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Dal’Rio I, Lopes EDS, Santaren KCF, Rosado AS, Seldin L. Co-inoculation of the endophytes Bacillus thuringiensis CAPE95 and Paenibacillus polymyxa CAPE238 promotes Tropaeolum majus L. growth and enhances its root bacterial diversity. Front Microbiol 2024; 15:1356891. [PMID: 38585693 PMCID: PMC10996857 DOI: 10.3389/fmicb.2024.1356891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 02/12/2024] [Indexed: 04/09/2024] Open
Abstract
Tropaeolum majus L. is a versatile edible plant that is widely explored due to its medicinal properties and as a key element in intercropping systems. Its growth could be improved by the use of biofertilizers that can enhance nutrient uptake by the plant or provide tolerance to different abiotic and biotic stresses. In a previous study, 101 endophytes isolated from T. majus roots showed more than three plant growth-promoting (PGP) features in vitro, such as phosphate mineralization/solubilization, production of siderophores, antimicrobial substances and indole-related compounds, and presence of the nifH gene. To provide sustainable alternatives for biofertilization, the genomes of two promising endophytes-CAPE95 and CAPE238-were sequenced to uncover metabolic pathways related to biofertilization. Greenhouse experiments were conducted with 216 seeds and 60 seedlings, half co-inoculated with the endophytes (treatment) and half inoculated with 1X PBS (control), and the impact of the co-inoculation on the plant's bacteriome was accessed through 16S rRNA gene metabarcoding. The strains CAPE95 and CAPE238 were taxonomically assigned as Bacillus thuringiensis and Paenibacillus polymyxa, respectively. Metabolic pathways related to the enhancement of nutrient availability (nitrogen fixation, sulfate-sulfur assimilation), biosynthesis of phytohormones (indole-3-acetic acid precursors) and antimicrobial substances (bacilysin, paenibacillin) were found in their genomes. The in vivo experiments showed that treated seeds exhibited faster germination, with a 20.3% higher germination index than the control on the eleventh day of the experiment. Additionally, treated seedlings showed significantly higher plant height and leaf diameters (p < 0.05). The bacterial community of the treated plants was significantly different from that of the control plants (p < 0.001) and showed a higher richness and diversity of species (Chao and Shannon indexes, p < 0.001). A higher relative abundance of potential synergistic PGP bacteria was also shown in the bacteriome of the treated plants, such as Lysinibacillus and Geobacter. For the first time, co-inoculation of B. thuringiensis and P. polymyxa was shown to have great potential for application as a biofertilizer to T. majus plants. The bacterial consortium used here could also be explored in other plant species in the future.
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Affiliation(s)
- Isabella Dal’Rio
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Bioscience, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Eliene dos Santos Lopes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Alexandre Soares Rosado
- Bioscience, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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de Sousa RDSDR, Lima GVS, Garcias JT, Gomes GDO, Mateus JR, Madeira LDPDS, Seldin L, Rogez HLG, Marques JM. The Microbial Community Structure in the Rhizosphere of Theobroma cacao L. and Euterpe oleracea Mart. Is Influenced by Agriculture System in the Brazilian Amazon. Microorganisms 2024; 12:398. [PMID: 38399802 PMCID: PMC10892126 DOI: 10.3390/microorganisms12020398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/25/2024] Open
Abstract
This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices.
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Affiliation(s)
- Rosiane do Socorro dos Reis de Sousa
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Giulia Victória Silva Lima
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Josinete Torres Garcias
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Graziane de Oliveira Gomes
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Jackeline Rossetti Mateus
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
| | - Lucimar Di Paula dos Santos Madeira
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
| | - Hervé Louis Ghislain Rogez
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
| | - Joana Montezano Marques
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-110, Pará, Brazil; (R.d.S.d.R.d.S.); (G.V.S.L.); (J.T.G.); (G.d.O.G.); (L.D.P.d.S.M.); (H.L.G.R.)
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil; (J.R.M.); (L.S.)
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da Silva MBF, da Mota FF, Cypriano J, Abreu F, Seldin L. Psychrobacillus antarcticus sp. nov., a psychrotolerant bioemulsifier producer isolated from King George Island, Antarctica. Int J Syst Evol Microbiol 2023; 73. [PMID: 38009904 DOI: 10.1099/ijsem.0.006181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
A Gram-stain-positive rod, psychrotolerant, aerobic and bioemulsifier-producing strain, denoted as Val9T, was isolated from soil sampled at Vale Ulman, King George Island, Antarctica. The strain grew at up to 30 °C (optimum, 15 °C), at pH 6-9 (optimum, pH 8) and with up to 5 % w/v NaCl (optimum, 3 %). The strain was motile and positive for catalase, oxidase and H2S. It did not hydrolyse starch, casein or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Val9T belonged to the genus Psychrobacillus and was closely related to Psychrobacillus psychrotolerans DSM 11706T (99.9 % similarity), Psychrobacillus psychrodurans DSM 11713T (99.8 %) and Psychrobacillus glaciei PB01T (99.2 %). Digital DNA-DNA hybridization and average nucleotide identity values were lower than 37.3 and 85.5 %, respectively, with the closest phylogenetic neighbours. The DNA G+C content of strain Val9T calculated from the complete genome sequence was 36.6 mol%. The predominant cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 1ω11c. Menaquinone-8 was the major respiratory quinone. The peptidoglycan type was A4β l-Orn-d-glu. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids. Based on 16S rRNA phylogenetic and multilocus sequence analyses (recA, rpoB and gyrB), as well as phylogenomic, chemotaxonomic and phenotypic tests, we demonstrate that strain Val9T represents a novel species of the genus Psychrobacillus, for which the name Psychrobacillus antarcticus sp. nov. is proposed. The type strain is Val9T (=DSM 115096T=CCGB 1952T=NRRL B-65674T).
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Affiliation(s)
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jefferson Cypriano
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Abreu
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Pinheiro LZ, da Silva FF, Queiroz MSR, Aguieiras ECG, Cipolatti EP, da Silva AS, Bassut J, Seldin L, Guimarães DO, Freire DMG, de Souza ROMA, Leal ICR. Activity of endophytic fungi in enantioselective biotransformation of chiral amines: New approach for solid-state fermentation. Biocatalysis and Agricultural Biotechnology 2023. [DOI: 10.1016/j.bcab.2023.102631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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de Lemos EA, Procópio L, da Mota FF, Jurelevicius D, Rosado AS, Seldin L. Molecular characterization of Paenibacillus antarcticus IPAC21, a bioemulsifier producer isolated from Antarctic soil. Front Microbiol 2023; 14:1142582. [PMID: 37025627 PMCID: PMC10072262 DOI: 10.3389/fmicb.2023.1142582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/28/2023] [Indexed: 04/08/2023] Open
Abstract
Paenibacillus antarcticus IPAC21, an endospore-forming and bioemulsifier-producing strain, was isolated from King George Island, Antarctica. As psychrotolerant/psychrophilic bacteria can be considered promising sources for novel products such as bioactive compounds and other industrially relevant substances/compounds, the IPAC21 genome was sequenced using Illumina Hi-seq, and a search for genes related to the production of bioemulsifiers and other metabolic pathways was performed. The IPAC21 strain has a genome of 5,505,124 bp and a G + C content of 40.5%. Genes related to the biosynthesis of exopolysaccharides, such as the gene that encodes the extracellular enzyme levansucrase responsible for the synthesis of levan, the 2,3-butanediol pathway, PTS sugar transporters, cold-shock proteins, and chaperones were found in its genome. IPAC21 cell-free supernatants obtained after cell growth in trypticase soy broth at different temperatures were evaluated for bioemulsifier production by the emulsification index (EI) using hexadecane, kerosene and diesel. EI values higher than 50% were obtained using the three oil derivatives when IPAC21 was grown at 28°C. The bioemulsifier produced by P. antarcticus IPAC21 was stable at different NaCl concentrations, low temperatures and pH values, suggesting its potential use in lower and moderate temperature processes in the petroleum industry.
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Affiliation(s)
- Ericka Arregue de Lemos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luciano Procópio
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Diogo Jurelevicius
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Soares Rosado
- Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: Lucy Seldin,
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Lopes ES, Parente CET, Picão RC, Seldin L. Irrigation Ponds as Sources of Antimicrobial-Resistant Bacteria in Agricultural Areas with Intensive Use of Poultry Litter. Antibiotics (Basel) 2022; 11:1650. [PMID: 36421294 PMCID: PMC9686582 DOI: 10.3390/antibiotics11111650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 10/17/2023] Open
Abstract
Poultry litter is widely used worldwide as an organic fertilizer in agriculture. However, poultry litter may contain high concentrations of antibiotics and/or antimicrobial-resistant bacteria (ARB), which can be mobilized through soil erosion to water bodies, contributing to the spread of antimicrobial resistance genes (ARGs) in the environment. To better comprehend this kind of mobilization, the bacterial communities of four ponds used for irrigation in agricultural and poultry production areas were determined in two periods of the year: at the beginning (low volume of rainfall) and at the end of the rainy season (high volume of rainfall). 16S rRNA gene sequencing revealed not only significantly different bacterial community structures and compositions among the four ponds but also between the samplings. When the DNA obtained from the water samples was PCR amplified using primers for ARGs, those encoding integrases (intI1) and resistance to sulfonamides (sul1 and sul2) and β-lactams (blaGES, blaTEM and blaSHV) were detected in three ponds. Moreover, bacterial strains were isolated from CHROMagar plates supplemented with sulfamethoxazole, ceftriaxone or ciprofloxacin and identified as belonging to clinically important Enterobacteriaceae. The results presented here indicate a potential risk of spreading ARB through water resources in agricultural areas with extensive fertilization with poultry litter.
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Affiliation(s)
- Eliene S. Lopes
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Cláudio E. T. Parente
- Laboratório de Radioisótopos Eduardo Penna Franca, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Renata C. Picão
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
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Jurelevicius D, Pereira RDS, da Mota FF, Cury JC, de Oliveira IC, Rosado AS, Mason OU, Jansson JK, Seldin L. Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica. Geobiology 2022; 20:98-111. [PMID: 34545693 DOI: 10.1111/gbi.12472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/28/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.
