1
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Gätjens-Boniche O, Jiménez-Madrigal JP, Whetten RW, Valenzuela-Diaz S, Alemán-Gutiérrez A, Hanson PE, Pinto-Tomás AA. Microbiome and plant cell transformation trigger insect gall induction in cassava. Front Plant Sci 2023; 14:1237966. [PMID: 38126017 PMCID: PMC10731979 DOI: 10.3389/fpls.2023.1237966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/18/2023] [Indexed: 12/23/2023]
Abstract
Several specialised insects can manipulate normal plant development to induce a highly organised structure known as a gall, which represents one of the most complex interactions between insects and plants. Thus far, the mechanism for insect-induced plant galls has remained elusive. To study the induction mechanism of insect galls, we selected the gall induced by Iatrophobia brasiliensis (Diptera: Cecidomyiidae) in cassava (Euphorbiaceae: Manihot esculenta Crantz) as our model. PCR-based molecular markers and deep metagenomic sequencing data were employed to analyse the gall microbiome and to test the hypothesis that gall cells are genetically transformed by insect vectored bacteria. A shotgun sequencing discrimination approach was implemented to selectively discriminate between foreign DNA and the reference host plant genome. Several known candidate insertion sequences were identified, the most significant being DNA sequences found in bacterial genes related to the transcription regulatory factor CadR, cadmium-transporting ATPase encoded by the cadA gene, nitrate transport permease protein (nrtB gene), and arsenical pump ATPase (arsA gene). In addition, a DNA fragment associated with ubiquitin-like gene E2 was identified as a potential accessory genetic element involved in gall induction mechanism. Furthermore, our results suggest that the increased quality and rapid development of gall tissue are mostly driven by microbiome enrichment and the acquisition of critical endophytes. An initial gall-like structure was experimentally obtained in M. esculenta cultured tissues through inoculation assays using a Rhodococcus bacterial strain that originated from the inducing insect, which we related to the gall induction process. We provide evidence that the modification of the endophytic microbiome and the genetic transformation of plant cells in M. esculenta are two essential requirements for insect-induced gall formation. Based on these findings and having observed the same potential DNA marker in galls from other plant species (ubiquitin-like gene E2), we speculate that bacterially mediated genetic transformation of plant cells may represent a more widespread gall induction mechanism found in nature.
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Affiliation(s)
- Omar Gätjens-Boniche
- Laboratorio de Biología Molecular, Escuela de Ciencias Naturales y Exactas, Campus Tecnológico Local San Carlos, Instituto Tecnológico de Costa Rica, Alajuela, Costa Rica
| | - Jose Pablo Jiménez-Madrigal
- Laboratorio de Biología Molecular, Escuela de Ciencias Naturales y Exactas, Campus Tecnológico Local San Carlos, Instituto Tecnológico de Costa Rica, Alajuela, Costa Rica
| | - Ross W. Whetten
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Sandro Valenzuela-Diaz
- Human Microbiome Research Program, Faculty of Medicine, The Helsinki University, Helsinki, Finland
| | - Alvaro Alemán-Gutiérrez
- Laboratorio de Biología Molecular, Escuela de Ciencias Naturales y Exactas, Campus Tecnológico Local San Carlos, Instituto Tecnológico de Costa Rica, Alajuela, Costa Rica
- Laboratorio de Genómica y Biodiversidad, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
| | - Paul E. Hanson
- Escuela de Biología, Universidad de Costa Rica, San Pedro, San José, Costa Rica
| | - Adrián A. Pinto-Tomás
- Center for Research in Microscopic Structures and Department of Biochemistry, School of Medicine, University of Costa Rica, San José, Costa Rica
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2
