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Moura FT, Delai CV, Klepa MS, Ribeiro RA, Nogueira MA, Hungria M. Unveiling remarkable bacterial diversity trapped by cowpea (Vigna unguiculata) nodules inoculated with soils from indigenous lands in Central-Western Brazil. Braz J Microbiol 2025; 56:545-562. [PMID: 39847210 PMCID: PMC11885751 DOI: 10.1007/s42770-025-01622-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 01/15/2025] [Indexed: 01/24/2025] Open
Abstract
Cowpea (Vigna unguiculata) is recognized as a promiscuous legume in its symbiotic relationships with rhizobia, capable of forming associations with a wide range of bacterial species. Our study focused on assessing the diversity of bacterial strains present in cowpea nodules when inoculated with soils from six indigenous lands of Mato Grosso do Sul state, Central-Western Brazil, comprising the Cerrado and the Pantanal biomes, which are known for their rich diversity. The DNA profiles (BOX-PCR) of 89 strains indicated great genetic diversity, with 20 groups and 23 strains occupying single positions, and all strains grouped at a final similarity level of only 25%. Further characterization using 16S rRNA gene sequencing revealed a diverse array of bacterial genera associated with the cowpea nodules. The strains (number in parenthesis) were classified into ten genera: Agrobacterium (47), Ancylobacter (2), Burkholderia (12), Ensifer (1), Enterobacter (1), Mesorhizobium (1), Microbacterium (1), Paraburkholderia (1), Rhizobium (22), and Stenotrophomonas (1), split into four different classes. Notably, only Ensifer, Mesorhizobium, Rhizobium, and Paraburkholderia are classified as rhizobia. Phylogenetic analysis was conducted based on the classes of the identified genera and the type strains of the closest species. Our integrated analyses, combining phenotypic, genotypic, and phylogenetic approaches, highlighted the significant promiscuity of cowpea in associating with a diverse array of bacteria within nodules, showcasing the Brazilian soils as a hotspot of bacterial diversity.
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Affiliation(s)
- Fernanda Terezinha Moura
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PR-445, Km 380, C.P. 10.011, CEP 86.057-970, Londrina, Paraná, Brazil
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, CEP 86.085-981, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, CEP 70.040-020, Brasília, Distrito Federal, Brazil
| | - Caroline Vanzzo Delai
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, CEP 86.085-981, Londrina, Paraná, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, CEP 70.040-020, Brasília, Distrito Federal, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10.011, CEP 86.057-970, Londrina, Paraná, Brazil
| | - Milena Serenato Klepa
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, CEP 86.085-981, Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71, 605-001, Brasília, Distrito Federal, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71, 605-001, Brasília, Distrito Federal, Brazil
| | - Marco Antonio Nogueira
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, CEP 86.085-981, Londrina, Paraná, Brazil
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10.011, CEP 86.057-970, Londrina, Paraná, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71, 605-001, Brasília, Distrito Federal, Brazil
| | - Mariangela Hungria
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PR-445, Km 380, C.P. 10.011, CEP 86.057-970, Londrina, Paraná, Brazil.
- Soil Biotechnology Laboratory, Embrapa Soja, C.P. 4006, CEP 86.085-981, Londrina, Paraná, Brazil.
- Department of Microbiology, Universidade Estadual de Londrina, C.P. 10.011, CEP 86.057-970, Londrina, Paraná, Brazil.
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71, 605-001, Brasília, Distrito Federal, Brazil.
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de Freitas AS, Carlos FS, Martins GL, Monteiro GGTN, Roesch LFW. Bacterial Resilience and Community Shifts Under 11 Draining-Flooding Cycles in Rice Soils. MICROBIAL ECOLOGY 2024; 87:149. [PMID: 39604741 PMCID: PMC11602802 DOI: 10.1007/s00248-024-02468-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 11/21/2024] [Indexed: 11/29/2024]
Abstract
Flooded rice cultivation, accounting for 75% of global rice production, significantly influences soil redox potential, element speciation, pH, and nutrient availability, presenting challenges such as extensive water usage and altered soil properties. This study investigates bacterial community dynamics in rice soils subjected to repeated draining and flooding in Rio Grande do Sul, Brazil. We demonstrate that bacterial communities exhibit remarkable resilience (the capacity to recover after being altered by a disturbance) but cannot remain stable after long-term exposure to environmental changes. The beta diversity analysis revealed four distinct community states after 11 draining/flooding cycles, indicating resilience over successive environment changes. However, the consistent environmental disturbance reduced microbial resilience, causing the bacterial community structure to shift over time. Those differences were driven by substitutions of taxa and functions and not by the loss of diversity. Notable shifts included a decline in Acidobacteria and an increase in Proteobacteria and Chloroflexi. Increased Verrucomicrobia abundance corresponded with lower pH levels. Functional predictions suggested dynamic metabolic responses, with increased nitrification during drained cycles and a surge in fermenters after the sixth cycle. Despite cyclic disturbances, bacterial communities exhibit resilience, contributing to stable ecosystem functioning in flooded rice soils. These findings enhance our understanding of microbial adaptation, providing insights into sustainable rice cultivation and soil management practices.
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Affiliation(s)
- Anderson Santos de Freitas
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Filipe Selau Carlos
- Soil Department, "Eliseu Maciel" Agronomy Faculty, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Guilherme Lucio Martins
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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Alves Ruislan AL, França Dias M, Daniela Lopes Júlio A, Mourão Silva UDC, Pagnin S, Veiga AA, Godinho Zanetti D, Santos VLD. Effects of antimicrobials over sessile and planktonic microbiota associated with an industrial cooling water system. BIOFOULING 2024; 40:499-513. [PMID: 39108059 DOI: 10.1080/08927014.2024.2384436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 08/20/2024]
Abstract
The bacterial community from a cooling water system was investigated through culture-dependent and independent strategies, and the responses of planktonic and sessile bacteria (grown in glass slides and stainless-steel coupons) to antimicrobials of industrial and clinical use were assessed. The morphotypes with higher biofilm-forming potential were Pseudoxanthomonas sp., Rheinheimera sp., Aeromonas sp. and Staphylococcus sp., and the first also exhibited lower susceptibility to all antibiotics and biocides tested. 16S rRNA high throughput sequencing indicated that Pseudomonadota (77.1% on average, sd 11.1%), Bacteroidota (8.4, sd 5.7%), and Planctomycetota (3.0, sd 1.3%) were the most abundant phyla. KEGG orthologs associated with antibiotics and biocide resistance were abundant in all samples. Although the minimum inhibitory and bactericidal concentrations were generally higher for biofilms, morphotypes in planktonic form also showed high levels of resistance, which could be associated with biofilm cells passing into the planktonic phase. Overall, monochloramine was the most effective biocide.
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Affiliation(s)
| | - Marcela França Dias
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Sergio Pagnin
- Research and Development Center (CENPES), Petróleo Brasileiro S.A., Rio de Janeiro, Brazil
| | - Andrea Azevedo Veiga
- Research and Development Center (CENPES), Petróleo Brasileiro S.A., Rio de Janeiro, Brazil
| | - Débora Godinho Zanetti
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Vera Lúcia Dos Santos
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Yaghjyan L, Mai V, Darville LNF, Cline J, Wang X, Ukhanova M, Tagliamonte MS, Martinez YC, Rich SN, Koomen JM, Egan KM. Associations of gut microbiome with endogenous estrogen levels in healthy postmenopausal women. Cancer Causes Control 2023; 34:873-881. [PMID: 37286847 DOI: 10.1007/s10552-023-01728-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023]
Abstract
PURPOSE The gut microbiome is a potentially important contributor to endogenous estrogen levels after menopause. In healthy postmenopausal women, we examined associations of fecal microbiome composition with levels of urinary estrogens, their metabolites, and relevant metabolic pathway ratios implicated in breast cancer risk. METHODS Eligible postmenopausal women (n = 164) had a body mass index (BMI) ≤ 35 kg/m2 and no history of hormone use (previous 6 months) or cancer/metabolic disorders. Estrogens were quantified in spot urine samples with liquid chromatography-high resolution mass spectrometry (corrected for creatinine). Bacterial DNA was isolated from fecal samples and the V1-V2 hypervariable regions of 16S rRNA were sequenced on the Illumina MiSeq platform. We examined associations of gut microbiome's indices of within-sample (alpha) diversity (i.e., Shannon, Chao1, and Inverse Simpson), phylogenetic diversity, and the ratio of the two main phyla (Firmicutes and Bacteroidetes; F/B ratio) with individual estrogens and metabolic ratios, adjusted for age and BMI. RESULTS In this sample of 164 healthy postmenopausal women, the mean age was 62.9 years (range 47.0-86.0). We found significant inverse associations of observed species with 4-pathway:total estrogens (p = 0.04) and 4-pathway:2-pathway (p = 0.01). Shannon index was positively associated with 2-catechols: methylated 2-catechols (p = 0.04). Chao1 was inversely associated with E1:total estrogens (p = 0.04), and 4-pathway:2-pathway (p = 0.02) and positively associated with 2-pathway:parent estrogens (p = 0.01). Phylogenetic diversity was inversely associated with 4-pathway:total estrogens (p = 0.02), 4-pathway:parent estrogens (p = 0.03), 4-pathway:2-pathway (p = 0.01), and 4-pathway:16-pathway (p = 0.03) and positively associated with 2-pathway:parent estrogens (p = 0.01). F/B ratio was not associated with any of the estrogen measures. CONCLUSION Microbial diversity was associated with several estrogen metabolism ratios implicated in breast cancer risk. Further studies are warranted to confirm these findings in a larger and more representative sample of postmenopausal women, particularly with enrichment of minority participants.
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Affiliation(s)
- Lusine Yaghjyan
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA.
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | | | | | - Maria Ukhanova
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Massimiliano S Tagliamonte
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | | | - Shannan N Rich
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA
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Moura FT, Helene LCF, Ribeiro RA, Nogueira MA, Hungria M. The outstanding diversity of rhizobia microsymbionts of common bean (Phaseolus vulgaris L.) in Mato Grosso do Sul, central-western Brazil, revealing new Rhizobium species. Arch Microbiol 2023; 205:325. [PMID: 37659972 DOI: 10.1007/s00203-023-03667-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 09/04/2023]
Abstract
Common bean is considered a legume of great socioeconomic importance, capable of establishing symbioses with a wide variety of rhizobial species. However, the legume has also been recognized for its low efficiency in fixing atmospheric nitrogen. Brazil is a hotspot of biodiversity, and in a previous study, we identified 13 strains isolated from common bean (Phaseolus vulgaris) nodules in three biomes of Mato Grosso do Sul state, central-western Brazil, that might represent new phylogenetic groups, deserving further polyphasic characterization. The phylogenetic tree of the 16S rRNA gene split the 13 strains into two large clades, seven in the R. etli and six in the R. tropici clade. The MLSA with four housekeeping genes (glnII, gyrB, recA, and rpoA) confirmed the phylogenetic allocation. Genomic comparisons indicated eight strains in five putative new species and the remaining five as R. phaseoli. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparing the putative new species and the closest neighbors ranged from 81.84 to 92.50% and 24.0 to 50.7%, respectively. Other phenotypic, genotypic, and symbiotic features were evaluated. Interestingly, some strains of both R. etli and R. tropici clades lost their nodulation capacity. The data support the description of the new species Rhizobium cerradonense sp. nov. (CNPSo 3464T), Rhizobium atlanticum sp. nov. (CNPSo 3490T), Rhizobium aureum sp. nov. (CNPSo 3968T), Rhizobium pantanalense sp. nov. (CNPSo 4039T), and Rhizobium centroccidentale sp. nov. (CNPSo 4062T).
