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Santos A, Gómez-Espinoza O, Núñez-Montero K, Zárate A, Andreote FD, Pylro VS, Bravo L, Barrientos L. Measuring the effect of climate change in Antarctic microbial communities: toward novel experimental approaches. Curr Opin Biotechnol 2023; 81:102918. [PMID: 36972633 DOI: 10.1016/j.copbio.2023.102918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/05/2023] [Accepted: 02/17/2023] [Indexed: 03/29/2023]
Abstract
The Antarctic continent is undergoing a rapid warming, affecting microbial communities throughout its ecosystems. This continent is a natural laboratory for studying the effect of climate change, however, assessing the microbial communities' responses to environmental changes is challenging from a methodological point of view. We suggest novel experimental designs, including multivariable assessments that apply multiomics methods in combination with continuous environmental data recording and new warming simulation systems. Moreover, we propose that climate change studies in Antarctica should consider three main objectives, including descriptive studies, short-term temporary adaptation studies, and long-term adaptive evolution studies. This will help us to understand and manage the effects of climate change on the Earth.
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Affiliation(s)
- Andrés Santos
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Olman Gómez-Espinoza
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Kattia Núñez-Montero
- Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica
| | - Ana Zárate
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Victor S Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | - León Bravo
- Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Leticia Barrientos
- Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco 4811230, Chile.
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Bizuti DTG, Robin A, Soares TM, Moreno¹ VS, Almeida DRA, Andreote FD, Casagrande JC, Guillemot J, Herrmann L, Melis J, Perim JEL, Medeiros SDS, Sorrini TB, Brancalion PHS. Multifunctional soil recovery during the restoration of Brazil's Atlantic Forest after bauxite mining. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Denise T. G. Bizuti
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Agnès Robin
- CIRADUMR Eco&Sols Piracicaba Brazil
- Eco&SolsUniversité de MontpellierCIRADINRAIRD Montpellier SupAgro, Montpellier France
- Department of Soil Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Thaís M. Soares
- Center for Nuclear Energy in Agriculture University of São Paulo Piracicaba Brazil
| | | | - Danilo R. A. Almeida
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Fernando D. Andreote
- Department of Soil Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - José Carlos Casagrande
- Department of Natural Resources and Environmental Protection Federal University of São Carlos Araras Brazil
| | - Joannès Guillemot
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
- CIRADUMR Eco&Sols Piracicaba Brazil
- Eco&SolsUniversité de MontpellierCIRADINRAIRD Montpellier SupAgro, Montpellier France
| | - Laetitia Herrmann
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT‐Asia)Common Microbial Biotechnology Platform (CMBP) Hanoi Vietnam
| | - Juliano Melis
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Júlia E. L. Perim
- Department of Soil Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Simone D. S. Medeiros
- Department of Informatics and Statistics Federal University of Santa Catarina Florianópolis Brazil
| | - Taísi B. Sorrini
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
| | - Pedro H. S. Brancalion
- Department of Forest Sciences, “Luiz de Queiroz” College of Agriculture University of São Paulo Piracicaba Brazil
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Florido FG, Regitano JB, Andrade PAM, Andreote FD, Brancalion PHS. A comprehensive experimental assessment of glyphosate ecological impacts in riparian forest restoration. Ecol Appl 2022; 32:e02472. [PMID: 34652865 DOI: 10.1002/eap.2472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/15/2021] [Accepted: 06/04/2021] [Indexed: 06/13/2023]
Abstract
Competition with invasive grasses is one of the most important drivers of tree planting failures, especially in tropical forests. A widely disseminated weeding approach has been glyphosate spraying, the most used herbicide globally in forestry and ecosystem restoration. However, glyphosate use in restoration is highly controversial and requires further studies to elucidate its effects on restoration processes and the environment. We evaluated the use of glyphosate in riparian forest restoration and its impacts on tree planting costs, weed control efficiency, planted seedling performance, herbaceous and woody species regeneration, soil bacteria, and environmental contamination, using mowing treatments as a reference and based on a controlled experiment established in the Brazilian Atlantic Forest. Glyphosate spraying reduced by one-half and one-third the accumulated aboveground biomass of, respectively, weeds in general and of the invasive grass Urochloa decumbens compared to mowing treatments, and it reduced the cost by half. The performance of planted tree seedlings was markedly favored by glyphosate spraying compared to mowing treatments, as expressed by improved seedling height (~twice higher), crown area (~5× higher), and basal area (~5× higher); the regeneration of both native woody and ruderal herbaceous plants were also enhanced. Neither glyphosate nor its metabolite Aminomethylphosphonic acid (AMPA) residues were detected in either water runoff or soil samples, but they were found at relatively high concentrations in the runoff sediments (from 1.32 to 24.75 mg/kg for glyphosate and from 1.75 to 76.13 mg/kg for AMPA). Soil bacteria communities differed before and after glyphosate spraying in comparison to mowing plots (without glyphosate). Glyphosate spraying was far more cost effective than mowing for controlling U. decumbens and greatly improved the performance of planted tree seedlings and natural regeneration, while not leaving residues in soil and water. However, the changes in the structure of bacterial communities and high concentration of glyphosate and AMPA residues in runoff sediments highlight the need for caution when using this herbicide in riparian buffers. We present alternatives for reducing glyphosate use and minimizing its risks in tree planting initiatives.
