhizosphere bacteria. J Appl Microbiol 2011; 111:915-24. [PMID: 21790914 DOI: 10.1111/j.1365-2672.2011.05115.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To develop a rapid and simple genus-specific polymerase chain reaction (PCR) method for detecting and identifying isolates of the genus Azospirillum which is well-recognized as plant growth-promoting rhizobacterium. METHODS AND RESULTS Nine pairs of PCR primers were designed based on the Azospirillum 16S rRNA, ipdC, nifA and nifH genes to assess their genus specificity by testing against 12 Azospirillum (from seven species) and 15 non-Azospirillum reference strains, as compared with the fAZO/rAZO pair reported by Baudoin et al. (J Appl Microbiol, 108, 2010, 25). Among the primer pairs assessed, the Az16S-A pair designed on the 16S rRNA gene sequence showed the highest genus specificity: it successfully yielded a single amplicon of the expected size in all the 12 Azospirillum strains and for a close relative, Rhodocista centenaria. The PCR with the Az16S-A primers generated a detectable amount of the amplicon from ≥10³ CFU ml⁻¹ of Azospirillum cell suspensions even in the presence of contaminants and accurately discriminated Azospirillum and non-Azospirillum species in both 35 Azospirillum-like and 70 unknown isolates from plant roots and rhizosphere soils. CONCLUSIONS We developed a rapid and simple PCR method for detecting and identifying Azospirillum isolates within populations of rhizosphere bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY The method developed would serve as a useful tool for isolating a variety of indigenous Azospirillum bacteria from agricultural samples.
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Affiliation(s)
- A Shime-Hattori
- National Agricultural Research Center for Hokkaido Region (NARCH), Hitsujigaoka 1, Toyohira-ku, Sapporo, Japan
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Altomare C, Tringovska I. Beneficial Soil Microorganisms, an Ecological Alternative for Soil Fertility Management. SUSTAINABLE AGRICULTURE REVIEWS 2011. [DOI: 10.1007/978-94-007-1521-9_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Donnarumma F, Capuana M, Vettori C, Petrini G, Giannini R, Indorato C, Mastromei G. Isolation and characterisation of bacterial colonies from seeds and in vitro cultures of Fraxinus spp. from Italian sites. PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:169-76. [PMID: 21143738 DOI: 10.1111/j.1438-8677.2010.00334.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Culturable bacteria were isolated from seeds, embryos and contaminated in vitro cultures of ash (Fraxinus excelsior L., F. ornus L. and F. angustifolia L.) and were identified using morphological and molecular analyses. Fourteen morphologically distinct isolates were recovered from seeds of Fraxinus spp. 16S rDNA sequencing categorised these isolates into ten separate genera. Three strains isolated from contaminated in vitro cultures, Pantoea agglomerans, Staphylococcus succinus and Aerococcus viridans, were used for comparative analysis with isolates from seeds. Antibiotic sensitivity testing of the isolated contaminants, including phytotoxicity of antibiotics on in vitro cultures of ash, was also investigated. Phytotoxic effects on explants immersed in ampicillin or cultured on medium containing ampicillin were negligible, however tetracycline, either alone or in combination with other antibiotics, had phytotoxic effects. We conclude that ampicillin is a suitable antibiotic to limit the growth of contaminating bacteria during the in vitro culture of ash.
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Affiliation(s)
- F Donnarumma
- Dipartimento di Biologia Evoluzionistica, Università di Firenze, Firenze, Italy
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Growth-promotion of strawberry plants inoculated with Azospirillum brasilense. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0169-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Verdenelli MC, Ghelfi F, Silvi S, Orpianesi C, Cecchini C, Cresci A. Probiotic properties of Lactobacillus rhamnosus and Lactobacillus paracasei isolated from human faeces. Eur J Nutr 2009; 48:355-63. [PMID: 19365593 DOI: 10.1007/s00394-009-0021-2] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 03/31/2009] [Indexed: 10/20/2022]
Abstract
BACKGROUND The possibility of using microbes to maintain health, and to prevent or treat disease is a topic as old as microbiology. The research of novel probiotic strains is important in order to satisfy the increasing request of the market and to obtain functional products in which the probiotic cultures are more active and with better probiotic characteristics than those already present on the market. AIM OF THE STUDY In this study, the probiotic potential of Lactobacillus strains isolated from Italian elderly human faeces was investigated. METHODS The Lactobacillus strains were identified and examined for resistance to gastric acidity and bile toxicity, adhesion to HT-29 cells, antimicrobial activities, antibiotic susceptibility and plasmid profile. Survival of the strains through human intestine was examined in a 3 months human feeding trial. RESULTS Two strains, Lactobacillus rhamnosus IMC 501 and Lactobacillus paracasei IMC 502, tolerated well low pH and bile acids. In antimicrobial activity assays, both strains showed inhibitory properties towards selected potential harmful microorganisms, particularly against Candida albicans. The two selected strains expressed high in vitro adherence to HT-29 cells increasing this characteristic when they are used in combination and they were resistant to vamcomycin, colistin sulphate, gentamicin, oxolinic acid and kanamycin. Moreover, the two strains could be recovered from stools of volunteers after the feeding trials. CONCLUSIONS Lactobacillus rhamnosus IMC 501 and L. paracasei IMC 502 present favourable strain-specific properties for their utilisation as probiotics in functional foods and the high adhesion ability of the L. rhamnosus IMC 501 and L. paracasei IMC 502 used in combination, confirmed by both in vitro and in vivo study, indicate that the two bacterial strains could be used as health-promoting bacteria.