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Matarrita-Carranza B, Murillo-Cruz C, Avendaño R, Ríos MI, Chavarría M, Gómez-Calvo ML, Tamayo-Castillo G, Araya JJ, Pinto-Tomás AA. Streptomyces sp. M54: an actinobacteria associated with a neotropical social wasp with high potential for antibiotic production. Antonie Van Leeuwenhoek 2021; 114:379-398. [PMID: 33587228 DOI: 10.1007/s10482-021-01520-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/17/2021] [Indexed: 11/28/2022]
Abstract
Streptomyces symbionts in insects have shown to be a valuable source of new antibiotics. Here, we report the genome sequence and the potential for antibiotic production of "Streptomyces sp. M54", an Actinobacteria associated with the eusocial wasp, Polybia plebeja. The Streptomyces sp. M54 genome is composed of a chromosome (7.96 Mb), and a plasmid (1.91 Kb) and harbors 30 biosynthetic gene clusters for secondary metabolites, of which only one third has been previously characterized. Growth inhibition bioassays show that this bacterium produces antimicrobial compounds that are active against Hirsutella citriformis, a natural fungal enemy of its host, and the human pathogens Staphylococcus aureus and Candida albicans. Analyses through TLC-bioautography, LC-MS/MS and NMR allowed the identification of five macrocyclic ionophore antibiotics, with previously reported antibacterial, antitumor and antiviral properties. Phylogenetic analyses placed Streptomyces sp. M54 in a clade of other host-associated strains taxonomically related to Streptomyces griseus. Pangenomic and ANI analyses confirm the identity of one of its closest relatives as Streptomyces sp. LaPpAH-199, a strain isolated from an ant-plant symbiosis in Africa. In summary, our results suggest an insect-microbe association in distant geographic areas and showcase the potential of Streptomyces sp. M54 and related strains for the discovery of novel antibiotics.
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Affiliation(s)
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | - María Isabel Ríos
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - María Luisa Gómez-Calvo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Juan J Araya
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, 11501-2060, San José, Costa Rica. .,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, 11501-2060, San José, Costa Rica. .,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.
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3
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Grubbs KJ, May DS, Sardina JA, Dermenjian RK, Wyche TP, Pinto-Tomás AA, Clardy J, Currie CR. Pollen Streptomyces Produce Antibiotic That Inhibits the Honey Bee Pathogen Paenibacillus larvae. Front Microbiol 2021; 12:632637. [PMID: 33613504 PMCID: PMC7889971 DOI: 10.3389/fmicb.2021.632637] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/13/2021] [Indexed: 01/11/2023] Open
Abstract
Humans use natural products to treat disease; similarly, some insects use natural products produced by Actinobacteria to combat infectious pathogens. Honey bees, Apis mellifera, are ecologically and economically important for their critical role as plant pollinators and are host to diverse and potentially virulent pathogens that threaten hive health. Here, we provide evidence that Actinobacteria that can suppress pathogenic microbes are associated with A. mellifera. We show through culture-dependent approaches that Actinobacteria in the genus Streptomyces are commonly isolated from foraging bees, and especially common in pollen stores. One strain, isolated from pollen stores, exhibited pronounced inhibitory activity against Paenibacillus larvae, the causative agent of American foulbrood. Bioassay-guided HPLC fractionation, followed by NMR and mass spectrometry, identified the known macrocyclic polyene lactam, piceamycin that was responsible for this activity. Further, we show that in its purified form, piceamycin has potent inhibitory activity toward P. larvae. Our results suggest that honey bees may use pollen-derived Actinobacteria and their associated small molecules to mediate colony health. Given the importance of honey bees to modern agriculture and their heightened susceptibility to disease, the discovery and development of antibiotic compounds from hives could serve as an important strategy in supporting disease management within apiaries.