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Affiliation(s)
- Diogo Jurelevicius
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raphael da Silva Pereira
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Juliano C Cury
- Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Ivan Cardoso de Oliveira
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre S Rosado
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lucy Seldin
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Calixto SD, Simão TLBV, de Almeida FM, Antunes SS, Romeiro NC, de Souza Borges W, das Chagas FO, Seldin L, de Carvalho ECQ, Andrioli WJ, Guimarães DO, Lasunskaia E, Muzitano MF. (R)-(+)-Lasiodiplodin isolated from the endophytic fungus Sordaria tamaensis exhibits potent antimycobacterial and anti-inflammatory activities in vitro and in vivo: a dual approach for the treatment of severe pulmonary tuberculosis. J Pharm Pharmacol 2021; 74:446-457. [PMID: 34850064 DOI: 10.1093/jpp/rgab165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES This study aimed to evaluate endophytic fungi isolated from Tocoyena bullata and Humiria balsamifera plant species for their antimycobacterial and anti-inflammatory activities, focusing on severe pulmonary tuberculosis cases which are often associated with exacerbated inflammation. METHODS Mycobacterium suspensions were incubated with the samples for 5 days. RAW 264.7 macrophages stimulated with LPS were also incubated with them for 24 h to assess the inhibition of inflammatory mediator production and cytotoxicity. C57BL/6 mice were infected with Mtb M299 and treated for 15 days with lasiodiplodin (Lasio). KEY FINDINGS Endophytic fungus Sordaria tamaensis, obtained from T. bullata, was the most promising. Its ethanolic extract impaired mycobacterial growth with MIC50 (µg/ml): 1.5 ± 0.6 (BCG), 66.8 ± 0.1 (H37Rv) and 80.0 ± 0.1 (M299). (R)-(+)-Lasio showed MIC50 92.2 ± 1.8 µg/ml (M299). In addition, Lasio was able to inhibit NO, IL-1β and TNF-α production and was not cytotoxic for macrophages. M. tuberculosis-infected C57BL/6 animals treated by Lasio reduced the number of acid-fast bacilli, lung pathology, leucocyte influx and proinflammatory cytokine production in the lungs. The class IIa fructose 1,6-bisphosphate aldolase was the predicted hypothetical target of Lasio. CONCLUSIONS (R)-(+)-Lasio stood out as a promising anti-TB compound, exhibiting anti-inflammatory and antimycobacterial effects, as well as low cytotoxicity.
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Affiliation(s)
- Sanderson Dias Calixto
- Laboratório de Biologia do Reconhecer, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil.,Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Thatiana Lopes Biá Ventura Simão
- Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Fabrício Moreira de Almeida
- Laboratório de Biologia do Reconhecer, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Stella Schuenck Antunes
- Laboratório Integrado de Computação Científica, Programa de Pós Graduação em Produtos Bioativos e Biociências, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Nelilma Correia Romeiro
- Laboratório Integrado de Computação Científica, Programa de Pós Graduação em Produtos Bioativos e Biociências, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Warley de Souza Borges
- Departamento de Química, Universidade Federal do Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Fernanda Oliveira das Chagas
- Instituto de Pesquisa de Produtos Naturais Walter Mors, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana CCS, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Willian Jonis Andrioli
- Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Denise Oliveira Guimarães
- Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
| | - Elena Lasunskaia
- Laboratório de Biologia do Reconhecer, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Michelle Frazão Muzitano
- Laboratório de Produtos Bioativos, Curso de Farmácia, Universidade Federal do Rio de Janeiro, Campus Macaé, Macaé, Rio de Janeiro, Brazil
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Guimarães CR, Pasqualino IP, de Sousa JS, Nogueira FCS, Seldin L, de Castilho LVA, Freire DMG. Bacillus velezensis H2O-1 surfactin efficiently maintains its interfacial properties in extreme conditions found in post-salt and pre-salt oil reservoirs. Colloids Surf B Biointerfaces 2021; 208:112072. [PMID: 34481248 DOI: 10.1016/j.colsurfb.2021.112072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 07/23/2021] [Accepted: 08/25/2021] [Indexed: 11/19/2022]
Abstract
Biosurfactants are molecules with surfactant properties produced by microorganisms, and can be used in various industrial sectors, e.g., the oil industry. These molecules can be used in enhanced oil recovery (EOR) in the pre-salt and post-salt reservoirs, where conditions of temperature, pressure, and salinity are quite varied, requiring a study of the stability of these molecules under these conditions. Bacillus velezensis H2O-1 produces five different surfactin homologs with a fatty-acid chain ranging from C11 to C16 and with a high capacity to reduce surface (24.8 mN.m-1) and interfacial tensions (1.5 and 0.8 8 mN.m-1 using light, medium oil and n-hexadecane, respectively). The critical micellar concentration (CMC) was 38.7 mg.L-1. Inversion wettability tests were carried out under the salinity conditions found in the post-salt (35 g.L-1) and pre-salt (70 g.L-1) reservoirs, in which it was observed that the surfactin reversed 100 % of the wettability of the calcite impregnated with light and medium oil. Using a central composite rotatable design, we demonstrated that surfactin maintained its interfacial properties when subjected simultaneously to extreme conditions of pressure, temperature and salinity commonly found in the post-salt (70 °C, 70 g.L-1 and 27.58 MPa) and pre-salt (100 °C, 150 g.L-1 and 48.2 MPa) layers. The results presented here highlight the efficiency and stability of H2O-1 surfactin in environmental conditions found in pre-salt and post-salt oil reservoirs.
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Affiliation(s)
| | - Ilson Paranhos Pasqualino
- Universidade Federal do Rio de Janeiro, Departamento de Engenharia Oceânica, COPPE, Rio de Janeiro, RJ, Brazil
| | - Joab Sampaio de Sousa
- Universidade Federal do Rio de Janeiro, Instituto de Química, Rio de Janeiro, RJ, Brazil
| | | | - Lucy Seldin
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil
| | - Livia Vieira Araujo de Castilho
- Universidade Federal do Rio de Janeiro, Instituto de Química, Rio de Janeiro, RJ, Brazil; Universidade Federal do Rio de Janeiro, Departamento de Engenharia Oceânica, COPPE, Rio de Janeiro, RJ, Brazil
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Tinôco D, de Castro AM, Seldin L, Freire DM. Production of (2R,3R)-butanediol by Paenibacillus polymyxa PM 3605 from crude glycerol supplemented with sugarcane molasses. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.03.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Jurelevicius D, Cotta SR, Montezzi LF, Dias ACF, Mason OU, Picão RC, Jansson JK, Seldin L. Enrichment of potential pathogens in marine microbiomes with different degrees of anthropogenic activity. Environ Pollut 2021; 268:115757. [PMID: 33168375 DOI: 10.1016/j.envpol.2020.115757] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Anthropogenic activities in coastal marine ecosystems can lead to an increase in the abundance of potentially harmful microorganisms in the marine environment. To understand anthropogenic impacts on the marine microbiome, we first used publicly available microbial phylogenetic and functional data to establish a dataset of bacterial genera potentially related to pathogens that cause diseases (BGPRD) in marine organisms. Representatives of low-, medium- and highly impacted marine coastal environments were selected, and the abundance and composition of their microbial communities were determined by quantitative PCR and 16 S rRNA gene sequencing. In total, 72 BGPRD were cataloged, and 11, 36 and 37 BGPRD were found in low-, medium- and highly human-impacted ecosystems, respectively. The absolute abundance of BGPRD and the co-occurrence of antibiotic resistance genes (AGR) increased with the degree of anthropogenic perturbation in these ecosystems. Anthropogenically impacted coastal microbiomes were compositionally and functionally distinct from those of less impacted sites, presenting features that may contribute to adverse outcomes for marine macrobiota in the Anthropocene era.
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Affiliation(s)
- Diogo Jurelevicius
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Simone R Cotta
- ESALQ - Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, Brazil
| | - Lara F Montezzi
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Armando C F Dias
- ESALQ - Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, Brazil
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA
| | - Renata C Picão
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Janet K Jansson
- Earth and Biological, Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Santos AF, Souza TFO, Freire DMG, Seldin L, Branquinha MH, Santos ALS. Halobacillus blutaparonensis Strain M9 as a Source of Extracellular Serine Peptidases with Properties for Biotechnological Purposes. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721010094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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13
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do Carmo Dias B, da Mota FF, Jurelevicius D, Seldin L. Genetics and regulation of nitrogen fixation in Paenibacillus brasilensis PB24. Microbiol Res 2020; 243:126647. [PMID: 33290933 DOI: 10.1016/j.micres.2020.126647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 12/23/2022]
Abstract
Biological nitrogen fixation (BNF), performed by diazotrophic prokaryotes, is responsible for reducing dinitrogen (N2) present in the biosphere into biologically available forms of nitrogen. Paenibacillus brasilensis PB24 is a diazotrophic Gram-positive bacterium and is considered ecologically and industrially important because it is able to produce antimicrobial substances and 2,3-butanediol. However, the genetics and regulation of its nitrogen fixing (nif) genes have never been assessed so far. Therefore, the present study aimed to (i) identify the structural and regulatory genes related to BNF in the PB24 genome, (ii) perform comparative genomics analysis of the nif operon among different Paenibacillus species and (iii) study the expression of these genes in the presence and absence of NH4. Strain PB24 showed a nif operon composed of nine genes (nifBHDKENXhesAV), with a conserved synteny (with small variations) among the Paenibacillus species evaluated. BNF regulatory genes, glnK and amtB (encoding GlnK signal transduction protein and AmtB transmembrane protein, respectively) and glnR and glnA genes (encoding the transcription factor GlnR and glutamine synthetase) were found in the PB24 genome. Primers were designed for qPCR amplification of the nitrogenase structural (nifH, nifD and nifK) and regulatory (glnA and amtB) BNF genes. The structural gene expression in PB24 was up- and downregulated in the absence and presence of NH4, respectively. The gene expression levels indicated a GlnR-mediated repression of genes associated with ammonium import (amtBglnK) and BNF (nif genes). Additionally, the regulatory mechanism of GlnR in P. brasilensis PB24 differed from the other Paenibacillus evaluated, considering the different distribution of binding sites recognized by GlnR.
