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de Sousa LP, Mondego JMC. Leaf surface microbiota transplantation confers resistance to the coffee leaf rust in susceptible Coffea arabica. FEMS Microbiol Ecol 2024:fiae049. [PMID: 38599638 DOI: 10.1093/femsec/fiae049] [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] [Indexed: 04/12/2024] Open
Abstract
Coffee leaf rust, caused by the fungus Hemileia vastatrix, became a major concern for coffee-producing countries. Additionally, there is an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers to use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora, Torula and bacteria such as Chryseobacterium, Sphingobium and especially Enterobacter and have their populations increased and may be related to the antagonism seen against H. vastatrix. Interestingly, relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplant, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust as well as help to optimize the development of biocontrol agents.
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Affiliation(s)
- Leandro Pio de Sousa
- Centro de Pesquisa e Desenvolvimento de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas, São Paulo, Brazil
| | - Jorge Maurício Costa Mondego
- Centro de Pesquisa e Desenvolvimento de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas, São Paulo, Brazil
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de Sousa LP, Filho OG, Mondego JMC. Age-Related Rhizosphere Analysis of Coffea arabica Plants. Curr Microbiol 2023; 80:130. [PMID: 36890285 DOI: 10.1007/s00284-023-03236-w] [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: 09/29/2022] [Accepted: 02/20/2023] [Indexed: 03/10/2023]
Abstract
The analysis of large-scale sequence data has revealed that plants over time recruit certain microbes that are efficient colonizers of the rhizosphere. This enrichment phenomenon is especially seen in annual crops, but we suggest that there could have been some type of enrichment in perennial crops such as coffee plants. To verify this hypothesis, we performed a metagenomic and chemical analysis in rhizosphere with three different plant ages (young, mature, and old) and cultivated on the same farm. We verified that from mature to old plants, there was a decrease in diversity, particularly Fusarium and Plenodomus, while there was an increase in Aspergillus, Cladosporium, Metarhizium, and Pseudomonas. We also detected that the abundance of anti-microbials and ACC-deaminase grows as plants age, although denitrification and carbon fixation had reduced abundances. In summary, we detected an enrichment in the microbial community, especially in the great increase in the participation of Pseudomonas, passing from 50% of the relative abundance as the plants get older. Such enrichment can occur through the dynamics of nutrients such as magnesium and boron.
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Affiliation(s)
- Leandro Pio de Sousa
- Centro de Pesquisa E Desenvolvimento de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas, São Paulo, Brazil.
| | | | - Jorge Maurício Costa Mondego
- Centro de Pesquisa E Desenvolvimento de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas, São Paulo, Brazil
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de Sousa LP, Cipriano MAP, da Silva MJ, Patrício FRA, Freitas SDS, Carazzolle MF, Mondego JMC. Functional genomics analysis of a phyllospheric Pseudomonas spp with potential for biological control against coffee rust. BMC Microbiol 2022; 22:222. [PMID: 36131235 PMCID: PMC9494895 DOI: 10.1186/s12866-022-02637-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/13/2022] [Indexed: 11/14/2022] Open
Abstract
Background Pseudomonas spp. promotes plant growth and colonizes a wide range of environments. During the annotation of a Coffea arabica ESTs database, we detected a considerable number of contaminant Pseudomonas sequences, specially associated with leaves. The genome of a Pseudomonas isolated from coffee leaves was sequenced to investigate in silico information that could offer insights about bacterial adaptation to coffee phyllosphere. In parallel, several experiments were performed to confirm certain physiological characteristics that could be associated with phyllospheric behavior. Finally, in vivo and in vitro experiments were carried out to verify whether this isolate could serve as a biocontrol agent against coffee rust and how the isolate could act against the infection. Results The isolate showed several genes that are associated with resistance to environmental stresses, such as genes encoding heat/cold shock proteins, antioxidant enzymes, carbon starvation proteins, proteins that control osmotic balance and biofilm formation. There was an increase of exopolysaccharides synthesis in response to osmotic stress, which may protect cells from dessication on phyllosphere. Metabolic pathways for degradation and incorporation into citrate cycle of phenolic compounds present in coffee were found, and experimentally confirmed. In addition, MN1F was found to be highly tolerant to caffeine. The experiments of biocontrol against coffee leaf rust showed that the isolate can control the progress of the disease, most likely through competition for resources. Conclusion Genomic analysis and experimental data suggest that there are adaptations of this Pseudomonas to live in association with coffee leaves and to act as a biocontrol agent.
Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02637-4.