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Affiliation(s)
- Maria Cristina Verdenelli
- Dipartimento di Scienze Morfologiche e Biochimiche Comparate, Università di Camerino, Camerino, Italy
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Reinhardt EL, Ramos PL, Manfio GP, Barbosa HR, Pavan C, Moreira-Filho CA. Molecular characterization of nitrogen-fixing bacteria isolated from brazilian agricultural plants at São Paulo state. Braz J Microbiol 2008; 39:414-22. [PMID: 24031239 PMCID: PMC3768443 DOI: 10.1590/s1517-83822008000300002] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 10/21/2007] [Accepted: 07/24/2008] [Indexed: 11/22/2022] Open
Abstract
Fourteen strains of nitrogen-fixing bacteria were isolated from different agricultural plant species, including cassava, maize and sugarcane, using nitrogen-deprived selective isolation conditions. Ability to fix nitrogen was verified by the acetylene reduction assay. All potentially nitrogen-fixing strains tested showed positive hybridization signals with a nifH probe derived from Azospirillum brasilense. The strains were characterized by RAPD, ARDRA and 16S rDNA sequence analysis. RAPD analyses revealed 8 unique genotypes, the remaining 6 strains clustered into 3 RAPD groups, suggesting a clonal origin. ARDRA and 16S rDNA sequence analyses allowed the assignment of 13 strains to known groups of nitrogen-fixing bacteria, including organisms from the genera Azospirillum, Herbaspirillum, Pseudomonas and Enterobacteriaceae. Two strains were classified as Stenotrophomonas ssp. Molecular identification results from 16S rDNA analyses were also corroborated by morphological and biochemical data.
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Cápiro NL, Da Silva MLB, Stafford BP, Rixey WG, Alvarez PJJ. Microbial community response to a release of neat ethanol onto residual hydrocarbons in a pilot-scale aquifer tank. Environ Microbiol 2008; 10:2236-44. [PMID: 18484998 DOI: 10.1111/j.1462-2920.2008.01645.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalie L Cápiro
- Department of Civil and Environmental Engineering, Rice University, 6100 Main Street - MS 317, Houston, TX 77005, USA.
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Characterisation and identification of arbuscular mycorrhizal fungi species by PCR/RFLP analysis of the rDNA internal transcribed spacer (ITS). ANN MICROBIOL 2008. [DOI: 10.1007/bf03175340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Ramya M, Anusha B, Kalavathy S. Decolorization and biodegradation of Indigo carmine by a textile soil isolate Paenibacillus larvae. Biodegradation 2007; 19:283-91. [PMID: 17554499 DOI: 10.1007/s10532-007-9134-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 05/11/2007] [Indexed: 11/26/2022]
Abstract
The potential of recently isolated bacteria Paenibacillus larvae for the effective decolorization of Indigo carmine was evaluated. The effects of operational parameters (temperature, pH, dye concentration, shaking/non shaking) were tested. Maximum extent of decolorization was observed when the medium was incorporated with 10 g/l of yeast extract and peptone. Decolorization was strongly inhibited at non-shaken conditions as well as incorporation of inorganic sources (sodium nitrite and ammonium chloride) in the medium. Maximum decolorization was observed at 30 degrees C (100%) and 40 degrees C (92%) at 8 h of incubation. The LC-MS and NMR analysis confirms the oxidation of Indigo carmine . The primary degradation products were found to be Isatin sulfonic acid and anthranilicacid.
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Affiliation(s)
- Mohandass Ramya
- Biotechnology Department, Bishop Heber College, Vyalur Road, Tiruchirapalli 620017 Tamilnadu, India.