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Affiliation(s)
- Beatriz do Carmo Dias
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Diogo Jurelevicius
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Coelho da Costa Waite C, Oliveira Andrade da Silva G, Pires Bitencourt JA, Pereira Torres Chequer L, Pennafirme S, de Azevedo Jurelevicius D, Seldin L, Araújo Carlos Crapez M. Potential application of Pseudomonas stutzeri W228 for removal of copper and lead from marine environments. PLoS One 2020; 15:e0240486. [PMID: 33104697 PMCID: PMC7588114 DOI: 10.1371/journal.pone.0240486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/27/2020] [Indexed: 11/18/2022] Open
Abstract
High concentrations of metals in the environment alter bacterial diversity, selecting resistant and tolerant species. The study evaluated the selection of a potential bacterial strain from Sepetiba Bay-Rio de Janeiro, Brazil marine sediments to remove Cu and Pb. The bacterial strain isolated from the sediments was used in three different bioassays: (1) Cu at concentrations of 0 (control), 6 and 50 μg.mL-1; (2) Pb at concentrations of 0 (control), 6 and 50 μg.mL-1; (3) Cu + Pb in concentrations of 3 μg.mL-1 Cu + 3 μg.mL-1 Pb (6 μg.mL-1) and 25 μg.mL-1 Cu + 25 μg.mL-1 Pb (50 μg.mL-1). The number of cells and the enzymatic activities of dehydrogenases and esterases were quantified. Results of taxonomic identification indicated the selection of the Pseudomonas stutzeri W228 strain, showing a greater degree of similarity (±73%) with the database used. There was no significant variation in the number of cells, 108 cells.mL-1, which represents a high biomass production in the presence of stressors. However, we observed a reduction in dehydrogenase activity at all tested concentrations of Cu, Pb and Cu + Pb. The activity of esterase increased, indicating a higher energy demand to complete the bacterial life cycle. The study showed significant results for the absorption of Pb by the extracellular polymeric substances (EPS) and the efflux of Cu. The capacity of Pb absorption by EPS can be considered a resistance mechanism, as well as the efflux of Cu, so that the available EPS sites could be occupied by the most toxic ions demonstrating that Pseudomonas stutzeri is resistant to Pb and Cu.
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Affiliation(s)
- Carolina Coelho da Costa Waite
- Programa de Biologia Marinha e Ambientes Costeiros, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
- * E-mail:
| | | | | | - Luciana Pereira Torres Chequer
- Programa de Biologia Marinha e Ambientes Costeiros, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Simone Pennafirme
- Programa de Biologia Marinha e Ambientes Costeiros, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Diogo de Azevedo Jurelevicius
- Instituto de Microbiologia Professor Paulo de Góes, Centro de Ciências da Saúde.CCS—Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Professor Paulo de Góes, Centro de Ciências da Saúde.CCS—Ilha do Fundão, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mirian Araújo Carlos Crapez
- Programa de Biologia Marinha e Ambientes Costeiros, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
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Alves J, Dias L, Mateus J, Marques J, Graças D, Ramos R, Seldin L, Henriques I, Silva A, Folador A. Resistome in Lake Bolonha, Brazilian Amazon: Identification of Genes Related to Resistance to Broad-Spectrum Antibiotics. Front Microbiol 2020; 11:67. [PMID: 32117110 PMCID: PMC7010645 DOI: 10.3389/fmicb.2020.00067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 01/14/2020] [Indexed: 01/02/2023] Open
Abstract
Resistance to antibiotics is one of the most relevant public health concerns in the world. Aquatic environments play an important role because they are reservoirs for antibiotic resistance genes and antibiotic-resistant strains, contributing to the spread of resistance. The present study investigated the resistome in Lake Bolonha (three sampling sites) in the Amazon region using a metagenomics approach and culture-dependent methods. Whole-metagenome-based results showed that the most abundant phyla were Protobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. The composition of the resistome demonstrated that the genes that confer resistance to β-lactams were prevalent at all sampling sites, followed by genes conferring resistance to aminoglycosides and tetracycline. Acquired genes encoding extended-spectrum β-lactamases (e.g., blaCTX–M) and resistance to carbapenems (e.g., blaIMP and blaVIM) were detected through metagenome analysis. Bacteria were isolated from culture medium supplemented with cefotaxime or imipenem, and isolates were identified and analyzed for their antibiotic susceptibility profiles and resistance genes. In total, 98 bacterial isolates belonging to the genera Pseudomonas (37), Acinetobacter (32), Klebsiella (13), Enterobacter (9), Pantoe (3), Stenotrophomonas (3), and Methylobacterium (1) were obtained. Among isolates, the most abundant genes were blaCTX–M (28.3%), blaSHV (22.6%) and blaTEM (18.8%) in isolates from cefotaxime-supplemented medium and blaVIM (28.8%) and blaIMP (22.2%) in isolates recovered from imipenem-supplemented medium. The genes intl1 and intl2 were detected in 19.3% and 7.1% of isolates. Antibiograms showed that 94.9% (from cefotaxime-supplemented medium) and 85.7% (from imipenem-supplemented medium) of the isolates were multidrug resistant. Besides cefotaxime and imipenem, isolates were mostly resistant to aztreonam (91.8%), amoxicillin (98.8%), ampicillin (82.6%), and nalidixic acid (77.5%). Hence, the present study demonstrates that Lake Bolonha is a reservoir of bacteria resistant to antibiotics and resistance genes, some of which are of critical importance to human health.
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Affiliation(s)
- Jorianne Alves
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Larissa Dias
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Jackeline Mateus
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joana Marques
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Diego Graças
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Rommel Ramos
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabel Henriques
- Center for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal.,Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Coimbra, Portugal
| | - Artur Silva
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
| | - Adriana Folador
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Brazil
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Procópio L, Pádula M, van Elsas JD, Seldin L. Oxidative damage induced by H2O2 reveals SOS adaptive transcriptional response of Dietzia cinnamea strain P4. World J Microbiol Biotechnol 2019; 35:53. [DOI: 10.1007/s11274-019-2628-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/08/2019] [Indexed: 11/28/2022]
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17
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Parente CET, Azeredo A, Vollú RE, Zonta E, Azevedo-Silva CE, Brito EMS, Seldin L, Torres JPM, Meire RO, Malm O. Fluoroquinolones in agricultural soils: Multi-temporal variation and risks in Rio de Janeiro upland region. Chemosphere 2019; 219:409-417. [PMID: 30551107 DOI: 10.1016/j.chemosphere.2018.11.184] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/21/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Our main goal was to investigate the potential accumulation of fluoroquinolones (FQs) in agricultural soils over extended periods of land use, predicting leaching and estimating risk quotients for soil microorganisms. Short to long-term of poultry litter fertilization (<1-30 years) were evaluated for enrofloxacin (ENR) and ciprofloxacin (CIP) input, in addition to the emergence of plasmid-mediated quinolone resistance (PMQR) genes. High FQs concentration (range 0.56-100 mg kg-1) were measured in poultry litter samples. In soils, FQs occurrence and risks have changed over the years. An accumulation trend was observed between short and medium-term fertilized soils (ST and MT soils), reaching a range of 330-6138 μg kg-1 ENR and 170-960 μg kg-1 CIP in MT soil, followed by decreased concentrations in long-term fertilized soils (LT soils). The environmental risk assessment showed a high ENR risk quotient (RQ ≥ 1) in ST and MT soils ranging (7-226) and high CIP risk (9-53) in LT soils. The detection of qnrS genes in the area with the lowest FQs concentration emphasizes the importance of a broader approach to environmental assessment, in which not only target compounds are considered. FQs soil-water migration model pointed out a high leaching risk in ST soil. To reduce risks, management measures to decrease antibiotic environmental load should be taken before poultry litter application. In addition, the high weathering of tropical soils contributing to possible fate of antibiotics to water resources through drainage basins should be considered.
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Affiliation(s)
- Cláudio E T Parente
- Laboratório de Radioisótopos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, Bloco G0, Sala 60, Subsolo, Rio de Janeiro, 21941-902, Brazil.
| | - Antonio Azeredo
- Laboratório de Toxicologia, Instituto de Estudos em Saúde Coletiva, Universidade Federal do Rio de Janeiro, Av. Horácio Macedo, s/n, Rio de Janeiro, 21941-598, Brazil
| | - Renata E Vollú
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, Bloco I, Sala 60, Rio de Janeiro, 21941-902, Brazil
| | - Everaldo Zonta
- Departamento de Solos, Universidade Federal Rural do Rio de Janeiro, BR 465 Km 7. Seropédica, Rio de Janeiro, 23897-000, Brazil
| | - Claudio E Azevedo-Silva
- Laboratório de Radioisótopos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, Bloco G0, Sala 60, Subsolo, Rio de Janeiro, 21941-902, Brazil
| | - Elcia M S Brito
- Ingenieria Ambiental, Div. Inginierías, Campus Guanajuato, Universidad de Guanajuato, Av. Juárez, 77; Zona Centro. Guanajuato, Gto, México, 36000, USA
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, Bloco I, Sala 60, Rio de Janeiro, 21941-902, Brazil
| | - João Paulo M Torres
- Laboratório de Radioisótopos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, Bloco G0, Sala 60, Subsolo, Rio de Janeiro, 21941-902, Brazil
| | - Rodrigo O Meire
- Laboratório de Radioisótopos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, Bloco G0, Sala 60, Subsolo, Rio de Janeiro, 21941-902, Brazil
| | - Olaf Malm
- Laboratório de Radioisótopos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho s/n, Bloco G0, Sala 60, Subsolo, Rio de Janeiro, 21941-902, Brazil
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Guimarães CR, Pasqualino IP, da Mota FF, de Godoy MG, Seldin L, de Castilho LVA, Freire DMG. Surfactin fromBacillus velezensisH2O‐1: Production and Physicochemical Characterization for Postsalt Applications. J SURFACTANTS DETERG 2019. [DOI: 10.1002/jsde.12250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
| | - Ilson Paranhos Pasqualino
- Departamento de Engenharia OceânicaUniversidade Federal do Rio de Janeiro COPPE, Rio de Janeiro RJ Brazil
| | | | - Mateus Gomes de Godoy
- Instituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Livia Vieira Araujo de Castilho
- Instituto de QuímicaUniversidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
- Departamento de Engenharia OceânicaUniversidade Federal do Rio de Janeiro COPPE, Rio de Janeiro RJ Brazil
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Mateus JR, Marques JM, Dal’Rio I, Vollú RE, Coelho MRR, Seldin L. Response of the microbial community associated with sweet potato (Ipomoea batatas) to Bacillus safensis and Bacillus velezensis strains. Antonie van Leeuwenhoek 2018; 112:501-512. [DOI: 10.1007/s10482-018-1181-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/06/2018] [Indexed: 10/28/2022]
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Alvarez VM, Jurelevicius D, Serrato RV, Barreto-Bergter E, Seldin L. Chemical characterization and potential application of exopolysaccharides produced by Ensifer adhaerens JHT2 as a bioemulsifier of edible oils. Int J Biol Macromol 2018; 114:18-25. [PMID: 29550419 DOI: 10.1016/j.ijbiomac.2018.03.06e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 05/26/2023]
Abstract
Bioemulsifiers are able to stabilize oil-in-water emulsions and are very important in several industrial processes, including food processing. In this study, a bioemulsifier produced by Ensifer adhaerens JHT2 was tested for its ability to emulsify edible oils (canola, corn, palm, olive and soy). Emulsification of soy and canola oils was detected, but the highest emulsification index (EI) was obtained when JHT2 culture supernatant was used for the emulsification of palm oil (EI=100%). Bioemulsifier production was evaluated using nine culture media and different NaCl concentrations (0.5 to 10%), pH (4 to 10) and temperatures (28 to 42°C). The highest emulsification activity was detected in the supernatants of JHT2 grown in trypticase soy broth containing 0.5-1.0% NaCl, pH6-7 and temperatures of 28-37°C. Characterization of the bioemulsifier produced by JHT2 revealed typical characteristics of exopolysaccharides (EPS), constituting a backbone of (1→4)-β-d-glucopyranosyl and (1→3)-β-D-galactopyranosyl alternating with (1→4)-α-d-mannopyranosyl units that branch from the structure at O-2. Side chains are composed of units of (1→6)-β-d-glucopyranosyl and 3-O-linked galactopyranosyl bearing a pyruvic acid acetal substitution at O-4 and O-6. Our results indicate that the EPS produced by Ensifer adhaerens JHT2 is a promising option for improving and maintaining stable emulsions in food prepared with edible oils.