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Affiliation(s)
- Kirk J. Grubbs
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Department of Cellular and Molecular Pathology, University of Wisconsin-Madison, Madison, WI, United States
| | - Daniel S. May
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Joseph A. Sardina
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Renee K. Dermenjian
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Thomas P. Wyche
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Adrián A. Pinto-Tomás
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
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4
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Abarca JG, Whitfield SM, Zuniga-Chaves I, Alvarado G, Kerby J, Murillo-Cruz C, Pinto-Tomás AA. Genotyping and differential bacterial inhibition of Batrachochytrium dendrobatidis in threatened amphibians in Costa Rica. Microbiology (Reading) 2021; 167. [PMID: 33529150 DOI: 10.1099/mic.0.001017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Amphibians have declined around the world in recent years, in parallel with the emergence of an epidermal disease called chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd). This disease has been associated with mass mortality in amphibians worldwide, including in Costa Rica, and Bd is considered an important contributor to the disappearance of this group of vertebrates. While many species are susceptible to the disease, others show tolerance and manage to survive infection with the pathogen. We evaluated the pathogen Bd circulating in Costa Rica and the capacity of amphibian skin bacteria to inhibit the growth of the pathogen in vitro. We isolated and characterized - genetically and morphologically - several Bd isolates from areas with declining populations of amphibians. We determined that the circulating chytrid fungus in Costa Rica belongs to the virulent strain Bd-GPL-2, which has been related to massive amphibian deaths worldwide; however, the isolates obtained showed genetic and morphological variation. Furthermore, we isolated epidermal bacteria from 12 amphibian species of surviving populations, some in danger of extinction, and evaluated their inhibitory activity against the collection of chytrid isolates. Through bioassays we confirmed the presence of chytrid-inhibitory bacterial genera in Costa Rican amphibians. However, we observed that the inhibition varied between different isolates of the same bacterial genus, and each bacterial isolation inhibited fungal isolation differently. In total, 14 bacterial isolates belonging to the genera Stenotrophomonas, Streptomyces, Enterobacter, Pseudomonas and Klebsiella showed inhibitory activity against all Bd isolates. Given the observed variation both in the pathogen and in the bacterial inhibition capacity, it is highly relevant to include local isolates and to consider the origin of the microorganisms when performing in vivo infection tests aimed at developing and implementing mitigation strategies for chytridiomycosis.
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Affiliation(s)
- Juan G Abarca
- Laboratorio de Recursos Naturales y Vida Silvestre (LARNAVISI), Escuela de Ciencias Biológicas, Universidad Nacional, Heredia, Costa Rica
| | - Steven M Whitfield
- Conservation and Research Department, Zoo Miami, St, Miami, FL 33177, USA
| | - Ibrahim Zuniga-Chaves
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Gilbert Alvarado
- Laboratorio de Patología Experimental y Comparada (LAPECOM), Escuela de Biología, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Jacob Kerby
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, San Pedro, Costa Rica.,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, San Pedro, Costa Rica.,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San Pedro, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
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5
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Gätjens-Boniche O, Sánchez-Valverde M, Trejos-Araya C, Espinoza-Obando R, Pinto-Tomás AA, Hanson PE. Plant galls recorded from Guanacaste Conservation Area-Costa Rica as an integrated concept of a biological database. Biota Neotrop 2021. [DOI: 10.1590/1676-0611-bn-2020-1153] [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] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract: Galling insects are specialist herbivorous that have the ability of manipulating plant tissue to form complex biological structures called galls. Even though different organisms have the ability to induce galls in plants, insect galls have the highest degree of structural complexity. The main goal of this study was to obtain a preliminary systematic record of plant gall morphotypes from the Guanacaste Conservation Area in Costa Rica and integrate the information into a biological database. Plant gall morphotypes were recorded, characterized and deposited into a specialized herbarium established as a reference for the inventory. Moreover, organisms associated with gall morphotypes were included in the inventory when it was possible to obtain and identify them. Galls were collected in the rainy season over a period of three years. In total, we recorded forty-four families, seventy genera, and eighty-seven host plant species. One hundred thirty-one morphotypes of plant galls were identified in the Guanacaste Conservation Area. The family with the highest number of gall morphotypes was Fabaceae (8.4%). Leaves were the organ with the largest number of galls (71%), followed by stems (17.6%), and apical buds (6.9%). The predominant gall shape was globular (25.2%), followed by discoid (18.3%). Fifty-nine percent of the galls had a glabrous texture, which was most common on leaves, with 77%. One hundred twenty of our field records (91.6%) of plant galls were new morphotypes not only for Costa Rica but also the world. As a consequence of this research and considering the prospect of future increases in new gall records (and associated organisms), we proposed having the biological entities resulting from the inventory placed in a cecidiarium. This repository represents a standardized and comprehensive way to manage the data and biological materials associated with the plant galls. We also suggest a nomenclature for standardizing gall morphotype registries and identifications. This work is the first and most detailed inventory of plant galls carried out thus far in the Guanacaste Conservation Area.