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Affiliation(s)
- Fernanda Terezinha Moura
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PR-445, Km 380, Cx. Postal 6001, Londrina, Paraná, CP 86.051-970, Brazil
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), SBN, Quadra 2, Bloco L, Lote 06, Edifício Capes, Brasília, Distrito Federal, 70.040-020, Brazil
| | - Luisa Caroline Ferraz Helene
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
- Vittia Fertilizantes e Biológicos, São Joaquim da Barra, São Paulo, Brazil
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | - Marco Antonio Nogueira
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil
| | - Mariangela Hungria
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina, PR-445, Km 380, Cx. Postal 6001, Londrina, Paraná, CP 86.051-970, Brazil.
- Soil Biotechnology Laboratory, Embrapa Soja, Cx. Postal 4006, Londrina, Paraná, 86.085-981, Brazil.
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, Brasília, Distrito Federal, 71605-001, Brazil.
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Giovanella P, Taketani RG, Gil-Solsona R, Saldanha LL, Naranjo SBE, Sancho JV, Portolés T, Andreote FD, Rodríguez-Mozaz S, Barceló D, Sette LD. A comprehensive study on diesel oil bioremediation under microcosm conditions using a combined microbiological, enzymatic, mass spectrometry, and metabarcoding approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:101250-101266. [PMID: 37648922 DOI: 10.1007/s11356-023-29474-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Abstract
This study aims at the application of a marine fungal consortium (Aspergillus sclerotiorum CRM 348 and Cryptococcus laurentii CRM 707) for the bioremediation of diesel oil-contaminated soil under microcosm conditions. The impact of biostimulation (BS) and/or bioaugmentation (BA) treatments on diesel-oil biodegradation, soil quality, and the structure of the microbial community were studied. The use of the fungal consortium together with nutrients (BA/BS) resulted in a TPH (Total Petroleum Hydrocarbon) degradation 42% higher than that obtained by natural attenuation (NA) within 120 days. For the same period, a 72 to 92% removal of short-chain alkanes (C12 to C19) was obtained by BA/BS, while only 3 to 65% removal was achieved by NA. BA/BS also showed high degradation efficiency of long-chain alkanes (C20 to C24) at 120 days, reaching 90 and 92% of degradation of icosane and heneicosane, respectively. In contrast, an increase in the levels of cyclosiloxanes (characterized as bacterial bioemulsifiers and biosurfactants) was observed in the soil treated by the consortium. Conversely, the NA presented a maximum of 37% of degradation of these alkane fractions. The 5-ringed PAH benzo(a)pyrene, was removed significantly better with the BA/BS treatment than with the NA (48 vs. 38 % of biodegradation, respectively). Metabarcoding analysis revealed that BA/BS caused a decrease in the soil microbial diversity with a concomitant increase in the abundance of specific microbial groups, including hydrocarbon-degrading (bacteria and fungi) and also an enhancement in soil microbial activity. Our results highlight the great potential of this consortium for soil treatment after diesel spills, as well as the relevance of the massive sequencing, enzymatic, microbiological and GC-HRMS analyses for a better understanding of diesel bioremediation.
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Affiliation(s)
- Patricia Giovanella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Rodrigo Gouvêa Taketani
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, SP, Brazil
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, United Kingdom
| | - Ruben Gil-Solsona
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research - Severo Ochoa Excellence Center (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain
| | - Luiz Leonardo Saldanha
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
| | - Samantha Beatríz Esparza Naranjo
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Universidade Federal da Integração Latino Americana, Parque tecnológico Itaipu, Foz do Iguaçu, PR, Brazil
| | - Juan V Sancho
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón de la Plana, Spain
| | - Tania Portolés
- Environmental and Public Health Analytical Chemistry, Research Institute for Pesticides and Water (IUPA), University Jaume I, Castellón de la Plana, Spain
| | - Fernando Dini Andreote
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo (USP), Piracicaba, SP, Brazil
| | - Sara Rodríguez-Mozaz
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA-CERCA), Parc Científic i Tecnològic de la Universitat de Girona, Girona, Spain
- University of Girona, Girona, Spain
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research - Severo Ochoa Excellence Center (IDAEA), Spanish Council of Scientific Research (CSIC), Barcelona, Spain
| | - Lara Durães Sette
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
- Centro de Estudos Ambientais (CEA), Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Rio Claro, SP, Brazil.
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Corrêa TAF, Tobaruela EDC, Capetini VC, Quintanilha BJ, Cortez RV, Taddei CR, Hassimotto NMA, Hoffmann C, Rogero MM, Lajolo FM. Blood orange juice intake changes specific bacteria of gut microbiota associated with cardiometabolic biomarkers. Front Microbiol 2023; 14:1199383. [PMID: 37469434 PMCID: PMC10352659 DOI: 10.3389/fmicb.2023.1199383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023] Open
Abstract
Blood orange juice is an important source of flavanones and anthocyanins, mainly hesperidin, narirutin, and cyanidin-3-O-glucoside. The benefits of these bioactive compounds have been reported, but the mechanistic details behind their biological effects are not well established. This study investigated the effects of Moro orange (Citrus sinensis L. Osbeck) juice (MOJ) on gut microbiota composition and cardiometabolic biomarkers in overweight women. In this study, 12 overweight women (BMI from 25.0 to 29.9 kg/m2), aged 18-37 years, consumed 500 mL of MOJ every day for 4 weeks. We assessed the gut microbiota composition, levels of short-chain fatty acids (SCFAs), cardiometabolic biomarkers, and insulin resistance (HOMA-IR) at baseline and after 2 weeks and 4 weeks of MOJ intake. The results suggested that MOJ intake affected the abundance of specific operational taxonomic units (OTUs) of the gut microbiota but did not significantly alter the diversity and general composition of the gut microbiota. However, MOJ intake increased the production of SCFAs, especially propionic and isobutyric acids, and significantly improved cardiometabolic biomarkers such as blood pressure and plasma VCAM-1 levels in the overweight women. Additionally, we observed significant associations between gut microbiota OTUs belonging to the Bacteroidetes phyla and Prevotella 9 genera and the cardiometabolic biomarkers. Furthermore, MOJ reduced fasting glucose and insulin levels and HOMA-IR values, thereby enhancing insulin sensitivity in the insulin-resistant overweight women. Finally, we highlighted the importance of orange juice intake duration because some beneficial changes such as blood pressure improvements were evident at the 2-week time interval of the intervention, but other changes became significant only at the 4-week interval of MOJ intake. In conclusion, our study demonstrated that changes in specific OTUs of the gut microbiota in response to MOJ intake were associated with significant improvements in some cardiometabolic biomarkers and SCFA levels in overweight women with insulin resistance.
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Affiliation(s)
- Telma Angelina Faraldo Corrêa
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), São Paulo, Brazil
| | - Eric de Castro Tobaruela
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), São Paulo, Brazil
| | - Vinicius Cooper Capetini
- Food Research Center (FoRC), São Paulo, Brazil
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Bruna Jardim Quintanilha
- Food Research Center (FoRC), São Paulo, Brazil
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Ramon Vitor Cortez
- Department of Clinical Analyses and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carla R. Taddei
- Department of Clinical Analyses and Toxicology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Neuza Mariko Aymoto Hassimotto
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), São Paulo, Brazil
| | - Christian Hoffmann
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), São Paulo, Brazil
| | - Marcelo Macedo Rogero
- Food Research Center (FoRC), São Paulo, Brazil
- Department of Nutrition, School of Public Health, University of São Paulo, São Paulo, Brazil
| | - Franco Maria Lajolo
- Department of Food and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), São Paulo, Brazil
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Reis AA, Monteiro MF, Bonilha GM, Saraiva L, Araújo C, Santamaria MP, Casati MZ, Kumar P, Casarin RCV. Parents with periodontitis drive the early acquisition of dysbiotic microbiomes in their offspring. J Clin Periodontol 2023; 50:890-904. [PMID: 37086047 DOI: 10.1111/jcpe.13815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 04/23/2023]
Abstract
AIM To evaluate the microbial colonization in different dentition phases on individuals from 0 to 18 years of age belonging to families with a history of periodontitis compared to descendants of periodontally healthy parents. MATERIALS AND METHODS The offspring of subjects with periodontitis ('Perio' group) and the offspring of periodontally healthy subjects ('Healthy' group), matched for gender and age, were included in this cross-sectional study and divided according to the dentition phase: pre-dentate, primary, mixed and permanent. The patients were clinically assessed, and their saliva was collected. DNA was extracted, and V1-V3 and V4-V5 regions of the 16S rRNA gene were sequenced. RESULTS Fifty children of parents with periodontitis and 50 from healthy parents were included in the study and divided according to the dentition phase: pre-dentate (n = 5/group), primary dentition (n = 15/group), mixed dentition (n = 15/group) and permanent dentition (n = 15/group) in each group. The microbiome composition was different between dentitions for both groups. Children of the Perio group presented a microbial diversity different from that of the Healthy group in mixed and permanent dentitions. The more intense shift in the community occurred between primary and mixed dentition in the Perio group, while the transition between mixed and permanent dentition was the period with greater changes in the microbiome for the Healthy group. Furthermore, a pathogen-rich environment-higher prevalence and abundance of periodontitis-associated species such as Prevotella spp., Selenomonas spp., Leptotrichia spp., Filifactor alocis, Prevotella intermedia, Treponema denticola and Tannerella forsythia- was observed in the Perio group. CONCLUSIONS The parents' periodontal status significantly affects the microbiome composition of their offspring from an early age. The mixed dentition was the phase associated with establishing a dysbiotic and pathogen-rich microbiome in descendants of parents with periodontitis.
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Affiliation(s)
| | | | | | - Luciana Saraiva
- School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Cassia Araújo
- Institute of Health Science, São Paulo State University, São Paulo, Brazil
| | | | | | - Purnima Kumar
- School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA
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9
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Mishra A, Singh L, Singh D. Unboxing the black box-one step forward to understand the soil microbiome: A systematic review. MICROBIAL ECOLOGY 2023; 85:669-683. [PMID: 35112151 PMCID: PMC9957845 DOI: 10.1007/s00248-022-01962-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.
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Affiliation(s)
- Apurva Mishra
- Academy of Scientific and Innovative Research [AcSIR], Ghaziabad, 201002, India
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Lal Singh
- Environmental Biotechnology and Genomics Division, , CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India
| | - Dharmesh Singh
- Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstrasse 30, 81675, Munich, Bavaria, Germany.