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Affiliation(s)
- Vanessa Marques Alvarez
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Diogo Jurelevicius
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Vassoler Serrato
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, CEP 81531-990 Curitiba, PR, Brazil
| | - Eliana Barreto-Bergter
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Alvarez VM, Jurelevicius D, Serrato RV, Barreto-Bergter E, Seldin L. Chemical characterization and potential application of exopolysaccharides produced by Ensifer adhaerens JHT2 as a bioemulsifier of edible oils. Int J Biol Macromol 2018; 114:18-25. [DOI: 10.1016/j.ijbiomac.2018.03.063] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 11/27/2022]
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Fasca H, de Castilho LVA, de Castilho JFM, Pasqualino IP, Alvarez VM, de Azevedo Jurelevicius D, Seldin L. Response of marine bacteria to oil contamination and to high pressure and low temperature deep sea conditions. Microbiologyopen 2018; 7:e00550. [PMID: 29057585 PMCID: PMC5912000 DOI: 10.1002/mbo3.550] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/05/2017] [Accepted: 09/12/2017] [Indexed: 01/16/2023] Open
Abstract
The effect of pressure and temperature on microbial communities of marine environments contaminated with petroleum hydrocarbons is understudied. This study aims to reveal the responses of marine bacterial communities to low temperature, high pressure, and contamination with petroleum hydrocarbons using seawater samples collected near an offshore Brazilian platform. Microcosms containing only seawater and those containing seawater contaminated with 1% crude oil were subjected to three different treatments of temperature and pressure as follows: (1) 22°C/0.1 MPa; (2) 4°C/0.1 MPa; and (3) 4°C/22 MPa. The effect of depressurization followed by repressurization on bacterial communities was also evaluated (4°C/22 MPaD). The structure and composition of the bacterial communities in the different microcosms were analyzed by PCR-DGGE and DNA sequencing, respectively. Contamination with oil influenced the structure of the bacterial communities in microcosms incubated either at 4°C or 22°C and at low pressure. Incubation at low temperature and high pressure greatly influenced the structure of bacterial communities even in the absence of oil contamination. The 4°C/22 MPa and 4°C/22 MPaD treatments resulted in similar DGGE profiles. DNA sequencing (after 40 days of incubation) revealed that the diversity and relative abundance of bacterial genera were related to the presence or absence of oil contamination in the nonpressurized treatments. In contrast, the variation in the relative abundances of bacterial genera in the 4°C/22 MPa-microcosms either contaminated or not with crude oil was less evident. The highest relative abundance of the phylum Bacteroidetes was observed in the 4°C/22 MPa treatment.
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Affiliation(s)
- Hanna Fasca
- Laboratório de Genética MicrobianaInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Livia V. A. de Castilho
- Laboratório de Tecnologia Submarina/PENO/COPPEUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | | | - Ilson P. Pasqualino
- Laboratório de Tecnologia Submarina/PENO/COPPEUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Vanessa M. Alvarez
- Laboratório de Genética MicrobianaInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Diogo de Azevedo Jurelevicius
- Laboratório de Genética MicrobianaInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Lucy Seldin
- Laboratório de Genética MicrobianaInstituto de Microbiologia Paulo de GóesUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
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Queiroz M, Pinheiro L, Sutili F, de Souza P, Seldin L, Muzitano M, de Souza R, Guimarães D, Leal I. Enantioselective biotransformation of sterically hindered amine substrates by the fungus
Stemphylium lycopersici. J Appl Microbiol 2018; 124:1107-1121. [DOI: 10.1111/jam.13684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/01/2017] [Accepted: 12/11/2017] [Indexed: 01/09/2023]
Affiliation(s)
- M.S.R. Queiroz
- Laboratório de Produtos Naturais e Ensaios Biológicos (LaProNEB) Faculdade de Farmácia DPNA, Cidade Universitária Rio de Janeiro RJ Brazil
| | - L.Z. Pinheiro
- Laboratório de Produtos Naturais e Ensaios Biológicos (LaProNEB) Faculdade de Farmácia DPNA, Cidade Universitária Rio de Janeiro RJ Brazil
| | - F.K. Sutili
- Departamento de Engenharia de Bioprocessos e Biotecnologia Unesp‐Universidade Estadual Paulista ‐ Campus Botucatu Botucatu SP Brazil
| | - P.M. de Souza
- Laboratório de Genética Microbiana CCS Instituto de Microbiologia UFRJ, Cidade Universitária Rio de Janeiro RJ Brazil
| | - L. Seldin
- Laboratório de Genética Microbiana CCS Instituto de Microbiologia UFRJ, Cidade Universitária Rio de Janeiro RJ Brazil
| | - M.F. Muzitano
- Laboratório de Produtos Bioativos (LPBio) Curso de Farmácia Pólo Novo Cavaleiro‐ IMCT UFRJ‐Macaé Macaé RJ Brazil
| | - R.O.M.A. de Souza
- Laboratório de Biocatálise e Síntese Orgânica (BOSS Group) IQ Centro de Tecnologia UFRJ‐ Cidade Universitária Rio de Janeiro Brazil
| | - D.O. Guimarães
- Laboratório de Produtos Bioativos (LPBio) Curso de Farmácia Pólo Novo Cavaleiro‐ IMCT UFRJ‐Macaé Macaé RJ Brazil
| | - I.C.R. Leal
- Laboratório de Produtos Naturais e Ensaios Biológicos (LaProNEB) Faculdade de Farmácia DPNA, Cidade Universitária Rio de Janeiro RJ Brazil
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Sampaio DS, Almeida JRB, de Jesus HE, Rosado AS, Seldin L, Jurelevicius D. Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica. Microb Ecol 2017; 74:810-820. [PMID: 28484799 DOI: 10.1007/s00248-017-0973-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.
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Affiliation(s)
- Dayanna Souza Sampaio
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Hugo E de Jesus
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Alexandre S Rosado
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Diogo Jurelevicius
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPPG), Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, 21941-590, Brazil.
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Couto CRDA, Jurelevicius DDA, Alvarez VM, van Elsas JD, Seldin L. Response of the bacterial community in oil-contaminated marine water to the addition of chemical and biological dispersants. J Environ Manage 2016; 184:473-479. [PMID: 28314395 DOI: 10.1016/j.jenvman.2016.10.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/13/2016] [Accepted: 10/18/2016] [Indexed: 05/20/2023]
Abstract
The use of dispersants in different stages of the oil production chain and for the remediation of water and soil is a well established practice. However, the choice for a chemical or biological dispersant is still a controversial subject. Chemical surfactants that persist long in the environment may pose problems of toxicity themselves; therefore, biosurfactants are considered to constitute an environmentally friendly and effective alternative. Nevertheless, the putative effects of such agents on the microbiomes of oil-contaminated and uncontaminated marine environments have not been sufficiently evaluated. Here, we studied the effects of the surfactant Ultrasperse II® and the surfactin (biosurfactant) produced by Bacillus sp. H2O-1 on the bacterial communities of marine water. Specifically, we used quantitative PCR and genetic fingerprint analyses to study the abundance and structure of the bacterial communities in marine water collected from two regions with contrasting climatic conditions. The addition of either chemical surfactant or biosurfactant influenced the structure and abundance of total and oil-degrading bacterial communities of oil-contaminated and uncontaminated marine waters. Remarkably, the bacterial communities responded similarly to the addition of oil and/or either the surfactant or the biosurfactant in both set of microcosms. After 30 days of incubation, the addition of surfactin enhanced the oil-degrading bacteria more than the chemical surfactant. However, no increase of hydrocarbon biodegradation values was observed, irrespective of the dispersant used. These data contribute to an increased understanding of the impact of novel dispersants on marine bacteriomes before commercial release into the environment.