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6
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Francoeur CB, Khadempour L, Moreira-Soto RD, Gotting K, Book AJ, Pinto-Tomás AA, Keefover-Ring K, Currie CR. Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System. mBio 2020; 11:e02146-20. [PMID: 32934088 PMCID: PMC7492740 DOI: 10.1128/mbio.02146-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Herbivores must overcome a variety of plant defenses, including coping with plant secondary compounds (PSCs). To help detoxify these defensive chemicals, several insect herbivores are known to harbor gut microbiota with the metabolic capacity to degrade PSCs. Leaf-cutter ants are generalist herbivores, obtaining sustenance from specialized fungus gardens that act as external digestive systems and which degrade the diverse collection of plants foraged by the ants. There is in vitro evidence that certain PSCs harm Leucoagaricus gongylophorus, the fungal cultivar of leaf-cutter ants, suggesting a role for the Proteobacteria-dominant bacterial community present within fungus gardens. In this study, we investigated the ability of symbiotic bacteria present within fungus gardens of leaf-cutter ants to degrade PSCs. We cultured fungus garden bacteria, sequenced the genomes of 42 isolates, and identified genes involved in PSC degradation, including genes encoding cytochrome P450 enzymes and genes in geraniol, cumate, cinnamate, and α-pinene/limonene degradation pathways. Using metatranscriptomic analysis, we showed that some of these degradation genes are expressed in situ Most of the bacterial isolates grew unhindered in the presence of PSCs and, using gas chromatography-mass spectrometry (GC-MS), we determined that isolates from the genera Bacillus, Burkholderia, Enterobacter, Klebsiella, and Pseudomonas degrade α-pinene, β-caryophyllene, or linalool. Using a headspace sampler, we show that subcolonies of fungus gardens reduced α-pinene and linalool over a 36-h period, while L. gongylophorus strains alone reduced only linalool. Overall, our results reveal that the bacterial communities in fungus gardens play a pivotal role in alleviating the effect of PSCs on the leaf-cutter ant system.IMPORTANCE Leaf-cutter ants are dominant neotropical herbivores capable of deriving energy from a wide range of plant substrates. The success of leaf-cutter ants is largely due to their external gut, composed of key microbial symbionts, specifically, the fungal mutualist L. gongylophorus and a consistent bacterial community. Both symbionts are known to have critical roles in extracting energy from plant material, yet comparatively little is known about their roles in the detoxification of plant secondary compounds. In this study, we assessed if the bacterial communities associated with leaf-cutter ant fungus gardens can degrade harmful plant chemicals. We identify plant secondary compound detoxification in leaf-cutter ant gardens as a process that depends on the degradative potential of both the bacterial community and L. gongylophorus Our findings suggest that the fungus garden and its associated microbial community influence the generalist foraging abilities of the ants, underscoring the importance of microbial symbionts in plant substrate suitability for herbivores.