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Affiliation(s)
- Flávia G Florido
- Department of Forest Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Pádua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Jussara B Regitano
- Department of Soil Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Pádua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Pedro A M Andrade
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Pádua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Fernando D Andreote
- Department of Soil Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Pádua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
| | - Pedro H S Brancalion
- Department of Forest Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Avenida Pádua Dias, 11, Piracicaba, Sao Paulo, 13418-900, Brazil
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Barbosa-Ribeiro M, Arruda-Vasconcelos R, Louzada LM, Dos Santos DG, Andreote FD, Gomes BPFA. Microbiological analysis of endodontically treated teeth with apical periodontitis before and after endodontic retreatment. Clin Oral Investig 2020; 25:2017-2027. [PMID: 32860137 DOI: 10.1007/s00784-020-03510-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/06/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To characterize the microbiota of teeth with endodontic treatment failure by 16S ribosomal RNA genetic sequencing (GS) and PCR at the different phases of the endodontic retreatment and to associate the presence of specific bacteria with clinical and radiographic features in teeth with apical periodontitis. MATERIALS AND METHODS Twenty infected root canals of single-rooted teeth were selected. Samples were collected with sterile paper points before chemo-mechanical preparation (CMP) (S1), after CMP (S2) and after 30 days of intracanal medication (ICM) (S3). Microbial identification was performed using GS and PCR. Tukey-Kramer post hoc test and post hoc ANOVA were used for intergroup analysis. Paired t test and repeated-measures ANOVA were applied for intragroup analysis, at a significance level of 5%. RESULTS A total of 89 strains were identified using GS. Sixty-five strains were recovered in S1 and 15 strains in S2, and 9 strains remained in S3. Enterococcus faecalis was the most predominant bacteria. Gram-positive cocci bacteria predominated. Gram-negative species were also detected. Using species-specific PCR primers to detect seven species, the most prevalent ones at all the phases of the endodontic retreatment were E. faecalis and Porphyromonas gingivalis. However, Parvimonas micra and P. gingivalis were associated with previous pain, P. gingivalis was associated with tenderness to percussion and E. faecalis, Fusobacterium nucleatum and P. gingivalis were associated with periapical lesion > 3 mm. CONCLUSIONS In conclusion, the microbiota of persistent infection is polymicrobial with predominance of E. faecalis and P. gingivalis in all phases of the endodontic retreatment, regardless of the method used for microbial identification. Associations were found between specific bacteria and clinical/radiographic features. CLINICAL RELEVANCE The characterization of the bacteria present at all phases of the endodontic retreatment is important for the monitoring of the effectiveness of the techniques used and to better understand the susceptibility of these species to the disinfection agent used during the procedures.
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Affiliation(s)
- Marlos Barbosa-Ribeiro
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas (UNICAMP), Av. Limeira 901, Bairro Areao, Piracicaba, São Paulo, Brazil.,Department of Endodontics School of Dentistry , University Center UniRuy- Wyden , BA, Salvador, Brazil
| | - Rodrigo Arruda-Vasconcelos
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas (UNICAMP), Av. Limeira 901, Bairro Areao, Piracicaba, São Paulo, Brazil
| | - Lidiane M Louzada
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas (UNICAMP), Av. Limeira 901, Bairro Areao, Piracicaba, São Paulo, Brazil
| | - Danielle G Dos Santos
- Department of Soil Science, Luiz de Queiroz College of Agriculture, University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Fernando D Andreote
- Department of Soil Science, Luiz de Queiroz College of Agriculture, University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Brenda P F A Gomes
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas (UNICAMP), Av. Limeira 901, Bairro Areao, Piracicaba, São Paulo, Brazil.