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Affiliation(s)
| | | | - Vanessa Marques Alvarez
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology Department, University of Groningen, Groningen, The Netherlands
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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de Lacerda JRM, da Silva TF, Vollú RE, Marques JM, Seldin L. Generally recognized as safe (GRAS) Lactococcus lactis strains associated with Lippia sidoides Cham. are able to solubilize/mineralize phosphate. Springerplus 2016; 5:828. [PMID: 27386277 PMCID: PMC4917509 DOI: 10.1186/s40064-016-2596-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 06/15/2016] [Indexed: 01/29/2023]
Abstract
Eight strains isolated from the stems of Lippia sidoides were identified as belonging to Lactococcus lactis, a bacterial species considered as "generally recognized as safe". Their capacity to solubilize/mineralize phosphate was tested in vitro with different inorganic and organic phosphorus (P) sources. All strains were able to solubilize calcium phosphate as an inorganic P source, and the best result was observed with strain 003.41 which solubilized 31 % of this P source. Rock phosphate, a mined rock containing high amounts of phosphate bearing minerals, was solubilized by five strains. When calcium phytate was the organic P source used, the majority of the strains tested showed phosphate mineralization activity. Moreover, all strains were able to solubilize/mineralize phosphate from poultry litter, a complex P source containing inorganic and predominantly organic P. The presence of genes coding for phytase and alkaline phosphatase was searched within the strains studied. However, only gene sequences related to alkaline phosphatase (phoA and phoD) could be detected in the majority of the strains (excepting strain 006.29) with identities varying from 67 to 88 %. These results demonstrate for the first time the potential of L. lactis strains for phosphate solubilization/mineralization activity using a broad spectrum of P sources; therefore, they are of great importance for the future development of more safe bioinoculants with possible beneficial effects for agriculture.
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Affiliation(s)
| | - Thais Freitas da Silva
- />Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-590 Brazil
| | - Renata Estebanez Vollú
- />Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-590 Brazil
| | - Joana Montezano Marques
- />Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-590 Brazil
- />Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA CEP 66075-900 Brazil
| | - Lucy Seldin
- />Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ CEP 21941-590 Brazil
- />Laboratório de Genética Microbiana, Centro de Ciências da Saúde, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ CEP 21941.590 Brazil
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Rosa JPD, Tibúrcio SRG, Marques JM, Seldin L, Coelho RRR. Streptomyces lunalinharesii 235 prevents the formation of a sulfate-reducing bacterial biofilm. Braz J Microbiol 2016; 47:603-9. [PMID: 27266627 PMCID: PMC4927686 DOI: 10.1016/j.bjm.2016.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/08/2015] [Indexed: 11/29/2022] Open
Abstract
Streptomyces lunalinharesii strain 235 produces an antimicrobial substance that is active against sulfate reducing bacteria, the major bacterial group responsible for biofilm formation and biocorrosion in petroleum reservoirs. The use of this antimicrobial substance for sulfate reducing bacteria control is therefore a promising alternative to chemical biocides. In this study the antimicrobial substance did not interfere with the biofilm stability, but the sulfate reducing bacteria biofilm formation was six-fold smaller in carbon steel coupons treated with the antimicrobial substance when compared to the untreated control. A reduction in the most probable number counts of planktonic cells of sulfate reducing bacteria was observed after treatments with the sub-minimal inhibitory concentration, minimal inhibitory concentration, and supra-minimal inhibitory concentration of the antimicrobial substance. Additionally, when the treated coupons were analyzed by scanning electron microscopy, the biofilm formation was found to be substantially reduced when the supra-minimal inhibitory concentration of the antimicrobial substance was used. The coupons used for the biofilm formation had a small weight loss after antimicrobial substance treatment, but corrosion damage was not observed by scanning electron microscopy. The absence of the dsrA gene fragment in the scraped cell suspension after treatment with the supra-minimal inhibitory concentration of the antimicrobial substance suggests that Desulfovibrio alaskensis was not able to adhere to the coupons. This is the first report on an antimicrobial substance produced by Streptomyces active against sulfate reducing bacteria biofilm formation. The application of antimicrobial substance as a potential biocide for sulfate reducing bacteria growth control could be of great interest to the petroleum industry.
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Affiliation(s)
- Juliana Pacheco da Rosa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Joana Montezano Marques
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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Cotta S, Cavalcante Franco Dias A, Seldin L, Andreote F, van Elsas J. The diversity and abundance of phytase genes (β
-propeller phytases) in bacterial communities of the maize rhizosphere. Lett Appl Microbiol 2016; 62:264-8. [DOI: 10.1111/lam.12535] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 01/27/2023]
Affiliation(s)
- S.R. Cotta
- Department of Soil Science; “Luiz de Queiroz” College of Agriculture; University of São Paulo; Piracicaba SP Brazil
- Department of Microbial Ecology, GELIFES; University of Groningen; Groningen The Netherlands
| | - A. Cavalcante Franco Dias
- Department of Soil Science; “Luiz de Queiroz” College of Agriculture; University of São Paulo; Piracicaba SP Brazil
| | - L. Seldin
- Institute of Microbiology Paulo de Góes; Federal University of Rio de Janeiro; Rio de Janeiro Brazil
| | - F.D. Andreote
- Department of Soil Science; “Luiz de Queiroz” College of Agriculture; University of São Paulo; Piracicaba SP Brazil
| | - J.D. van Elsas
- Department of Microbial Ecology, GELIFES; University of Groningen; Groningen The Netherlands
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Alvarez VM, Jurelevicius D, Marques JM, de Souza PM, de Araújo LV, Barros TG, de Souza ROMA, Freire DMG, Seldin L. Bacillus amyloliquefaciens TSBSO 3.8, a biosurfactant-producing strain with biotechnological potential for microbial enhanced oil recovery. Colloids Surf B Biointerfaces 2015; 136:14-21. [DOI: 10.1016/j.colsurfb.2015.08.046] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/11/2015] [Accepted: 08/25/2015] [Indexed: 12/21/2022]
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de Almeida Couto CR, Alvarez VM, Marques JM, de Azevedo Jurelevicius D, Seldin L. Exploiting the aerobic endospore-forming bacterial diversity in saline and hypersaline environments for biosurfactant production. BMC Microbiol 2015; 15:240. [PMID: 26511622 PMCID: PMC4625932 DOI: 10.1186/s12866-015-0575-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/16/2015] [Indexed: 11/30/2022] Open
Abstract
Background Biosurfactants are surface-active biomolecules with great applicability in the food, pharmaceutical and oil industries. Endospore-forming bacteria, which survive for long periods in harsh environments, are described as biosurfactant producers. Although the ubiquity of endospore-forming bacteria in saline and hypersaline environments is well known, studies on the diversity of the endospore-forming and biosurfactant-producing bacterial genera/species in these habitats are underrepresented. Methods In this study, the structure of endospore-forming bacterial communities in sediment/mud samples from Vermelha Lagoon, Massambaba, Dois Rios and Abraão Beaches (saline environments), as well as the Praia Seca salterns (hypersaline environments) was determined via denaturing gradient gel electrophoresis. Bacterial strains were isolated from these environmental samples and further identified using 16S rRNA gene sequencing. Strains presenting emulsification values higher than 30 % were grouped via BOX-PCR, and the culture supernatants of representative strains were subjected to high temperatures and to the presence of up to 20 % NaCl to test their emulsifying activities in these extreme conditions. Mass spectrometry analysis was used to demonstrate the presence of surfactin. Results A diverse endospore-forming bacterial community was observed in all environments. The 110 bacterial strains isolated from these environmental samples were molecularly identified as belonging to the genera Bacillus, Thalassobacillus, Halobacillus, Paenibacillus, Fictibacillus and Paenisporosarcina. Fifty-two strains showed emulsification values of at least 30%, and they were grouped into18 BOX groups. The stability of the emulsification values varied when the culture supernatants of representative strains were subjected to high temperatures and to the presence of up to 20% NaCl. The presence of surfactin was demonstrated in one of the most promising strains. Conclusion The environments studied can harbor endospore-forming bacteria capable of producing biosurfactants with biotechnological applications. Various endospore-forming bacterial genera/species are presented for the first time as biosurfactant producers.
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Affiliation(s)
- Camila Rattes de Almeida Couto
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
| | - Vanessa Marques Alvarez
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
| | - Joana Montezano Marques
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
| | - Diogo de Azevedo Jurelevicius
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
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Mello ICT, Ribeiro ASD, Dias VHG, Silva R, Sabino BD, Garrido RG, Seldin L, de Moura Neto RS. A segment of rbcL gene as a potential tool for forensic discrimination of Cannabis sativa seized at Rio de Janeiro, Brazil. Int J Legal Med 2015; 130:353-6. [DOI: 10.1007/s00414-015-1170-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
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da Silva DAF, Cotta SR, Vollú RE, Jurelevicius DDA, Marques JM, Marriel IE, Seldin L. Endophytic microbial community in two transgenic maize genotypes and in their near-isogenic non-transgenic maize genotype. BMC Microbiol 2014; 14:332. [PMID: 25540019 PMCID: PMC4327796 DOI: 10.1186/s12866-014-0332-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 12/17/2014] [Indexed: 11/23/2022] Open
Abstract
Background Despite all the benefits assigned to the genetically modified plants, there are still no sufficient data available in literature concerning the possible effects on the microbial communities associated with these plants. Therefore, this study was aimed at examining the effects of the genetic modifications of two transgenic maize genotypes (MON810 – expressing the insecticidal Bt-toxin and TC1507 – expressing the insecticidal Bt-toxin and the herbicide resistance PAT [phosphinothricin-N-acetyltransferase]) on their endophytic microbial communities, in comparison to the microbial community found in the near-isogenic non-transgenic maize (control). Results The structure of the endophytic communities (Bacteria, Archaea and fungi) and their composition (Bacteria) were evaluated by denaturing gradient gel electrophoresis (DGGE) and the construction of clone libraries, respectively. DGGE analysis and the clone libraries of the bacterial community showed that genotype TC1507 slightly differed from the other two genotypes. Genotype TC1507 showed a higher diversity within its endophytic bacterial community when compared to the other genotypes. Although some bacterial genera were found in all genotypes, such as the genera Burkholderia, Achromobacer and Stenotrophomonas, some were unique to genotype TC1507. Moreover, OTUs associated with Enterobacter predominated only in TC1507 clone libraries. Conclusion The endophytic bacterial community of the maize genotype TC1507 differed from the communities of the maize genotype MON810 and of their near-isogenic parental genotypes (non-Bt or control). The differences observed among the maize genotypes studied may be associated with insertion of the gene coding for the protein PAT present only in the transgenic genotype TC1507.
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Affiliation(s)
| | - Simone Raposo Cotta
- Departamento de Ciências do Solo, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo, Brazil.
| | - Renata Estebanez Vollú
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | | | - Joana Montezano Marques
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil.
| | - Ivanildo Evódio Marriel
- EMBRAPA/CNPMS- Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisas de Milho e Sorgo, Sete Lagoas, MG, Brazil.
| | - Lucy Seldin
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brazil. .,Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil.
