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Vázquez-Guerrero E, Kneubehl AR, Pellegrini-Hernández P, González-Quiroz JL, Domínguez-López ML, Krishnavajhala A, Estrada-de Los Santos P, Ibarra JA, Lopez JE. Borrelia turicatae from Ticks in Peridomestic Setting, Camayeca, Mexico. Emerg Infect Dis 2024; 30:380-383. [PMID: 38270112 PMCID: PMC10826751 DOI: 10.3201/eid3002.231053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
We conducted surveillance studies in Sinaloa, Mexico, to determine the circulation of tick-borne relapsing fever spirochetes. We collected argasid ticks from a home in the village of Camayeca and isolated spirochetes. Genomic analysis indicated that Borrelia turicatae infection is a threat to those living in resource-limited settings.
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Vázquez-Guerrero E, González-Quiroz JL, Domínguez-López ML, Kneubehl AR, Krishnavajhala A, Curtis MW, Ponce-Mendoza A, Estrada-de Los Santos P, Lopez JE, Ibarra JA. New records of Ornithodoros turicata (Ixodida: Argasidae) in rural and urban sites in the Mexican states of Aguascalientes and Zacatecas indicate the potential for tick-borne relapsing fever. Exp Appl Acarol 2023; 91:99-110. [PMID: 37584844 DOI: 10.1007/s10493-023-00830-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023]
Abstract
Soft ticks from the Ornithodoros genus are vectors of relapsing fever (RF) spirochetes around the world. In Mexico, they were originally described in the 19th century. However, few recent surveillance studies have been conducted in Mexico, and regions where RF spirochetes circulate remain vague. Here, the presence of soft ticks in populated areas was assessed in two sites from the Mexican states of Aguascalientes and Zacatecas. Argasidae ticks were collected, identified by morphology and mitochondrial 16S rDNA gene sequencing, and tested for RF borreliae. The specimens in both sites were identified as Ornithodoros turicata but no RF spirochetes were detected. These findings emphasize the need to update the distribution of these ticks in multiple regions of Mexico and to determine the circulation of RF borreliosis in humans and domestic animals.
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Affiliation(s)
- Edwin Vázquez-Guerrero
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - José Luis González-Quiroz
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - María Lilia Domínguez-López
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Alexander R Kneubehl
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Aparna Krishnavajhala
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Michael W Curtis
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Alejandro Ponce-Mendoza
- Comisión Nacional para el conocimiento y Uso de la Biodiversidad, CONABIO, Ciudad de México, México
| | - Paulina Estrada-de Los Santos
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Job E Lopez
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| | - J Antonio Ibarra
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México.
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3
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Arroyo-Herrera I, Román-Ponce B, Bustamante-Brito R, Guevara-Luna J, Larios-Serrato V, Carro L, Mariano Igual J, Geiger O, Sánchez-Reyes A, Estrada-de Los Santos P, Wang ET, Vásquez-Murrieta MS. Microbacterium plantarum sp. nov. and Microbacterium thalli sp. nov., two endophytic metal-resistant bacteria isolated from Sphaeralcea angustifolia (Cav.) G. Don and Prosopis laevigata (Humb. et Bonpl. ex Willd) M.C. Johnston. Int J Syst Evol Microbiol 2023; 73. [PMID: 37754346 DOI: 10.1099/ijsem.0.006052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Four Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped, motile endophytic bacterial strains, designated NM3R9T, NE1TT3, NE2TL11 and NE2HP2T, were isolated from the inner tissues (leaf and stem) of Sphaeralcea angustifolia and roots of Prosopis laevigata. They were characterized using a polyphasic approach, which revealed that they represent two novel Microbacterium species. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the species closest to NE2HP2T was Microbacterium arborescens DSM 20754T (99.6 %) and that closest to NM3R9T, NE2TL11 and NE2TT3 was Microbacterium oleivorans NBRC 103075T (97.4 %). The whole-genome average nucleotide identity value between strain NM3R9T and Microbacterium imperiale DSM 20530T was 90.91 %, and that between strain NE2HP2T and M. arborecens DSM 20754T was 91.03 %. Digital DNA-DNA hybridization showed values of less than 70 % with the type strains of related species. The polar lipids present in both strains included diphosphatidylglycerol, phosphatidylglycerol, glycolipids and unidentified lipids, whereas the major fatty acids included anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Whole-cell sugars included mannose, rhamnose and galactose. Strains NM3R9T and NE2HP2T showed physiological characteristics different from those present in closely related Microbacterium species. According to the taxonomic analysis, both strains belong to two novel species. The name Microbacterium plantarum sp. nov. is proposed for strain NE2HP2T (=LMG 30875T=CCBAU 101117T) and Microbacterium thalli sp. nov. for strains NM3R9T (=LMG 30873T=CCBAU 101116T), NE1TT3 (=CCBAU 101114) and NE2TL11 (=CCBAU 101115).