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Rigotto A, Cotta SR, Dias ACF, Carvalho JLN, Andreote FD. Shifting abundances of communities associated with nitrogen cycling in soils promoted by sugarcane harvest systems. Lett Appl Microbiol 2020; 71:444-450. [PMID: 32395843 DOI: 10.1111/lam.13314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 11/26/2022]
Abstract
Sugarcane cultivation supports Brazil as one of the largest world sugar and ethanol producer. In order to understand the impact of changing sugarcane harvest from manual to mechanized harvest, we studied the effect of machinery traffic on soil and consequently soil compaction upon soil microbial communities involved in nitrogen cycling. The impact of sugarcane harvest was dependent on soil depth and texture. At deeper soil layers, mechanized harvesting increases the abundance of nitrogen fixers and denitrifying communities (specifically nosZ clade I and II) while manual harvesting increases the abundance of ammonia oxidizers (specifically AOA) and increases denitrifying communities (nosZ clade I and II) on top and at intermediate depth. The effect of change on the harvest system is more evident on sandy soil than on clay soil, where soil indicators of compaction (bulk density and penetration resistance) were negatively correlated with soil microorganisms associated with the nitrogen cycle. Our results point to connections between soil compaction and N transformations in sugarcane fields, besides naming biological variables to be used as proxies for alterations in soil structure.
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Affiliation(s)
- A Rigotto
- Department of Soil Science, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, SP, Brazil
| | - S R Cotta
- Department of Soil Science, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, SP, Brazil.,Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - A C F Dias
- Department of Soil Science, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, SP, Brazil
| | - J L N Carvalho
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - F D Andreote
- Department of Soil Science, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba, SP, Brazil
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Núñez-Montero K, Quezada-Solís D, Khalil ZG, Capon RJ, Andreote FD, Barrientos L. Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds. Biomolecules 2020; 10:E673. [PMID: 32349314 PMCID: PMC7277857 DOI: 10.3390/biom10050673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new "-omics" comparative approaches for drug discovery.
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Affiliation(s)
- Kattia Núñez-Montero
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
- Biotechnology Investigation Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago 159-7050, Costa Rica
| | - Damián Quezada-Solís
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
| | - Zeinab G. Khalil
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Fernando D. Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil;
| | - Leticia Barrientos
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
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Lopes LD, Weisberg AJ, Davis EW, Varize CDS, Pereira e Silva MDC, Chang JH, Loper JE, Andreote FD. Genomic and metabolic differences between Pseudomonas putida populations inhabiting sugarcane rhizosphere or bulk soil. PLoS One 2019; 14:e0223269. [PMID: 31581220 PMCID: PMC6776310 DOI: 10.1371/journal.pone.0223269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 09/17/2019] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas putida is one of 13 major groups of Pseudomonas spp. and contains numerous species occupying diverse niches and performing many functions such as plant growth promotion and bioremediation. Here we compared a set of 19 P. putida isolates obtained from sugarcane rhizosphere or bulk soil using a population genomics approach aiming to assess genomic and metabolic differences between populations from these habitats. Phylogenomics placed rhizosphere versus bulk soil strains in separate clades clustering with different type strains of the P. putida group. Multivariate analyses indicated that the rhizosphere and bulk soil isolates form distinct populations. Comparative genomics identified several genetic functions (GO-terms) significantly different between populations, including some exclusively present in the rhizosphere or bulk soil strains, such as D-galactonic acid catabolism and cellulose biosynthesis, respectively. The metabolic profiles of rhizosphere and bulk soil populations analyzed by Biolog Ecoplates also differ significantly, most notably by the higher oxidation of D-galactonic/D-galacturonic acid by the rhizosphere population. Accordingly, D-galactonate catabolism operon (dgo) was present in all rhizosphere isolates and absent in the bulk soil population. This study showed that sugarcane rhizosphere and bulk soil harbor different populations of P. putida and identified genes and functions potentially associated with their soil niches.
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Affiliation(s)
- Lucas Dantas Lopes
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
- * E-mail: (LDL); (FDA)
| | - Alexandra J. Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Edward W. Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Camila de S. Varize
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Michele de C. Pereira e Silva
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Joyce E. Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States of America
| | - Fernando D. Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- * E-mail: (LDL); (FDA)
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9
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Lopes LD, Pereira E Silva MDC, Weisberg AJ, Davis EW, Yan Q, Varize CDS, Wu CF, Chang JH, Loper JE, Andreote FD. Genome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population. Environ Microbiol 2018; 20:4401-4414. [PMID: 30033663 DOI: 10.1111/1462-2920.14363] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 11/28/2022]
Abstract
Bulk soil and rhizosphere are soil compartments selecting different microbial communities. However, it is unknown whether this selection also can change the genome content of specific bacterial taxa, splitting a population in distinct ecotypes. To answer this question we compared the genome sequences of 53 isolates obtained from sugarcane rhizosphere (28) and bulk soil (25). These isolates were previously classified in the Pseudomonas koreensis subgroup of the P. fluorescens complex. Phylogenomics showed a trend of separation between bulk soil and rhizosphere isolates. Discriminant analysis of principal components (DAPC) identified differences in the accessory genome of rhizosphere and bulk soil sub-populations. We found significant changes in gene frequencies distinguishing rhizosphere from bulk soil ecotypes, for example, enrichment of phosphatases and xylose utilization (xut) genes, respectively. Phenotypic assays and deletion of xutA gene indicated that accumulation of xut genes in the bulk soil sub-population provided a higher growth capacity in a d-xylose medium, supporting the corresponding genomic differences. Despite the clear differences distinguishing the two ecotypes, all 53 isolates were classified in a single 16S rRNA gene OTU. Collectively, our results revealed that the gene pool and ecological behavior of a bacterial population can be different for ecotypes living in neighbouring soil habitats.