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Dias VHG, Ribeiro ASD, Mello ICT, Silva R, Sabino BD, Garrido RG, Seldin L, Moura-Neto RS. Genetic identification of Cannabis sativa using chloroplast trnL-F gene. Forensic Sci Int Genet 2014; 14:201-2. [PMID: 25450794 DOI: 10.1016/j.fsigen.2014.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/02/2014] [Accepted: 10/06/2014] [Indexed: 10/24/2022]
Affiliation(s)
- V H G Dias
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, UFRJ, Brazil
| | - A S D Ribeiro
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, UFRJ, Brazil; Instituto Nacional de Metrologia, Qualidade e Tecnologia, INMETRO, Brazil
| | - I C T Mello
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, UFRJ, Brazil
| | - R Silva
- Laboratório de Metabolismo Macromolecular Firmino Torres de Castro, Instituto de Biofísica Carlos Chagas Filho, UFRJ, UFRJ, Brazil
| | - B D Sabino
- Instituto de Criminalística Carlos Éboli, DGPTC, PCERJ, Brazil
| | - R G Garrido
- Instituto de Pesquisas e Perícias em Genética Forense, DGPTC, PCERJ, Brazil; Mestrado em Desenvolvimento Local, UNISUAM, Brazil
| | - L Seldin
- Instituto de Microbiologia Paulo de Góes, UFRJ, Brazil
| | - R S Moura-Neto
- Laboratório de Biologia Molecular Forense, Instituto de Biologia, UFRJ, Brazil; Instituto Nacional de Metrologia, Qualidade e Tecnologia, INMETRO, Brazil.
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D Santos AF, Pacheco CA, Valle RDS, Seldin L, D Santos ALS. Enzymes produced by halotolerant spore-forming gram-positive bacterial strains isolated from a resting habitat (Restinga de Jurubatiba) in Rio de Janeiro, Brazil: focus on proteases. Appl Biochem Biotechnol 2014; 174:2748-61. [PMID: 25227686 DOI: 10.1007/s12010-014-1223-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 09/03/2014] [Indexed: 11/25/2022]
Abstract
The screening for hydrolases-producing, halotolerant, and spore-forming gram-positive bacteria from the root, rhizosphere, and non-rhizosphere soil of Blutaparon portulacoides, a plant found in the Restinga de Jurubatiba located at the northern region of Rio de Janeiro State, Brazil, resulted in the isolation of 22 strains. These strains were identified as Halobacillus blutaparonensis (n = 2), Oceanobacillus picturae (n = 5), and Oceanobacillus iheyensis (n = 15), and all showed the ability to produce different extracellular enzymes. A total of 20 isolates (90.9 %) showed activity for protease, 5 (22.7 %) for phytase, 3 (13.6 %) for cellulase, and 2 (9.1 %) for amylase. Some bacterial strains were capable of producing three (13.6 %) or two (9.1 %) distinct hydrolytic enzymes. However, no bacterial strain with ability to produce esterase and DNase was observed. The isolate designated M9, belonging to the species H. blutaparonensis, was the best producer of protease and also yielded amylase and phytase. This strain was chosen for further studies regarding its protease activity. The M9 strain produced similar amounts of protease when grown either without or with different NaCl concentrations (from 0.5 to 10 %). A simple inspection of the cell-free culture supernatant by gelatin-sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) revealed the presence of three major alkaline proteases of 40, 50, and 70 kDa, which were fully inhibited by phenylmethylsulfonyl fluoride (PMSF) and tosyl-L-phenylalanine chloromethyl ketone (TPCK) (two classical serine protease inhibitors). The secreted proteases were detected in a wide range of temperature (from 4 to 45 °C) and their hydrolytic activities were stimulated by NaCl (up to 10 %). The serine proteases produced by the M9 strain cleaved gelatin, casein, albumin, and hemoglobin, however, in different extensions. Collectively, these results suggest the potential use of the M9 strain in biotechnological and/or industrial processes.
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Affiliation(s)
- Anderson Fragoso D Santos
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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Marques JM, da Silva TF, Vollu RE, Blank AF, Ding GC, Seldin L, Smalla K. Plant age and genotype affect the bacterial community composition in the tuber rhizosphere of field-grown sweet potato plants. FEMS Microbiol Ecol 2014; 88:424-35. [PMID: 24597529 DOI: 10.1111/1574-6941.12313] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 02/21/2014] [Accepted: 02/23/2014] [Indexed: 11/30/2022] Open
Abstract
The hypothesis that sweet potato genotypes containing different starch yields in their tuberous roots can affect the bacterial communities present in the rhizosphere (soil adhering to tubers) was tested in this study. Tuberous roots of field-grown sweet potato of genotypes IPB-149 (commercial genotype), IPB-052, and IPB-137 were sampled three and six months after planting and analyzed by denaturing gradient gel electrophoresis (DGGE) and pyrosequencing analysis of 16S rRNA genes PCR-amplified from total community DNA. The statistical analysis of the DGGE fingerprints showed that both plant age and genotypes influenced the bacterial community structure in the tuber rhizosphere. Pyrosequencing analysis showed that the IPB-149 and IPB-052 (both with high starch content) displayed similar bacterial composition in the tuber rhizosphere, while IPB-137 with the lowest starch content was distinct. In comparison with bulk soil, higher 16S rRNA gene copy numbers (qPCR) and numerous genera with significantly increased abundance in the tuber rhizosphere of IPB-137 (Sphingobium, Pseudomonas, Acinetobacter, Stenotrophomonas, Chryseobacterium) indicated a stronger rhizosphere effect. The genus Bacillus was strongly enriched in the tuber rhizosphere samples of all sweet potato genotypes studied, while other genera showed a plant genotype-dependent abundance. This is the first report on the molecular identification of bacteria being associated with the tuber rhizosphere of different sweet potato genotypes.
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Affiliation(s)
- Joana M Marques
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Santos AF, Valle RS, Pacheco CA, Alvarez VM, Seldin L, Santos ALS. Extracellular proteases of Halobacillus blutaparonensis strain M9, a new moderately halophilic bacterium. Braz J Microbiol 2014; 44:1299-304. [PMID: 24688526 PMCID: PMC3958202 DOI: 10.1590/s1517-83822014005000015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 04/04/2013] [Indexed: 12/05/2022] Open
Abstract
Halophilic microorganisms are source of potential hydrolytic enzymes to be used in industrial and/or biotechnological processes. In the present study, we have investigated the ability of the moderately halophilic bacterium Halobacillus blutaparonensis (strain M9), a novel species described by our group, to release proteolytic enzymes. This bacterial strain abundantly proliferated in Luria-Bertani broth supplemented with 2.5% NaCl as well as secreted proteases to the extracellular environment. The production of proteases occurred in bacterial cells grown under different concentration of salt, ranging from 0.5% to 10% NaCl, in a similar way. The proteases secreted by H. blutaparonensis presented the following properties: (i) molecular masses ranging from 30 to 80 kDa, (ii) better hydrolytic activities under neutral-alkaline pH range, (iii) expression modulated according to the culture age, (iv) susceptibility to phenylmethylsulphonyl fluoride, classifying them as serine-type proteases, (v) specific cleavage over the chymotrypsin substrate, and (vi) enzymatic stability in the presence of salt (up to 20% NaCl) and organic solvents (e.g., ether, isooctane and cyclohexane). The proteases described herein are promising for industrial practices due to its haloalkaline properties.
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Affiliation(s)
- Anderson F Santos
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. ; Programa de Pós-Graduação em Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Roberta S Valle
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Clarissa A Pacheco
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. ; Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Vanessa M Alvarez
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - André L S Santos
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. ; Programa de Pós-Graduação em Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Pylro VS, Roesch LFW, Ortega JM, do Amaral AM, Tótola MR, Hirsch PR, Rosado AS, Góes-Neto A, da Costa da Silva AL, Rosa CA, Morais DK, Andreote FD, Duarte GF, de Melo IS, Seldin L, Lambais MR, Hungria M, Peixoto RS, Kruger RH, Tsai SM, Azevedo V. Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects. Microb Ecol 2014; 67:237-241. [PMID: 24173537 DOI: 10.1007/s00248-013-0302-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 09/27/2013] [Indexed: 06/02/2023]
Abstract
The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.
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Affiliation(s)
- Victor Satler Pylro
- Microbiology Department, Federal University of Vicosa, Vicosa, Minas Gerais, 365700-000, Brazil,
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Ribeiro ASD, Dias VHG, Mello ICT, Silva R, Sabino BD, Garrido RG, Seldin L, Moura-Neto RS. O gene rbcL como barcode para identificação forense de Cannabis sativa. Saúde, Ét Just 2013. [DOI: 10.11606/issn.2317-2770.v18ispep67-71] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
<em>Cannabis sativa</em> é uma das espécies mais antigas de plantas domesticadas e permanece como uma das culturas mais amplamente difundida e a droga ilícita mais consumida no mundo. Há uma grande difi culdade em identifi car e individualizar as amostras de Cannabis sp, difi cultando a correlação a prováveis locais de plantações ilegais, o que permitiria revelar rotas de tráfi co, relacionar grupos criminosos e distinguir amostras legais daquelas comercializadas como droga, onde o cultivo é permitido. A principal fi nalidade do DNA Barcode é o de proporcionar uma rápida e precisa identifi cação de organismos a partir de uma pequena região padronizada do genoma que ajuda a caracterizar e distinguir espécies e indivíduos não identifi cados para atribuir à espécie. Um dos genes candidatos é o ribulose-1,5-bisfosfato carboxilase/oxigenase (rbcL), utilizado como um sistema de DNA Barcode e presente no DNA dos cloroplastos das plantas, sendo o responsável pela produção subunidade maior da que converte dióxido de carbono e água em carboidratos.Nosso objetivo é o desenvolvimento de um protocolo efi ciente de extração de DNA e de sequenciamento do gene rbcL para análise forense de amostras apreendidas da Polícia Judiciária. DNA de amostras de Cannabis sativa,caracterizadas no ICCE/DGPTC/PCERJ, foi extraído utilizandoo Mini DNeasy Plant (Qiagen)no IPPGF/DGPTC/PCERJ. O material foi transferido para o LabFor/UFRJe um fragmento de 735 pb do gene rbcL foi amplifi cado através de um par de iniciadores descritos na literatura como universais para plantas.O fragmento foi sequenciado, com o protocolo do BigDye v3.1, usando ABI 3500 (Life Technologies). As comparações das sequências foram realizadas no software Geneious (Biomatters). A nossa sequência consenso de 559 pb foi comparada às seqüências que correspondem às regiões rbcL em <em>Cannabis sativa</em> depositadas no GenBank, e observamos a ocorrência de polimorfi smos (SNPs) entre as amostras dos Estados unidos, Reino Unido e China, sugerindo que se trata de uma assinatura genética para análise forense.