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Affiliation(s)
- Leandro Pio de Sousa
- Instituto Agronômico de Campinas, IAC, Campinas, SP, Brazil.,Programa de Pós-Graduação Em Genética E Biologia Molecular, UNICAMP, Campinas, SP, Brazil
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de Sousa LP, Cipriano MAP, Freitas SDS, Carazzolle MF, da Silva MJ, Mondego JMC. Genomic and physiological evaluation of two root associated Pseudomonas from Coffea arabica. Microbiol Res 2022; 263:127129. [PMID: 35907286 DOI: 10.1016/j.micres.2022.127129] [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: 09/24/2021] [Revised: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 10/17/2022]
Abstract
Many Pseudomonas species promote plant growth and colonize a wide range of environments. The annotation of a Coffea arabica ESTs database revealed a considerable number of Pseudomonas sequences. To evaluate the genomic and physiology of Pseudomonas that inhabit coffee plants, fluorescent Pseudomonas from C. arabica root environment were isolated. Two of them had their genomes sequenced; one from rhizospheric soil, named as MNR3A, and one from internal part of the root, named as EMN2. In parallel, we performed biochemical and physiological experiments to confirm genomic analyses results. Interestingly, EMN2 has achromobactin and aerobactin siderophore receptors, but does not have the genes responsible for the production of these siderophores, suggesting an interesting bacterial competition strategy. The two bacterial isolates were able to degrade and catabolize plant phenolic compounds for their own benefit. Surprisingly, MNR3A and EMN2 do not contain caffeine methylases that are responsible for the catabolism of caffeine. In fact, bench experiments confirm that the bacteria did not metabolize caffeine, but were resistant and chemically attracted to it. Furthermore, both bacteria, most especially MNR3A, were able to increase growth of lettuce plants. Our results indicate MNR3A as a potential plant growth promoting bacteria.
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Affiliation(s)
- Leandro Pio de Sousa
- Instituto Agronômico de Campinas, IAC, Campinas, SP, Brazil; UNICAMP, Programa de Pós-graduação em Genética e Biologia Molecular, Campinas, SP, Brazil
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de Sousa LP. Genomic and pathogenicity of a Bacillus paranthracis isolated from book page surface. Infect Genet Evol 2021; 92:104867. [PMID: 33872786 DOI: 10.1016/j.meegid.2021.104867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
I report here the genome sequences of a Bacillus paranthracis strain isolated from book page surface. The presented data show a new study field for this species, which is frequently encountered in several environment, including soil, rhizosphere and notably human samples. I provide some insights about genomic content of Bacillus paranthracis, for example the presence of multiple antibiotic resistance genes, genes for polyhydroxybutyrate metabolism, 120 genes related to stress resistance and pathogenicity-related genes such as phospholipase C, metalloprotease and a cluster for non-hemolytic enterotoxin. In vitro tests showed that this isolate has motility, ability to produce biofilm, cytotoxic and enterotoxic ability, which makes this isolate a potential pathogen.
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Affiliation(s)
- Leandro Pio de Sousa
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas, Brazil.
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Abstract
Microbes have been identified as fundamental for the good health of bees, acting as pathogens, protective agent against infection/inorganic toxic compounds, degradation of recalcitrant secondary plant metabolites, definition of social group membership, carbohydrate metabolism, honey and bee pollen production. However, study of microbiota associated with bees have been largely confined to the honeybees and solitary bees. Here, I characterized the microbiota of indoor surface nest of four brazilian stingless bee species (Apidae: Meliponini) with different construction behaviors and populations. Bees that use predominantly plant material to build the nest (Frieseomelitta varia and Tetragonisca angustula) have a microbiome dominated by bacteria found in the phylloplane and flowers such as Pseudomonas sp. and Sphingomonas sp. Species that use mud and feces (Trigona spinipes) possess a microbiome dominated by coliforms such as Escherichia coli and Alcaligenes faecalis. Melipona quadrifasciata, which uses both mud / feces and plant resin, showed a hybrid microbiome with microbes found in soil, feces and plant material. These findings indicate that indoor surface microbiome varies widely among bees and reflects the materials used in the construction of the nests.
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Affiliation(s)
- Leandro Pio de Sousa
- Department of Genetic, Evolution, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas, Brazil
- * E-mail:
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Sousa LPD, da Silva MJD, Mondego JMC. Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves. Genet Mol Biol 2018; 41:455-465. [PMID: 29782032 PMCID: PMC6082234 DOI: 10.1590/1678-4685-gmb-2017-0255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/14/2017] [Indexed: 01/16/2023] Open
Abstract
Coffee is one of the most valuable agricultural commodities and the plants’
leaves are the primary site of infection for most coffee diseases, such as the
devastating coffee leaf rust. Therefore, the use of bacterial microbiota that
inhabits coffee leaves to fight infections could be an alternative agricultural
method to protect against coffee diseases. Here, we report the leaf-associated
bacteria in three coffee genotypes over the course of a year, with the aim to
determine the diversity of bacterial microbiota. The results indicate a
prevalence of Enterobacteriales in Coffea canephora,
Pseudomonadales in C. arabica ‘Obatã’, and an intriguing lack
of bacterial dominance in C. arabica ‘Catuaí’. Using PERMANOVA
analyses, we assessed the association between bacterial abundance in the coffee
genotypes and environmental parameters such as temperature, precipitation, and
mineral nutrients in the leaves. We detected a close relationship between the
amount of Mn and the abundance of Pseudomonadales in ‘Obatã’ and the amount of
Ca and the abundance of Enterobacteriales in C. canephora. We
suggest that mineral nutrients can be key drivers that shape leaf microbial
communities.
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Affiliation(s)
- Leandro Pio de Sousa
- Instituto Agronômico, Campinas, SP, Brazil.,Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia Universidade de Campinas (UNICAMP), Campinas, SP, Brazil.,Programa de Pós Graduação em Genética e Biologia Molecular, Instituto de Biologia, Universidade de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Marcio José da da Silva
- Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade de Campinas (UNICAMP), Campinas, SP, Brazil
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