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Affiliation(s)
- Charlotte B Francoeur
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lily Khadempour
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Rolando D Moreira-Soto
- Sección de Entomología Medica, Departamento de Parasitología, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Kirsten Gotting
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adam J Book
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San José, Costa Rica
- Departamento de Bioquímica, Facultad de Medicina, Universidad de Costa Rica, San José, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San José, Costa Rica
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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7
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Cambronero-Heinrichs JC, Matarrita-Carranza B, Murillo-Cruz C, Araya-Valverde E, Chavarría M, Pinto-Tomás AA. Phylogenetic analyses of antibiotic-producing Streptomyces sp. isolates obtained from the stingless-bee Tetragonisca angustula (Apidae: Meliponini). Microbiology (Reading) 2019; 165:292-301. [DOI: 10.1099/mic.0.000754] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Juan Carlos Cambronero-Heinrichs
- 1Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
- 2Centro de Investigación en Contaminación Ambiental (CICA), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | | | - Catalina Murillo-Cruz
- 1Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
- 4Centro de Investigación en Biología Molecular y Celular (CIBCM), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
- 5Escuela de Medicina, Departamento de Bioquímica, Universidad de Costa Rica, 11501-2060 SanJosé, Costa Rica
| | - Emanuel Araya-Valverde
- 6Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200 San José, Costa Rica
| | - Max Chavarría
- 6Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200 San José, Costa Rica
- 7Escuela de Química & Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
| | - Adrián A. Pinto-Tomás
- 1Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
- 5Escuela de Medicina, Departamento de Bioquímica, Universidad de Costa Rica, 11501-2060 SanJosé, Costa Rica
- 4Centro de Investigación en Biología Molecular y Celular (CIBCM), Universidad de Costa Rica, 11501-2060 San José, Costa Rica
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8
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Chevrette MG, Carlson CM, Ortega HE, Thomas C, Ananiev GE, Barns KJ, Book AJ, Cagnazzo J, Carlos C, Flanigan W, Grubbs KJ, Horn HA, Hoffmann FM, Klassen JL, Knack JJ, Lewin GR, McDonald BR, Muller L, Melo WGP, Pinto-Tomás AA, Schmitz A, Wendt-Pienkowski E, Wildman S, Zhao M, Zhang F, Bugni TS, Andes DR, Pupo MT, Currie CR. The antimicrobial potential of Streptomyces from insect microbiomes. Nat Commun 2019; 10:516. [PMID: 30705269 PMCID: PMC6355912 DOI: 10.1038/s41467-019-08438-0] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [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: 10/18/2018] [Accepted: 01/11/2019] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial resistance is a global health crisis and few novel antimicrobials have been discovered in recent decades. Natural products, particularly from Streptomyces, are the source of most antimicrobials, yet discovery campaigns focusing on Streptomyces from the soil largely rediscover known compounds. Investigation of understudied and symbiotic sources has seen some success, yet no studies have systematically explored microbiomes for antimicrobials. Here we assess the distinct evolutionary lineages of Streptomyces from insect microbiomes as a source of new antimicrobials through large-scale isolations, bioactivity assays, genomics, metabolomics, and in vivo infection models. Insect-associated Streptomyces inhibit antimicrobial-resistant pathogens more than soil Streptomyces. Genomics and metabolomics reveal their diverse biosynthetic capabilities. Further, we describe cyphomycin, a new molecule active against multidrug resistant fungal pathogens. The evolutionary trajectories of Streptomyces from the insect microbiome influence their biosynthetic potential and ability to inhibit resistant pathogens, supporting the promise of this source in augmenting future antimicrobial discovery.
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Affiliation(s)
- Marc G Chevrette
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Caitlin M Carlson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Humberto E Ortega
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14040-903, SP, Brazil
| | - Chris Thomas
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - Gene E Ananiev
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - Kenneth J Barns
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - Adam J Book
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Julian Cagnazzo
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Will Flanigan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Kirk J Grubbs
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - F Michael Hoffmann
- McArdle Laboratory for Cancer Research, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, 06269, CT, USA
| | - Jennifer J Knack
- Department of Biology, Large Lakes Observatory, University of Minnesota-Duluth, Duluth, 55812, MN, USA
| | - Gina R Lewin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, 30332, GA, USA
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Laura Muller
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | - Weilan G P Melo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14040-903, SP, Brazil
| | - Adrián A Pinto-Tomás
- Center for Research in Microscopic Structures and Department of Biochemistry, School of Medicine, University of Costa Rica, San José, 10102, Costa Rica
| | - Amber Schmitz
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA
| | | | - Scott Wildman
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - Miao Zhao
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, 53705, WI, USA
| | - Fan Zhang
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, 53705, WI, USA
| | - David R Andes
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, 53705, WI, USA
| | - Monica T Pupo
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14040-903, SP, Brazil
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, 53706, WI, USA.
