Genomic diversity of culturable Paraburkholderia and Burkholderia species isolated from Bornean rainforest rhizosphere

Alswat, Amal, Webster, Gordon ORCID: https://orcid.org/0000-0002-9530-7835, Mullins, Alex J. ORCID: https://orcid.org/0000-0001-5804-9008, Petrova, Yoana D., Davies, Benjamin J., Jones, Angharad R. ORCID: https://orcid.org/0000-0001-7493-9625, Murray, James A.H., Weightman, Andrew J. ORCID: https://orcid.org/0000-0002-6671-2209, Goossens, Benoit ORCID: https://orcid.org/0000-0003-2360-4643 and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2026. Genomic diversity of culturable Paraburkholderia and Burkholderia species isolated from Bornean rainforest rhizosphere. Microbial Genomics 12 (5) 10.1099/mgen.0.001720

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Abstract

The genus Paraburkholderia was formally separated from Burkholderia in 2014 and now encompasses an expanding diversity of environmental species. To further resolve the taxonomy and functional potential of both genera, we conducted a comprehensive survey of 98 rhizosphere samples from the Bornean rainforest in Sabah, Malaysia, recovering 95 isolates spanning Burkholderia (n=15), Paraburkholderia (n=46) and other bacterial genera (n=34). Given the complexity of Burkholderiaceae classification, genome sequencing of 57 representative isolates coupled with average nucleotide identity (ANI) enabled accurate species assignment. ANI revealed that Burkholderia isolates comprised Burkholderia cepacia (n=7), Burkholderia vietnamiensis (n=2) and Burkholderia diffusa-like (n=3) taxa. Among Paraburkholderia, 22 isolates were assigned to Paraburkholderia tropica, eight to Paraburkholderia bannensis and single isolates to Paraburkholderia heleia and Paraburkholderia guartelaensis. Notably, 12 Paraburkholderia isolates represented putative novel species forming eight distinct genomic taxa. Although Paraburkholderia genomes encoded a broader repertoire of biosynthetic gene cluster classes, detectable antimicrobial activity and known bioactive metabolites (cepacin and pyrrolnitrin) were restricted to Burkholderia. In contrast, Paraburkholderia exhibited strong plant growth–promotion potential, with genomic predictions validated by phosphate solubilization, auxin production and extensive root-associated interactions. These findings reveal the Bornean rainforest rhizosphere as a rich reservoir of Burkholderiaceae diversity, particularly unexplored Paraburkholderia lineages.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Schools > Biosciences
Publisher:	Microbiology Society
ISSN:	2057-5858
Funders:	BBSRC
Projects:	BB/S007652/1, APP2180, BB/Y008537/1, BB/X010619/1
Date of First Compliant Deposit:	26 May 2026
Date of Acceptance:	24 April 2026
Last Modified:	17 Aug 2026 13:19
URI:	https://orca.cardiff.ac.uk/id/eprint/187205

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