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10
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Porsani MV, Poitevin CG, Tralamazza SM, de Souza MT, de Souza MT, da Silva ÉDB, Zawadneak MAC, Pimentel IC, de Melo IS. Streptomyces spp. Isolated from Marine and Caatinga Biomes in Brazil for the Biological Control of Duponchelia fovealis. NEOTROPICAL ENTOMOLOGY 2022; 51:299-310. [PMID: 35020183 DOI: 10.1007/s13744-022-00942-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Actinobacteria have been drawing attention due to their potential for the development of new pest control products. We hereby assess the effects of Streptomyces isolated from marine and caatinga biomes against Duponchelia fovealis Zeller (Lepidoptera: Crambidae), a pest associated with the strawberry culture at a global scale. To this end, eggs deposited by adults were immersed for 5 s in a bacterial suspension, and the larvae were fed on leaflets placed in glass tubes containing bacterial suspensions. In both treatments, the control was a saline solution. The bioassays demonstrated that the Streptomyces strains were able to cause the death of D. fovealis eggs (≈ 40%) and larvae (≈ 65%) compared to untreated eggs (1.4%) and larvae (2.0%). The crude extract of strain T49 and the chitinase extract of strain T26 affected larval growth when applied directly to the thorax of first-instar larvae (larval-adult lifespan of 65.3 ± 0.5 days and 67.5 ± 0.7 days, respectively; survival of 61.2 ± 1.2%) in relation to the control treatment (larval-adult lifespan of 41.75 ± 0.2 days and survival of 83.7 ± 2.6%). The Streptomyces spp. strains T41, T49, and T50 caused antifeeding activity. Apart from larval mortality, the adults that emerged from the larvae exposed to the extracts presented morphological abnormalities, and the moths' chitin spectra showed clear alterations to the pupa and wings. Our studies show, for the very first time, that Streptomyces isolated from the marine environment and the Caatinga biome are effective at provoking the mortality of D. fovealis and are promising agents for developing new products with biological control properties.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Itamar Soares de Melo
- Embrapa Environment, Brazilian Agricultural Research Corporation, Jaguariúna, São Paulo, Brazil
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11
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Portela VO, Moro A, Santana NA, Baldoni DB, de Castro IA, Antoniolli ZI, Dalcol II, Seminoti Jacques RJ. First report on the production of phytotoxic metabolites by Mycoleptodiscus indicus under optimized conditions of submerged fermentation. ENVIRONMENTAL TECHNOLOGY 2022; 43:1458-1470. [PMID: 33044125 DOI: 10.1080/09593330.2020.1836030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
An alternative to controlling weeds resistant to conventional herbicides is the isolation of new active principles. Fungi can produce phytotoxic metabolites that may be used in the development of new herbicides. The objectives of this study were: (1) isolate, select, and identify a fungus producer of phytotoxic metabolites and (2) optimize the culture conditions of this fungus in a low-cost culture medium, with the aim of increasing the phytotoxic effects of their metabolites in weeds and commercial plants. Fungi were isolated from the leaves of Conyza sp. with disease symptoms and selected according to the production of phytotoxic metabolites in solid and submerged fermentation in a low-cost culture medium. A Plackett-Burman Design and Central Composite Rotational Design were used to optimize the conditions of temperature, agitation, pH, and concentrations of glucose and yeast extract in submerged fermentation. The phytotoxic metabolites produced under optimal conditions were tested on 10 commercial plants and weeds that are difficult to control. Of the nine fungi isolated, Mycoleptodiscus indicus UFSM54 produced higher leaf lesions. The production of phytotoxic metabolites was optimized when the fungus was cultivated at 35°C, 50 rpm, and 1.5 g L-1 of glucose in submerged fermentation. The metabolites of M. indicus caused severe phytotoxic effects on germination and seedling growth, and enhanced lesion development on detached plant leaves. The present study is the first to report on the production of phytotoxic metabolites by M. indicus, a potential producer of bioherbicides.
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Affiliation(s)
| | - Anderson Moro
- Department of Soils, Federal University of Santa Maria, Santa Maria, Brazil
| | - Natielo Almeida Santana
- Department of Sanitary and Environmental Engineering, Federal University of Santa Maria, Santa Maria, Brazil
| | | | | | | | - Ionara Irion Dalcol
- Department of Chemistry, Federal University of Santa Maria, Santa Maria, Brazil
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12
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Fernanda FV, Gleison GRQM, Atilon AVDA, Leila LPP, Clarice CMC. NATIVE AMAZONIAN FUNGI TO CONTROL TERMITES Nasutitermes sp. (BLATTODEA: TERMITIDAE). ACTA BIOLÓGICA COLOMBIANA 2021. [DOI: 10.15446/abc.v27n1.86848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Termites of the Nasutitermes genus are considered one of the main urban and agroforestry pests in Brazil, where the main method of control is the application of pesticides. The uso of entomopathogenic fungi to reduce the population of this plague in the environment could be use as an alternative. The goal of this study was to evaluate the virulence of isolates native Amazonian fungi belonging to the Tolypocladium endophyticum, Metarhizium anisopliae and Metarhizium marquandii species for the control of Nasutitermes sp. The strains of T. endophyticum (4.439), M. anisopliae (4.443) and M. marquandii (4.472) with their respective isolation codes, were evaluated using suspensions at concentrations of 105, 106, 107 and 108 conidia/mL against the termites. The fungi were characterized to species level by molecular analysis. The greatest virulence was registered with T. endophyticum (4.439), with a mortality of 100 % on the 4th day of treatment for all analyzed concentrations. The M. anisopliae strain (4.443) proved to be efficient, causing a mortality of 100 % on the 7th and 6th days at dilutions of 107 and 108 conidia/mL, respectively. Rates lower than 100 % were registered with M. marquandii (4.472). Therefore, the three fungal strains showed virulence against the termites Nasutitermes sp. In this study, the fungi Tolypocladium endophyticum and Metarhizium marquandii are reported for the first time for the biological control of pests, indicating the potential of native Amazonian fungi for the biological control of thermites Nasutitermes sp.
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13
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Paz HES, Monteiro MF, Stolf CS, Altabtbaei K, Casati MZ, Casarin RCV, Kumar PS. Predicted functional and taxonomic analysis of subgingival biofilm of grade C periodontitis in young patients under maintenance therapy. J Periodontol 2021; 93:1119-1130. [PMID: 34727386 DOI: 10.1002/jper.21-0411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND In Grade C periodontitis in young patients (PerioC-Y), the functional roles of the subgingival community after years of periodontal treatment are still underexplored. This study evaluated the taxonomic and predicted functional content of the subgingival microbiome of PerioC-Y patients under supportive periodontal therapy (SPT). METHODS Clinical and microbiological data from subgingival biofilm were assessed from 10 PerioC-Y patients at two time points: at baseline and after 5.7±1.3 years of SPT. This was compared to 15 patients without a history of periodontitis. The V1-V3 and V4-V5 regions of the 16S rRNA were sequenced using the Illumina Miseq. Microbial composition was evaluated by the core microbiome, and alpha- and beta-diversity. The microbiome functional content was predicted using Picrust2, and the gene differential abundance was analyzed with DESeq2. RESULTS Clinical improvements were seen in PerioC-Y-SPT. Differences in β-diversity between PerioC-Y and Health were observed (Health x PerioC-Y-baseline, p = 0.02; Health x PerioC-Y-SPT, p = 0.05). Moreover, although β-diversity did not statistically change between baseline and SPT in PerioC-Y, the microbial correlation evidenced increased Streptococcus and decreased Treponema network contributions during SPT. Based on predicted functional data, treatment induced a reduction in genes related to flagellar protein and signal transduction in PerioC-Y. However, compared to healthy individuals, some genes remained more highly abundant in PerioC-Y-SPT, such as quorum sensing and efflux pump transporters. CONCLUSION Despite clinical improvements and a shift in taxonomic composition, the PerioC-Y patients' periodontal treatment was not enough to reach a similar microbiome to patients without disease experience. Some functional content in this biofilm remained altered in PerioC-Y regardless of disease control. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hélvis E S Paz
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Mabelle F Monteiro
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Camila S Stolf
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Khaled Altabtbaei
- Department of Periodontology, School of Dentistry, University of Alberta, Edmonton, Canada
| | - Márcio Z Casati
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Renato C V Casarin
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Purnima S Kumar
- Department of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH, USA
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14
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Arruda B, George PBL, Robin A, de L C Mescolotti D, Herrera WFB, Jones DL, Andreote FD. Manipulation of the soil microbiome regulates the colonization of plants by arbuscular mycorrhizal fungi. MYCORRHIZA 2021; 31:545-558. [PMID: 34363527 DOI: 10.1007/s00572-021-01044-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of many plant species, facilitating the acquisition of soil nutrients by roots. We hypothesized that AMF root colonization is strongly influenced by the composition of the soil microbiome. Here, we evaluated mycorrhizal colonization of two plants, the grass Urochloa brizantha (Brachiaria) and the legume Crotalaria juncea (Crotalaria). These were cultivated in the same soil but hosting eight distinct microbiomes: natural soil (i); soil exposed to heat treatments for 1 h at 50 ºC (ii), 80 ºC (iii), or 100 ºC (iv); sterilized soil by autoclaving (AS) followed by re-inoculation of dilutions of the natural soil community at 10-1 (v), 10-3 (vi), and 10-6 (vii); and AS without re-inoculation (viii). Microbial diversity (bacteria and fungi) was assessed through 16S rDNA and ITS1 metabarcoding, respectively, and the soil acid phosphatase activity (APASE) was measured. Sequencing results showed the formation of distinct microbial communities according to the soil manipulations, which also correlated with the decline of APASE. Subsequently, seedlings of Brachiaria and Crotalaria were grown in those soils inoculated separately with three AMF (Acaulospora colombiana, Rhizophagus clarus, and Dentiscutata heterogama) which were compared to an AMF-free control treatment. Brachiaria showed higher colonization in natural soil when compared to the microbial community manipulations, regardless of the AMF species inoculated. In contrast, two mycorrhiza species were able to colonize Crotalaria under modified microbial communities at similar rates to natural soil. Furthermore, Brachiaria showed a possible inverse relationship between APASE and mycorrhization, but this trend was absent for Crotalaria. We conclude that mycorrhizal root colonization and soil acid phosphatase activity were associated with the structure of the soil microbiome, depending on the plant species evaluated.
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Affiliation(s)
- Bruna Arruda
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, Gwynedd, UK
| | - Paul B L George
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, Gwynedd, UK
- Département de Médecine Moléculaire, Université Laval, Québec, Canada
| | - Agnès Robin
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
- UMR Eco&Sols, CIRAD, Piracicaba, Brazil
- Eco&Sols, CIRAD, INRAE, IRD, Université Montpellier, Montpellier, France
| | - Denise de L C Mescolotti
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Davey L Jones
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, Gwynedd, UK
- SoilsWest, School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, Brazil.
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15
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Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index-A Pilot Study. Microorganisms 2021; 9:microorganisms9061222. [PMID: 34200004 PMCID: PMC8228046 DOI: 10.3390/microorganisms9061222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
The potential role of the salivary microbiome in human diseases has increasingly been explored. The salivary microbiome has been characterized in several global populations, except the Arabian Gulf region. Hence, in this pilot study, we profiled the salivary microbiome of Kuwaiti adolescents with varied body mass indexes (BMI). The analyses of core microbiome composition showed Firmicutes, Bacteroidota, Proteobacteria, Patescibacteria, Fusobacteriota, Actinobacteriota, and Campylobacterota as the common phylum found in the Kuwaiti adolescent population. We also illustrated a diverse microbial community among the sampled individuals grouped according to their BMI. Notably, the overweight group was found with a higher number of distinct taxa than other groups. As such, the core microbiome composition was found to be significantly different (p-value < 0.001) across different BMI groups. Overall, this pilot investigation outlined the microbial diversity and suggested that changes in salivary microbiome composition in people with obese or overweight BMI might reflect their susceptibility to oral diseases.
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16
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Melkonian C, Fillinger L, Atashgahi S, da Rocha UN, Kuiper E, Olivier B, Braster M, Gottstein W, Helmus R, Parsons JR, Smidt H, van der Waals M, Gerritse J, Brandt BW, Röling WFM, Molenaar D, van Spanning RJM. High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. Commun Biol 2021; 4:530. [PMID: 33953314 PMCID: PMC8099898 DOI: 10.1038/s42003-021-01948-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/03/2021] [Indexed: 01/04/2023] Open
Abstract
A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.