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Chaia EE, Valverde C, Wall LG. Local Adaptation of Frankia to Different Discaria (Rhamnaceae) Host Species Growing in Patagonia. Curr Microbiol 2006; 53:523-8. [PMID: 17106801 DOI: 10.1007/s00284-006-0306-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Accepted: 08/14/2006] [Indexed: 11/29/2022]
Abstract
Frankia BCU110601 (Da) and Frankia BCU110345 (Dc) were isolated from root nodules of Discaria articulata and Discaria chacaye, respectively; Frankia BCU110501 (Dt) was previously isolated from Discaria trinervis. The strains were identical at the 16S sequence and after analysis of RFLP of 16S and 23S rDNA intergenic region. Diversity was revealed at the molecular level after fingerprint analysis by BOX-polymerase chain reaction. The strains were infective and effective on the original host plants. A cross-inoculation assay intra Discaria genus, including D. trinervis, D. articulata, and D. chacaye, with each of these isolated Frankia strains caused effective symbioses with a similar dry weight in each plant species regardless of the inoculated strain. Nevertheless, a differential degree of recognition was revealed: Homologous symbiotic pairs in the case of D. chacaye-Frankia BCU110345 (Dc), D. articulata-Frankia BCU110601 (Da), and D. trinervis-Frankia BCU110501 (Dt) had faster nodulation rates than heterologous pairs. The differences in nodulation rate would suggest the existence of a subspecific level of recognition within a certain cross-inoculation group, pointing to subspecific adaptation occurring in this actinorhizal symbiosis.
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Affiliation(s)
- Eugenia E Chaia
- Centro Regional Universitario Bariloche, Universidad Nacional del Comahue, Quintral 1250, 8400 S.C., Bariloche, Argentina
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Barionovi D, Giorgi S, Stoeger AR, Ruppitsch W, Scortichini M. Characterization of Erwinia amylovora strains from different host plants using repetitive-sequences PCR analysis, and restriction fragment length polymorphism and short-sequence DNA repeats of plasmid pEA29. J Appl Microbiol 2006; 100:1084-94. [PMID: 16630009 DOI: 10.1111/j.1365-2672.2006.02813.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS The three main aims of the study were the assessment of the genetic relationship between a deviating Erwinia amylovora strain isolated from Amelanchier sp. (Maloideae) grown in Canada and other strains from Maloideae and Rosoideae, the investigation of the variability of the PstI fragment of the pEA29 plasmid using restriction fragment length polymorphism (RFLP) analysis and the determination of the number of short-sequence DNA repeats (SSR) by DNA sequence analysis in representative strains. METHODS AND RESULTS Ninety-three strains obtained from 12 plant genera and different geographical locations were examined by repetitive-sequences PCR using Enterobacterial Repetitive Intergenic Consensus, BOX and Repetitive Extragenic Palindromic primer sets. Upon the unweighted pair group method with arithmetic mean analysis, a deviating strain from Amelanchier sp. was analysed using amplified ribosomal DNA restriction analysis (ARDRA) analysis and the sequencing of the 16S rDNA gene. This strain showed 99% similarity to other E. amylovora strains in the 16S gene and the same banding pattern with ARDRA. The RFLP analysis of pEA29 plasmid using MspI and Sau3A restriction enzymes showed a higher variability than that previously observed and no clear-cut grouping of the strains was possible. The number of SSR units reiterated two to 12 times. The strains obtained from pear orchards showing for the first time symptoms of fire blight had a low number of SSR units. CONCLUSIONS The strains from Maloideae exhibit a wider genetic variability than previously thought. The RFLP analysis of a fragment of the pEA29 plasmid would not seem a reliable method for typing E. amylovora strains. A low number of SSR units was observed with first epidemics of fire blight. SIGNIFICANCE AND IMPACT OF THE STUDY The current detection techniques are mainly based on the genetic similarities observed within the strains from the cultivated tree-fruit crops. For a more reliable detection of the fire blight pathogen also in wild and ornamentals Rosaceous plants the genetic features of deviating E. amylovora strains have to be studied in detail.