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Affiliation(s)
- Lucas Dantas Lopes
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Michele de C Pereira E Silva
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, 97331, USA
| | - Qing Yan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Camila de S Varize
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Chih-Feng Wu
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, 97331, USA
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR, 97331, USA
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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10
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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: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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11
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Withers PJA, Rodrigues M, Soltangheisi A, de Carvalho TS, Guilherme LRG, Benites VDM, Gatiboni LC, de Sousa DMG, Nunes RDS, Rosolem CA, Andreote FD, Oliveira AD, Coutinho ELM, Pavinato PS. Transitions to sustainable management of phosphorus in Brazilian agriculture. Sci Rep 2018; 8:2537. [PMID: 29416090 PMCID: PMC5803245 DOI: 10.1038/s41598-018-20887-z] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/21/2018] [Indexed: 11/13/2022] Open
Abstract
Brazil's large land base is important for global food security but its high dependency on inorganic phosphorus (P) fertilizer for crop production (2.2 Tg rising up to 4.6 Tg in 2050) is not a sustainable use of a critical and price-volatile resource. A new strategic analysis of current and future P demand/supply concluded that the nation's secondary P resources which are produced annually (e.g. livestock manures, sugarcane processing residues) could potentially provide up to 20% of crop P demand by 2050 with further investment in P recovery technologies. However, the much larger legacy stores of secondary P in the soil (30 Tg in 2016 worth over $40 billion and rising to 105 Tg by 2050) could provide a more important buffer against future P scarcity or sudden P price fluctuations, and enable a transition to more sustainable P input strategies that could reduce current annual P surpluses by 65%. In the longer-term, farming systems in Brazil should be redesigned to operate profitably but more sustainably under lower soil P fertility thresholds.
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Affiliation(s)
- Paul J A Withers
- School of Environment, Natural Resources and Geography, Bangor University, Thoday Building, LL57 2UW, Bangor, UK.
| | - Marcos Rodrigues
- School of Environment, Natural Resources and Geography, Bangor University, Thoday Building, LL57 2UW, Bangor, UK
- College of Agriculture 'Luiz de Queiroz', University of São Paulo - ESALQ-USP. Av. Pádua Dias, 11. CEP, 13418-900, Piracicaba, SP, Brazil
| | - Amin Soltangheisi
- College of Agriculture 'Luiz de Queiroz', University of São Paulo - ESALQ-USP. Av. Pádua Dias, 11. CEP, 13418-900, Piracicaba, SP, Brazil
| | - Teotonio S de Carvalho
- Federal University of Lavras - UFLA. Campus Universitário, PO Box 3037, CEP 37200-000, Lavras, MG, Brazil
| | - Luiz R G Guilherme
- Federal University of Lavras - UFLA. Campus Universitário, PO Box 3037, CEP 37200-000, Lavras, MG, Brazil
| | - Vinicius de M Benites
- Brazilian Agricultural Research Corporation, Embrapa Soils. Rua Jardim Botânico, 1024, CEP 22460-000, Rio de Janeiro, RJ, Brazil
| | - Luciano C Gatiboni
- Santa Catarina State University - UDESC. Av. Luís de Camões, 2090, CEP 88520-000, Lages, SC, Brazil
| | - Djalma M G de Sousa
- Brazilian Agricultural Research Corporation, Embrapa Cerrados. BR 020, Km 18 Planaltina. PO Box 08223, CEP 73310-970, Brasília, DF, Brazil
| | - Rafael de S Nunes
- Brazilian Agricultural Research Corporation, Embrapa Cerrados. BR 020, Km 18 Planaltina. PO Box 08223, CEP 73310-970, Brasília, DF, Brazil
| | - Ciro A Rosolem
- São Paulo State University, FCA/UNESP. Rua José Barbosa de Barros, 1780, CEP 186010-307, Botucatu, SP, Brazil
| | - Fernando D Andreote
- College of Agriculture 'Luiz de Queiroz', University of São Paulo - ESALQ-USP. Av. Pádua Dias, 11. CEP, 13418-900, Piracicaba, SP, Brazil
| | - Adilson de Oliveira
- Brazilian Agricultural Research Corporation, Embrapa Soybean, PO Box 231, CEP 86001-970, Londrina, PR, Brazil
| | - Edson L M Coutinho
- São Paulo State University, FCAV/UNESP. Via de acesso prof. Paulo Donato Castellane, s/n. km 5, CEP 14884-900, Jaboticabal, SP, Brazil
| | - Paulo S Pavinato
- College of Agriculture 'Luiz de Queiroz', University of São Paulo - ESALQ-USP. Av. Pádua Dias, 11. CEP, 13418-900, Piracicaba, SP, Brazil