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Affiliation(s)
- Chrats Melkonian
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Lucas Fillinger
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Esther Kuiper
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brett Olivier
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Martin Braster
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Willi Gottstein
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - John R Parsons
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Jan Gerritse
- Unit Subsurface and Groundwater Systems, Deltares, Utrecht, The Netherlands
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wilfred F M Röling
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Douwe Molenaar
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Rob J M van Spanning
- Department of Molecular Cell Biology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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Camacho-Montealegre CM, Rodrigues EM, Morais DK, Tótola MR. Prokaryotic community diversity during bioremediation of crude oil contaminated oilfield soil: effects of hydrocarbon concentration and salinity. Braz J Microbiol 2021; 52:787-800. [PMID: 33813729 DOI: 10.1007/s42770-021-00476-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/26/2021] [Indexed: 02/01/2023] Open
Abstract
Crude oil extracted from oilfield reservoirs brings together hypersaline produced water. Failure in pipelines transporting this mixture causes contamination of the soil with oil and hypersaline water. Soil salinization is harmful to biological populations, impairing the biodegradation of contaminants. We simulated the contamination of a soil from an oilfield with produced water containing different concentrations of NaCl and crude oil, in order to evaluate the effect of salinity and hydrocarbon concentration on prokaryote community structure and biodegradation activity. Microcosms were incubated in CO2-measuring respirometer. After the incubation, residual aliphatic hydrocarbons were quantified and were performed 16S rRNA gene sequencing. An increase in CO2 emission and hydrocarbon biodegradation was observed with increasing oil concentration up to 100 g kg-1. Alpha diversity decreased in oil-contaminated soils with an increase in the relative abundance of Actinobacteria and reduction of Bacteroidetes with increasing oil concentration. In the NaCl-contaminated soils, alpha diversity, CO2 emission, and hydrocarbon biodegradation decreased with increasing NaCl concentration. There was an increase in the relative abundance of Firmicutes and Proteobacteria and a reduction of Actinobacteria with increasing salt concentration. Our results highlight the need to adopt specific bioremediation strategies in soils impacted by mixtures of crude oil and hypersaline produced water.
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Affiliation(s)
- Celia Marcela Camacho-Montealegre
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.,Facultad de Ciencias, Universidad del Tolima, Ibagué, Tolima, Colombia
| | - Edmo Montes Rodrigues
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. .,Instituto Federal de Educação, Ciência e Tecnologia do Ceará - IFCE - Campus Camocim, Camocim, Ceará, Brazil.
| | - Daniel Kumazawa Morais
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences - CAS, Prague, Czech Republic
| | - Marcos Rogério Tótola
- Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente, Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
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18
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Yaghjyan L, Mai V, Wang X, Ukhanova M, Tagliamonte M, Martinez YC, Rich SN, Egan KM. Gut microbiome, body weight, and mammographic breast density in healthy postmenopausal women. Cancer Causes Control 2021; 32:681-692. [PMID: 33772705 DOI: 10.1007/s10552-021-01420-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 03/16/2021] [Indexed: 12/17/2022]
Abstract
PURPOSE We examined gut microbiome (GM) profiles in relation to mammographic breast density (BD) and body mass index (BMI) in healthy postmenopausal women. METHODS Eligible women were postmenopausal, had a BMI ≤ 35 kg/m2, and had not recently taken oral/IV antibiotics. All women provided a fecal sample and information on breast cancer risk factors. Mammographic BD was classified with the American College of Radiology's BI-RADS BD classification system. Bacterial DNA was isolated from fecal samples and the V1-V2 hypervariable regions of 16S rRNA were sequenced on the Illumina MiSeq platform. We examined associations of GM with indices of within-sample (alpha) diversity and the ratio of the two main phyla (Firmicutes and Bacteroidetes; F/B ratio) with BD and BMI. RESULTS Among 69 women with BD data, 39 had low BD (BI-RADS I/II) and 30 had high BD (BI-RADS III/IV). BMI was inversely associated with BD (mean BMI = 23.8 and 28.0 in women with high and low BD, respectively, p = 1.07 × 10-5). Similar levels of GM diversity were found across weight groups according to Shannon (p = 0.83); Inverse Simpson (p = 0.97); and Chao1 (p = 0.31) indices. F/B ratio and microbiota diversity were suggestively greater in women with high vs. low BD (p = 0.35, 0.14, 0.15, and 0.17 for F/B ratio, Shannon, Inverse Simpson and Chao1, respectively). CONCLUSION Suggestive differences observed in women with high and low BD with respect to GM alpha diversity and prevalence of specific GM taxa need to be confirmed in larger studies.
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Affiliation(s)
- Lusine Yaghjyan
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | - Maria Ukhanova
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | | | - Shannan N Rich
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Kathleen M Egan
- H. Lee Moffitt Cancer Center, Tampa, FL, USA. .,Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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de Paula A, Medeiros JD, Fernandes G, da Silva V, Diniz CG. Microbiome of industrialized Minas Frescal Cheese reveals high prevalence of putative bacteria: A concern in the One Health context. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Parents with periodontitis impact the subgingival colonization of their offspring. Sci Rep 2021; 11:1357. [PMID: 33446688 PMCID: PMC7809442 DOI: 10.1038/s41598-020-80372-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023] Open
Abstract
Early acquisition of a pathogenic microbiota and the presence of dysbiosis in childhood is associated with susceptibility to and the familial aggregation of periodontitis. This longitudinal interventional case-control study aimed to evaluate the impact of parental periodontal disease on the acquisition of oral pathogens in their offspring. Subgingival plaque and clinical periodontal metrics were collected from 18 parents with a history of generalized aggressive periodontitis and their children (6-12 years of age), and 18 periodontally healthy parents and their parents at baseline and following professional oral prophylaxis. 16S rRNA amplicon sequencing revealed that parents were the primary source of the child's microbiome, affecting their microbial acquisition and diversity. Children of periodontitis parents were preferentially colonized by Filifactor alocis, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Streptococcus parasanguinis, Fusobacterium nucleatum and several species belonging to the genus Selenomonas even in the absence of periodontitis, and these species controlled inter-bacterial interactions. These pathogens also emerged as robust discriminators of the microbial signatures of children of parents with periodontitis. Plaque control did not modulate this pathogenic pattern, attesting to the microbiome's resistance to change once it has been established. This study highlights the critical role played by parental disease in microbial colonization patterns in their offspring and the early acquisition of periodontitis-related species and underscores the need for greater surveillance and preventive measures in families of periodontitis patients.
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Kaminsky LM, Esker PD, Bell TH. Abiotic conditions outweigh microbial origin during bacterial assembly in soils. Environ Microbiol 2020; 23:358-371. [PMID: 33185966 DOI: 10.1111/1462-2920.15322] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022]
Abstract
Understanding the processes guiding microbial community assembly in soils is essential for predicting microbiome structure and function following soil disturbance events like agricultural soil fumigation. However, assembly outcomes are complex and variable, being affected by both selective abiotic forces and by the history of colonizing microorganisms. To untangle the interactions between these factors, we conducted a controlled microcosm study tracking bacterial assembly in cleared soils over 7 weeks. We used mesh bags to connect five unsterilized source soils, differing in land use history (forested, agricultural, or fallow), with four sterile recipient soil treatments, differing in abiotic conditions (no soil additives, salt addition, urea addition, or mixed salt/urea addition). We found that 59%-96% of bacterial colonizers after 1 week were Firmicutes, but by 7 weeks Actinobacteria and Bacteroidetes were also dominant. Salt and nitrogen additions reshaped bacterial assembly by constraining alpha diversity by up to half and biomass accumulation by up to an order of magnitude. Within-treatment dispersion was significantly lower for salt and nutrient addition microcosms, suggesting deterministic selective pressures. In contrast, source soil origin had little impact on assembly trajectories. These results suggest that abiotic conditions can overshadow microbial source history in shaping community assembly outcomes.
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Affiliation(s)
- Laura M Kaminsky
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
| | - Paul D Esker
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.,Graduate Faculty in International Agriculture and Development, The Pennsylvania State University, University Park, PA, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.,Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, USA
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Meconium microbiome and its relation to neonatal growth and head circumference catch-up in preterm infants. PLoS One 2020; 15:e0238632. [PMID: 32956415 PMCID: PMC7505439 DOI: 10.1371/journal.pone.0238632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 08/20/2020] [Indexed: 12/21/2022] Open
Abstract
The purpose was identify an association between meconium microbiome, extra-uterine growth restriction, and head circumference catch-up. MATERIALS AND METHODS Prospective study with preterm infants born <33 weeks gestational age (GA), admitted at Neonatal Unit and attending the Follow-Up Preterm Program of a tertiary hospital. Excluded out born infants; presence of congenital malformations or genetic syndromes; congenital infections; HIV-positive mothers; and newborns whose parents or legal guardians did not authorize participation. Approved by the institution's ethics committee. Conducted 16S rRNA sequencing using PGM Ion Torrent meconium samples for microbiota analysis. RESULTS Included 63 newborns, GA 30±2.3 weeks, mean weight 1375.80±462.6 grams, 68.3% adequate weight for GA at birth. Polynucleobacter (p = 0.0163), Gp1 (p = 0.018), and Prevotella (p = 0.038) appeared in greater abundance in meconium of preterm infants with adequate birth weight for GA. Thirty (47.6%) children reached head circumference catch-up before 6 months CA and 33 (52.4%) after 6 months CA. Salmonella (p<0.001), Flavobacterium (p = 0.026), and Burkholderia (p = 0.026) were found to be more abundant in meconium in the group of newborns who achieved catch-up prior to 6th month CA. CONCLUSION Meconium microbiome abundance was related to adequacy of weight for GA. Meconium microbiome differs between children who achieve head circumference catch-up by the 6th month of corrected age or after this period.
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Microbiota composition in bilateral healthy breast tissue and breast tumors. Cancer Causes Control 2020; 31:1027-1038. [PMID: 32844256 DOI: 10.1007/s10552-020-01338-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE Previous reports suggest that a complex microbiome exists within the female human breast that might contribute to breast cancer etiology. The purpose of this pilot study was to assess the variation in microbiota composition by breast side (left versus right) within individual women and compare the microbiota of normal and breast tumor tissue between women. We aimed to determine whether microbiota composition differs between these groups and whether certain bacterial taxa may be associated with breast tumors. METHODS Bilateral normal breast tissue samples (n = 36) were collected from ten women who received routine mammoplasty procedures. Archived breast tumor samples (n = 10) were obtained from a biorepository. DNA was extracted, amplified, and sequenced. Microbiota data were analyzed using QIIME and RStudio. RESULTS The most abundant phyla in both tumor and normal tissues were Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. There were statistically significant differences in the relative abundance of various bacterial taxa between groups. Alpha diversity (Simpson's index) was significantly higher in normal compared to tumor samples (0.968 vs. 0.957, p = 0.022). Based on unweighted UniFrac measures, breast tumor samples clustered distinctly from normal samples (R2 = 0.130; p = 0.01). Microbiota composition in normal samples clustered within women (R2 = 0.394; p = 0.01) and by breast side (left or right) within a woman (R2 = 0.189; p = 0.03). CONCLUSION Significant differences in diversity between tumor and normal tissue and in composition between women and between breasts of the same woman were identified. These results warrant further research to investigate the relationship between microbiota and breast cancer.