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Affiliation(s)
- Ivan Arroyo-Herrera
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Del Miguel Hidalgo, Mexico City, 11340, Mexico
| | - Brenda Román-Ponce
- Universidad Politécnica del Estado de Morelos. Boulevard Cuauhnáhuac #566, Col. Lomas del Texcal, Jiutepec, Morelos, 62550, Mexico
| | - Rafael Bustamante-Brito
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Joseph Guevara-Luna
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Del Miguel Hidalgo, Mexico City, 11340, Mexico
| | - Violeta Larios-Serrato
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Del Miguel Hidalgo, Mexico City, 11340, Mexico
| | - Lorena Carro
- Departamento de Microbiología y Genética, Facultad de CC Agrarias y Ambientales, Universidad de Salamanca, Plaza Doctores de la Reina, Lab 230, 37007, Salamanca, Spain
| | - Jose Mariano Igual
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas (IRNASA-CSIC), c/Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - Otto Geiger
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Colonia Chamilpa, Cuernavaca, Morelos, 62210, Mexico
| | - Ayixon Sánchez-Reyes
- Investigador por México, CONAHCYT-Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, Cuernavaca, Morelos, 62209, Mexico
| | - Paulina Estrada-de Los Santos
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Del Miguel Hidalgo, Mexico City, 11340, Mexico
| | - En Tao Wang
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Del Miguel Hidalgo, Mexico City, 11340, Mexico
| | - María Soledad Vásquez-Murrieta
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. de Carpio y Plan de Ayala s/n, Col. Santo Tomás, Del Miguel Hidalgo, Mexico City, 11340, Mexico
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4
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Vázquez-Guerrero E, Reyes-Solís GC, Cano-Ravell AE, Machain-Williams C, Leyva-Gastélum M, Estrada-de Los Santos P, Álvarez-Hernández G, Ibarra JA. Detection of Rickettsia amblyommatis and Rickettsia bellii in ticks collected from pet dogs in peri-urban and rural areas in Yucatan, Mexico. Exp Appl Acarol 2023:10.1007/s10493-023-00825-z. [PMID: 37498401 DOI: 10.1007/s10493-023-00825-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023]
Abstract
Rickettsia species are bacteria that may cause multiple diseases in animals and humans, via transmission through multiple arthropod vectors. Routine surveillance of Rickettsia spp. within vectors is critical to determine their presence and risk to mammalian hosts within human populations. Therefore, to better characterize the circulating Rickettsia species in an understudied region we targeted pet dogs to survey. Ticks were collected from pet dogs in three populations of the Yucatan where we tested for the presence of Rickettsia spp. by PCR in metagenomic DNA. In these ticks removed from pet dogs we detected Rickettsia amblyommatis and Rickettsia bellii in Amblyomma auriculatum, Amblyomma ovale and Amblyomma mixtum ticks obtained in a rural community in the Mexican state of Yucatan. This is the first report detecting both species for this state in Mexico, underpinning the importance of more routine surveillance.
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Affiliation(s)
- Edwin Vázquez-Guerrero
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Guadalupe C Reyes-Solís
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico.
| | - Alan E Cano-Ravell
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Carlos Machain-Williams
- Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán, Mérida, Mexico
| | - Marcia Leyva-Gastélum
- Departamento de Medicina y Ciencias de la Salud, Universidad de Sonora, Sonora, Mexico
| | - Paulina Estrada-de Los Santos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | | | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico.
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5
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Gómez-de la Cruz I, Chávez-Ramírez B, Avendaño-Arrazate CH, Morales-García YE, Muñoz-Rojas J, Estrada-de Los Santos P. Optimization of Paenibacillus sp. NMA1017 Application as a Biocontrol Agent for Phytophthora tropicalis and Moniliophthora roreri in Cacao-Growing Fields in Chiapas, Mexico. Plants (Basel) 2023; 12:2336. [PMID: 37375961 DOI: 10.3390/plants12122336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
In Mexico, cacao production is endangered by pathogenic fungi, such as Phytophthora spp. and Moniliophthora rorei, that cause black pod rot and moniliasis, respectively. In this study the biocontrol agent Paenibacillus sp. NMA1017 was tested in cacao fields against the previous diseases. The treatments applied were shade management, inoculation of the bacterial strain with or without an adherent, and use of chemical control. The statistical analysis showed that the incidence of black pod rot in tagged cacao trees diminished when the bacterium was applied (reduction of 44.24 to 19.11%). The same result was observed with moniliasis when the pods were tagged (reduction of 66.6 to 27%). The use of Paenibacillus sp. NMA1017 with an integrated management might be a solution to cacao diseases and to having a sustainable production of cacao in Mexico.