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Affiliation(s)
- D Barionovi
- C.R.A.-Istituto Sperimentale per la Frutticoltura, Ciampino Aeroporto, Rome, Italy
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Decorosi F, Mengoni A, Baldi F, Fani R. Identification of alkane monoxygenase genes inAcinetobacter venetianus VE-C3 and analysis of mutants impaired in diesel fuel degradation. ANN MICROBIOL 2006. [DOI: 10.1007/bf03175007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Rodriguez H, Mendoza A, Cruz MA, Holguin G, Glick BR, Bashan Y. Pleiotropic physiological effects in the plant growth-promoting bacterium Azospirillum brasilense following chromosomal labeling in the clpX gene. FEMS Microbiol Ecol 2006; 57:217-25. [PMID: 16867140 DOI: 10.1111/j.1574-6941.2006.00111.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Azospirillum brasilense 8-I was chromosomally labeled with green fluorescent protein (gfp) genes, using either the native promoterless gfp gene or the mutant gfpmut2 gene under the transcriptional control of the neomycin phosphate transferase (npt2) promoter inserted into Tn5 suicide plasmid vectors. One A. brasilense exconjugant, showing a steady and strong fluorescence following irradiation with 365-nm UV light was characterized in detail. This strain, A. brasilense 8-I-gfp showed increased N(2)-fixation of approximately threefold, up to a twofold increase in exopolysaccharide production, and a significant decrease in indole-3-acetic acid and poly-beta-hydroxybutyrate production over the parental strain. Sequence analysis showed that the Tn5 carrying the gfp gene was inserted in the clpX gene encoding a heat-shock protein. This data is consistent with a model in which the observed physiological changes are a consequence of pleiotropic changes that occur as a consequence of impaired heat shock (stress) protein synthesis. In summary, (i) chromosomally labelled Azospirillum brasilense was obtained carrying either native or mutant gfp genes, (ii) Pleiotropic physiological effects were caused by disruption of the clpX gene as the consequence of the insertion, (iii) a new indole-3-acetic acid-attenuated mutant of A. brasilense producing only 0.25% of the indole-3-acetic acid produced by the wild-type is presented.
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Affiliation(s)
- Hilda Rodriguez
- Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, BCS 23090, Mexico
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Mehnaz S, Lazarovits G. Inoculation effects of Pseudomonas putida, Gluconacetobacter azotocaptans, and Azospirillum lipoferum on corn plant growth under greenhouse conditions. MICROBIAL ECOLOGY 2006; 51:326-35. [PMID: 16598630 DOI: 10.1007/s00248-006-9039-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Accepted: 10/18/2005] [Indexed: 05/08/2023]
Abstract
Alcohol production from corn is gaining importance in Ontario, Canada, and elsewhere. A major cost of corn production is the cost of chemical fertilizers and these continue to increase in price. The competitiveness of alcohol with fossil fuels depends on access to low-cost corn that allows growers to earn a sustainable income. In this study we set out to determine if we can identify root-associated microorganisms from Ontario-grown corn that can enhance the nutrient flow to corn roots, directly or indirectly, and help minimize the use of extraneous fertilizer. Bacteria were isolated from corn rhizosphere and screened for their capacity to enhance corn growth. The bacteria were examined for their ability to fix nitrogen, solubilize phosphate, and produce indole acetic acid (IAA) and antifungal substances on potato dextrose agar. Bacterial suspensions were applied to pregerminated seed of four corn varieties (39D82, 39H84, 39M27, and 39T68) planted in sterilized sand and unsterilized cornfield soil. The plants were grown under greenhouse conditions for 30 days. Three isolates were identified as having growth-promoting effect. These bacteria were identified as to species by biochemical tests, fatty acid profiles, and 16S rDNA sequence analysis. Corn rhizosphere isolates, Gluconacetobacter azotocaptans DS1, Pseudomonas putida CQ179, and Azospirillum lipoferum N7, provided significant plant growth promotion expressed as increased root/shoot weight when compared to uninoculated plants, in sand and/or soil. All strains except P. putida CQ179 were capable of nitrogen fixation and IAA production. Azospirillum brasilense, however, produced significantly more IAA than the other isolates. Although several of the strains were also able to solubilize phosphate and produce metabolites inhibitory to various fungal pathogens, these properties are not considered as contributing to growth promotion under the conditions used in this study. These bacteria will undergo field tests for their effect on corn growth.
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Affiliation(s)
- Samina Mehnaz
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada, N5V4T3
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Liu B, Zhang F, Feng X, Liu Y, Yan X, Zhang X, Wang L, Zhao L. Thauera and Azoarcus as functionally important genera in a denitrifying quinoline-removal bioreactor as revealed by microbial community structure comparison. FEMS Microbiol Ecol 2006; 55:274-86. [PMID: 16420635 DOI: 10.1111/j.1574-6941.2005.00033.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Structural shifts associated with functional dynamics in a bacterial community may provide clues for identifying the most valuable members in an ecosystem. A laboratory-scale denitrifying reactor was adapted from use of non-efficient seeding sludge and was utilized to degrade quinoline and remove the chemical oxygen demand. Stable removal efficiencies were achieved after an adaptation period of six weeks. Both denaturing gradient gel electrophoresis profiling of the 16S rRNA gene V3 region and comparison of the 16S rRNA gene sequence clone libraries (LIBSHUFF analysis) demonstrated that microbial communities in the denitrifying reactor and seeding sludge were significantly distinct. The percentage of the clones affiliated with the genera Thauera and Azoarcus was 74% in the denitrifying reactor and 4% in the seeding sludge. Real-time quantitative PCR also indicated that species of the genera Thauera and Azoarcus increased in abundance by about one order of magnitude during the period of adaptation. The greater abundance of Thauera and Azoarcus in association with higher efficiency after adaptation suggested that these phylotypes might play an important role for quinoline and chemical oxygen demand removal under denitrifying conditions.