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12
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Lopes LD, Davis EW, Pereira E Silva MDC, Weisberg AJ, Bresciani L, Chang JH, Loper JE, Andreote FD. Tropical soils are a reservoir for fluorescent Pseudomonas spp. biodiversity. Environ Microbiol 2017; 20:62-74. [PMID: 29027341 DOI: 10.1111/1462-2920.13957] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/07/2017] [Accepted: 10/08/2017] [Indexed: 11/30/2022]
Abstract
Fluorescent Pseudomonas spp. are widely studied for their beneficial activities to plants. To explore the genetic diversity of Pseudomonas spp. in tropical regions, we collected 76 isolates from a Brazilian soil. Genomes were sequenced and compared to known strains, mostly collected from temperate regions. Phylogenetic analyses classified the isolates in the P. fluorescens (57) and P. putida (19) groups. Among the isolates in the P. fluorescens group, most (37) were classified in the P. koreensis subgroup and two in the P. jessenii subgroup. The remaining 18 isolates fell into two phylogenetic subclades distinct from currently recognized P. fluorescens subgroups, and probably represent new subgroups. Consistent with their phylogenetic distance from described subgroups, the genome sequences of strains in these subclades are asyntenous to the genome sequences of members of their neighbour subgroups. The tropical isolates have several functional genes also present in known fluorescent Pseudomonas spp. strains. However, members of the new subclades share exclusive genes not detected in other subgroups, pointing to the potential for novel functions. Additionally, we identified 12 potential new species among the 76 isolates from the tropical soil. The unexplored diversity found in the tropical soil is possibly related to biogeographical patterns.
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Affiliation(s)
- Lucas Dantas Lopes
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
| | - Michele de C Pereira E Silva
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Luana Bresciani
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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13
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Pylro VS, Mui TS, Rodrigues JL, Andreote FD, Roesch LF. A Step Forward to Empower Global Microbiome Research Through Local Leadership. Trends Microbiol 2016; 24:767-771. [DOI: 10.1016/j.tim.2016.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/12/2016] [Accepted: 07/25/2016] [Indexed: 11/30/2022]
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14
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Lopes LD, Pereira E Silva MDC, Andreote FD. Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization. Front Microbiol 2016; 7:1341. [PMID: 27610108 PMCID: PMC4997060 DOI: 10.3389/fmicb.2016.01341] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/15/2016] [Indexed: 11/13/2022] Open
Abstract
The rhizosphere harbors one of the most complex, diverse, and active plant-associated microbial communities. This community can be recruited by the plant host to either supply it with nutrients or to help in the survival under stressful conditions. Although selection for the rhizosphere community is evident, the specific bacterial traits that make them able to colonize this environment are still poorly understood. Thus, here we used a combination of community level physiological profile (CLPP) analysis and 16S rRNA gene quantification and sequencing (coupled with in silico analysis and metagenome prediction), to get insights on bacterial features and processes involved in rhizosphere colonization of sugarcane. CLPP revealed a higher metabolic activity in the rhizosphere compared to bulk soil, and suggested that D-galacturonic acid plays a role in bacterial selection by the plant roots (supported by results of metagenome prediction). Quantification of the 16S rRNA gene confirmed the higher abundance of bacteria in the rhizosphere. Sequence analysis showed that of the 252 classified families sampled, 24 were significantly more abundant in the bulk soil and 29 were more abundant in the rhizosphere. Furthermore, metagenomes predicted from the 16S rRNA gene sequences revealed a significant higher abundance of predicted genes associated with biofilm formation and with horizontal gene transfer (HGT) processes. In sum, this study identified major bacterial groups and their potential abilities to occupy the sugarcane rhizosphere, and indicated that polygalacturonase activity and HGT events may be important features for rhizosphere colonization.