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Affiliation(s)
- Irene Gómez-de la Cruz
- Laboratorio de Biotecnología Microbiana, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s/n, Col. Santo Tomas, Alcaldía Miguel Hidalgo 11340, Ciudad de México, Mexico
| | - Belén Chávez-Ramírez
- Laboratorio de Fitopatología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s/n, Col. Santo Tomas, Alcaldía Miguel Hidalgo 11340, Ciudad de México, Mexico
| | - Carlos Hugo Avendaño-Arrazate
- Campo Experimental Rosario Izapa, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Km 18, Carretera Tapachula-Cacahoatán, Tuxtla Chico 30870, Chiapas, Mexico
| | - Yolanda Elizabeth Morales-García
- Ecology and Survival of Microoganisms Gropu, Laboratorio de Ecología Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, San Manuel, Puebla 72570, Puebla, Mexico
| | - Jesús Muñoz-Rojas
- Ecology and Survival of Microoganisms Gropu, Laboratorio de Ecología Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, San Manuel, Puebla 72570, Puebla, Mexico
| | - Paulina Estrada-de Los Santos
- Laboratorio de Biotecnología Microbiana, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala s/n, Col. Santo Tomas, Alcaldía Miguel Hidalgo 11340, Ciudad de México, Mexico
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6
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Morales-Ruíz LM, Rodríguez-Cisneros M, Kerber-Díaz JC, Rojas-Rojas FU, Ibarra JA, Estrada-de Los Santos P. Burkholderia orbicola sp. nov., a novel species within the Burkholderia cepacia complex. Arch Microbiol 2022; 204:178. [PMID: 35174425 DOI: 10.1007/s00203-022-02778-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/30/2022]
Abstract
Genome analysis of strains placed in the NCBI genome database as Burkholderia cenocepacia defined nine genomic species groups. The largest group (259 strains) corresponds to B. cenocepacia and the second largest group (58 strains) was identified as "Burkholderia servocepacia", a Burkholderia species classification which has not been validly published. The publication of "B. servocepacia" did not comply with Rule 27 and Recommendation 30 from the International Code of Nomenclature of Prokaryotes (ICNP) and have errors in the type strain name and the protologue describing the novel species. Here, we correct the position of this species by showing essential information that meets the criteria defined by ICNP. After additional analysis complying with taxonomic criteria, we propose that the invalid "B. servocepacia" be renamed as Burkholderia orbicola sp. nov. The original study proposing "B. servocepacia" was misleading, because this name derives from the Latin "servo" meaning "to protect/watch over", and the authors proposed this based on the beneficial biocontrol properties of several strains within the group. However, it is clear that "B. servocepacia" isolates are capable of opportunistic infection, and the proposed name Burkholderia orbicola sp. nov. takes into account these diverse phenotypic traits. The type strain is TAtl-371 T (= LMG 30279 T = CM-CNRG 715 T).
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Affiliation(s)
- Leslie-Mariana Morales-Ruíz
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Mariana Rodríguez-Cisneros
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Jeniffer-Chris Kerber-Díaz
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Fernando-Uriel Rojas-Rojas
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León UNAM), Blvd. UNAM 2011, 37684, León, Guanajuato, México.,Laboratorio Nacional PlanTECC, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (ENES-León), Blvd. UNAM 2011, 37684, León, Guanajuato, México
| | - J Antonio Ibarra
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México
| | - Paulina Estrada-de Los Santos
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo, C.P. 11340, Mexico City, México.
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7
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Cortés-Avalos D, Martínez-Pérez N, Ortiz-Moncada MA, Juárez-González A, Baños-Vargas AA, Estrada-de Los Santos P, Pérez-Rueda E, Ibarra JA. An update of the unceasingly growing and diverse AraC/XylS family of transcriptional activators. FEMS Microbiol Rev 2021; 45:6219864. [PMID: 33837749 DOI: 10.1093/femsre/fuab020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/31/2021] [Indexed: 01/09/2023] Open
Abstract
Transcriptional factors play an important role in gene regulation in all organisms, especially in Bacteria. Here special emphasis is placed in the AraC/XylS family of transcriptional regulators. This is one of the most abundant as many predicted members have been identified and more members are added because more bacterial genomes are sequenced. Given the way more experimental evidence has mounded in the past decades, we decided to update the information about this captivating family of proteins. Using bioinformatics tools on all the data available for experimentally characterized members of this family, we found that many members that display a similar functional classification can be clustered together and in some cases they have a similar regulatory scheme. A proposal for grouping these proteins is also discussed. Additionally, an analysis of surveyed proteins in bacterial genomes is presented. Altogether, the current review presents a panoramic view into this family and we hope it helps to stimulate future research in the field.
