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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

Journal Article · · Genes
DOI:https://doi.org/10.3390/genes9080389· OSTI ID:1544040
 [1];  [2];  [1];  [2];  [2];  [3];  [3];  [4];  [4];  [3];  [3];  [5];  [6];  [7];  [8];  [9];  [10];  [11];  [3];  [2] more »;  [4] « less
  1. Escuela Nacional de Ciencias Biológicas (Mexico)
  2. Univ. of Pretoria, Pretoria (South Africa)
  3. Univ. of California, Los Angeles, CA (United States)
  4. The James Hutton Inst., Dundee (United Kingdom)
  5. Weber State Univ., Ogden, UT (United States)
  6. Santa Cruz State Univ., Ilheus (Brazil)
  7. Embrapa CENARGEN, Distrito Federal (Brazil)
  8. Embrapa Cerrados, Distrito Federal (Brazil)
  9. Univ. of Georgia, Athens, GA (United States)
  10. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  11. Univ. of Oxford, Oxford (United Kingdom)
+ Show Author Affiliations

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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1544040
Journal Information:
Genes, Vol. 9, Issue 8; ISSN 2073-4425
Publisher:
MDPICopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 131 works
Citation information provided by
Web of Science

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Cited By (56)

Trinickia dabaoshanensis sp. nov., a new name for a lost species journal July 2019
Paraburkholderia guartelaensis sp. nov., a nitrogen-fixing species isolated from nodules of Mimosa gymnas in an ecotone considered as a hotspot of biodiversity in Brazil journal August 2019
Draft Genome of Burkholderia cenocepacia TAtl-371, a Strain from the Burkholderia cepacia Complex Retains Antagonism in Different Carbon and Nitrogen Sources journal February 2019
Paraburkholderia strydomiana sp. nov. and Paraburkholderia steynii sp. nov.: rhizobial symbionts of the fynbos legume Hypocalyptus sophoroides journal May 2019
Structure elucidation and biosynthetic locus of trinickiabactin from the plant pathogenic bacterium Trinickia caryophylli journal October 2019
Chromids Aid Genome Expansion and Functional Diversification in the Family Burkholderiaceae journal January 2019
List of new names and new combinations previously effectively, but not validly, published journal April 2015
Trinickia dinghuensis sp. nov. and Trinickia fusca sp. nov., isolated from forest soil journal May 2019
Paraburkholderia dinghuensis sp. nov., isolated from soil journal June 2019
Minimal standards for the description of new genera and species of rhizobia and agrobacteria journal July 2019
Reclassification of Burkholderia insecticola as Caballeronia insecticola comb. nov. and reliability of conserved signature indels as molecular synapomorphies journal July 2019
Paraburkholderia pallida sp. nov. and Paraburkholderia silviterrae sp. nov., isolated from forest soil journal December 2019
Pararobbsia silviterrae gen. nov., sp. nov., isolated from forest soil and reclassification of Burkholderia alpina as Pararobbsia alpina comb. nov. journal February 2020
Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil journal March 2020
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
Engineering root microbiomes for healthier crops and soils using beneficial, environmentally safe bacteria journal February 2019
Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans journal November 2019
Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status journal March 2020
Both Alpha- and Beta-Rhizobia Occupy the Root Nodules of Vachellia karroo in South Africa journal June 2019
A Genomotaxonomy View of the Bradyrhizobium Genus journal June 2019
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
Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance journal June 2018
Genomic Features and Insights into the Taxonomy, Virulence, and Benevolence of Plant-Associated Burkholderia Species journal December 2018
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