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Affiliation(s)
- Binbin Liu
- Laboratory of Molecular Microbial Ecology and Ecogenomics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China
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Kim C, Kecskés ML, Deaker RJ, Gilchrist K, New PB, Kennedy IR, Kim S, Sa T. Wheat root colonization and nitrogenase activity byAzospirillumisolates from crop plants in Korea. Can J Microbiol 2005; 51:948-56. [PMID: 16333334 DOI: 10.1139/w05-052] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nitrogen-fixing bacteria were isolated from the rhizosphere of different crops of Korea. A total of 16 isolates were selected and characterized. Thirteen of the isolates produced characteristics similar to those of the reference strains of Azospirillum, and the remaining 3 isolates were found to be Enterobacter spp. The isolates could be categorized into 3 groups based on their ARDRA patterns, and the first 2 groups comprised Azospirillum brasilense and Azospirillum lipoferum. The acetylene reduction activity (ARA) of these isolates was determined for free cultures and in association with wheat roots. There was no correlation between pure culture and plant-associated nitrogenase activity of the different strains. The isolates that showed higher nitrogenase activities in association with wheat roots in each group were selected and sequenced. Isolates of Azospirillum brasilense CW301, Azospirillum brasilense CW903, and Azospirillum lipoferum CW1503 were selected to study colonization in association with wheat roots. We observed higher expression of β-galactosidase activity in A. brasilense strains than in A. lipoferum strains, which could be attributed to their higher population in association with wheat roots. All strains tested colonized and exhibited the strongest β-galactosidase activity at the sites of lateral roots emergence.Key words: Azospirillum, acetylene reduction activity, 16S rDNA, ARDRA patterns, lacZ fusion.
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Affiliation(s)
- Chungwoo Kim
- Dept. Of Agricultural Chemistry, Chungbuk National University, Cheongju 361-763, Korea
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Scortichini M, Rossi MP, Loreti S, Bosco A, Fiori M, Jackson RW, Stead DE, Aspin A, Marchesi U, Zini M, Janse JD. Pseudomonas syringae pv. coryli, the Causal Agent of Bacterial Twig Dieback of Corylus avellana. PHYTOPATHOLOGY 2005; 95:1316-24. [PMID: 18943363 DOI: 10.1094/phyto-95-1316] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
ABSTRACT Thirty-eight bacterial strains isolated from hazelnut (Corylus avellana) cv. Tonda Gentile delle Langhe showing a twig dieback in Piedmont and Sardinia, Italy, were studied by a polyphasic approach. All strains were assessed by fatty acids analysis and repetitive sequence-based polymerase chain reaction (PCR) fingerprinting using BOX and ERIC primer sets. Representative strains also were assessed by sequencing the 16S rDNA and hrpL genes, determining the presence of the syrB gene, testing their biochemical and nutritional characteristics, and determining their pathogenicity to hazelnut and other plants species or plant organs. Moreover, they were compared with reference strains of other phytopathogenic pseudomonads. The strains from hazelnut belong to Pseudomonas syringae (sensu latu), LOPAT group Ia. Both fatty acids and repetitive-sequence-based PCR clearly discriminate such strains from other Pseudomonas spp., including P. avellanae and other P. syringae pathovars as well as P. syringae pv. syringae strains from hazelnut. Also, the sequencing of 16S rDNA and hrpL genes differentiated them from P. avellanae and from P. syringae pv. syringae. They did not possess the syrB gene. Some nutritional tests also differentiated them from related P. syringae pathovars. Upon artificial inoculation, these strains incited severe twig diebacks only on hazelnut. Our results justify the creation of a new pathovar because the strains from hazelnut constitute a homogeneous group and a discrete phenon. The name of P. syringae pv. coryli is proposed and criteria for routine identification are presented.
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Cao Y, Wang L, Xu K, Kou C, Zhang Y, Wei G, He J, Wang Y, Zhao L. Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates. BMC Bioinformatics 2005; 6:190. [PMID: 16042814 PMCID: PMC1183192 DOI: 10.1186/1471-2105-6-190] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Accepted: 07/26/2005] [Indexed: 11/10/2022] Open
Abstract
Background A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information transfer process. Results Primer sequence is converted to a vector of the full potential hydrogen numbers (3 for G or C, 2 for A or T), while template sequence is converted to a vector of the actual hydrogen bond numbers formed after primer annealing. The former is considered as source information and the latter destination information. An information coefficient is calculated as a measure for fidelity of this information transfer process and thus a measure of similarity between primer and potential annealing site on template. Conclusion Successful prediction of PCR products from whole genomic sequences with a computer program based on the algorithm demonstrated the potential of this new algorithm in areas like in silico PCR and gene finding.