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Affiliation(s)
- Daniel Cortés-Avalos
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Noemy Martínez-Pérez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Mario A Ortiz-Moncada
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Aylin Juárez-González
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Arturo A Baños-Vargas
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Paulina Estrada-de Los Santos
- Laboratorio de Biotecnología Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México.,Facultad de Ciencias, Centro de Genómica y Bioinformática, Universidad Mayor, Santiago, Chile
| | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
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8
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Alvarez-Hernandez G, Cruz-Loustaunau D, Ibarra JA, Rascon-Alcantar A, Contreras-Soto J, Meza-Radilla G, Torres AG, Estrada-de Los Santos P. Description of two fatal cases of melioidosis in Mexican children with acute pneumonia: case report. BMC Infect Dis 2021; 21:204. [PMID: 33622263 PMCID: PMC7903701 DOI: 10.1186/s12879-021-05910-5] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melioidosis is an infectious disease caused by Burkholderia pseudomallei. In Mexico, the disease is rarely diagnosed in humans and there is no evidence of simultaneous environmental isolation of the pathogen. Here, we describe clinical profiles of fatal cases of melioidosis in two children, in a region without history of that disease. CASE PRESENTATION About 48 h before onset of symptoms, patients swam in a natural body of water, and thereafter they rapidly developed fatal septicemic illness. Upon necropsy, samples from liver, spleen, lung, cerebrospinal fluid, and bronchial aspirate tissues contained Burkholderia pseudomallei. Environmental samples collected from the locations where the children swam also contained B. pseudomallei. All the clinical and environmental strains showed the same BOX-PCR pattern, suggesting that infection originated from the area where the patients were swimming. CONCLUSIONS The identification of B. pseudomallei confirmed that melioidosis disease exists in Sonora, Mexico. The presence of B. pseudomallei in the environment may suggest endemicity of the pathogen in the region. This study highlights the importance of strengthening laboratory capacity to prevent and control future melioidosis cases.
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Affiliation(s)
- Gerardo Alvarez-Hernandez
- Department of Medicine and Health Sciences, University of Sonora, Hermosillo, Sonora, Mexico
- Ministry of Health of Sonora, Hermosillo, Sonora, Mexico
| | | | - J Antonio Ibarra
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo. C.P., 11340, Mexico City, Mexico
| | | | | | - Georgina Meza-Radilla
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo. C.P., 11340, Mexico City, Mexico
| | | | - Paulina Estrada-de Los Santos
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomás, Alcaldía Miguel Hidalgo. C.P., 11340, Mexico City, Mexico.
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9
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Author Correction: Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 6:136. [PMID: 33184503 PMCID: PMC7752755 DOI: 10.1038/s41564-020-00827-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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10
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Aguilar-Rangel EJ, Prado BL, Vásquez-Murrieta MS, Los Santos PED, Siebe C, Falcón LI, Santillán J, Alcántara-Hernández RJ. Temporal analysis of the microbial communities in a nitrate-contaminated aquifer and the co-occurrence of anammox, n-damo and nitrous-oxide reducing bacteria. J Contam Hydrol 2020; 234:103657. [PMID: 32777591 DOI: 10.1016/j.jconhyd.2020.103657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/13/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
Groundwater-N pollution derives from agricultural and urban activities, and compromises water quality in shallow aquifers, putting human and environmental health at risk. Nonetheless, subsurface microbiota can transform dissolved inorganic nitrogen into N2. In this study, we surveyed the microbial community of a shallow aquifer by sampling one well, one piezometer and a spring within an agricultural area that receives N-inputs of more than 700 kg/ha per year through irrigation with wastewater. The survey was conducted during a year with a 16S rRNA next-gen approach. In parallel, we quantified the number of gene copies and transcripts related to anaerobic ammonium oxidation (anammox, hzo), nitrite-dependent anaerobic methane oxidation (n-damo, nod and pmoA) and nitrous oxide reduction (last step of denitrification, nosZ), during the dry and rainy seasons. Our results showed that the groundwater samples had 17.7 to 22.5 mg/L of NO3--N. The bacterial and archaeal community structure was distinctive at each site, and it remained relatively stable over time. We verified the co-occurrence of N-transforming bacteria, which was correlated with the concentration of NO2-/NO3- and ORP/DO values (DO: ~3.0 mg/L). Our analyses suggest that these conditions may allow the presence of nitrifying microorganisms which can couple with anammox, n-damo and denitrifying bacteria in interrelated biogeochemical pathways. Gene density (as the number of gene copies per litre) was lower in the rainy season than in the dry season, possibly due to dilution by rainwater infiltration. Yet, the numbers of hzo gene copies here found were similar to those reported in oceanic oxygen minimum zones and in a carbonate-rock aquifer. The transcript sequences showed that Candidatus Brocadia spp. (anammox), Candidatus Methylomirabilis spp. (n-damo) and autotrophic denitrifying Betaproteobacteria coexist in the groundwater environment, with the potential to attenuate the concentration of dissolved inorganic nitrogen by reducing it to N2 rather than N2O; delivering thus, an important ecosystem service to remove contaminants.
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Affiliation(s)
- Eduardo J Aguilar-Rangel
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Blanca L Prado
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - María Soledad Vásquez-Murrieta
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340 Ciudad de México, Mexico
| | - Paulina Estrada-de Los Santos
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340 Ciudad de México, Mexico
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Yucatán, Mexico
| | - Jazmín Santillán
- Posgrado en Ciencias de la Tierra, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Rocío J Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico.