List of new names and new combinations previously effectively, but not validly, published journal March 2020
Impact of Soil Salinity on the Cowpea Nodule-Microbiome and the Isolation of Halotolerant PGPR Strains to Promote Plant Growth under Salinity Stress journal January 2020
List of new names and new combinations previously effectively, but not validly, published journal November 2017
The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential. journalarticle January 2019
List of new names and new combinations previously effectively, but not validly, published journal July 2019
List of new names and new combinations previously effectively, but not validly, published journal September 2013
Exemplar Abstract for Paraburkholderia endofungorum (Partida-Martinez et al. 2007) Sawana et al. 2015, Mycetohabitans endofungorum (Partida-Martinez et al. 2007) Estrada-de los Santos et al. 2018 and Burkholderia endofungorum Partida-Martinez et al. 2007. dataset January 2013
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Exemplar Abstract for Burkholderia caryophylli (Burkholder 1942) Yabuuchi et al. 1993, Paraburkholderia caryophylli (Burkholder 1942) Sawana et al. 2015, Pseudomonas caryophylli (Burkholder 1942) Starr and Burkholder 1942 (Approved Lists 1980) and Trinickia caryophylli (Burkholder 1942) Estrada-de los Santos et al. 2018. dataset January 2013
Exemplar Abstract for Burkholderia dabaoshanensis Zhu et al. 2012 and Trinickia dabaoshanensis (Zhu et al. 2012) Estrada-de Los Santos et al. 2019. dataset January 2018
Nomenclature Abstract for Paraburkholderia caryophylli (Burkholder 1942) Sawana et al. 2015. dataset January 2015
Nomenclature Abstract for Paraburkholderia endofungorum (Partida-Martinez et al. 2007) Sawana et al. 2015. dataset January 2015
Nomenclature Abstract for Paraburkholderia rhizoxinica (Partida-Martinez et al. 2007) Sawana et al. 2015. dataset January 2015
Nomenclature Abstract for Paraburkholderia soli (Yoo et al. 2007) Sawana et al. 2015. dataset January 2015
Nomenclature Abstract for Paraburkholderia symbiotica (Sheu et al. 2012) Sawana et al. 2015. dataset January 2015
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Nomenclature Abstract for Mycetohabitans endofungorum (Partida-Martinez et al. 2007) Estrada-de los Santos et al. 2018. dataset January 2018
Nomenclature Abstract for Mycetohabitans rhizoxinica (Partida-Martinez et al. 2007) Estrada-de los Santos et al. 2018. dataset January 2018
Nomenclature Abstract for Trinickia Estrada-de los Santos et al. 2018. dataset January 2018
Nomenclature Abstract for Trinickia symbiotica (Sheu et al. 2012) Estrada-de los Santos et al. 2018. dataset January 2018
Nomenclature Abstract for Trinickia caryophylli (Burkholder 1942) Estrada-de los Santos et al. 2018. dataset January 2018
Nomenclature Abstract for Trinickia soli (Yoo et al. 2007) Estrada-de los Santos et al. 2018. dataset January 2018
Nomenclature Abstract for Burkholderia dabaoshanensis Zhu et al. 2012. dataset January 2018
Nomenclature Abstract for Trinickia dabaoshanensis (Zhu et al. 2012) Estrada-de Los Santos et al. 2019. dataset January 2018
Taxonomic Abstract for the families. dataset January 2013
Taxonomic Abstract for the genera. dataset January 2018
Taxonomic Abstract for the species. dataset January 2018
Taxonomic Abstract for the species. dataset January 2018
Taxonomic Abstract for the genera. dataset January 2018
Taxonomic Abstract for the species. dataset January 2018
Taxonomic Abstract for the species. dataset January 2018
Taxonomic Abstract for the species. dataset January 2018

Figures / Tables (7)

Table 1(p. 4)table Table 1
Figure 1(p. 8)figure Figure 1
Figure 2(p. 9)figure Figure 2
Table 2(p. 11)table Table 2
Figure 3(p. 13)figure Figure 3
Table 3(p. 14)table Table 3
Figure 4(p. 16)figure Figure 4

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59 BASIC BIOLOGICAL SCIENCES
Genetics & Heredity
Burkholderia
Paraburkholderia
Caballeronia
Robbsia
Mimosa
Rhizopus
symbionts
diazotrophy
root nodulation