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Article

Bacillus velezensis SM1: A Promising Biocontrol Solution for Phytophthora Durian Root Rot

by
Ashara Pengnoo
1,*,
Usman Lohlaeh
1,
Fadila Maduerehand
1,
Chuthamard Kaewmano
1,
Sudanai Krualee
2,
Pimchana Wongpisal
2,
Wipa Homhaul
3,
Pawika Boonyapipat
4,
Sukhumaporn Saeng-ngam
5,
Abbas Äkbärjan
6 and
Vipaporn Phuntumart
6
1
Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
2
Faculty of Agriculture, Nakhon Si Thammarat Campus, Rajamangala University of Srivijaya, Nakhon Si Thammarat 80240, Thailand
3
Faculty of Agriculture, Natural Resources and Environment Naresuan University, Phitsanulok 65000, Thailand
4
Faculty of Agricultural Technology, Songkhla Rajabhat University, Songkhla 90000, Thailand
5
Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
6
Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43402, USA
*
Author to whom correspondence should be addressed.
Appl. Microbiol. 2025, 5(1), 21; https://doi.org/10.3390/applmicrobiol5010021
Submission received: 20 January 2025 / Revised: 9 February 2025 / Accepted: 12 February 2025 / Published: 17 February 2025
(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2025))
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Abstract

:
Plant diseases, particularly root rot caused by Phytophthora species, pose a significant threat to plants. In this study, we investigated the antagonistic activity of a Bacillus velezensis strain (Bv-SM1) against Phytophthora palmivora isolates, NKST002 and CP002, which cause root rot in durian. In vitro assays using dual-plate, pour-plate, and volatile organic compounds demonstrated a strong inhibition of Phytophthora mycelial growth by Bv-SM1. Phylogenomic analysis based on 1000 genes confirmed that Bv-SM1 is most closely related to B. velezensis. Genome analysis revealed the presence of key genes that contribute to biocontrol activity, including genes encoding cell wall-degrading enzymes (β-glucanase and cellulase) and siderophore production. Additionally, 13 biosynthetic gene clusters are responsible for the production of various antimicrobial compounds, such as fengycin, bacillaene, macrolactin, and bacilysin. These findings are the first to demonstrate the potential of Bv-SM1 as a promising biocontrol agent for managing Phytophthora-induced root rot in durian, with potential applications in other crops.