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9
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Abarca JG, Vargas G, Zuniga I, Whitfield SM, Woodhams DC, Kerby J, McKenzie VJ, Murillo-Cruz C, Pinto-Tomás AA. Assessment of Bacterial Communities Associated With the Skin of Costa Rican Amphibians at La Selva Biological Station. Front Microbiol 2018; 9:2001. [PMID: 30233511 PMCID: PMC6129598 DOI: 10.3389/fmicb.2018.02001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 10/31/2017] [Accepted: 08/08/2018] [Indexed: 12/15/2022] Open
Abstract
Amphibian skin is a suitable environment for rich communities of microorganisms, both beneficial and detrimental to the host. The amphibian cutaneous microbiota has been hypothesized to play an important role as symbionts, protecting their hosts against disease. Costa Rica has one of the most diverse assemblages of amphibians in the world and we know very little about the microbiota of these tropical animals. For comparison with other studies, we explore the diversity of the skin bacterial communities employing16S rRNA amplicon sequencing of swab samples from twelve species of frogs at La Selva Biological Station in Sarapiquí, Heredia province. The predominant phylum detected in our studies was Proteobacteria, followed by Bacteroidetes and Actinobacteria, with these three phyla representing 89.9% of the total bacterial taxa. At the family level, Sphingobacteriaceae and Comamonadaceae were highly represented among samples. Our results suggest that host species and host family are significant predictors of the variation in microbiota composition. This study helps set the foundation for future research about microbiota composition and resilience to unfavorable conditions, leading to improvement in managing strategies for endangered amphibian species.
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Affiliation(s)
- Juan G. Abarca
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Gabriel Vargas
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Ibrahim Zuniga
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Steven M. Whitfield
- Department of Conservation and Research, Zoo Miami, Miami, FL, United States
| | - Douglas C. Woodhams
- Department of Biology, University of Massachusetts, Boston, MA, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jacob Kerby
- Department of Biology, University of South Dakota, Vermillion, SD, United States
| | - Valerie J. McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Adrián A. Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
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10
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Abarca JG, Zuniga I, Ortiz-Morales G, Lugo A, Viquez-Cervilla M, Rodriguez-Hernandez N, Vázquez-Sánchez F, Murillo-Cruz C, Torres-Rivera EA, Pinto-Tomás AA, Godoy-Vitorino F. Characterization of the Skin Microbiota of the Cane Toad Rhinella cf. marina in Puerto Rico and Costa Rica. Front Microbiol 2018; 8:2624. [PMID: 29354109 PMCID: PMC5760547 DOI: 10.3389/fmicb.2017.02624] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/15/2017] [Indexed: 12/22/2022] Open
Abstract
Rhinella marina is a toad native to South America that has been introduced in the Antilles, likely carrying high loads of microorganisms, potentially impacting local community diversity. The amphibian skin is involved in pathogen defense and its microbiota has been relatively well studied, however, research focusing on the cane toad microbiota is lacking. We hypothesize that the skin microbial communities will differ between toads inhabiting different geographical regions in Central America and the Caribbean. To test our hypothesis, we compared the microbiota of three populations of R. cf. marina toads, two from Costa Rican (native) and one Puerto Rican (exotic) locations. In Costa Rica, we collected 11 toads, 7 in Sarapiquí and 4 from Turrialba while in Puerto Rico, 10 animals were collected in Santa Ana. Separate swab samples were collected from the dorsal and ventral sites resulting in 42 samples. We found significant differences in the structure of the microbial communities between Puerto Rico and Costa Rica. We detected as much as 35 different phyla; however, communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Alpha diversity and richness were significantly higher in toads from Puerto Rico and betadiversity revealed significant differences between the microbiota samples from the two countries. At the genus level, we found in Santa Ana, Puerto Rico, a high dominance of Kokuria, Niabella, and Rhodobacteraceae, while in Costa Rica we found Halomonas and Pseudomonas in Sarapiquí, and Acinetobacter and Citrobacter in Turrialba. This is the first report of Niabella associated with the amphibian skin. The core microbiome represented 128 Operational Taxonomic Units (OTUs) mainly from five genera shared among all samples, which may represent the symbiotic Rhinella's skin. These results provide insights into the habitat-induced microbial changes facing this amphibian species. The differences in the microbial diversity in Puerto Rican toads compared to those in Costa Rica provide additional evidence of the geographically induced patterns in the amphibian skin microbiome, and highlight the importance of discussing the microbial tradeoffs in the colonization of new ecosystems.