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Affiliation(s)
- Lucas D Lopes
- Soil Microbiology Lab, Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo Piracicaba, Brazil
| | - Michele de Cássia Pereira E Silva
- Soil Microbiology Lab, Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo Piracicaba, Brazil
| | - Fernando D Andreote
- Soil Microbiology Lab, 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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Rigonato J, Kent AD, Alvarenga DO, Andreote FD, Beirigo RM, Vidal-Torrado P, Fiore MF. Drivers of cyanobacterial diversity and community composition in mangrove soils in south-east Brazil. Environ Microbiol 2012; 15:1103-14. [DOI: 10.1111/j.1462-2920.2012.02830.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Miqueletto PB, Andreote FD, Dias ACF, Ferreira JC, dos Santos Neto EV, de Oliveira VM. Cultivation-independent methods applied to the microbial prospection of oil and gas in soil from a sedimentary basin in Brazil. AMB Express 2011; 1:35. [PMID: 22018208 PMCID: PMC3282667 DOI: 10.1186/2191-0855-1-35] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 10/22/2011] [Indexed: 11/10/2022] Open
Abstract
The upper parts of oil field structures may leak gas which is supposed to be indirectly detected by the soil bacterial populations. Such microorganisms are capable of consuming this gas, supporting the Microbial Prospection of Oil and Gas (MPOG) methodology. The goal of the present work was to characterize microbial communities involved in short-chain alkane metabolism, namely methane, ethane and propane, in samples from a petroliferous (P) soil through clone libraries of the 16S rRNA gene of the Domains Bacteria and Archaea and the catabolic gene coding for the soluble di-iron monooxygenase (SDIMO) enzyme alpha subunit. The microbial community presented high abundance of the bacterial phylum Actinobacteria, which represented 53% of total clones, and the Crenarchaeota group I.1b from the Archaea Domain. The analysis of the catabolic genes revealed the occurrence of seven Operational Protein Families (OPF) and higher richness (Chao = 7; Ace = 7.5) and diversity (Shannon = 1.09) in P soil when compared with a non-petroliferous (Np) soil (Chao = 2; Ace = 0, Shannon = 0.44). Clones related to the ethene monooxygenase (EtnC) and methane monooxygenase (MmoX) coding genes occurred only in P soil, which also presented higher levels of methane and lower levels of ethane and propane, revealed by short-chain hydrocarbon measures. Real-time PCR results suggested that the SDIMO genes occur in very low abundance in the soil samples under study. Further investigations on SDIMOs genes in natural environments are necessary to unravel their still uncharted diversity and to provide reliable tools for the prospection of degrading populations.
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Affiliation(s)
- Paula B Miqueletto
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, CP 6171, CEP 13081-970, Campinas, SP, Brazil
- Biomedical Sciences Institute (ICB-IV), University of São Paulo, São Paulo, Brazil
| | - Fernando D Andreote
- Departament of Soil Sciences, ESALQ, University of São Paulo, CP 09, CEP: 13418-900, Piracicaba, SP, Brazil
| | - Armando CF Dias
- Departament of Soil Sciences, ESALQ, University of São Paulo, CP 09, CEP: 13418-900, Piracicaba, SP, Brazil
| | - Justo C Ferreira
- PETROBRAS R&D Center, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21949-900, Brazil
| | - Eugênio V dos Santos Neto
- PETROBRAS R&D Center, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, RJ, CEP 21949-900, Brazil
| | - Valéria M de Oliveira
- Division of Microbial Resources, Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, CP 6171, CEP 13081-970, Campinas, SP, Brazil
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17
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Rossetto PB, Dourado MN, Quecine MC, Andreote FD, Araújo WL, Azevedo JL, Pizzirani-Kleiner AA. Specific plant induced biofilm formation in Methylobacterium species. Braz J Microbiol 2011; 42:878-83. [PMID: 24031703 PMCID: PMC3768801 DOI: 10.1590/s1517-83822011000300006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 09/27/2010] [Accepted: 03/14/2011] [Indexed: 05/27/2023] Open
Abstract
Two endophytic strains of Methylobacterium spp. were used to evaluate biofilm formation on sugarcane roots and on inert wooden sticks. Results show that biofilm formation is variable and that plant surface and possibly root exudates have a role in Methylobacterium spp. host recognition, biofilm formation and successful colonization as endophytes.
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Affiliation(s)
- Priscilla B Rossetto
- Laboratório de Biotecnologia Vegetal, Centro de Energia Nuclear na Agricultura Universidade de São Paulo , Piracicaba, SP, Brasil
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18
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Carneiro-Leão MP, Andreote FD, Araújo WL, Oliveira NT. Differential expression of genes involved in entomopathogenicity of the fungi Metarhizium anisopliae var. anisopliae and M. anisopliae var. acridum (Clavicipitaceae). Genet Mol Res 2011; 10:769-78. [PMID: 21563071 DOI: 10.4238/vol10-2gmr1094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Expression analysis of the genes involved in germination, conidiogenisis and pathogenesis of Metarhizium anisopliae during its saprophytic and pathogenic life stages can help plan strategies to increase its efficacy as a biological control agent. We quantified relative expression levels of the nitrogen response regulator gene (nrr1) and a G-protein regulator of genes involved in conidiogenesis (cag8), using an RT-qPCR assay. Comparisons were made between M. anisopliae var. anisopliae and M. anisopliae var. acridum during germination and conidiogenesis and at different stages of pathogenesis. The cag8 gene was repressed during germination and induced during conidial development and the pathogenic phase, and the nrr1 gene was induced during germination, conidiogenesis and the pathogenic phase. Both genes were more expressed in M. anisopliae var. anisopliae, demonstrating that different varieties of M. anisopliae differ in activation of genes linked to virulence for certain environments and hosts. This suggests that differences among these varieties in the ability to adapt could be attributed not only to specific genomic regions and genes, but also to differential gene expression in this fungus, modulating its ability to respond to environmental stimuli.