1. Introduction

Durian (Durio zibethinus Murr.) often referred to as the “king of fruits”, is economically and culturally significant in Southeast Asia [1]. According to the report on Durian Global Trade Overview 2023 by the Food and Agriculture Organization of the United Nations, global durian exports have increased more than tenfold over the past decade, rising from around 80,000 tons in 2003 to approximately 870,000 tons in 2022. Thailand is the leading exporter of durian, representing an average of 94 percent of global shipments from 2020 to 2022, with the export value at an average of USD 3.3 billion in 2021–2022 [2]. Despite its dominance in the global market, plant pathogens represent one of the most significant threats to durian cultivation, often causing substantial damage to the crop. In recent years, durian cultivation has faced challenges from oomycete pathogens belonging to the genus Phytophthora and Pythium, which are responsible for causing root rot [3,4,5,6]. Phytophthora palmivora (E.J. Butler) E.J. Butler, in particular, has been found in most orchards in Thailand and poses significant economic impacts on durian production [3,4,5]. Traditional chemical treatments are not fully effective and have raised concerns due to environmental pollution, pathogen resistance, and negative impacts on non-target organisms. This is because most fungicides are designed to target true fungi rather than oomycetes. Moreover, the pathogens developed resistance to these fungicides [4,5,6]. Another commonly employed method in fruit tree production includes grafting, in which Phytophthora-resistant rootstocks were used to provide protection against the diseases of susceptible plants [7,8,9]. This method, however, can reduce genetic diversity, lead to pathogen adaptation, cause incompatibility or growth issues, and potentially disrupt local ecosystems, while also being costly and less sustainable in the long term.
In recent years, the search for sustainable alternatives has brought biological control agents to the forefront of plant disease management. Among these, bacteria in the Bacillus genus have shown promise as effective biocontrol agents against plant pathogens. Bacillus subtilis, for example, has been demonstrated to effectively control soilborne pathogens like Fusarium spp., Rhizoctonia spp., Phytophthora spp., and Pythium spp. in crops such as tomato, peppers, and cucumbers [10,11,12,13]. Several strains of Bacillus amyloliquefaciens have also been used successfully to control fungal pathogens such as Colletotrichum dematium (mulberry) [14], F. oxysporum f. sp. cubense (banana) [15], Botrytis cinerea (tomato) [16], F. oxysporum f. sp. lycopersici (tomato) [17], and Colletotrichum truncatum (alfalfa) [18]. Due to its effectiveness against Botrytis cinerea, B. velezensis has been commercialized as the fungicide Botrybel by Agricaldes, Spain (review in ref. [19]). This successful application of Bacillus strains underscores the importance of precise bacterial identification. In fact, genomic analysis led to the reclassification of some bacteria such as B. amyloliquefaciens strains as B. velezensis, including strain FZB42 [20]. This taxonomic revision highlights the role of genomics in accurate bacterial identification, crucial for optimizing biocontrol applications.
Most microbial biocontrol agents suppress pathogens by outcompeting them for nutrients and producing antifungal compounds. In addition to these mechanisms, many biocontrol agents also enhance plant defense responses, induce systemic resistance, and promote beneficial soil microbiomes [21,22,23]. Some biocontrol microbes can produce enzymes that degrade pathogen cell walls, further inhibiting pathogen growth [10,24,25,26]. These natural biocontrol agents offer a sustainable alternative to chemical fungicides, enhancing crop resilience and contributing to environmentally friendly agricultural practices.
This study explores the efficacy of Bacillus velezensis SM1 (Bv-SM1) and its mechanisms of action in controlling Phytophthora root rot in durian. We combine experimental methods with genomic approaches to evaluate the effectiveness of Bv-SM1 in suppressing Phytophthora growth and to examine the underlying mechanisms through genome analysis. The ultimate goal is to contribute to the development of integrated pest management strategies that are both effective and ecologically responsible.

2. Materials and Methods

2.1. Isolation and Identification of a Bacterial Biocontrol Agent

Soil samples were collected from a para-rubber (Hevea brasiliensis) plantation located in southern Thailand, at a depth of approximately 20 cm from the surface. The isolation of potential biocontrol agents was performed as described in refs. [27,28]. Briefly, each soil sample was added to sterile water (1: 10, w/v). The mixture was homogenized and serial dilutions were prepared. To select spore-forming bacteria, the dilution was heated at 80 °C for 20 min in a water bath. Following the heat treatment, 100 μL of the soil suspension was plated on potato dextrose agar (PDA). Colonies resembling Bacillus species were selected and subjected to further analysis for identification. Physical and biochemical tests were performed according to the UK Standards for Microbiology Investigations (Public Health England, 2018). For molecular identification, PCR was performed using primers 27F and 1525R to amplify the rRNA genes [29]. The amplicons were sequenced by Gibthai (Bangkok, Thailand) and the DNA Sequencing and Genotyping Facility, University of Chicago Comprehensive Cancer Center (Chicago, IL, USA), followed by nucleotide sequence analysis (BLASTN) against the National Center for Biotechnology Information (NCBI) database (https://blast.ncbi.nlm.nih.gov/Blast.cgi, accessed on 1 December 2024).