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Affiliation(s)
- Youfang Cao
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lianjie Wang
- Department of Food Science and Engineering, Northwest Institute of Light Industry, Xianyang 712081, Shaanxi, China
| | - Kexue Xu
- Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chunhai Kou
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yulei Zhang
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guifang Wei
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junjian He
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yunfang Wang
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liping Zhao
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Verma SC, Chowdhury SP, Tripathi AK. Phylogeny based on 16S rDNA andnifHsequences ofRalstonia taiwanensisstrains isolated from nitrogen-fixing nodules ofMimosa pudica, in India. Can J Microbiol 2004; 50:313-22. [PMID: 15213739 DOI: 10.1139/w04-020] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacterial symbionts present in the indeterminate-type nitrogen (N)-fixing nodules of Mimosa pudica grown in North and South India showed maximum similarity to Ralstonia taiwanensis on the basis of carbon-source utilization patterns and 16S rDNA sequence. Isolates from the nodules of M. pudica from North India and South India showed identical ARDRA (Amplified Ribosomal DNA Restriction Analysis) patterns with Sau3AI and RsaI, but AluI revealed dimorphy between the North Indian and South Indian isolates. Alignment of 16S rDNA sequences revealed similarity of North Indian isolates with an R. taiwanensis strain isolated from M. pudica in Taiwan, whereas South Indian isolates showed closer relatedness with the isolates from Mimosa diplotricha. Alignment of nifH sequences from both North Indian and South Indian isolates with that of the related isolates revealed their closer affinity to α-rhizobia, suggesting that nif genes in the β-rhizobia might have been acquired from α-rhizobia via lateral transfer during co-occupancy of nodules by α-rhizobia and progenitors of R. taiwanensis, members of the β-subclass of Proteobacteria. Immunological cross-reaction of the bacteroid preparation of M. pudica nodules showed strong a positive signal with anti-dinitrogenase reductase antibody, whereas a weak positive cross-reaction was observed with free-living R. taiwanensis grown microaerobically in minimal medium with and without NH4Cl. In spite of the expression of dinitrogenase reductase under free-living conditions, acetylene reduction was not observed under N-free conditions even after prolonged incubation.Key words: symbiotic nitrogen fixation, Mimosa pudica, rhizobia, phylogeny, 16S rDNA, nifH, Ralstonia taiwanensis.
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MESH Headings
- Bacterial Typing Techniques
- Carbohydrate Metabolism
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/analysis
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Gene Transfer, Horizontal
- Genes, rRNA
- India
- Mimosa/microbiology
- Molecular Sequence Data
- Nitrogen Fixation/genetics
- Oxidoreductases/genetics
- Oxidoreductases/immunology
- Oxidoreductases/metabolism
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Ralstonia/classification
- Ralstonia/genetics
- Ralstonia/isolation & purification
- Sequence Analysis, DNA
- Sequence Homology
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Affiliation(s)
- Subhash Chandra Verma
- School of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi, India
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44
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Michaud L, Di Cello F, Brilli M, Fani R, Lo Giudice A, Bruni V. Biodiversity of cultivable psychrotrophic marine bacteria isolated from Terra Nova Bay (Ross Sea, Antarctica). FEMS Microbiol Lett 2004; 230:63-71. [PMID: 14734167 DOI: 10.1016/s0378-1097(03)00857-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A set of 146 Antarctic marine isolates from the Ross Sea was characterized by a combination of molecular techniques in order to determine the degree of inter- and intraspecific variability. Isolates were analyzed by amplified rDNA restriction analysis (ARDRA) using the tetrameric enzyme AluI, resulting in 52 different groups, corresponding to at least 52 different bacterial species, indicating a high degree of interspecific variability. The phylogenetic position of bacteria belonging to some ARDRA groups was obtained by sequencing of 16S rDNA. Random amplified polymorphic DNA (RAPD) analysis, carried out on the largest ARDRA groups, revealed a high intraspecific genetic variability, too. The analysis of plasmid content revealed the existence of horizontal gene transfer between strains belonging to the same and to different species. A comparison of the whole body of morphological, physiological and biochemical data was finally carried out.