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11
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 5:987-994. [PMID: 32514073 PMCID: PMC7381421 DOI: 10.1038/s41564-020-0733-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [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: 06/14/2019] [Accepted: 05/01/2020] [Indexed: 11/09/2022]
Abstract
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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12
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Arroyo-Herrera I, Rojas-Rojas FU, Lozano-Cervantes KD, Larios-Serrato V, Vásquez-Murrieta MS, Whtiman WB, Ibarra JA, Estrada-de Los Santos P. Draft genome of five Cupriavidus plantarum strains: agave, maize and sorghum plant-associated bacteria with resistance to metals. 3 Biotech 2020; 10:242. [PMID: 32405446 DOI: 10.1007/s13205-020-02210-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/15/2020] [Indexed: 11/27/2022] Open
Abstract
Five strains of Cupriavidus plantarum, a metal-resistant, plant-associated bacterium, were selected for genome sequencing through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) Phase IV project at the Joint Genome Institute (JGI) of the U.S. Department of Energy (DOE). The genome of the strains was in the size range of 6.2-6.4 Mbp and encoded 5605-5834 proteins; 16.9-23.7% of these genes could not be assigned to a COG-associated functional category. The G + C content was 65.83-65.99%, and the genomes encoded 59-67 stable RNAs. The strains were resistant in vitro to arsenite, arsenate, cobalt, chromium, copper, nickel and zinc, and their genomes possessed the resistance genes for these metals. The genomes also encoded the biosynthesis of potential antimicrobial compounds, such as terpenes, phosphonates, bacteriocins, betalactones, nonribosomal peptides, phenazine and siderophores, as well as the biosynthesis of cellulose and enzymes such as chitinase and trehalase. The average nucleotide identity (ANI) and DNA-DNA in silico hybridization of the genomes confirmed that C. plantarum is a single species. Moreover, the strains cluster within a single group upon multilocus sequence analyses with eight genes and a phylogenomic analyses. Noteworthy, the ability of the species to tolerate high concentrations of different metals might prove useful for bioremediation of naturally contaminated environments.
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Affiliation(s)
- Ivan Arroyo-Herrera
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Fernando Uriel Rojas-Rojas
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
- 2Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores, Universidad Nacional Autónoma de México, León, Guanajuato, Mexico
| | - Karla Daniela Lozano-Cervantes
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Violeta Larios-Serrato
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - María Soledad Vásquez-Murrieta
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | | | - J Antonio Ibarra
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
| | - Paulina Estrada-de Los Santos
- 1Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala S/N. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340 Cd. de México, Mexico
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13
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Chávez-Ramírez B, Kerber-Díaz JC, Acoltzi-Conde MC, Ibarra JA, Vásquez-Murrieta MS, Estrada-de Los Santos P. Inhibition of Rhizoctonia solani RhCh-14 and Pythium ultimum PyFr-14 by Paenibacillus polymyxa NMA1017 and Burkholderia cenocepacia CACua-24: A proposal for biocontrol of phytopathogenic fungi. Microbiol Res 2020; 230:126347. [PMID: 31586859 DOI: 10.1016/j.micres.2019.126347] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/20/2019] [Accepted: 09/25/2019] [Indexed: 02/06/2023]
Abstract
Biocontrol has emerged in recent years as an alternative to pesticides. Given the importance of environmental preservation using biocontrol, in this study two antagonistic bacteria against phytopathogenic fungi were isolated and evaluated. These bacterial strains, identified as Paenibacillus polymyxa NMA1017 and Burkholderia cenocepacia CACua-24, inhibited (70 to 80%) the development of two phytopathogens of economic importance: the fungus Rhizoctonia solani RhCh-14, isolated from chili pepper, and the oomycete Pythium ultimum PyFr-14, isolated from tomato. The spectrum was not limited to the previous pathogens, but also to other phytopathogenic fungus, some bacteria and other oomycetes. Fungi-bacteria microcultures observed with optical and scanning electron microscopy revealed hyphae disintegration and pores formation. The antifungal activity was found also in the supernatant, suggesting a diffusible compound is present. Innocuous tests on tobacco leaves, blood agar, bean seed germination and in Galleria mellonella larvae showed that strain NMA1017 has the potential to be a biocontrol agent. Greenhouse experiments with bean plants inoculated with P. polymyxa exhibited the efficacy to inhibit the growth of R. solani and P. ultimum. Furthermore, P. polymyxa NMA1017 showed plant growth promotion activities, such as siderophore synthesis and nitrogen fixation which can contribute to the crop development.
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Affiliation(s)
- Belén Chávez-Ramírez
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, C.P. 11340, Mexico City, Mexico.
| | - Jeniffer Chris Kerber-Díaz
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, C.P. 11340, Mexico City, Mexico.
| | - Marí Carmen Acoltzi-Conde
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, C.P. 11340, Mexico City, Mexico.
| | - J Antonio Ibarra
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, C.P. 11340, Mexico City, Mexico.
| | - María-Soledad Vásquez-Murrieta
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, C.P. 11340, Mexico City, Mexico.
| | - Paulina Estrada-de Los Santos
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n, Col. Santo Tomas, C.P. 11340, Mexico City, Mexico.
