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
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.
- Authors:
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- Escuela Nacional de Ciencias Biológicas (Mexico)
- Univ. of Pretoria, Pretoria (South Africa)
- Univ. of California, Los Angeles, CA (United States)
- The James Hutton Inst., Dundee (United Kingdom)
- Weber State Univ., Ogden, UT (United States)
- Santa Cruz State Univ., Ilheus (Brazil)
- Embrapa CENARGEN, Distrito Federal (Brazil)
- Embrapa Cerrados, Distrito Federal (Brazil)
- Univ. of Georgia, Athens, GA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of Oxford, Oxford (United Kingdom)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1544040
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Genes
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 8; Journal ID: ISSN 2073-4425
- Publisher:
- MDPI
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; Burkholderia; Paraburkholderia; Caballeronia; Robbsia; Mimosa; Rhizopus; symbionts; diazotrophy; root nodulation
Citation Formats
Estrada-de los Santos, Paulina, Palmer, Marike, Chávez-Ramírez, Belén, Beukes, Chrizelle, Steenkamp, Emma T., Briscoe, Leah, Khan, Noor, Maluk, Marta, Lafos, Marcel, Humm, Ethan, Arrabit, Monique, Crook, Matthew, Gross, Eduardo, Simon, Marcelo F., dos Reis Junior, Fábio, Whitman, William, Shapiro, Nicole, Poole, Philip S., Hirsch, Ann M., Venter, Stephanus N., and James, Euan K. 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. United States: N. p., 2018.
Web. doi:10.3390/genes9080389.
Estrada-de los Santos, Paulina, Palmer, Marike, Chávez-Ramírez, Belén, Beukes, Chrizelle, Steenkamp, Emma T., Briscoe, Leah, Khan, Noor, Maluk, Marta, Lafos, Marcel, Humm, Ethan, Arrabit, Monique, Crook, Matthew, Gross, Eduardo, Simon, Marcelo F., dos Reis Junior, Fábio, Whitman, William, Shapiro, Nicole, Poole, Philip S., Hirsch, Ann M., Venter, Stephanus N., & James, Euan K. 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. United States. doi:https://doi.org/10.3390/genes9080389
Estrada-de los Santos, Paulina, Palmer, Marike, Chávez-Ramírez, Belén, Beukes, Chrizelle, Steenkamp, Emma T., Briscoe, Leah, Khan, Noor, Maluk, Marta, Lafos, Marcel, Humm, Ethan, Arrabit, Monique, Crook, Matthew, Gross, Eduardo, Simon, Marcelo F., dos Reis Junior, Fábio, Whitman, William, Shapiro, Nicole, Poole, Philip S., Hirsch, Ann M., Venter, Stephanus N., and James, Euan K. Wed .
"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". United States. doi:https://doi.org/10.3390/genes9080389. https://www.osti.gov/servlets/purl/1544040.
@article{osti_1544040,
title = {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},
author = {Estrada-de los Santos, Paulina and Palmer, Marike and Chávez-Ramírez, Belén and Beukes, Chrizelle and Steenkamp, Emma T. and Briscoe, Leah and Khan, Noor and Maluk, Marta and Lafos, Marcel and Humm, Ethan and Arrabit, Monique and Crook, Matthew and Gross, Eduardo and Simon, Marcelo F. and dos Reis Junior, Fábio and Whitman, William and Shapiro, Nicole and Poole, Philip S. and Hirsch, Ann M. and Venter, Stephanus N. and James, Euan K.},
abstractNote = {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.},
doi = {10.3390/genes9080389},
journal = {Genes},
number = 8,
volume = 9,
place = {United States},
year = {2018},
month = {8}
}
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Figures / Tables:
Table 1: The genome sequencing statistics for Burkholderia sensu lato strains sequenced in this study.
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Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies
journal, July 2019
- Dobritsa, Anatoly P.; Samadpour, Mansour
- International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 7
The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential
journal, August 2019
- Webster, Gordon; Mullins, Alex J.; Bettridge, Aimee S.
- Microbiology Resource Announcements, Vol. 8, Issue 34
Potential of Novel Sequence Type of Burkholderia cenocepacia for Biological Control of Root Rot of Maize (Zea mays L.) Caused by Fusarium temperatum
journal, February 2019
- Tagele, Setu; Kim, Sang; Lee, Hyun
- International Journal of Molecular Sciences, Vol. 20, Issue 5
Chromids Aid Genome Expansion and Functional Diversification in the Family Burkholderiaceae
journal, January 2019
- diCenzo, George C.; Mengoni, Alessio; Perrin, Elena
- Molecular Biology and Evolution, Vol. 36, Issue 3
Paraburkholderia strydomiana sp. nov. and Paraburkholderia steynii sp. nov.: rhizobial symbionts of the fynbos legume Hypocalyptus sophoroides
journal, May 2019
- Beukes, Chrizelle W.; Steenkamp, Emma T.; van Zyl, Elritha
- Antonie van Leeuwenhoek, Vol. 112, Issue 9
Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil
journal, March 2020
- Wilhelm, Roland C.; Murphy, Sean J. L.; Feriancek, Nicole M.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3
Genomic Features and Insights into the Taxonomy, Virulence, and Benevolence of Plant-Associated Burkholderia Species
journal, December 2018
- Mannaa, Mohamed; Park, Inmyoung; Seo, Young-Su
- International Journal of Molecular Sciences, Vol. 20, Issue 1
Paraburkholderia dinghuensis sp. nov., isolated from soil
journal, June 2019
- Fu, Jia-cheng; Lv, Ying-ying; You, Jia
- International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 6
Trinickia dabaoshanensis sp. nov., a new name for a lost species
journal, July 2019
- Estrada-de los Santos, Paulina; Palmer, Marike; Steenkamp, Emma T.
- Archives of Microbiology, Vol. 201, Issue 9
A Genomotaxonomy View of the Bradyrhizobium Genus
journal, June 2019
- Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza
- Frontiers in Microbiology, Vol. 10
Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status
journal, March 2020
- Jin, Yuan; Zhou, Jianglin; Zhou, Jing
- Biology Direct, Vol. 15, Issue 1
Deciphering the Symbiotic Plant Microbiome: Translating the Most Recent Discoveries on Rhizobia for the Improvement of Agricultural Practices in Metal-Contaminated and High Saline Lands
journal, September 2019
- Bellabarba, Agnese; Fagorzi, Camilla; diCenzo, George C.
- Agronomy, Vol. 9, Issue 9
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