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Procópio L, de Cassia Pereira e Silva M, van Elsas JD, Seldin L. Transcriptional profiling of genes involved in n-hexadecane compounds assimilation in the hydrocarbon degrading Dietzia cinnamea P4 strain. Braz J Microbiol 2013; 44:633-41. [PMID: 24294263 PMCID: PMC3833169 DOI: 10.1590/s1517-83822013000200044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/23/2012] [Indexed: 11/24/2022] Open
Abstract
The petroleum-derived degrading Dietzia cinnamea strain P4 recently had its genome sequenced and annotated. This allowed employing the data on genes that are involved in the degradation of n-alkanes. To examine the physiological behavior of strain P4 in the presence of n-alkanes, the strain was grown under varying conditions of pH and temperature. D. cinnamea P4 was able to grow at pH 7.0–9.0 and at temperatures ranging from 35 ºC to 45 ºC. Experiments of gene expression by real-time quantitative RT-PCR throughout the complete growth cycle clearly indicated the induction of the regulatory gene alkU (TetR family) during early growth. During the logarithmic phase, a large increase in transcriptional levels of a lipid transporter gene was noted. Also, the expression of a gene that encodes the protein fused rubredoxin-alkane monooxygenase was enhanced. Both genes are probably under the influence of the AlkU regulator.
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Affiliation(s)
- Luciano Procópio
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Ilha do Fundão, Rio de Janeiro, RJ, Brazil. ; Department of Microbial Ecology, University of Groningen, Kerklaan, Haren, The Netherlands
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Korenblum E, Regina de Vasconcelos Goulart F, de Almeida Rodrigues I, Abreu F, Lins U, Alves PB, Blank AF, Valoni É, Sebastián GV, Alviano DS, Alviano CS, Seldin L. Antimicrobial action and anti-corrosion effect against sulfate reducing bacteria by lemongrass (Cymbopogon citratus) essential oil and its major component, the citral. AMB Express 2013; 3:44. [PMID: 23938023 PMCID: PMC3751693 DOI: 10.1186/2191-0855-3-44] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/02/2013] [Indexed: 11/10/2022] Open
Abstract
The anti-corrosion effect and the antimicrobial activity of lemongrass essential oil (LEO) against the planktonic and sessile growth of a sulfate reducing bacterium (SRB) were evaluated. Minimum inhibitory concentration (MIC) of LEO and its major component, the citral, was 0.17 mg ml-1. In addition, both LEO and citral showed an immediate killing effect against SRB in liquid medium, suggesting that citral is responsible for the antimicrobial activity of LEO against SRB. Transmission electron microscopy revealed that the MIC of LEO caused discernible cell membrane alterations and formed electron-dense inclusions. Neither biofilm formation nor corrosion was observed on carbon steel coupons after LEO treatment. LEO was effective for the control of the planktonic and sessile SRB growth and for the protection of carbon steel coupons against biocorrosion. The application of LEO as a potential biocide for SRB growth control in petroleum reservoirs and, consequently, for souring prevention, and/or as a coating protection against biocorrosion is of great interest for the petroleum industries.
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Affiliation(s)
- Elisa Korenblum
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Igor de Almeida Rodrigues
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernanda Abreu
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ulysses Lins
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Péricles Barreto Alves
- Departamento de Engenharia Agronômica, Universidade Federal de Sergipe, Aracajú, SE, Brazil
| | - Arie Fitzgerald Blank
- Departamento de Engenharia Agronômica, Universidade Federal de Sergipe, Aracajú, SE, Brazil
| | - Érika Valoni
- CENPES, Petrobras, Ilha do Fundão, Rio de Janeiro, Brazil
| | | | - Daniela Sales Alviano
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Celuta Sales Alviano
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucy Seldin
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Jurelevicius D, Alvarez VM, Peixoto R, Rosado AS, Seldin L. The Use of a Combination of alkB Primers to Better Characterize the Distribution of Alkane-Degrading Bacteria. PLoS One 2013; 8:e66565. [PMID: 23825163 PMCID: PMC3688950 DOI: 10.1371/journal.pone.0066565] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 05/08/2013] [Indexed: 11/22/2022] Open
Abstract
The alkane monooxygenase AlkB, which is encoded by the alkB gene, is a key enzyme involved in bacterial alkane degradation. To study the alkB gene within bacterial communities, researchers need to be aware of the variations in alkB nucleotide sequences; a failure to consider the sequence variations results in the low representation of the diversity and richness of alkane-degrading bacteria. To minimize this shortcoming, the use of a combination of three alkB-targeting primers to enhance the detection of the alkB gene in previously isolated alkane-degrading bacteria was proposed. Using this approach, alkB-related PCR products were detected in 79% of the strains tested. Furthermore, the chosen set of primers was used to study alkB richness and diversity in different soils sampled in Carmópolis, Brazil and King George Island, Antarctica. The DNA extracted from the different soils was PCR amplified with each set of alkB-targeting primers, and clone libraries were constructed, sequenced and analyzed. A total of 255 alkB phylotypes were detected. Venn diagram analyses revealed that only low numbers of alkB phylotypes were shared among the different libraries derived from each primer pair. Therefore, the combination of three alkB-targeting primers enhanced the richness of alkB phylotypes detected in the different soils by 45% to 139%, when compared to the use of a single alkB-targeting primer. In addition, a dendrogram analysis and beta diversity comparison of the alkB composition showed that each of the sampling sites studied had a particular set of alkane-degrading bacteria. The use of a combination of alkB primers was an efficient strategy for enhancing the detection of the alkB gene in cultivable bacteria and for better characterizing the distribution of alkane-degrading bacteria in different soil environments.
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Affiliation(s)
- Diogo Jurelevicius
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vanessa Marques Alvarez
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Peixoto
- Laboratório de Ecologia Molecular Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre S. Rosado
- Laboratório de Ecologia Molecular Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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da Silva TF, Vollú RE, Jurelevicius D, Alviano DS, Alviano CS, Blank AF, Seldin L. Does the essential oil of Lippia sidoides Cham. (pepper-rosmarin) affect its endophytic microbial community? BMC Microbiol 2013; 13:29. [PMID: 23387945 PMCID: PMC3626855 DOI: 10.1186/1471-2180-13-29] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 01/30/2013] [Indexed: 11/28/2022] Open
Abstract
Background Lippia sidoides Cham., also known as pepper-rosmarin, produces an essential oil in its leaves that is currently used by the pharmaceutical, perfumery and cosmetic industries for its antimicrobial and aromatic properties. Because of the antimicrobial compounds (mainly thymol and carvacrol) found in the essential oil, we believe that the endophytic microorganisms found in L. sidoides are selected to live in different parts of the plant. Results In this study, the endophytic microbial communities from the stems and leaves of four L. sidoides genotypes were determined using cultivation-dependent and cultivation-independent approaches. In total, 145 endophytic bacterial strains were isolated and further grouped using either ERIC-PCR or BOX-PCR, resulting in 76 groups composed of different genera predominantly belonging to the Gammaproteobacteria. The endophytic microbial diversity was also analyzed by PCR-DGGE using 16S rRNA-based universal and group-specific primers for total bacteria, Alphaproteobacteria, Betaproteobacteria and Actinobacteria and 18S rRNA-based primers for fungi. PCR-DGGE profile analysis and principal component analysis showed that the total bacteria, Alphaproteobacteria, Betaproteobacteria and fungi were influenced not only by the location within the plant (leaf vs. stem) but also by the presence of the main components of the L. sidoides essential oil (thymol and/or carvacrol) in the leaves. However, the same could not be observed within the Actinobacteria. Conclusion The data presented here are the first step to begin shedding light on the impact of the essential oil in the endophytic microorganisms in pepper-rosmarin.
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Affiliation(s)
- Thais Freitas da Silva
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Rio de Janeiro, Brazil
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Procópio L, Macrae A, van Elsas JD, Seldin L. The putative α/β-hydrolases of Dietzia cinnamea P4 strain as potential enzymes for biocatalytic applications. Antonie Van Leeuwenhoek 2012; 103:635-46. [PMID: 23142860 DOI: 10.1007/s10482-012-9847-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
Abstract
The draft genome of the soil actinomycete Dietzia cinnamea P4 reveals a versatile group of α/β-hydrolase fold enzymes. Phylogenetic and comparative sequence analyses were used to classify the α/β-hydrolases of strain P4 into six different groups: (i) lipases, (ii) esterases, (iii) epoxide hydrolases, (iv) haloacid dehalogenases, (v) C-C breaking enzymes and (vi) serine peptidases. The high number of lipases/esterases (41) and epoxide hydrolase enzymes (14) present in the relatively small (3.6 Mb) P4 genome is unusual; it is likely to be linked to the survival of strain P4 in its natural environment. Strain P4 is thus equipped with a large number of genes which would appear to confer survivability in harsh hot tropical soil. As such, this highly resilient soil bacterial strain provides an interesting genome for enzyme mining for applications in the field of biotransformations of polymeric compounds.
