Exploring How PN-1 Bacteria Can Protect Ginseng Roots from Rot

Jim Crocker
31st March, 2024

Exploring How PN-1 Bacteria Can Protect Ginseng Roots from Rot

Image Source: Natural Science News, 2024

Key Findings

  • Researchers at Yunnan Normal University found a soil bacterium, Burkholderia arboris PN-1, that stops a plant disease
  • The bacterium was effective against the disease in both lab tests and on living plants
  • The study also mapped the bacterium's genome, revealing genes that may explain its disease-fighting abilities
Panax notoginseng, a plant used in traditional Chinese medicine, is under threat from a disease called root rot, caused by the fungus Fusarium solani. This disease can severely affect the plant's yield and quality, posing a problem for farmers and practitioners who rely on it. However, a recent study by researchers at Yunnan Normal University[1] has found a potential natural solution to this problem in the form of a soil bacterium named Burkholderia arboris PN-1. Burkholderia arboris PN-1 was isolated from the soil surrounding P. notoginseng plants and showed a unique ability to stop the growth of the harmful F. solani fungus. The researchers conducted a series of tests to understand how this bacterium works. They discovered that B. arboris PN-1 could suppress root rot not only in laboratory conditions (in vitro) but also when applied to living plants (in vivo), indicating its potential as a biocontrol agent. To gain deeper insight into the genetic makeup of B. arboris PN-1, the researchers sequenced its entire genome. They found that it consisted of three circular chromosomes with a total of 7,550 genes that code for proteins. Interestingly, unlike some bacteria, B. arboris PN-1 does not carry any plasmids, which are small DNA molecules that can be transferred between bacteria. The genome's high GC content—referring to the proportion of the DNA bases guanine (G) and cytosine (C)—was consistent with the characteristics of the Burkholderia genus. Phylogenetic analysis, which is like creating a family tree based on genetic information, showed that B. arboris PN-1 is closely related to other members of its species. This was further confirmed by comparing the average nucleotide identity (ANI), a measure of genetic similarity, to other B. arboris strains. The study also explored the broader genetic diversity within B. arboris by performing a comparative analysis with seven other strains of the same species. This revealed a set of 4,628 core genes common to all strains, hinting at the essential functions required by the species to survive and thrive. The concept of a pan-genome, as mentioned in previous research[2], encompasses all the genes found within a bacterial species, including core (essential), accessory (optional), and unique (strain-specific) genes. The pan-genome of B. arboris appears to be 'open', suggesting that new genes are still being discovered as more strains are sequenced, although it may eventually reach a point where most of the genetic diversity has been uncovered. Within the genome of B. arboris PN-1, researchers identified specific gene clusters that might hold the key to its biocontrol properties. These include 265 carbohydrate-active enzymes, which may help the bacterium break down plant materials or fungal cell walls, and 9 clusters that could produce secondary metabolites—chemical compounds that are not essential for the bacterium's survival but may have important ecological functions, such as fighting off competitors like F. solani. These findings build upon earlier studies that have recognized Burkholderia species as a new source of natural products with potential applications in drug discovery[3]. The identification of natural product biosynthetic gene clusters (BGCs) in the genomes of Burkholderia species, including the strain S-53, has highlighted the untapped potential of these bacteria in producing new secondary metabolites. Furthermore, the study's approach aligns with advances in genomic analysis tools that have improved our ability to identify genomic islands (GIs)[4]. These are clusters of genes that bacteria can acquire from other organisms, potentially endowing them with new abilities, such as antibiotic resistance or novel metabolic pathways. The improved accuracy of tools like IslandPath-DIMOB in predicting GIs can aid in understanding the genetic basis of microbial adaptability and biocontrol capabilities. In summary, the research conducted by Yunnan Normal University not only offers hope for protecting P. notoginseng from root rot but also contributes to our understanding of the genetic diversity and potential applications of Burkholderia species. The study's integration of phenotypic, phylogenetic, and genomic analyses exemplifies the power of modern genomics to uncover the secrets of microbial life and its potential to solve agricultural problems.

AgricultureBiotechGenetics

References

Main Study

1) Comprehensive genomic analysis of Burkholderia arboris PN-1 reveals its biocontrol potential against Fusarium solani-induced root rot in Panax notoginseng.

Published 30th March, 2024

https://doi.org/10.1007/s00294-024-01288-4

Related Studies

2) BPGA- an ultra-fast pan-genome analysis pipeline.

https://doi.org/10.1038/srep24373

3) Isolation, complete genome sequencing and in silico genome mining of Burkholderia for secondary metabolites.

https://doi.org/10.1186/s12866-022-02692-x

4) Improved genomic island predictions with IslandPath-DIMOB.

https://doi.org/10.1093/bioinformatics/bty095


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