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14
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Rojas-Rojas FU, Sánchez-López D, Tapia-García EY, Arroyo-Herrera I, Maymon M, Humm E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Ivanova N, Kyrpides N, Woyke T, Shapiro N, Hirsch AM, Ibarra JA, Estrada-de Los Santos P. Draft Genome of Burkholderia cenocepacia TAtl-371, a Strain from the Burkholderia cepacia Complex Retains Antagonism in Different Carbon and Nitrogen Sources. Curr Microbiol 2019; 76:566-574. [PMID: 30820638 DOI: 10.1007/s00284-019-01657-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/20/2019] [Indexed: 02/06/2023]
Abstract
Burkholderia cenocepacia TAtl-371 was isolated from the rhizosphere of a tomato plant growing in Atlatlahucan, Morelos, Mexico. This strain exhibited a broad antimicrobial spectrum against bacteria, yeast, and fungi. Here, we report and describe the improved, high-quality permanent draft genome of B. cenocepacia TAtl-371, which was sequenced using a combination of PacBio RS and PacBio RS II sequencing methods. The 7,496,106 bp genome of the TAtl-371 strain is arranged in three scaffolds, contains 6722 protein-coding genes, and 99 RNA only-encoding genes. Genome analysis revealed genes related to biosynthesis of antimicrobials such as non-ribosomal peptides, siderophores, chitinases, and bacteriocins. Moreover, analysis of bacterial growth on different carbon and nitrogen sources shows that the strain retains its antimicrobial ability.
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Affiliation(s)
- Fernando Uriel Rojas-Rojas
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - David Sánchez-López
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Erika Yanet Tapia-García
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Ivan Arroyo-Herrera
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Maskit Maymon
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Ethan Humm
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Marcel Huntemann
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Alicia Clum
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Manoj Pillay
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | | | - Neha Varghese
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Natalia Mikhailova
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Dimitrios Stamatis
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - T B K Reddy
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Natalia Ivanova
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Nicole Shapiro
- DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Ann M Hirsch
- Department of Molecular, Cell and Developmental Biology, University of California-Los Angeles, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - J Antonio Ibarra
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Paulina Estrada-de Los Santos
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Prol. Carpio y Plan de Ayala s/n. Col. Santo Tomás, Del. Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico.
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15
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Estrada-de Los Santos P, Palmer M, Chávez-Ramírez B, Beukes C, Steenkamp ET, Briscoe L, Khan N, Maluk M, Lafos M, Humm E, Arrabit M, Crook M, Gross E, Simon MF, Dos Reis Junior FB, Whitman WB, Shapiro N, Poole PS, Hirsch AM, Venter SN, James EK. Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera ( Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae. Genes (Basel) 2018; 9:genes9080389. [PMID: 30071618 PMCID: PMC6116057 DOI: 10.3390/genes9080389] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/19/2018] [Accepted: 07/24/2018] [Indexed: 11/21/2022] Open
Abstract
Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4–7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia, Caballeronia, Paraburkholderia, and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N2-fixing legume symbionts) and Caballeronia, while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum, which are both symbionts of the fungal phytopathogen Rhizopus microsporus. The second group comprises the Mimosa-nodulating bacterium Paraburkholderia symbiotica, the phytopathogen Paraburkholderia caryophylli, and the soil bacteria Burkholderia dabaoshanensis and Paraburkholderia soli. In order to clarify their positions within Burkholderia sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 Burkholderia sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera Mycetohabitans gen. nov. and Trinickia gen. nov. The newly proposed combinations are Mycetohabitans endofungorum comb. nov., Mycetohabitansrhizoxinica comb. nov., Trinickia caryophylli comb. nov., Trinickiadabaoshanensis comb. nov., Trinickia soli comb. nov., and Trinickiasymbiotica comb. nov. Given that the division between the genera that comprise Burkholderia s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits—diazotrophy and/or symbiotic nodulation, and pathogenesis—were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in Trinickia via-à-vis other Burkholderiaceae were determined, and the possibility of pathogenesis in Mycetohabitans and Trinickia was tested by performing infection experiments on plants and the nematode Caenorhabditis elegans. It is concluded that (1) T. symbiotica nif and nod genes fit within the wider Mimosa-nodulating Burkholderiaceae but appear in separate clades and that T. caryophyllinif genes are basal to the free-living Burkholderia s.l. strains, while with regard to pathogenesis (2) none of the Mycetohabitans and Trinickia strains tested are likely to be pathogenic, except for the known phytopathogen T. caryophylli.