2.2. In Vitro Screening of Antifungal Activity Against P. palmivora Isolates NKST002 and CP002

The antimicrobial activity against two isolates of P. palmivora was performed using a dual culture method [27,28]. Briefly, an agar disk (4 mm) of each five-day-old Phytophthora was placed at the center of the PDA plate and the bacterial isolate was streaked in a single line at the opposite side of the test pathogen approximately 2 cm from the edge of the PDA plates and incubated at 28 °C. The plates were incubated at room temperature for a duration of 14 days or until Phytophthora in the control plate almost covered the entire surface, whichever occurred first. Phytophthora plugs placed on uninoculated PDA plates served as controls. The experiment was repeated three times and performed in ten replicates. The percentage of inhibition was evaluated daily by measuring the diameter of the Phytophthora colony in each plate. The percentage of inhibition of radial growth (PIRG) was assessed using the formula: PIRG (%) = 100 × (R1 − R2)/R1, where R1 represents the radial growth of Phytophthora in the control group and R2 represents the radial growth of the test group [30].

2.3. Antifungal Activity of Volatile Organic Compounds from Bv-SM1 on P. palmivora Isolates NKST002 and CP002

To examine the impact of volatile organic compounds (VOCs) produced by Bv-SM1 on the mycelial growth of Phytophthora, we conducted a dual-Petri dish assay to examine the impact on the mycelial growth of Phytophthora [31]. Briefly, Phytophthora strains and Bv-SM1 were cultured on PDA plates for 7 days. The lid of each plate was removed, and a second PDA plate was placed upside down over the first plate. The two plates were then sealed together using Parafilm. The dual-culture setup was incubated at 23–25 °C for 7 days. Control plates, containing only Phytophthora without Bv-SM1, were also prepared. After incubation, the colony diameter of Phytophthora in both the control and treatment groups was measured, and colony morphology was observed under microscope. The experiment was performed in triplicate and repeated three times.

2.4. Assessing the Efficacy of Bv-SM1 in Controlling Phytophthora

A detached leaf method was used to assess the efficacy of Bv-SM1 [32]. Monthong durian leaf was rinsed with sterile water and surface sterilized with 10% bleach, followed by rinsing three times with sterile distilled water to remove any residual bleach. Each leaf was then treated with a Bv-SM1 suspension prepared from an overnight culture (OD 1.0) adjusted to a concentration of 107 CFU/mL, and then left to dry for an hour at room temperature. Following treatment, the leaves were inoculated with a 4-day-old agar plaque of either P. palmivora NKST002 or P. palmivora CP002. Control leaves, which were not treated with Bv-SM1, were also inoculated with both Phytophthora isolates for comparison. The experiment included four replicates, with each replicate consisting of four leaves per treatment. The leaves were incubated at room temperature for seven days. The brown rot around the wound was measured in diameter and photographed.

2.5. Genome Sequencing and Annotation

The genome of Bv-SM1 was sequenced by SeqCenter (Pittsburgh, PA, USA) using combined Nanopore and Illumina sequencing. For Nanopore sequencing, genomic DNA was prepared using the Rapid Barcoding Kit (SQK-RBK004) with size selection on a Blue Pippin system to remove fragments below 8 kb. Libraries were loaded onto R9.4.1 flow cells and sequenced on the MinION device for 48 h. For Illumina sequencing, sample libraries were prepared using the Illumina DNA Prep kit and IDT 10 bp UDI indices and sequenced on an Illumina NextSeq 2000, producing 2 × 151 bp reads, which were then sequenced on an Illumina NextSeq 2000. A hybrid assembly was generated by combining both read types in Unicycler version 0.4.8 [33] by using a hybrid strategy that combined sample libraries, which were prepared using the Illumina DNA Prep kit and IDT 10 bp UDI indices, and then sequenced on an Illumina NextSeq 2000, producing 2 × 151 bp reads. Demultiplexing, quality control, and adapter trimming were performed with bcl-convert (v3.9.3), a proprietary Illumina software for the conversion of bcl files to base calls (https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html, accessed on 5 January 2025). Read files were imported into the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) (https://www.bv-brc.org/, accessed on 5 January 2025). An automated pipeline of programs was used to assemble reads into genomes with the default parameters. Biosynthetic gene clusters were identified using the antiSMASH web server (version 7.1.0; https://antismash.secondarymetabolites.org/, accessed on 5 January 2025) in “relaxed” mode with all additional features enabled.