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Affiliation(s)
- Luigi Michaud
- Department of Animal Biology and Marine Ecology, University of Messina, Salita Sperone 31, 98166 S. Agata, Messina, Italy
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45
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Mocali S, Bertelli E, Di Cello F, Mengoni A, Sfalanga A, Viliani F, Caciotti A, Tegli S, Surico G, Fani R. Fluctuation of bacteria isolated from elm tissues during different seasons and from different plant organs. Res Microbiol 2003; 154:105-14. [PMID: 12648725 DOI: 10.1016/s0923-2508(03)00031-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this work we isolated a culturable endophytic aerobic heterotrophic bacterial community from the stem and root tissues of elm trees (Ulmus spp.) and analyzed its fluctuations. A total of 724 bacterial isolates were collected at different times (April, June, September and December) from two elm trees, one infected with Elm Yellows phytoplasmas, and one which was healthy-looking. The isolates were grouped into 82 haplotypes, identified by means of amplified ribosomal DNA restriction analysis (ARDRA) using the restriction enzyme AluI, suggesting that the genetic diversity of the bacterial community was very high. The taxonomic position of the isolates belonging to the twelve main haplotypes, representing more than 72% of the total population, was determined by 16S rDNA sequencing. The main genera were Bacillus, Curtobacterium, Pseudomonas, Stenotrophomonas, Sphingomonas, Enterobacter, and Staphylococcus. The fluctuations in the bacterial community, determined by different parameters (seasonal changes, plant organ, presence of phytoplasmas) were studied, revealing that they were influenced both by variations in temperature (warm or cold according to the season) and by the organ examined (roots or stems). The role of the phytopathogenic status in these fluctuations was also discussed.
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Affiliation(s)
- Stefano Mocali
- Dipartimento di Biologia Animale e Genetica, Via Romana 17-19, 50125 Firenze, Italy
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46
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Scortichini M, Marchesi U, Rossi MP, Di Prospero P. Bacteria associated with hazelnut (Corylus avellana L.) decline are of two groups: Pseudomonas avellanae and strains resembling P. syringae pv. syringae. Appl Environ Microbiol 2002; 68:476-84. [PMID: 11823181 PMCID: PMC126672 DOI: 10.1128/aem.68.2.476-484.2002] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A total of 118 fluorescent pseudomonads associated with hazelnut decline, which has been occurring for many years in different areas of northern Greece and Italy, were assessed by performing a repetitive PCR analysis with enterobacterial repetitive intergenic consensus, box element, and repetive extragenic palindromic primer sets, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell protein extracts, a carbon compound utilization analysis, and an analysis to determine the presence of the syrB gene. A subset of 53 strains was also characterized by amplified 16S ribosomal DNA restriction analysis (ARDRA) by using nine restriction endonucleases. The virulence of 40 representative strains was assessed by using serial doses. The pathogenic specificities of the strains were also verified. ARDRA carried out with HinfI revealed two main groups of strains, groups A and B, which exhibited a level of similarity of 57%. The other eight restriction endonucleases used did not separate the strains. In addition, a cluster analysis performed by the unweighted pair group method using arithmetic averages after repetitive PCR and SDS-PAGE of protein extracts also revealed the same two groups. Furthermore, the differential utilization of some carbon compounds made it possible to differentiate the groups. Virulence assessment clearly indicated that the group A strains are very virulent, whereas the group B strains proved to be mildly virulent for hazelnut. Group A included the strains isolated in northern Greece and central Italy (i.e., the province of Viterbo); these strains do not have the syrB gene, are pathogenically restricted to Corylus avellana, and belong to Pseudomonas avellanae. Group B includes the other strains obtained from hazelnut cultivated in Piedmont, Campania, Latium, Sicily, and Sardinia. They represent a distinct taxon closely related to Pseudomonas syringae pv. syringae.
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Affiliation(s)
- Marco Scortichini
- Istituto Sperimentale per la Frutticoltura, Via di Fioranello, 52 I-00040 Ciampino Aeroporto, Rome, Italy.
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47
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Potrich DP, Passaglia LM, Schrank IS. Partial characterization of nif genes from the bacterium Azospirillum amazonense. Braz J Med Biol Res 2001; 34:1105-13. [PMID: 11514833 DOI: 10.1590/s0100-879x2001000900002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Azospirillum amazonense revealed genomic organization patterns of the nitrogen fixation genes similar to those of the distantly related species A. brasilense. Our work suggests that A. brasilense nifHDK, nifENX, fixABC operons and nifA and glnB genes may be structurally homologous to the counterpart genes of A. amazonense. This is the first analysis revealing homology between A. brasilense nif genes and the A. amazonense genome. Sequence analysis of PCR amplification products revealed similarities between the amino acid sequences of the highly conserved nifD and glnB genes of A. amazonense and related genes of A. brasilense and other bacteria. However, the A. amazonense non-coding regions (the upstream activator sequence region and the region between the nifH and nifD genes) differed from related regions of A. brasilense even in nitrogenase structural genes which are highly conserved among diazotrophic bacteria. The feasibility of the 16S ribosomal RNA gene-based PCR system for specific detection of A. amazonense was shown. Our results indicate that the PCR primers for 16S rDNA defined in this article are highly specific to A. amazonense and can distinguish this species from A. brasilense.