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Affiliation(s)
- M P Carneiro-Leão
- Departamento de Micologia, Universidade Federal de Pernambuco, Recife, PE, Brasil.
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19
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Dias ACF, Andreote FD, Rigonato J, Fiore MF, Melo IS, Araújo WL. The bacterial diversity in a Brazilian non-disturbed mangrove sediment. Antonie Van Leeuwenhoek 2010; 98:541-51. [PMID: 20563848 DOI: 10.1007/s10482-010-9471-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 06/08/2010] [Indexed: 11/25/2022]
Abstract
The bacterial diversity present in sediments of a well-preserved mangrove in Ilha do Cardoso, located in the extreme south of São Paulo State coastline, Brazil, was assessed using culture-independent molecular approaches (denaturing gradient gel electrophoresis (DGGE) and analysis of 166 sequences from a clone library). The data revealed a bacterial community dominated by Alphaproteobacteria (40.36% of clones), Gammaproteobacteria (19.28% of clones) and Acidobacteria (27.71% of clones), while minor components of the assemblage were affiliated to Betaproteobacteria, Deltaproteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. The clustering and redundancy analysis (RDA) based on DGGE were used to determine factors that modulate the diversity of bacterial communities in mangroves, such as depth, seasonal fluctuations, and locations over a transect area from the sea to the land. Profiles of specific DGGE gels showed that both dominant ('universal' Bacteria and Alphaproteobacteria) and low-density bacterial communities (Betaproteobacteria and Actinobacteria) are responsive to shifts in environmental factors. The location within the mangrove was determinant for all fractions of the community studied, whereas season was significant for Bacteria, Alphaproteobacteria, and Betaproteobacteria and sample depth determined the diversity of Alphaproteobacteria and Actinobacteria.
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Affiliation(s)
- Armando C F Dias
- Center of Biotechnological Researches, ICB-IV, University of São Paulo, Brazil
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20
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Silva CC, Vieiro AF, Dias ACF, Andreote FD, Jesus EC, Paula SOD, Torres APR, Santiago VMJ, Oliveira VM. Monitoring the Bacterial Community Dynamics in a Petroleum Refinery Wastewater Membrane Bioreactor Fed with a High Phenolic Load. J Microbiol Biotechnol 2010. [DOI: 10.4014/jmb.0906.06001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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21
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Silva CC, Viero AF, Dias ACF, Andreote FD, Jesus EC, De Paula SO, Torres APR, Santiago VMJ, Oliveira VM. Monitoring the bacterial community dynamics in a petroleum refinery wastewater membrane bioreactor fed with a high phenolic load. J Microbiol Biotechnol 2010; 20:21-29. [PMID: 20134229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.
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Affiliation(s)
- Cynthia C Silva
- Division of Microbial Resources, Campinas University - UNICAMP CP 6171, Campinas, SP, Brazil.
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22
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Abreu-Tarazi MF, Navarrete AA, Andreote FD, Almeida CV, Tsai SM, Almeida M. Endophytic bacteria in long-term in vitro cultivated “axenic” pineapple microplants revealed by PCR–DGGE. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0191-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Dias ACF, Costa FEC, Andreote FD, Lacava PT, Teixeira MA, Assumpção LC, Araújo WL, Azevedo JL, Melo IS. Isolation of micropropagated strawberry endophytic bacteria and assessment of their potential for plant growth promotion. World J Microbiol Biotechnol 2008. [DOI: 10.1007/s11274-008-9878-0] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Andreote FD, Rossetto PB, Souza LCA, Marcon J, Maccheroni W, Azevedo JL, Araújo WL. Endophytic population ofPantoea agglomeransin citrus plants and development of a cloning vector for endophytes. J Basic Microbiol 2008; 48:338-46. [DOI: 10.1002/jobm.200700341] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Andreote FD, Mendes R, Dini-Andreote F, Rossetto PB, Labate CA, Pizzirani-Kleiner AA, van Elsas JD, Azevedo JL, Araújo WL. Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development. Antonie Van Leeuwenhoek 2008; 93:415-24. [PMID: 18181027 DOI: 10.1007/s10482-007-9219-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 12/28/2007] [Indexed: 10/22/2022]
Abstract
The rhizosphere constitutes a complex niche that may be exploited by a wide variety of bacteria. Bacterium-plant interactions in this niche can be influenced by factors such as the expression of heterologous genes in the plant. The objective of this work was to describe the bacterial communities associated with the rhizosphere and rhizoplane regions of tobacco plants, and to compare communities from transgenic tobacco lines (CAB1, CAB2 and TRP) with those found in wild-type (WT) plants. Samples were collected at two stages of plant development, the vegetative and flowering stages (1 and 3 months after germination). The diversity of the culturable microbial community was assessed by isolation and further characterization of isolates by amplified ribosomal RNA gene restriction analysis (ARDRA) and 16S rRNA sequencing. These analyses revealed the presence of fairly common rhizosphere organisms with the main groups Alphaproteobacteria, Betaproteobacteria, Actinobacteria and Bacilli. Analysis of the total bacterial communities using PCR-DGGE (denaturing gradient gel electrophoresis) revealed that shifts in bacterial communities occurred during early plant development, but the reestablishment of original community structure was observed over time. The effects were smaller in rhizosphere than in rhizoplane samples, where selection of specific bacterial groups by the different plant lines was demonstrated. Clustering patterns and principal components analysis (PCA) were used to distinguish the plant lines according to the fingerprint of their associated bacterial communities. Bands differentially detected in plant lines were found to be affiliated with the genera Pantoea, Bacillus and Burkholderia in WT, CAB and TRP plants, respectively. The data revealed that, although rhizosphere/rhizoplane microbial communities can be affected by the cultivation of transgenic plants, soil resilience may be able to restore the original bacterial diversity after one cycle of plant cultivation.