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Affiliation(s)
- Juan G. Abarca
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Ibrahim Zuniga
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Gilmary Ortiz-Morales
- Department of Natural Sciences, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Armando Lugo
- Department of Natural Sciences, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Mariel Viquez-Cervilla
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Natalia Rodriguez-Hernandez
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Frances Vázquez-Sánchez
- Department of Natural Sciences, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Ernesto A. Torres-Rivera
- Department of Natural Sciences, Center for Environmental Education, Conservation and Interpretation, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
| | - Adrián A. Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Filipa Godoy-Vitorino
- Department of Natural Sciences, Microbial Ecology and Genomics Laboratory, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico
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11
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Pinto-Tomás AA, Sittenfeld A, Uribe-Lorío L, Chavarría F, Mora M, Janzen DH, Goodman RM, Simon HM. Comparison of midgut bacterial diversity in tropical caterpillars (Lepidoptera: Saturniidae) fed on different diets. Environ Entomol 2011; 40:1111-1122. [PMID: 22251723 DOI: 10.1603/en11083] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
As primary consumers of foliage, caterpillars play essential roles in shaping the trophic structure of tropical forests. The caterpillar midgut is specialized in plant tissue processing; its pH is exceptionally alkaline and contains high concentrations of toxic compounds derived from the ingested plant material (secondary compounds or allelochemicals) and from the insect itself. The midgut, therefore, represents an extreme environment for microbial life. Isolates from different bacterial taxa have been recovered from caterpillar midguts, but little is known about the impact of these microorganisms on caterpillar biology. Our long-term goals are to identify midgut symbionts and to investigate their functions. As a first step, different diet formulations were evaluated for rearing two species of tropical saturniid caterpillars. Using the polymerase chain reaction (PCR) with primers hybridizing broadly to sequences from the bacterial domain, 16S rRNA gene libraries were constructed with midgut DNA extracted from caterpillars reared on different diets. Amplified rDNA restriction analysis indicated that bacterial sequences recovered from the midguts of caterpillars fed on foliage were more diverse than those from caterpillars fed on artificial diet. Sequences related to Methylobacterium sp., Bradyrhizobium sp., and Propionibacterium sp. were detected in all caterpillar libraries regardless of diet, but were not detected in a library constructed from the diet itself. Furthermore, libraries constructed with DNA recovered from surface-sterilized eggs indicated potential for vertical transmission of midgut symbionts. Taken together, these results suggest that microorganisms associated with the tropical caterpillar midgut may engage in symbiotic interactions with these ecologically important insects.
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12
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Pinto-Tomás AA, Anderson MA, Suen G, Stevenson DM, Chu FST, Cleland WW, Weimer PJ, Currie CR. Symbiotic nitrogen fixation in the fungus gardens of leaf-cutter ants. Science 2009; 326:1120-3. [PMID: 19965433 DOI: 10.1126/science.1173036] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Bacteria-mediated acquisition of atmospheric N2 serves as a critical source of nitrogen in terrestrial ecosystems. Here we reveal that symbiotic nitrogen fixation facilitates the cultivation of specialized fungal crops by leaf-cutter ants. By using acetylene reduction and stable isotope experiments, we demonstrated that N2 fixation occurred in the fungus gardens of eight leaf-cutter ant species and, further, that this fixed nitrogen was incorporated into ant biomass. Symbiotic N2-fixing bacteria were consistently isolated from the fungus gardens of 80 leaf-cutter ant colonies collected in Argentina, Costa Rica, and Panama. The discovery of N2 fixation within the leaf-cutter ant-microbe symbiosis reveals a previously unrecognized nitrogen source in neotropical ecosystems.
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Affiliation(s)
- Adrián A Pinto-Tomás
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706, USA
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