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Rabêlo FHS, Borgo L, Merloti LF, Pylro VS, Navarrete AA, Mano RH, Thijs S, Vangronsveld J, Alleoni LRF. Effects of winter and summer conditions on Cd fractionation and bioavailability, bacterial communities and Cd phytoextraction potential of Brachiaria decumbens and Panicum maximum grown in a tropical soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 728:138885. [PMID: 32361355 DOI: 10.1016/j.scitotenv.2020.138885] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 05/04/2023]
Abstract
The interactions between soil properties, microorganisms, plant species and climate affect cadmium (Cd) availability in tropical soils. In this study, we investigated the effects of simulated summer and winter conditions on Cd fractionation and bacterial communities in Oxisols and on growth of two high biomass production-grasses (Brachiaria decumbens and Panicum maximum) that were evaluated for their Cd phytoextraction potential. We also assessed how these interactions could influence the availability of Cd and its possible phytoextraction by these grasses. The Cd fraction bound to carbonates was higher in the winter conditions, while Cd bound to Fe- and Mn oxides was higher in the summer conditions, which resulted in a higher Cd availability in winter compared to summer conditions. B. decumbens and P. maximum took up more Cd when grown in the winter conditions, but their biomasses were not affected by the higher Cd uptake. The occurrence and relative abundance of bacterial taxa in the bare soil differed from the soils cultivated with grasses, where the Gammaproteobacteria predominated. However, no positive correlations were observed between the rhizosphere bacterial community in the cultivated soils and Cd availability, irrespective of the season conditions.
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Affiliation(s)
- Flávio Henrique Silveira Rabêlo
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil; Hasselt University, Centre for Environmental Sciences, Diepenbeek, Belgium.
| | - Lucélia Borgo
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil; Hasselt University, Centre for Environmental Sciences, Diepenbeek, Belgium
| | - Luis Fernando Merloti
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | | | | | - Rodrigo Hideki Mano
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Sofie Thijs
- Hasselt University, Centre for Environmental Sciences, Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Hasselt University, Centre for Environmental Sciences, Diepenbeek, Belgium; Maria Curie-Skłodowska University, Faculty of Biology and Biotechnology, Lublin, Poland
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Microbial patterns in rumen are associated with gain of weight in beef cattle. Antonie Van Leeuwenhoek 2020; 113:1299-1312. [PMID: 32577920 DOI: 10.1007/s10482-020-01440-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Ruminal microorganisms play a pivotal role in cattle nutrition. The discovery of the main microbes or of a microbial community responsible for enhancing the gain of weight in beef cattle might be used in therapeutic approaches to increase animal performance and cause less environmental damages. Here, we examined the differences in bacterial and fungal composition of rumen samples of Braford heifers raised in natural grassland of the Pampa Biome in Brazil. We aimed to detect microbial patterns in the rumen that could be correlated with the gain of weight. We hypothesized that microorganisms important to digestion process are increased in animals with a higher gain of weight. The gain of weight of seventeen healthy animals was monitored for 60 days. Ruminal samples were obtained and the 16S and ITS1 genes were amplified and sequenced to identify the closest microbial relatives within the microbial communities. A predictive model based on microbes responsible for the gain of weight was build and further tested using the entire dataset., The main differential abundant microbes between groups included the bacterial taxa RFN20, Prevotella, Anaeroplasma and RF16 and the fungal taxa Aureobasidium, Cryptococcus, Sarocladium, Pleosporales and Tremellales. The predictive model detected some of these taxa associated with animals with the high gain of weight group, most of them being organisms that have been correlated to the production of substances that improve the ruminal digestion process. These findings provide new insights about cattle nutrition and suggest the use of these microbes to improve beef cattle breeding.
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Dagher DJ, de la Providencia IE, Pitre FE, St-Arnaud M, Hijri M. Arbuscular Mycorrhizal Fungal Assemblages Significantly Shifted upon Bacterial Inoculation in Non-Contaminated and Petroleum-Contaminated Environments. Microorganisms 2020; 8:E602. [PMID: 32326329 PMCID: PMC7232219 DOI: 10.3390/microorganisms8040602] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 11/16/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) have been shown to reduce plant stress and improve their health and growth, making them important components of the plant-root associated microbiome, especially in stressful conditions such as petroleum hydrocarbons (PHs) contaminated environments. Purposely manipulating the root-associated AMF assemblages in order to improve plant health and modulate their interaction with the rhizosphere microbes could lead to increased agricultural crop yields and phytoremediation performance by the host plant and its root-associated microbiota. In this study, we tested whether repeated inoculations with a Proteobacteria consortium influenced plant productivity and the AMF assemblages associated with the root and rhizosphere of four plant species growing either in non-contaminated natural soil or in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was performed in a randomized complete block design in four blocks with two factors: (1) substrate contamination (contaminated or not contaminated), and (2) inoculation (or not) with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over four months, after which the effect of treatments on plant biomass and petroleum hydrocarbon concentrations in the substrate were determined. MiSeq amplicon sequencing, targeting the 18S rRNA gene, was used to assess AMF community structures in the roots and rhizosphere of plants growing in both contaminated and non-contaminated substrates. We also investigated the contribution of plant identity and biotope (plant roots and rhizospheric soil) in shaping the associated AMF assemblages. Our results showed that while inoculation caused a significant shift in AMF communities, the substrate contamination had a much stronger influence on their structure, followed by the biotope and plant identity to a lesser extent. Moreover, inoculation significantly increased plant biomass production and was associated with a decreased petroleum hydrocarbons dissipation in the contaminated soil. The outcome of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with indigenous plants following repeated inoculation of a bacterial consortium. It highlights the dominance of soil chemical properties, such as petroleum hydrocarbon presence, over biotic factors and inputs, such as plant species and microbial inoculations, in determining the plant-associated arbuscular mycorrhizal fungi communities.
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Affiliation(s)
- Dimitri J. Dagher
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal, 4101 Sherbrooke est, Montréal, QC H1X 2B2, Canada; (D.J.D.); (F.E.P.); (M.S.-A.)
| | | | - Frédéric E. Pitre
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal, 4101 Sherbrooke est, Montréal, QC H1X 2B2, Canada; (D.J.D.); (F.E.P.); (M.S.-A.)
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal, 4101 Sherbrooke est, Montréal, QC H1X 2B2, Canada; (D.J.D.); (F.E.P.); (M.S.-A.)
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin botanique de Montréal, 4101 Sherbrooke est, Montréal, QC H1X 2B2, Canada; (D.J.D.); (F.E.P.); (M.S.-A.)
- AgroBioSciences, University Mohammed VI Polytechnic, Lot 660–Hay Moulay Rachid, Ben Guerir 43150, Morocco
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Edge TA, Baird DJ, Bilodeau G, Gagné N, Greer C, Konkin D, Newton G, Séguin A, Beaudette L, Bilkhu S, Bush A, Chen W, Comte J, Condie J, Crevecoeur S, El-Kayssi N, Emilson EJS, Fancy DL, Kandalaft I, Khan IUH, King I, Kreutzweiser D, Lapen D, Lawrence J, Lowe C, Lung O, Martineau C, Meier M, Ogden N, Paré D, Phillips L, Porter TM, Sachs J, Staley Z, Steeves R, Venier L, Veres T, Watson C, Watson S, Macklin J. The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:135906. [PMID: 31926407 DOI: 10.1016/j.scitotenv.2019.135906] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.
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Affiliation(s)
- Thomas A Edge
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Donald J Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.
| | | | - Nellie Gagné
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Charles Greer
- National Research Council Canada, Montreal, Quebec, Canada
| | - David Konkin
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Glen Newton
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | | | - Lee Beaudette
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Satpal Bilkhu
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Alexander Bush
- Environment and Climate Change Canada @ Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Wen Chen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jérôme Comte
- Environment and Climate Change Canada, Burlington, Ontario, Canada; Institut National de la Recherche Scientifique, Québec, Québec, Canada
| | - Janet Condie
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | | | | | - Erik J S Emilson
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Donna-Lee Fancy
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Iyad Kandalaft
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Izhar U H Khan
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Ian King
- Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - David Kreutzweiser
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - David Lapen
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - John Lawrence
- Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Lowe
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Oliver Lung
- Canadian Food Inspection Agency, Winnipeg, Manitoba, Canada
| | | | - Matthew Meier
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Nicholas Ogden
- Public Health Agency of Canada, St. Hyacinthe, Quebec, Canada
| | - David Paré
- Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Lori Phillips
- Agriculture and Agri-Food Canada, Harrow, Ontario, Canada
| | - Teresita M Porter
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada; Biodiversity Institute of Ontario, University of Guelph, Ontario, Canada
| | - Joel Sachs
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Zachery Staley
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Royce Steeves
- Fisheries and Oceans Canada, Moncton, New Brunswick, Canada
| | - Lisa Venier
- Natural Resources Canada, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Teodor Veres
- National Research Council Canada, Ottawa, Ontario, Canada
| | - Cynthia Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Susan Watson
- Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - James Macklin
- Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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Santos LFD, Lana RP, Silva MCSDA, Veloso TGR, Kasuya MCM, Ribeiro KG. Effective microorganisms inoculant: Diversity and effect on the germination of palisade grass seeds. AN ACAD BRAS CIENC 2020; 92:e20180426. [PMID: 32159585 DOI: 10.1590/0001-3765202020180426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 12/28/2018] [Indexed: 11/22/2022] Open
Abstract
Effective microorganisms (EM) are inoculants formed by fungi and bacteria isolated from soil. EM are commonly used by farmers on agronomic crops to stimulate plant growth, but their composition and their benefits has been controverted. This study aimed to analyze the diversity of microorganisms growing in three EM inoculants, as well as to evaluate their efficiency in the germination of palisade grass seeds. The total DNA of the three EM inoculants was extracted, the 16S rRNA and ITS genes were amplified by PCR and sequenced on the Illumina MiSeq platform. Germination tests were conducted with three type of the EM, in three concentration and two times of the immersion. The bacterial group was the most abundant in EM, followed by fungi. Bacterial operational taxonomic units OTUs were shared by all EMs. Pre-treatments of palisade grass seeds with EMs resulted in a higher germination percentage (% G) and germination speed index (IVG) when EM was used at concentration of 1 or 2% in water. Seed immersion for 5 min was more efficient than immersion for 24 h. We can conclude that EM of different origin can share microbial groups and diversity of microorganisms, besides being an alternative to increase palisade grass seeds germination.
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Affiliation(s)
- Lidiane F Dos Santos
- Departamento de Agroecologia, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, 36571-000 Viçosa, MG, Brazil
| | - Rogério P Lana
- Departamento de Zootecnia, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, 36571-000 Viçosa, MG, Brazil
| | - Marliane C S DA Silva
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, 36571-000 Viçosa, MG, Brazil
| | - Tomás G R Veloso
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, 36571-000 Viçosa, MG, Brazil
| | - Maria Catarina M Kasuya
- Departamento de Microbiologia, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, 36571-000 Viçosa, MG, Brazil
| | - Karina G Ribeiro
- Departamento de Zootecnia, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, 36571-000 Viçosa, MG, Brazil
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de Andrade PAM, Giovani PA, Araujo DS, de Souza AJ, Pedroni-Pereira A, Kantovitz KR, Andreote FD, Castelo PM, Nociti-Jr FH. Shifts in the bacterial community of saliva give insights on the relationship between obesity and oral microbiota in adolescents. Arch Microbiol 2020; 202:1085-1095. [PMID: 32034425 DOI: 10.1007/s00203-020-01817-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/19/2020] [Accepted: 01/22/2020] [Indexed: 02/06/2023]
Abstract
The current study aimed at the determination of the impact of obesity on the salivary microbiome in adolescents. Sixty subjects ranging 14-17 years old were enrolled (obese: n = 30-50% females, and normal weight: n = 30-50% females). Stimulated saliva was collected for denaturing gradient gel electrophoresis (DGGE) band patterns and massive 16S rRNA gene sequencing using the Ion Torrent platform. Overall, data analysis revealed that male subjects harbored a higher diverse salivary microbiome, defined by a significant higher richness (32.48 versus 26.74) and diversity (3.36 versus 3.20), higher Simpson values (0.96 versus 0.95) and distinct bacterial community structure considering either sex or condition (p < 0.05). Bacterial community fingerprinting analysis in human saliva showed a positive correlation with increased body mass index (BMI) in adolescents. Veillonella, Haemophilus and Prevotella occurrence was found to be affected by BMI, whereas Neisseria and Rothia occurrence was significantly impacted by sex in obese subjects. Our findings suggest that male and female adolescents may harbor a naturally distinct salivary microbiota and that obesity may specifically have an impact on their oral bacterial community. The potential dysbiotic oral microbiome in obese adolescents raises new insights on the etiology and prevention of future conditions in these populations.