3. Results

3.1. Bacterial Isolation and Identification

Approximately 60 bacterial isolates resembling Bacillus were obtained from a soil sample. The visual characteristics of the colonies were round, white, rough, and slightly glossy. These isolates are gram-positive bacteria with rod-shaped morphology and the ability to form spores. Biochemical tests showed positive results for catalase, nitrate reductase, and starch hydrolase activities. They were grown and maintained on potato dextrose agar (PDA) at room temperature (28 °C). This study focuses on Bv-SM1 due to its highest efficiency observed in the agar plate assay. A PCR amplicon of the 16S rRNA gene was 1555 bp. The GenBank accession number for the nucleotide sequence of 16S rRNA is OR056195.1 (https://www.ncbi.nlm.nih.gov/nuccore/OR056195.1, accessed on 5 January 2025). BLAST analysis indicated that Bv-SM1 is a member of the Bacillus group but could not be accurately assigned to a specific species due to low discrimination.
To improve accuracy, nucleotide and amino acid sequences from 1000 genes were utilized to construct a phylogenomic tree using the Phylogenetic Tree Building tool provided by the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) [34]. The phylogenetic analysis indicated that Bv-SM1 clusters with B. velezensis with 100% bootstrap support. Notably, Bv-SM1 also exhibits 100% bootstrap support with B. subtilis, suggesting a high degree of genetic similarity between these two species. However, the shorter branch length observed for B. velezensis (Figure 1) supports the conclusion that Bv-SM1 is more closely related to B. velezensis.

3.2. In Vitro Antagonistic Assays

Bv-SM1 was tested against two isolates, P. palmivora NKST002 (OQ940455.1) (https://www.ncbi.nlm.nih.gov/nuccore/OQ940455.1/, accessed on 5 January 2025) and P. palmivora CP002 (OQ940453.1) (https://www.ncbi.nlm.nih.gov/search/all/?term=OQ940453.1, accessed on 5 January 2025). The colonies were measured daily for 14 days. The results for days 7 and 14 are shown in Table 1. On day 7, the growth of P. palmivora NKST002 in the presence of Bv-SM1 was 0.88 ± 0.09 cm, compared to 3.01 ± 0.03 cm in the control. On day 14, the growth of P. palmivora NKST002 was 1.06 ± 0.06 cm in the presence of Bv-SM1, compared to 5.02 ± 0.07 cm in the control. For P. palmivora CP002, the colony growth in the presence of Bv-SM1 was 1.06 ± 0.06 cm on day 7, compared to 3.00 ± 0.04 cm in the control, and 1.20 ± 0.05 cm on day 14, compared to 5.00 ± 0.12 cm in the control (Figure 2, Table 1). Using the PIRG formula, the results showed that Bv-SM1 exhibited antagonistic activity against both isolates, with inhibition rates of 79% and 76% at day 14, respectively.

3.3. Antifungal Activity of Volatile Organic Compounds

The antifungal activity of VOCs produced by Bv-SM1 on the mycelial growth of Phytophthora was assessed using a dual-Petri dish assay. After 6 days of incubation, the results showed that Phytophthora growth was significantly inhibited in the presence of VOCs from Bv-SM1. The colony diameter of P. palmivora NKST002 was reduced from 5 cm to 2.11 cm in the presence of VOCs compared to the control, and P. palmivora CP002 was reduced from 5 cm to 2.0 cm in the presence of VOCs compared to the control (Figure 3, Table 2). This corresponded to growth inhibition of 57.75 ± 1.71% for P. palmivora NKST002 and 60.00 ± 4.08% for P. palmivora CP002.