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Affiliation(s)
- Fernando D Andreote
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, São Paulo, Brazil.
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Andreote FD, Lacava PT, Gai CS, Araújo WL, Maccheroni W, van Overbeek LS, van Elsas JD, Azevedo JL. Model plants for studying the interaction between Methylobacterium mesophilicum and Xylella fastidiosa. Can J Microbiol 2006; 52:419-26. [PMID: 16699566 DOI: 10.1139/w05-142] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Over the last few years, endophytic bacterial communities associated with citrus have been studied as key components interacting with Xylella fastidiosa. In this study, we investigated the possible interaction between the citrus endophyte Methylobacterium mesophilicum SR1.6/6 and X. fastidiosa in model plants such as Catharanthus roseus (Madagaskar periwinkle) and Nicotiana clevelandii (Clevelands tobacco). The aim of this study was to establish the fate of M. mesophilicum SR1.6/6 after inoculation of C. roseus and N. clevelandii plants, using PCR-DGGE (polymerase chain reaction--denaturing gradient gel electrophoresis) and plating techniques. Shifts in the indigenous endophytic bacterial communities were observed in plants inoculated with strain SR1.6/6, using specific primers targeting alpha- and beta-Proteobacteria. Cells of strain SR1.6/6 were observed in a biofilm structure on the root and hypocotyl surfaces of in vitro seedlings inoculated with M. mesophilicum SR1.6/6. This emphasizes the importance of these tissues as main points of entrance for this organism. The results showed that C. roseus and N. clevelandii could be used as model plants to study the interaction between M. mesophilicum and X. fastidiosa.
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Affiliation(s)
- Fernando D Andreote
- Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, ESALQ/USP, Piracicaba, Brazil
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Lima AOS, Quecine MC, Fungaro MHP, Andreote FD, Maccheroni W, Araújo WL, Silva-Filho MC, Pizzirani-Kleiner AA, Azevedo JL. Molecular characterization of a β-1,4-endoglucanase from an endophytic Bacillus pumilus strain. Appl Microbiol Biotechnol 2004; 68:57-65. [PMID: 15538558 DOI: 10.1007/s00253-004-1740-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2004] [Revised: 08/14/2004] [Accepted: 08/31/2004] [Indexed: 10/26/2022]
Abstract
Endophytes comprise mainly microorganisms that colonize inner plant tissues, often living with the host in a symbiotic manner. Several ecological roles have been assigned to endophytic fungi and bacteria, such as antibiosis to phytopathogenic agents and plant growth promotion. Nowadays, endophytes are viewed as a new source of genes, proteins and biochemical compounds that may be used to improve industrial processes. In this study, the gene EglA was cloned from a citrus endophytic Bacillus strain. The EglA encodes a beta-1,4-endoglucanase capable of hydrolyzing cellulose under in vitro conditions. The predicted protein, EglA, has high homology to other bacterial cellulases and shows a modular structure containing a catalytic domain of the glycosyl hydrolase family 9 (GH9) and a cellulose-binding module type 3 (CBM3). The enzyme was expressed in Escherichia coli, purified to homogeneity, and characterized. EglA has an optimum pH range of 5-8, and remarkable heat stability, retaining more than 85% activity even after a 24-h incubation at pH 6-8.6. This characteristic is an important feature for further applications of this enzyme in biotechnological processes in which temperatures of 50-60 degrees C are required over long incubation periods.
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Affiliation(s)
- André O S Lima
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias 11, Piracicaba, SP, 13418-900, Brazil.
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