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Affiliation(s)
- Pedro Avelino Maia de Andrade
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo (Esalq-USP), Piracicaba, São Paulo, Brazil. .,Department of Genetics, College of Agriculture "Luiz de Queiroz", University of São Paulo (Esalq-USP), Piracicaba, São Paulo, Brazil.
| | - Priscila Alves Giovani
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Darlle Santos Araujo
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Adijailton José de Souza
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo (Esalq-USP), Piracicaba, São Paulo, Brazil
| | - Aline Pedroni-Pereira
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Kamila Rosamilia Kantovitz
- Department of Pediatric Dentistry, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil.,Department of Dental Materials, São Leopoldo Mandic Research Center, Campinas, São Paulo, Brazil
| | - Fernando Dini Andreote
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo (Esalq-USP), Piracicaba, São Paulo, Brazil
| | - Paula Midori Castelo
- Department of Biological Sciences, Federal University of São Paulo, São Paulo, Brazil
| | - Francisco Humberto Nociti-Jr
- Division of Periodontics, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, São Paulo, Brazil
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da Silva LL, Veloso TGR, Manhães JHC, da Silva CC, de Queiroz MV. The plant organs and rhizosphere determine the common bean mycobiome. Braz J Microbiol 2020; 51:765-772. [PMID: 31898247 DOI: 10.1007/s42770-019-00217-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
The plant microbiota diversity is often underestimated when approaches developed mainly for the identification of cultivable microorganisms are used. High-throughput sequencing allows a deeper understanding of the microbial diversity associated with plants. The amplification of ITS1 was used to analyze fungal diversity in several plant organs and rhizosphere of three common bean (Phaseolus vulgaris) varieties grown in a greenhouse. The fungal diversity diverged between those plant organs and the rhizosphere, with the highest found in the rhizosphere and the lowest in the stem. In each organ different numbers of genus, OTUs were identified, in a total of 283 OTUs evenly distributed among the varieties. In the co-occurrence network, a larger number of positive interactions were found in the organs of the aerial part in all varieties. We observed that the diversity of the endophytic microbiota differed more between plant organs than between common bean varieties. Our results show that the diversity of endophytic fungi can be efficiently accessed with the sequencing of ITS amplicons and that this diversity may vary among distinct plant organs and the rhizosphere of a single plant variety.
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Affiliation(s)
- Leandro L da Silva
- Departamento de Microbiologia/ Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tomás G R Veloso
- Departamento de Microbiologia/ Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Jonathan H C Manhães
- Departamento de Microbiologia/ Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Cynthia C da Silva
- Departamento de Microbiologia/ Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marisa V de Queiroz
- Departamento de Microbiologia/ Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Ceccon DM, Faoro H, Lana PDC, Souza EMD, Pedrosa FDO. Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 694:133609. [PMID: 31400683 DOI: 10.1016/j.scitotenv.2019.133609] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/18/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.
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Affiliation(s)
- Denny Marcel Ceccon
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Paulo da Cunha Lana
- Center for Marine Studies, Universidade Federal do Paraná, Pontal do Paraná, Brazil
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Botina LL, Vélez M, Barbosa WF, Mendonça AC, Pylro VS, Tótola MR, Martins GF. Behavior and gut bacteria of Partamona helleri under sublethal exposure to a bioinsecticide and a leaf fertilizer. CHEMOSPHERE 2019; 234:187-195. [PMID: 31212205 DOI: 10.1016/j.chemosphere.2019.06.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
The exposure of bees to agrochemicals during foraging and feeding has been associated with their population decline. Sublethal exposure to agrochemicals can affect behavior and the microbiota. Gut microbiota is associated with insect nutritional health, immunocompetence, and is essential for neutralizing the damage caused by pathogens and xenobiotics. Research on the effect of the bioinsecticides and fertilizers on the microbiota of bees remains neglected. In this study, we assessed the sublethal effect of both bioinsecticide spinosad and the fertilizer copper sulfate (CuSO4) on the behavior and gut microbiota in forager adults of the stingless bee Partamona helleri (Friese), which is an important pollinator in the Neotropical region. Behavioral assays and gut microbiota profiles were assessed on bees orally exposed to estimated LC5 values for spinosad and CuSO4. The microbiota were characterized through 16S rRNA gene target sequencing. Acute and oral sublethal exposure to spinosad and CuSO4 did not affect the overall activity, flight take-off, and food consumption. However, CuSO4 decreased bee respiration rate and copper accumulated in exposed bees. Exposure to spinosad increased the proportional abundance of the genus Gilliamella, but CuSO4 did not alter the composition of the gut microbiota. In conclusion, sublethal exposure to CuSO4 induces changes in respiration, and spinosad changes the abundance of gut microorganisms of P. helleri.
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Affiliation(s)
- L L Botina
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - M Vélez
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil; Facultad de Ciencias Agrarias, Universidad Técnica Estatal de Quevedo, Quevedo-Los Ríos, 120508, Ecuador
| | - W F Barbosa
- Departamento de Entomologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - A C Mendonça
- Departmento de Ciência de Solos, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - V S Pylro
- Departamento de Biologia, Universidade Federal de Lavras - UFLA, Lavras, MG 37200-000, Brazil
| | - M R Tótola
- Departmento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - G F Martins
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
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Tagliamonte MS, Waugh SG, Prosperi M, Mai V. An Integrated Approach for Efficient Multi-Omics Joint Analysis. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019; 2019:619-625. [PMID: 31588431 DOI: 10.1145/3307339.3343476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The challenges associated with multi-omics analysis, e.g. DNA-seq, RNA-seq, metabolomics, methylomics and microbiomics domains, include: (1) increased high-dimensionality, as all -omics domains include ten thousands to hundreds of thousands of variables each; (2) increased complexity in analyzing domain-domain interactions, quadratic for pairwise correlation, and exponential for higher-order interactions; (3) variable heterogeneity, with highly skewed distributions in different units and scales for methylation and microbiome. Here, we developed an efficient strategy for joint-domain analysis, applying it to an analysis of correlations between colon epithelium methylomics and fecal microbiomics data with colorectal cancer risk as estimated by colorectal polyp prevalence. First, we applied domain-specific standard pipelines for quality assessment, cleaning, batch-effect removal, et cetera. Second, we performed variable homogenization for both the methylation and microbiome data sets, using domain-specific normalization and dimension reduction, obtaining scale-free variables that could be compared across the two domains. Finally, we implemented a joint-domain network analysis to identify relevant microbial-methylation island patterns. The network analysis considered all possible species-island pairs, thus being quadratic in its complexity. However, we were able to pre-select the unpaired variables by performing a preliminary association analysis on the outcome polyp prevalence. All results from association and interaction analyses were adjusted for multiple comparisons. Although the limited sample size did not provide good power (80% to detect medium to large effect sizes with 5% alpha error), a number of potentially significant association (dozens in the uncorrected analysis, reducing to just a few in the corrected one) were identified As a last step, we linked the network patterns identified by our approach to the KEGG functional ontology, showing that the method can generate new mechanistic hypotheses for the biological causes of polyp development.
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Affiliation(s)
| | - Sheldon G Waugh
- Army Public Health Center, Aberdeen Proving Ground, Aberdeen, MD, USA
| | - Mattia Prosperi
- Department of Epidemiology University of Florida Gainesville, FL, USA
| | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida
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Dagher DJ, de la Providencia IE, Pitre FE, St-Arnaud M, Hijri M. Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments. Front Microbiol 2019; 10:2144. [PMID: 31572347 PMCID: PMC6753587 DOI: 10.3389/fmicb.2019.02144] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 08/30/2019] [Indexed: 01/21/2023] Open
Abstract
Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.
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Affiliation(s)
- Dimitri J. Dagher
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
| | | | - Frédéric E. Pitre
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
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Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation. Sci Rep 2019; 9:11731. [PMID: 31409826 PMCID: PMC6692397 DOI: 10.1038/s41598-019-47921-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/20/2019] [Indexed: 01/07/2023] Open
Abstract
Metataxonomic approach was used to describe the bacterial community from a creosote-contaminated aquifer and to access the potential for in situ bioremediation of the polycyclic aromatic hydrocarbons (PAHs) by biostimulation. In general, the wells with higher PAH contamination had lower richness and diversity than others, using the Shannon and Simpson indices. By the principal coordinate analysis (PCoA) it was possible to observe the clustering of the bacterial community of most wells in response of the presence of PAH contamination. The significance analysis using edgeR package of the R program showed variation in the abundance of some Operational Taxonomic Units (OTUs) of contaminated wells compared to uncontaminated ones. Taxons enriched in the contaminated wells were correlated positively (p < 0.05) with the hydrocarbons, according to redundancy analysis (RDA). All these enriched taxa have been characterized as PAH degrading agents, such as the genus Comamonas, Geobacter, Hydrocarboniphaga, Anaerolinea and Desulfomonile. Additionally, it was possible to predict, with the PICRUSt program, a greater proportion of pathways and genes related to the degradation of PAHs in the wells with higher contamination levels. We conclude that the contaminants promoted the enrichment of several groups of degrading bacteria in the area, which strengthens the feasibility of applying biostimulation as an aquifer remediation strategy.