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Affiliation(s)
| | - Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Belén Chávez-Ramírez
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, 11340 Cd. de Mexico, Mexico.
| | - Chrizelle Beukes
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Leah Briscoe
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Noor Khan
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Marta Maluk
- The James Hutton Institute, Dundee DD2 5DA, UK.
| | | | - Ethan Humm
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Monique Arrabit
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Matthew Crook
- 450G Tracy Hall Science Building, Weber State University, Ogden, 84403 UT, USA.
| | - Eduardo Gross
- Center for Electron Microscopy, Department of Agricultural and Environmental Sciences, Santa Cruz State University, 45662-900 Ilheus, BA, Brazil.
| | - Marcelo F Simon
- Embrapa CENARGEN, 70770-917 Brasilia, Distrito Federal, Brazil.
| | | | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Ann M Hirsch
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
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16
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Martínez-Aguilar L, Caballero-Mellado J, Estrada-de Los Santos P. Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov. Int J Syst Evol Microbiol 2012; 63:208-211. [PMID: 22389284 DOI: 10.1099/ijs.0.038729-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis of the 16S rRNA gene sequences of strains TE26(T) and K6 belonging to Wautersia numazuensis Kageyama et al. 2005 showed the strains to be deeply intermingled among the species of the genus Cupriavidus. The comparison showed that strain TE26(T) was closely related to the type strains of Cupriavidus pinatubonensis (99.1 % 16S rRNA gene sequence similarity), C. basilensis (98.7 %), C. necator (98.7 %) and C. gilardii (98.0 %). However, DNA-DNA hybridization experiments (less than 20 % relatedness) demonstrated that strain TE26(T) is different from these Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA gene sequence phylogenetic analysis and the DNA-DNA hybridization results supported the incorporation of Wautersia numazuensis into the genus Cupriavidus as Cupriavidus numazuensis comb. nov.; the type strain is TE26(T) (=LMG 26411(T) =DSM 15562(T) = CIP 108892(T)).
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Affiliation(s)
- Lourdes Martínez-Aguilar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Jesús Caballero-Mellado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Paulina Estrada-de Los Santos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, Cuernavaca, Morelos, Mexico
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17
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Gyaneshwar P, Hirsch AM, Moulin L, Chen WM, Elliott GN, Bontemps C, Estrada-de Los Santos P, Gross E, Dos Reis FB, Sprent JI, Young JPW, James EK. Legume-nodulating betaproteobacteria: diversity, host range, and future prospects. Mol Plant Microbe Interact 2011; 24:1276-88. [PMID: 21830951 DOI: 10.1094/mpmi-06-11-0172] [Citation(s) in RCA: 207] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Rhizobia form specialized nodules on the roots of legumes (family Fabaceae) and fix nitrogen in exchange for carbon from the host plant. Although the majority of legumes form symbioses with members of genus Rhizobium and its relatives in class Alphaproteobacteria, some legumes, such as those in the large genus Mimosa, are nodulated predominantly by betaproteobacteria in the genera Burkholderia and Cupriavidus. The principal centers of diversity of these bacteria are in central Brazil and South Africa. Molecular phylogenetic studies have shown that betaproteobacteria have existed as legume symbionts for approximately 50 million years, and that, although they have a common origin, the symbiosis genes in both subclasses have evolved separately since then. Additionally, some species of genus Burkholderia, such as B. phymatum, are highly promiscuous, effectively nodulating several important legumes, including common bean (Phaseolus vulgaris). In contrast to genus Burkholderia, only one species of genus Cupriavidus (C. taiwanensis) has so far been shown to nodulate legumes. The recent availability of the genome sequences of C. taiwanensis, B. phymatum, and B. tuberum has paved the way for a more detailed analysis of the evolutionary and mechanistic differences between nodulating strains of alpha- and betaproteobacteria. Initial analyses of genome sequences have suggested that plant-associated Burkholderia spp. have lower G+C contents than Burkholderia spp. that are opportunistic human pathogens, thus supporting previous suggestions that the plant- and human-associated groups of Burkholderia actually belong in separate genera.
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Affiliation(s)
- Prasad Gyaneshwar
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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18
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Caballero-Mellado J, Onofre-Lemus J, Estrada-de Los Santos P, Martínez-Aguilar L. The tomato rhizosphere, an environment rich in nitrogen-fixing Burkholderia species with capabilities of interest for agriculture and bioremediation. Appl Environ Microbiol 2007; 73:5308-19. [PMID: 17601817 PMCID: PMC1950987 DOI: 10.1128/aem.00324-07] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia strains are promising candidates for biotechnological applications. Unfortunately, most of these strains belong to species of the Burkholderia cepacia complex (Bcc) involved in human infections, hampering potential applications. Novel diazotrophic Burkholderia species, phylogenetically distant from the Bcc species, have been discovered recently, but their environmental distribution and relevant features for agro-biotechnological applications are little known. In this work, the occurrence of N2-fixing Burkholderia species in the rhizospheres and rhizoplanes of tomato plants field grown in Mexico was assessed. The results revealed a high level of diversity of diazotrophic Burkholderia species, including B. unamae, B. xenovorans, B. tropica, and two other unknown species, one of them phylogenetically closely related to B. kururiensis. These N2-fixing Burkholderia species exhibited activities involved in bioremediation, plant growth promotion, or biological control in vitro. Remarkably, B. unamae and B. kururiensis grew with aromatic compounds (phenol and benzene) as carbon sources, and the presence of aromatic oxygenase genes was confirmed in both species. The rhizospheric and endophyte nature of B. unamae and its ability to degrade aromatic compounds suggest that it could be used in rhizoremediation and for improvement of phytoremediation. B. kururiensis and other Burkholderia sp. strains grew with toluene. B. unamae and B. xenovorans exhibited ACC (1-aminocyclopropane-1-carboxylic acid) deaminase activity, and the occurrence of acdS genes encoding ACC deaminase was confirmed. Mineral phosphate solubilization through organic acid production appears to be the mechanism used by most diazotrophic Burkholderia species, but in B. tropica, there presumably exists an additional unknown mechanism. Most of the diazotrophic Burkholderia species produced hydroxamate-type siderophores. Certainly, the N2-fixing Burkholderia species associated with plants have great potential for agro-biotechnological applications.