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Affiliation(s)
- D P Potrich
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brasil
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48
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Barberio C, Pagliai L, Cavalieri D, Fani R. Biodiversity and horizontal gene transfer in culturable bacteria isolated from activated sludge enriched in nonylphenol ethoxylates. Res Microbiol 2001; 152:105-12. [PMID: 11281319 DOI: 10.1016/s0923-2508(00)01173-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
One hundred and twenty bacterial isolates, from activated sludge of a treatment plant collecting wastes enriched in ethoxylated nonylphenols, were studied. Sixty isolates were selected on rich medium and 60 on mineral medium containing two nonylphenol ethoxylates as the sole carbon source. Analysis of biodiversity at the species level was performed by comparing the AluI restriction patterns of the 16S ribosomal DNA amplified by PCR from 120 isolates. The rDNA restriction analysis enabled us to cluster the isolates into 15 groups, five of which represented nearly 77% of the community. Phylogenetic analysis of five strains belonging to these main groups made it possible to assign four of them to the genera Acinetobacter, Aeromonas and Shewanella and one to the Proteus group. The analysis of plasmid content showed a high variability and suggested that horizontal gene transfer had taken place at the intraspecific, interspecific and intergeneric levels.
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MESH Headings
- Culture Media
- DNA, Bacterial/analysis
- DNA, Bacterial/genetics
- DNA, Ribosomal/analysis
- DNA, Ribosomal/genetics
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Ethylene Glycols/metabolism
- Gene Transfer, Horizontal
- Gram-Negative Bacteria/classification
- Gram-Negative Bacteria/genetics
- Gram-Negative Bacteria/isolation & purification
- Industrial Waste
- Molecular Sequence Data
- Phylogeny
- Plasmids/genetics
- RNA, Ribosomal, 16S
- Restriction Mapping
- Sequence Analysis, DNA
- Sewage/chemistry
- Sewage/microbiology
- Waste Disposal, Fluid
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Affiliation(s)
- C Barberio
- Dipartimento di Biologia Animale e Genetica, Florence, Italy.
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49
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Vaneechoutte M, Heyndrickx M. Application and Analysis of ARDRA Patterns in Bacterial Identification, Taxonomy and Phylogeny. NEW APPROACHES FOR THE GENERATION AND ANALYSIS OF MICROBIAL TYPING DATA 2001:211-247. [DOI: 10.1016/b978-044450740-2/50010-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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50
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Picard C, Di Cello F, Ventura M, Fani R, Guckert A. Frequency and biodiversity of 2,4-diacetylphloroglucinol-producing bacteria isolated from the maize rhizosphere at different stages of plant growth. Appl Environ Microbiol 2000; 66:948-55. [PMID: 10698757 PMCID: PMC91928 DOI: 10.1128/aem.66.3.948-955.2000] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/1999] [Accepted: 12/12/1999] [Indexed: 11/20/2022] Open
Abstract
A Pseudomonas 2,4-diacetylphloroglucinol (DAPG)-producing population that occurred naturally on the roots, in rhizosphere soil of Zea mays and in the nonrhizosphere soil was investigated in order to assess the microbial diversity at five stages of plant growth. A total of 1,716 isolates were obtained, and 188 of these isolates were able to produce DAPG. DAPG producers were isolated at each stage of plant growth, indicating that the maize rhizosphere is colonized by natural DAPG producers throughout development. The frequency of DAPG producers was very low in the first stage of plant growth and increased over time. An analysis of the level of biodiversity of the DAPG producers at the species level was performed by comparing the AluI restriction patterns of the 16S ribosomal DNAs (rDNAs) amplified by PCR from 167 isolates. This comparison allowed us to cluster the isolates into four amplified rDNA restriction analysis (ARDRA) groups, and the main group (ARDRA group 1) contained 89.8% of the isolates. The diversity of the 150 isolates belonging to ARDRA group 1 was analyzed by the random amplified polymorphic DNA (RAPD) technique. An analysis of RAPD patterns by a molecular variance method revealed that there was a high level of genetic diversity in this population and that the genetic diversity was related to plant age. Finally, we found that some of the DAPG producers, which originated from all stages of plant growth, had the same genotype. These DAPG producers could be exploited in future screening programs for biocontrol agents.
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Affiliation(s)
- C Picard
- Laboratoire Agronomie et Environnement, ENSAIA-INRA, 54505 Vandouvre les Nancy, France.
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