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Perez‐Lamarque B, Morlon H. Characterizing symbiont inheritance during host–microbiota evolution: Application to the great apes gut microbiota. Mol Ecol Resour 2019; 19:1659-1671. [DOI: 10.1111/1755-0998.13063] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Benoît Perez‐Lamarque
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM PSL University Paris France
- Muséum national d'Histoire naturelleUMR 7205 CNRS‐MNHN‐UPMC‐EPHE “Institut de Systématique, Evolution, Biodiversité – ISYEB” Herbier National 16 rue Buffon Paris France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM PSL University Paris France
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Gouveia JG, Silva ALDS, Santos ECLD, Martins ES, López AMQ. OPTIMIZATION OF BIOFLOCCULANT PRODUCTION BY Bacillus spp. FROM SUGARCANE CROP SOIL OR FROM SLUDGE OF THE AGROINDUSTRIAL EFFLUENT. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2019. [DOI: 10.1590/0104-6632.20190362s20180360] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bacterial communities associated with anthracnose symptomatic and asymptomatic leaves of guarana, an endogenous tropical crop, and their pathogen antagonistic effects. Arch Microbiol 2019; 201:1061-1073. [PMID: 31123792 DOI: 10.1007/s00203-019-01677-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 04/22/2019] [Accepted: 05/11/2019] [Indexed: 10/26/2022]
Abstract
Plants are colonized by diverse microorganisms that can substantially impact their health and growth. Understanding bacterial diversity and the relationships between bacteria and phytopathogens may be key to finding effective biocontrol agents. We evaluated the bacterial community associated with anthracnose symptomatic and asymptomatic leaves of guarana, a typical tropical crop. Bacterial communities were assessed through culture-independent techniques based on extensive 16S rRNA sequencing, and cultured bacterial strains were evaluated for their ability to inhibit the growth of Colletotrichum sp. as well as for enzyme and siderophore production. The culture-independent method revealed that Proteobacteria was the most abundant phylum, but many sequences were unclassified. The emergence of anthracnose disease did not significantly affect the bacterial community, but the abundance of the genera Acinetobacter, Pseudomonas and Klebsiella were significantly higher in the symptomatic leaves. In vitro growth of Colletotrichum sp. was inhibited by 11.38% of the cultured bacterial strains, and bacteria with the highest inhibition rates were isolated from symptomatic leaves, while asymptomatic leaves hosted significantly more bacteria that produced amylase and polygalacturonase. The bacterial isolate Bacillus sp. EpD2-5 demonstrated the highest inhibition rate against Colletotrichum sp., whereas the isolates EpD2-12 and FD5-12 from the same genus also had high inhibition rates. These isolates were also able to produce several hydrolytic enzymes and siderophores, indicating that they may be good candidates for the biocontrol of anthracnose. Our work demonstrated the importance of using a polyphasic approach to study microbial communities from plant diseases, and future work should focus on elucidating the roles of culture-independent bacterial communities in guarana anthracnose disease.
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Casero MC, Velázquez D, Medina-Cobo M, Quesada A, Cirés S. Unmasking the identity of toxigenic cyanobacteria driving a multi-toxin bloom by high-throughput sequencing of cyanotoxins genes and 16S rRNA metabarcoding. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 665:367-378. [PMID: 30772567 DOI: 10.1016/j.scitotenv.2019.02.083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Cyanobacterial harmful algal blooms (CyanoHABs) are complex communities that include coexisting toxic and non-toxic strains only distinguishable by genetic methods. This study shows a water-management oriented use of next generation sequencing (NGS) to specifically pinpoint toxigenic cyanobacteria within a bloom simultaneously containing three of the most widespread cyanotoxins (the hepatotoxins microcystins, MCs; and the neurotoxins anatoxin-a, ATX, and saxitoxins, STXs). The 2013 summer bloom in Rosarito reservoir (Spain) comprised 33 cyanobacterial OTUs based on 16S rRNA metabarcoding, 7 of which accounted for as much as 96.6% of the community. Cyanotoxins and their respective biosynthesis genes were concurrently present throughout the entire bloom event including: MCs and mcyE gene; ATX and anaF gene; and STXs and sxtI gene. NGS applied to amplicons of cyanotoxin-biosynthesis genes unveiled 6 toxigenic OTUs, comprising 3 involved in MCs production (Planktothrix agardhii and 2 Microcystis spp.), 2 in ATX production (Cuspidothrix issatschenkoi and Phormidium/Tychonema spp.) and 1 in STXs production (Aphanizomenon gracile). These toxigenic taxa were also present in 16S rRNA OTUs list and their relative abundance was positively correlated with the respective toxin concentrations. Our results point at MC-producing P. agardhii and ATX-producing C. issatschenkoi as the main contributors to the moderate toxin concentrations observed, and suggest that their distribution in Southern Europe is broader than previously thought. Our findings also stress the need for monitoring low-abundance cyanobacteria (<1% relative abundance) in cyanotoxicity studies, and provide novel data on the presence of picocyanobacteria and potentially ATX-producing benthic taxa (e.g., Phormidium) in deep thermally-stratified water bodies. This study showcases a straightforward use of amplicon metagenomics of cyanotoxin biosynthesis genes in a multi-toxin bloom thus illustrating the broad applicability of NGS for water management in risk-oriented monitoring of CyanoHABs.
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Affiliation(s)
- María Cristina Casero
- Departamento de Biología, C/Darwin, 2, Universidad Autónoma de Madrid, ES-28049 Madrid, Spain
| | - David Velázquez
- Departamento de Biología, C/Darwin, 2, Universidad Autónoma de Madrid, ES-28049 Madrid, Spain
| | - Miguel Medina-Cobo
- Centro de Estudios Hidrográficos, Paseo Bajo de la Virgen del Puerto, 3, CEDEX, ES-28005 Madrid, Spain
| | - Antonio Quesada
- Departamento de Biología, C/Darwin, 2, Universidad Autónoma de Madrid, ES-28049 Madrid, Spain
| | - Samuel Cirés
- Departamento de Biología, C/Darwin, 2, Universidad Autónoma de Madrid, ES-28049 Madrid, Spain.
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Sanitá Lima M, Coutinho de Lucas R, Lima N, Polizeli MDLTDM, Santos C. Fungal Community Ecology Using MALDI-TOF MS Demands Curated Mass Spectral Databases. Front Microbiol 2019; 10:315. [PMID: 30873137 PMCID: PMC6401475 DOI: 10.3389/fmicb.2019.00315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Matheus Sanitá Lima
- Department of Biology, University of Western Ontario, London, ON, Canada.,Biology Department, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Rosymar Coutinho de Lucas
- Biology Department, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Nelson Lima
- CEB - Biological Engineering Centre, University of Minho, Braga, Portugal
| | | | - Cledir Santos
- Department of Chemical Science and Natural Resources, BIOREN-UFRO, Universidad de La Frontera, Temuco, Chile
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Mateus-Barros E, Meneghine AK, Bagatini IL, Fernandes CC, Kishi LT, Vieira AAH, Sarmento H. Comparison of two DNA extraction methods widely used in aquatic microbial ecology. J Microbiol Methods 2019; 159:12-17. [PMID: 30738110 DOI: 10.1016/j.mimet.2019.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 11/20/2022]
Abstract
In recent years, the rapid advances of culture-independent methods and new molecular tools have revolutionized our understanding of microbial biodiversity and ecological functions. DNA extraction from microbial communities is a critical step in this process and several methods have been proposed and used, but the influence of the extraction method on the outcome and ultimately on ecological inferences from the results is not yet precisely determined. Here, we compared two of the most commonly used extraction methods in aquatic microbial ecology, and investigated whether the two methods yielded comparable results for community ecology analyses. We extracted DNA from 15 different shallow lakes with phenol:chloroform, a classical and widely used extraction method, and with the PowerSoil DNA isolation Kit, often suggested as the standard DNA extraction method, with some adaptations for aquatic environments. We found that although only 5% of all OTUs showed significant differences in pairwise comparisons (using the 15 lakes as replicates), these OTUs accounted for >35% (on average) of the relative abundance. Diversity and richness did not differ significantly between the two extraction methods, but the beta-dispersion of the communities indicated that the organic extraction yielded more homogeneous communities, while the kit extraction generated variability. Consequently, we conclude that despite the small number of OTUs with significant differences, their impact on the community composition obtained was not negligible, and therefore the results from these two extraction methods were not comparable.
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Affiliation(s)
- Erick Mateus-Barros
- Universidade Federal de São Carlos (UFSCar), Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, São Carlos, SP 13565-905, Brazil; Post Graduate Program in Ecology and Natural Resources (PPGERN), UFSCar, São Carlos, SP 13565-905, Brazil
| | - Aylan K Meneghine
- Universidade Federal de São Carlos (UFSCar), Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, São Carlos, SP 13565-905, Brazil
| | | | - Camila C Fernandes
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Plantas - LBMP, Jaboticabal, SP 14884-900, Brazil; UNESP, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica - LMSeq, Jaboticabal, SP 14884-900, Brazil
| | - Luciano T Kishi
- Universidade Estadual Paulista (UNESP), Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Plantas - LBMP, Jaboticabal, SP 14884-900, Brazil; UNESP, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica - LMSeq, Jaboticabal, SP 14884-900, Brazil
| | - Armando A H Vieira
- UFSCar, Department of Botany, Laboratory of Phycology, São Carlos, SP 13565-905, Brazil
| | - Hugo Sarmento
- Universidade Federal de São Carlos (UFSCar), Department of Hydrobiology, Laboratory of Microbial Processes and Biodiversity, São Carlos, SP 13565-905, Brazil.
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Ortiz-Vera MP, Olchanheski LR, da Silva EG, de Lima FR, Martinez LRDPR, Sato MIZ, Jaffé R, Alves R, Ichiwaki S, Padilla G, Araújo WL. Influence of water quality on diversity and composition of fungal communities in a tropical river. Sci Rep 2018; 8:14799. [PMID: 30287878 PMCID: PMC6172213 DOI: 10.1038/s41598-018-33162-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/21/2018] [Indexed: 11/09/2022] Open
Abstract
Freshwater fungi are key decomposers of organic material and play important roles in nutrient cycling, bio-remediation and ecosystem functioning. Although aquatic fungal communities respond to pollution, few studies have quantitatively assessed the effect of freshwater contamination on fungal diversity and composition; and knowledge is scarcer for tropical systems. Here we help fill this knowledge gap by studying a heavily-contaminated South American river spanning a biodiversity hotspot. We collected 30 water samples scattered across a quality gradient over two seasons and analyzed them using Terminal Restriction Fragment Length Polymorphisms (T-RFLP) coupled with 454 Pyrosequencing. Using T-RFLP we identified 451 and 442 Operational Taxonomy Units (OTUs) in the dry and rainy seasons respectively, whereas Pyrosequencing revealed 48,553 OTUs from which 11% were shared between seasons. Although 68% of all identified OTUs and 51% of all identified phyla remained unidentified, dominant fungal phyla included the Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, Zygomycota and Neocallimastigomycota, while Calcarisporiella, Didymosphaeria, Mycosphaerella (Ascomycota) and Rhodotorula (Basidiomycota) were the most abundant genera. Fungal diversity was affected by pH and dissolved iron, while community composition was influenced by dissolved oxygen, pH, nitrate, biological oxygen demand, total aluminum, total organic carbon, total iron and seasonality. The presence of potentially pathogenic species was associated with high pH. Furthermore, geographic distance was positively associated with community dissimilarity, suggesting that local conditions allowed divergence among fungal communities. Overall, our findings raise potential concerns for human health and the functioning of tropical river ecosystems and they call for improved water sanitation systems.
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Affiliation(s)
- Mabel Patricia Ortiz-Vera
- NAP-BIOP, LABMEM, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1374, Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, Brazil
| | - Luiz Ricardo Olchanheski
- NAP-BIOP, LABMEM, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1374, Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, Brazil
| | - Eliane Gonçalves da Silva
- NAP-BIOP, LABMEM, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1374, Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, Brazil
| | - Felipe Rezende de Lima
- NAP-BIOP, LABMEM, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1374, Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, Brazil
| | - Lina Rocío Del Pilar Rada Martinez
- NAP-BIOP, LABMEM, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1374, Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, Brazil
| | - Maria Inês Zanoli Sato
- Department of Environmental Analysis, Environmental Company of São Paulo State (CETESB), Av. Prof. Frederico Hermann Jr., 345, São Paulo, SP, Brazil
| | - Rodolfo Jaffé
- Instituto Tecnológico Vale - Desenvolvimento Sustentável. Rua Boaventura da Silva, 955, Nazaré, 66055-090, Belém, PA, Brazil
| | - Ronnie Alves
- Instituto Tecnológico Vale - Desenvolvimento Sustentável. Rua Boaventura da Silva, 955, Nazaré, 66055-090, Belém, PA, Brazil
| | - Simone Ichiwaki
- NAP-BIOP, LABMEM, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1374, Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, Brazil
| | - Gabriel Padilla
- NAP-BIOP, LABMEM, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1374, Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, Brazil
| | - Welington Luiz Araújo
- NAP-BIOP, LABMEM, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1374, Ed. Biomédicas II, Cidade Universitária, São Paulo, SP, Brazil.