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Affiliation(s)
- Jesús Caballero-Mellado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, Cuernavaca, Morelos, México.
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19
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Valdés M, Pérez NO, Estrada-de Los Santos P, Caballero-Mellado J, Peña-Cabriales JJ, Normand P, Hirsch AM. Non-Frankia actinomycetes isolated from surface-sterilized roots of Casuarina equisetifolia fix nitrogen. Appl Environ Microbiol 2005; 71:460-6. [PMID: 15640222 PMCID: PMC544234 DOI: 10.1128/aem.71.1.460-466.2005] [Citation(s) in RCA: 67] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Accepted: 08/18/2004] [Indexed: 11/20/2022] Open
Abstract
Based on partial 16S sequences, we previously described a novel group of nonsymbiotic, acetylene reduction activity-positive actinomycetes which were isolated from surface-sterilized roots of Casuarina equisetifolia growing in Mexico. An amplified rRNA restriction analysis confirmed that these actinomycetes are distinct from Frankia, a finding substantiated by a 16S rRNA gene phylogenetic analysis of two of the Mexican isolates. Further support for these actinomycetes being separate from Frankia comes from the very low DNA-DNA homology that was found. Nevertheless, the Mexican isolates may be diazotrophs based not only on their ability to grow in N-free medium and reduce acetylene to ethylene but also on the results from (15)N isotope dilution analysis and the finding that a nifH gene was PCR amplified. A comparison of the nifH sequences from the various isolates showed that they are closely related to nifH from Frankia; the similarity was 84 to 98% depending on the host specificity group. An analysis of complete 16S rRNA gene sequences demonstrated that the two strains analyzed in detail are most closely related to actinobacteria in the Thermomonosporaceae and the Micromonosporaceae.
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Affiliation(s)
- María Valdés
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, I. P. N., Plan De Ayala y Carpio, México
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Caballero-Mellado J, Martínez-Aguilar L, Paredes-Valdez G, Santos PEDL. Burkholderia unamae sp. nov., an N2-fixing rhizospheric and endophytic species. Int J Syst Evol Microbiol 2004; 54:1165-1172. [PMID: 15280286 DOI: 10.1099/ijs.0.02951-0] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It was shown recently that the genus Burkholderia is rich in N2-fixing bacteria that are associated with plants. A group of these diazotrophic isolates with identical or very similar 16S rDNA restriction patterns [designated amplified rDNA restriction analysis (ARDRA) genotypes 13, 14 and 15] was selected and a polyphasic taxonomic study was performed, which included new isolates that were recovered from rhizospheres, rhizoplanes or internal tissues of maize, sugarcane and coffee plants. Morphological, physiological and biochemical features, as well as multi-locus enzyme electrophoresis profiles and whole-cell protein patterns, of 20 strains were analysed. In addition, analysis of cellular fatty acid profiles, 16S rDNA sequence analysis and DNA–DNA reassociation experiments were performed with representative strains. The taxonomic data indicated that the strains analysed belong to a novel diazotrophic Burkholderia species, for which the name Burkholderia unamae sp. nov. is proposed. Strain MTl-641T (=ATCC BAA-744T=CIP 107921T), isolated from the rhizosphere of maize, was designated as the type strain. B. unamae was found as an endophyte of plants grown in regions with climates ranging from semi-hot subhumid to hot humid, but not from plants grown in regions with semi-hot or hot dry climates. Moreover, B. unamae was isolated from rhizospheres and plants growing in soils with pH values in the range 4·5–7·1, but not from soils with pH values higher than 7·5.
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Affiliation(s)
- Jesús Caballero-Mellado
- Programa de Ecología Molecular y Microbiana, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, México
| | - Lourdes Martínez-Aguilar
- Programa de Ecología Molecular y Microbiana, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, México
| | - Guadalupe Paredes-Valdez
- Programa de Ecología Molecular y Microbiana, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, México
| | - Paulina Estrada-de Los Santos
- Programa de Ecología Molecular y Microbiana, Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de México, Apdo. Postal 565-A, Cuernavaca, Morelos, México
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