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Affiliation(s)
- Luciano Procópio
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Prof. Paulo de Góes, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Bloco I, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941.590, Brazil
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Korenblum E, de Araujo LV, Guimarães CR, de Souza LM, Sassaki G, Abreu F, Nitschke M, Lins U, Freire DMG, Barreto-Bergter E, Seldin L. Purification and characterization of a surfactin-like molecule produced by Bacillus sp. H2O-1 and its antagonistic effect against sulfate reducing bacteria. BMC Microbiol 2012; 12:252. [PMID: 23131170 PMCID: PMC3577442 DOI: 10.1186/1471-2180-12-252] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/01/2012] [Indexed: 12/02/2022] Open
Abstract
Background Bacillus sp. H2O-1, isolated from the connate water of a Brazilian reservoir, produces an antimicrobial substance (denoted as AMS H2O-1) that is active against sulfate reducing bacteria, which are the major bacterial group responsible for biogenic souring and biocorrosion in petroleum reservoirs. Thus, the use of AMS H2O-1 for sulfate reducing bacteria control in the petroleum industry is a promising alternative to chemical biocides. However, prior to the large-scale production of AMS H2O-1 for industrial applications, its chemical structure must be elucidated. This study also analyzed the changes in the wetting properties of different surfaces conditioned with AMS H2O-1 and demonstrated the effect of AMS H2O-1 on sulfate reducing bacteria cells. Results A lipopeptide mixture from AMS H2O-1 was partially purified on a silica gel column and identified via mass spectrometry (ESI-MS). It comprises four major components that range in size from 1007 to 1049 Da. The lipid moiety contains linear and branched β-hydroxy fatty acids that range in length from C13 to C16. The peptide moiety contains seven amino acids identified as Glu-Leu-Leu-Val-Asp-Leu-Leu. Transmission electron microscopy revealed cell membrane alteration of sulfate reducing bacteria after AMS H2O-1 treatment at the minimum inhibitory concentration (5 μg/ml). Cytoplasmic electron dense inclusions were observed in treated cells but not in untreated cells. AMS H2O-1 enhanced the osmosis of sulfate reducing bacteria cells and caused the leakage of the intracellular contents. In addition, contact angle measurements indicated that different surfaces conditioned by AMS H2O-1 were less hydrophobic and more electron-donor than untreated surfaces. Conclusion AMS H2O-1 is a mixture of four surfactin-like homologues, and its biocidal activity and surfactant properties suggest that this compound may be a good candidate for sulfate reducing bacteria control. Thus, it is a potential alternative to the chemical biocides or surface coating agents currently used to prevent SRB growth in petroleum industries.
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Affiliation(s)
- Elisa Korenblum
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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Cotta SR, Dias ACF, Marriel IE, Gomes EA, van Elsas JD, Seldin L. Temporal dynamics of microbial communities in the rhizosphere of two genetically modified (GM) maize hybrids in tropical agrosystems. Antonie Van Leeuwenhoek 2012; 103:589-601. [PMID: 23124960 DOI: 10.1007/s10482-012-9843-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/25/2012] [Indexed: 11/30/2022]
Abstract
The use of genetically modified (GM) plants still raises concerns about their environmental impact. The present study aimed to evaluate the possible effects of GM maize, in comparison to the parental line, on the structure and abundance of microbial communities in the rhizosphere. Moreover, the effect of soil type was addressed. For this purpose, the bacterial and fungal communities associated with the rhizosphere of GM plants were compared by culture-independent methodologies to the near-isogenic parental line. Two different soils and three stages of plant development in two different periods of the year were included. As evidenced by principal components analysis (PCA) of the PCR-DGGE profiles of evaluated community, clear differences occurred in these rhizosphere communities between soils and the periods of the year that maize was cultivated. However, there were no discernible effects of the GM lines as compared to the parental line. For all microbial communities evaluated, soil type and the period of the year that the maize was cultivated were the main factors that influenced their structures. No differences were observed in the abundances of total bacteria between the rhizospheres of GM and parental plant lines.
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Affiliation(s)
- Simone Raposo Cotta
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I Ilha do Fundão, Rio de Janeiro, RJ, CEP 21941-590, Brazil
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Castro ALMD, Vollú RE, Peixoto RS, Grigorevski-Lima AL, Coelho RRR, Bon EPS, Rosado AS, Seldin L. Cellulolytic potential of a novel strain of Paenibacillus sp. isolated from the armored catfish Parotocinclus maculicauda gut. Braz J Microbiol 2011. [DOI: 10.1590/s1517-83822011000400048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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de Castro ALM, Vollú RE, Peixoto RS, Grigorevski-Lima AL, Coelho RRR, Bon EPS, Rosado AS, Seldin L. Cellulolytic potential of a novel strain of Paenibacillus sp. isolated from the armored catfish Parotocinclus maculicauda gut. Braz J Microbiol 2011; 42:1608-15. [PMID: 24031795 PMCID: PMC3768713 DOI: 10.1590/s1517-838220110004000048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 05/30/2011] [Indexed: 11/22/2022] Open
Abstract
A cellulolytic bacterial strain, designated P118, isolated from the gut of the tropical fish Parotocinclus maculicauda was identified as belonging to the genus Paenibacillus based on phenotypic and chemotaxonomic characteristics and the 16S rRNA gene sequence. The novel strain was Gram-positive, spore-forming and rod-shaped. Catalase but not oxidase was produced. Carboxymethylcellulose was hydrolyzed but starch or gelatin was not. Acetoin production was negative whereas nitrate reduction and urease production were positive. Many carbohydrates served as carbon sources for growth. MK-7 was the predominant isoprenoid quinone. Anteiso-C15:0 (38.73%) and C16:0 (20.85%) were the dominant cellular fatty acids. Strain P118 was closely related to Paenibacillus amylolyticus NRRL NRS-290, P. pabuli HSCC 492, P. tundrae Ab10b, P. xylanexedens B22a, and P. tylopili MK2 with 98.3-98.8% 16S rRNA gene sequence similarity. The results presented here suggest that strain P118 represents a novel species of the genus Paenibacillus and it is a potential strain for further studies concerning its role in the production of industrially important products from cellulosic biomass.
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Affiliation(s)
- André L. M. de Castro
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brasil
| | - Renata E. Vollú
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brasil
| | - Raquel S. Peixoto
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brasil
| | - André L. Grigorevski-Lima
- Laboratório de Biotecnologia de Actinomicetos, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brasil
| | - Rosalie R. R. Coelho
- Laboratório de Biotecnologia de Actinomicetos, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brasil
| | - Elba P. S. Bon
- Instituto de Química, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brasil
| | - Alexandre S. Rosado
- Laboratório de Ecologia Molecular Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brasil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, RJ, Brasil
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Procópio L, Alvarez VM, Jurelevicius DA, Hansen L, Sørensen SJ, Cardoso JS, Pádula M, Leitão ÁC, Seldin L, van Elsas JD. Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential. Antonie Van Leeuwenhoek 2011; 101:289-302. [PMID: 21901521 PMCID: PMC3261415 DOI: 10.1007/s10482-011-9633-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 08/20/2011] [Indexed: 01/17/2023]
Abstract
The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO2 fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation.
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Affiliation(s)
- Luciano Procópio
- Microbial Ecology Laboratory, Department of Microbial Ecology, CEES, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Vanessa M. Alvarez
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Diogo A. Jurelevicius
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Lars Hansen
- Department of Microbiology, Institute of Biology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen, Denmark
| | - Søren J. Sørensen
- Department of Microbiology, Institute of Biology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen, Denmark
| | - Janine S. Cardoso
- Laboratório de Diagnóstico Molecular e Hematologia, Faculdade de Farmácia, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Marcelo Pádula
- Laboratório de Diagnóstico Molecular e Hematologia, Faculdade de Farmácia, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Álvaro C. Leitão
- Laboratório de Radiobiologia Molecular, Instituto de Biofísica Carlos Chagas Filho, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology Laboratory, Department of Microbial Ecology, CEES, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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Jurelevicius D, Korenblum E, Casella R, Vital RL, Seldin L. Polyphasic analysis of the bacterial community in the rhizosphere and roots of Cyperus rotundus L. grown in a petroleum-contaminated soil. J Microbiol Biotechnol 2010; 20:862-70. [PMID: 20519908 DOI: 10.4014/jmb.0910.10012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Cyperus rotundus L. is a perennial herb which was found prevailing in an area in the northeast of Brazil previously contaminated with petroleum. In order to enlarge the knowledge of microorganism-plant interaction in phytoremediation, the bacterial community present in the rhizosphere and roots of C. rotundus was evaluated by culture-dependent and molecular approaches. PCR-DGGE analyses based on the 16S rRNA gene showed that the profiles of bulk soil, rhizosphere and root samples had a high degree of similarity. A complex community of alkane utilizing-bacteria and a variable nitrogen-fixing community were observed when the PCR-DGGE analyses were based on the genes alkB and nifH, respectively. In addition, two clone libraries were generated from the alkB fragments of bulk and rhizosphere soils. Statistical analyses showed that the libraries were different concerning the alkB population composition. Using culture-dependent techniques, 209 bacterial strains were isolated from the rhizosphere and rhizoplane/roots of C. rotundus. Dot blotting analysis showed that the DNA from 17 strains hybridized, simultaneously, with the alkB and nifH probes. After partial 16S rRNA gene sequencing, these strains were affiliated with the genera Bosea, Cupriavidus, Enterobacter, Gordonia, Mycoplana, Pandoraea, Pseudomonas, Rhizobium and Rhodococcus. They can be considered of great potential for phytoremediation in this tropical soil area.
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Affiliation(s)
- Diogo Jurelevicius
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Korenblum E, Valoni E, Penna M, Seldin L. Bacterial diversity in water injection systems of Brazilian offshore oil platforms. Appl Microbiol Biotechnol 2010; 85:791-800. [PMID: 19830416 DOI: 10.1007/s00253-009-2281-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2009] [Revised: 09/26/2009] [Accepted: 09/28/2009] [Indexed: 10/20/2022]
Abstract
Biogenic souring and microbial-influenced corrosion is a common scenario in water-flooded petroleum reservoirs. Water injection systems are continuously treated to control bacterial contamination, but some bacteria that cause souring and corrosion can persist even after different treatments have been applied. Our aim was to increase our knowledge of the bacterial communities that persist in the water injection systems of three offshore oil platforms in Brazil. To achieve this goal, we used a culture-independent molecular approach (16S ribosomal RNA gene clone libraries) to analyze seawater samples that had been subjected to different treatments. Phylogenetic analyses revealed that the bacterial communities from the different platforms were taxonomically different. A predominance of bacterial clones affiliated with Gammaproteobacteria, mostly belonging to the genus Marinobacter (60.7%), were observed in the platform A samples. Clones from platform B were mainly related to the genera Colwellia (37.9%) and Achromobacter (24.6%), whereas clones obtained from platform C were all related to unclassified bacteria. Canonical correspondence analyses showed that different treatments such as chlorination, deoxygenation, and biocide addition did not significantly influence the bacterial diversity in the platforms studied. Our results demonstrated that the injection water used in secondary oil recovery procedures contained potentially hazardous bacteria, which may ultimately cause souring and corrosion.
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Affiliation(s)
- Elisa Korenblum
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Ilha do Fundão, Rio de Janeiro, RJ, Brazil
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