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44
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Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado. Commun Biol 2018; 1:135. [PMID: 30272014 PMCID: PMC6127325 DOI: 10.1038/s42003-018-0129-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/06/2018] [Indexed: 01/13/2023] Open
Abstract
Biodiversity underlies ecosystem functioning. While aboveground biodiversity is often well studied, the belowground microbiome, in particular protists, remains largely unknown. Indeed, holistic insights into soil microbiome structures in natural soils, especially in hyperdiverse biomes such as the Brazilian Cerrado, remain unexplored. Here, we study the soil microbiome across four major vegetation zones of the Cerrado, ranging from grass-dominated to tree-dominated vegetation with a focus on protists. We show that protist taxon richness increases towards the tree-dominated climax vegetation. Early successional habitats consisting of primary grass vegetation host most potential plant pathogens and least animal parasites. Using network analyses combining protist with prokaryotic and fungal sequences, we show that microbiome complexity increases towards climax vegetation. Together, this suggests that protists are key microbiome components and that vegetation succession towards climax vegetation is stimulated by higher loads of animal and plant pathogens. At the same time, an increase in microbiome complexity towards climax vegetation might enhance system stability. Araujo et al. investigate the soil microbiome across four major vegetation zones of the Brazilian Cerrado and find that protist taxon richness increases towards the tree-dominated climax vegetation. Their findings suggest that increased microbiome complexity might enhance system stability towards climax vegetation.
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45
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Tonato D, Marcuz C, Vendruscolo RG, Bevilacqua C, Jacques RJS, Wagner R, Kuhn RC, Mazutti MA. PRODUCTION OF POLYUNSATURATED FATTY ACIDS BY MICROORGANISMS ISOLATED IN THE BRAZILIAN PAMPA BIOME. BRAZILIAN JOURNAL OF CHEMICAL ENGINEERING 2018. [DOI: 10.1590/0104-6632.20180353s20170155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Morais D, Roesch LFW, Redmile-Gordon M, Santos FG, Baldrian P, Andreote FD, Pylro VS. BTW-Bioinformatics Through Windows: an easy-to-install package to analyze marker gene data. PeerJ 2018; 6:e5299. [PMID: 30083449 PMCID: PMC6074753 DOI: 10.7717/peerj.5299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/03/2018] [Indexed: 11/20/2022] Open
Abstract
Recent advances in Next-Generation Sequencing (NGS) make comparative analyses of the composition and diversity of whole microbial communities possible at a far greater depth than ever before. This brings new challenges, such as an increased dependence on computation to process these huge datasets. The demand on system resources usually requires migrating from Windows to Linux-based operating systems and prior familiarity with command-line interfaces. To overcome this barrier, we developed a fully automated and easy-to-install package as well as a complete, easy-to-follow pipeline for microbial metataxonomic analysis operating in the Windows Subsystem for Linux (WSL)-Bioinformatics Through Windows (BTW). BTW combines several open-access tools for processing marker gene data, including 16S rRNA, bringing the user from raw sequencing reads to diversity-related conclusions. It includes data quality filtering, clustering, taxonomic assignment and further statistical analyses, directly in WSL, avoiding the prior need of migrating from Windows to Linux. BTW is expected to boost the use of NGS amplicon data by facilitating rapid access to a set of bioinformatics tools for Windows users. Moreover, several Linux command line tools became more reachable, which will enhance bioinformatics accessibility to a wider range of researchers and practitioners in the life sciences and medicine. BTW is available in GitHub (https://github.com/vpylro/BTW). The package is freely available for noncommercial users.
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Affiliation(s)
- Daniel Morais
- Institute of Microbiology of the CAS, Prague, Czech Republic
| | - Luiz F W Roesch
- Centro para Pesquisa Interdisciplinar em Biotecnologia, Universidade Federal do Pampa, São Gabriel, Rio Grande do Sul, Brazil
| | | | - Fausto G Santos
- Biosystems Informatics and Genomics, Instituto René Rachou, Belo Horizonte, Brazil
| | - Petr Baldrian
- Institute of Microbiology of the CAS, Prague, Czech Republic
| | - Fernando D Andreote
- Soil Department, "Luiz de Queiroz" College of Agriculture - ESALQ/USP, Piracicaba, São Paulo, Brazil
| | - Victor S Pylro
- Soil Department, "Luiz de Queiroz" College of Agriculture - ESALQ/USP, Piracicaba, São Paulo, Brazil.,Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
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47
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Chou MY, Vanden Heuvel J, Bell TH, Panke-Buisse K, Kao-Kniffin J. Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts. Sci Rep 2018; 8:11039. [PMID: 30038291 PMCID: PMC6056419 DOI: 10.1038/s41598-018-29346-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 07/03/2018] [Indexed: 12/02/2022] Open
Abstract
The microbiome of a vineyard may play a critical role in fruit development, and consequently, may impact quality properties of grape and wine. Vineyard management approaches that have directly manipulated the microbiome of grape clusters have been studied, but little is known about how vineyard management practices that impact the soil microbial pool can influence this dynamic. We examined three under-vine soil management practices: 1) herbicide application, 2) soil cultivation (vegetation removal), and 3) natural vegetation (no vegetation removal) in a Riesling vineyard in New York over a three-year period. The microbiomes associated with soil and grapes were profiled using high-throughput sequencing of the bacterial 16 S rRNA gene and fungal ITS regions. Our results showed that soil bacterial composition under natural vegetation differs from that seen in glyphosate-maintained bare soil. Soil fungal composition under the natural vegetation treatment was distinct from other treatments. Although our study revealed soil microbiome shifts based on under-vine management, there were no corresponding changes in fruit-associated microbial composition. These results suggested that other vineyard management practices or environmental factors are more influential in shaping the grape-associated microbiome.
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Affiliation(s)
- Ming-Yi Chou
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA.,New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Justine Vanden Heuvel
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA.,New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Kevin Panke-Buisse
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Madison, WI, 53706, USA
| | - Jenny Kao-Kniffin
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA.
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48
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de Lima LA, Diniz RHS, de Queiroz MV, Fietto LG, da Silveira WB. Screening of Yeasts Isolated from Brazilian Environments for the 2-Phenylethanol (2-PE) Production. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0119-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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49
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Gomes ACSM, Santos SRD, Ribeiro MC, Cravo PVL, Vieira JDG, Souza KMCDE, Amaral AC. Is there still room to explore cyclodextrin glycosyltransferase-producers in Brazilian biodiversity? AN ACAD BRAS CIENC 2018; 90:1473-1480. [PMID: 29898106 DOI: 10.1590/0001-3765201820170670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/30/2017] [Indexed: 11/22/2022] Open
Abstract
In the present work, different Brazilian biomes aiming to identify and select cyclodextrin glycosyltransferase-producer bacteria are explored. This enzyme is responsible for converting starch to cyclodextrin, which are interesting molecules to carry other substances of economic interest applied by textile, pharmaceutical, food, and other industries. Based on the enzymatic index, 12 bacteria were selected and evaluated, considering their capacity to produce the enzyme in culture media containing different starch sources. It was observed that the highest yields were presented by the bacteria when grown in cornstarch. These bacteria were also characterized by sequencing of the 16S rRNA region and were classified as Bacillus, Paenibacillus, Gracilibacillus and Solibacillus.
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Affiliation(s)
- Andrea C S M Gomes
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Rua 235, s/n, Setor Universitário, 74605-050 Goiânia, GO, Brazil
| | - Samuel R Dos Santos
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Rua 235, s/n, Setor Universitário, 74605-050 Goiânia, GO, Brazil.,Instituto de Ciências Biomédicas II, Universidade de São Paulo, Av. Prof. Lineu Prestes, 1374, 05508-900 Butantã, SP, Brazil
| | - Maycon C Ribeiro
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Rua 235, s/n, Setor Universitário, 74605-050 Goiânia, GO, Brazil
| | - Pedro V L Cravo
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - José Daniel G Vieira
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Rua 235, s/n, Setor Universitário, 74605-050 Goiânia, GO, Brazil
| | - Keili M C DE Souza
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Rua 235, s/n, Setor Universitário, 74605-050 Goiânia, GO, Brazil
| | - Andre C Amaral
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Rua 235, s/n, Setor Universitário, 74605-050 Goiânia, GO, Brazil
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50
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Lay CY, Bell TH, Hamel C, Harker KN, Mohr R, Greer CW, Yergeau É, St-Arnaud M. Canola Root-Associated Microbiomes in the Canadian Prairies. Front Microbiol 2018; 9:1188. [PMID: 29937756 PMCID: PMC6002653 DOI: 10.3389/fmicb.2018.01188] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/16/2018] [Indexed: 01/16/2023] Open
Abstract
Canola is one of the most economically important crops in Canada, and the root and rhizosphere microbiomes of a canola plant likely impact its growth and nutrient uptake. The aim of this study was to determine whether canola has a core root microbiome (i.e., set of microbes that are consistently selected in the root environment), and whether this is distinct from the core microbiomes of other crops that are commonly grown in the Canadian Prairies, pea, and wheat. We also assessed whether selected agronomic treatments can modify the canola microbiome, and whether this was associated to enhanced yield. We used a field experiment with a randomized complete block design, which was repeated at three locations across the canola-growing zone of Canada. Roots and rhizosphere soil were harvested at the flowering stage of canola. We separately isolated total extractable DNA from plant roots and from adjacent rhizosphere soil, and constructed MiSeq amplicon libraries for each of 60 samples, targeting bacterial, and archaeal 16S rRNA genes and the fungal ITS region. We determined that the microbiome of the roots and rhizosphere of canola was consistently different from those of wheat and pea. These microbiomes comprise several putative plant-growth-promoting rhizobacteria, including Amycolatopsis sp., Serratia proteamaculans, Pedobacter sp., Arthrobacter sp., Stenotrophomonas sp., Fusarium merismoides, and Fusicolla sp., which correlated positively with canola yield. Crop species had a significant influence on bacterial and fungal assemblages, especially within the roots, while higher nutrient input or seeding density did not significantly alter the global composition of bacterial, fungal, or archaeal assemblages associated with canola roots. However, the relative abundance of Olpidium brassicae, a known pathogen of members of the Brassicaceae, was significantly reduced in the roots of canola planted at higher seeding density. Our results suggest that seeding density and plant nutrition management modified the abundance of other bacterial and fungal taxa forming the core microbiomes of canola that are expected to impact crop growth. This work helps us to understand the microbial assemblages associated with canola grown under common agronomic practices and indicates microorganisms that can potentially benefit or reduce the yield of canola.
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Affiliation(s)
- Chih-Ying Lay
- Biodiversity Centre, Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
| | - Terrence H Bell
- Biodiversity Centre, Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada.,Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA, United States
| | - Chantal Hamel
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - K Neil Harker
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Ramona Mohr
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Charles W Greer
- Energy, Mining and Environment, National Research Council Canada, Montreal, QC, Canada
| | - Étienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, Montreal, QC, Canada.,Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Laval, QC, Canada
| | - Marc St-Arnaud
- Biodiversity Centre, Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
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