3.4. Efficacy of Bv-SM1 in Controlling Phytophthora on Durian Leaves

After inoculating the durian leaves with P. palmivora NKST002 and applying Bacillus suspended cells, it was observed that at day 3, Bv-SM1 did not cause any lesions on the durian leaves, compared to slight lesions in the control group (no Bv-SM1). At day 5, lesions on the durian leaves were observed only in the control group. At day 7, durian leaves pre-treated with suspended Bv-SM1 exhibited reduced lesion sizes of 3.78 cm and 2.16 cm when challenged with P. palmivora NKST002 (A) and P. palmivora CP002 (B), respectively. In contrast, untreated control leaves developed larger lesions measuring 5.06 cm and 4.73 cm when inoculated with P. palmivora NKST002 (C) and P. palmivora CP002 (D), respectively. (Table 3, Figure 4).

3.5. General Genomic Feature

The raw genome sequence data of Bv-SM1 are deposited in NCBI under BioProject at accession PRJNA1205391 (https://submit.ncbi.nlm.nih.gov/subs/bioproject/SUB14983505/overview, accessed on 5 January 2025). The draft genome is 3,964,444 bp in length with a G + C content of 46.19 mol% and an N50 score of 2,988,422 bp. Sequence analysis using BV-BRC revealed that the Bv-SM1 genome contains 4100 putative protein-coding genes. Of these, 1129 were assigned to hypothetical proteins, and 2971 proteins were assigned to the function, including 86 genes encoding tRNAs and 27 genes encoding rRNAs (Table 4). The completeness and contamination of the genome of strain R-35 were 100% and 0.2%, respectively.

3.6. Genes Associated with Antagonistic Features

3.6.1. Hydrolytic Enzymes

A genome analysis of Bv-SM1 revealed gene encoding of the hydrolytic enzyme cellulase, specifically endo-beta-1,3-1,4 glucanase, which hydrolyzes both 1,3- and 1,4-β-D-glycosidic bonds in cellulose, a major component of Phytophthora cell walls, releasing glucose [35,36,37,38]. Bv-SM1 also produces putative protease, which breaks down the protein matrix in the cell wall and degrades phytopathogen proteins into peptides and amino acids, disrupting their function [35,37,38,39,40]. Additionally, it contains different types of lipase genes, including phospholipase and acetyl esterases, which degrade acetyl groups in pathogen cell walls, weakening structural integrity and enhancing antimicrobial penetration. This process also releases carbon sources for beneficial microorganisms and can trigger plant defense responses [39,41,42,43]. Lysophospholipase and monoglyceride lipase further contribute to pathogen control by disrupting membrane lipids, leading to cell lysis and death, while releasing fatty acids for microbial nutrition.

3.6.2. Siderophores

Siderophores play a crucial role in the biocontrol of plant pathogens by acting as iron-chelating molecules. They deprive pathogens of the essential iron needed for their growth and development, thereby inhibiting infection and disease progression [41,42,44]. Essentially, siderophores “out-compete” pathogens by binding iron in the environment, making it unavailable to the pathogen and limiting its ability to cause disease [44,45,46]. Bv-SM1 contains a large number of genes associated with siderophore production, indicating its potential biocontrol capabilities. These 85 siderophore-related genes include nine non-ribosomal peptide synthetase modules involved in siderophore biosynthesis, five siderophore biosynthesis genes, and 24 siderophore transporter systems. The remaining genes encode enzymes involved in the biosynthesis of siderophores.

3.6.3. Secondary Metabolites

Secondary metabolite gene cluster analysis using antiSMASH identified 13 biosynthetic gene clusters (Figure 5). Sequence homology ranged from 7% to 100% similarity to known BGCs. Region 1 contained seven non-ribosomal peptide synthetase clusters: fengycin, bacillaene, macrolactin H, butirosin A, surfactin, bacilysin, and bacillibactin. Region 2 showed one type III polyketide synthase (T3PKS) cluster. Region 3 contained plipastatin and terpene clusters (Table 5). Notably, the T3PKS and terpene BGCs contained essential domains but showed no sequence homology to previously characterized BGCs.

4. Discussion

Plant diseases pose a critical threat to crop production. While chemical pesticides are commonly used, they can lead to fungal resistance and harm non-target organisms. This has driven interest in biological control methods as sustainable alternatives. Our study examined the antifungal activity of an orchard-isolated bacterium against Phytophthora root rot disease in durian. Phylogenetic trees based on the 16S rRNA genes and a concatenated tree of five housekeeping genes showed that it belongs to B. velezensis. Full genome analysis of ANI analysis proves that the identity of our strain is closely related to B. velezensis FZB42. Bacillus velezensis has emerged as a significant biocontrol agent due to its wide spectrum of antagonistic activity against phytopathogens, including Fusarium oxysporum, Fusarium graminearum, Botrytis cinerea, and Alternaria alternata [15,17,19,20,24,25,47,48,49,50]. For controlling Phytophthora species, B. velezensis strains exhibit antagonistic activity against several species, including P. sojae, P. infestans, and P. nicotianae [20,51,52].
In this study, we investigated the antagonistic activity of Bv-SM1 against two Phytophthora pathogens that cause root rot in durian: Phytophthora palmivora and Phytophthora palmivora. Our in vitro assays demonstrated that Bv-SM1 strongly inhibited the growth of these durian pathogens. This antagonism is known to occur through multiple mechanisms, including bioactive compounds, enzyme production, nutrient competition, plant defense induction, and siderophore-mediated iron sequestration [11,53,54,55,56]. Genome analysis of Bv-SM1 revealed the presence of cell wall-degrading enzymes, including β-glucanase and cellulase, consistent with prior studies that demonstrated their role in fungal cell wall degradation and pathogen control [10,17,23]. The genome also contains a large number of genes associated with siderophore production and transport, suggesting that these iron-chelating compounds contribute significantly to its biocontrol capabilities [10,11,17,57,58,59]. Secondary metabolites play key roles in the antagonistic activity of biocontrol agents. Many species of B. velezensis produce these bioactive compounds [23,60,61,62,63,64]. AntiSMASH identified 13 biosynthetic gene clusters responsible for producing various antimicrobial compounds: polyketide antibiotics (fengycin, bacillaene, macrolactin, butirosin, difficidin), cyclic lipopeptides (fengycin, surfactin), a siderophore (bacillibactin), and lipopeptides (bacilysin and plipastatin). Notably, bacilysin, produced by B. velezensis FZB42, has been shown to control Phytophthora sojae in soybeans [20]. Fengycin exhibits antifungal activity against both plant and human pathogenic fungi, while bacilysin and plipastatin disrupt bacterial membrane permeability and biofilm formation [10,18,23,47,60,61,63,65]. These findings highlight the potential of Bv-SM1 as a promising biocontrol agent for protecting durian and potentially other crops against pathogenic infection.

5. Conclusions

This is the first study to demonstrate the effectiveness of the Bacillus velezensis strain SM1 in controlling the growth of Phytophthora palmivora, which causes root rot in durian. The strain shows strong antagonistic activity through multiple mechanisms, supported by genomic evidence of biocontrol-related genes and antimicrobial compound production. These findings highlight Bv-SM1’s potential as a promising biocontrol agent for managing Phytophthora infections in durian and potentially other crops.

Author Contributions

Conceptualization, A.P., U.L., W.H., and V.P.; Data curation, U.L., S.K., A.Ä., and V.P.; Formal analysis, U.L., F.M., and V.P.; Funding acquisition, A.P., S.K., W.H., S.S.-n., and P.B.; Investigation, A.P., U.L., F.M., C.K., S.K., W.H., S.S.-n., P.W., W.H., and A.Ä.; Methodology, A.P., U.L., F.M., C.K., S.K., P.W., W.H., and P.B.; Project administration, A.P., S.K., W.H., S.S.-n., and P.B.; Resources, A.P., S.K., W.H., P.B., and A.Ä.; Software, U.L., F.M., P.W., A.Ä., and V.P.; Supervision, A.P., W.H., and P.B.; Validation, U.L., C.K., and V.P.; Visualization, A.P., A.Ä., and V.P.; Writing—original draft, V.P.; Writing—review and editing, A.P., U.L., F.M., C.K., S.K., P.W., W.H., P.B., S.S.-n., A.Ä., and V.P. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Research Council of Thailand (NRCT), grant number N21A650768; Bowling Green State University Building Strength (Award No. 33000339); and the Fulbright U.S. Scholar Program (2023).

Data Availability Statement

The raw genome sequence of Bv-SM1 has been deposited at the NCBI and is publicly available under the BioProject PRJNA1205391 (https://submit.ncbi.nlm.nih.gov/subs/bioproject/SUB14983505/overview, accessed on 5 January 2025).

Acknowledgments

We thank Leela Cromwell, Paul Morris, and Dan Pavuk of Bowling Green State University, as well as the anonymous reviewers for their critical reading of the manuscripts.

Conflicts of Interest

The authors declare no conflicts of interest.

Abbreviations

The following abbreviations are used in this manuscript:
Bacillus velezensis strain SM1
BGCs		Bv-SM1
Biosynthetic gene clusters
Phytophthora palmivora
Phytophthora palmivora isolate NKST002		P. palmivora
NKST002
Phytophthora palmivora isolate CP002CP002

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Applmicrobiol 05 00021 g001
Figure 1. A phylogenomic tree of B. velezensis SM1 (in red), inferred from the alignment of nucleotide and amino acid sequences of 1000 shared genes across 10 genomes each from Bacillus subtilis and Bacillus velezensis, generated using the BV-BRC Phylogenetic Tree Building tool. Bootstrap values are shown in black and branch lengths are represented in gray.
Figure 1. A phylogenomic tree of B. velezensis SM1 (in red), inferred from the alignment of nucleotide and amino acid sequences of 1000 shared genes across 10 genomes each from Bacillus subtilis and Bacillus velezensis, generated using the BV-BRC Phylogenetic Tree Building tool. Bootstrap values are shown in black and branch lengths are represented in gray.
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Figure 2. Bv-SM1 antagonistic activity against P. palmivora: (A) isolate NKST002 by dual culture; (B) by pour plate; (C) isolate CP002 by dual culture; (D) by pour plate.
Figure 2. Bv-SM1 antagonistic activity against P. palmivora: (A) isolate NKST002 by dual culture; (B) by pour plate; (C) isolate CP002 by dual culture; (D) by pour plate.
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Figure 3. Antagonistic activity of volatile organic compounds from Bv-SM1 against (A) P. palmivora NKST002 and (B) P. palmivora CP002.
Figure 3. Antagonistic activity of volatile organic compounds from Bv-SM1 against (A) P. palmivora NKST002 and (B) P. palmivora CP002.
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Figure 4. Detached leaf assays of Bv-SM1 antagonistic activity against (A) P. palmivora NKST002 without Bv-SM1; (B) P. palmivora NKST002 treated with Bv-SM1; (C) P. palmivora CP002 without Bv-SM1; (D) P. palmivora CP002 treated with Bv-SM1.
Figure 4. Detached leaf assays of Bv-SM1 antagonistic activity against (A) P. palmivora NKST002 without Bv-SM1; (B) P. palmivora NKST002 treated with Bv-SM1; (C) P. palmivora CP002 without Bv-SM1; (D) P. palmivora CP002 treated with Bv-SM1.
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Figure 5. AntiSMASH output of biosynthetic gene clusters detected in the draft genome assembly of Bv-SM1.
Figure 5. AntiSMASH output of biosynthetic gene clusters detected in the draft genome assembly of Bv-SM1.
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Table 1. Growth inhibition of mycelial Phytophthotra by Bv-SM1.
Table 1. Growth inhibition of mycelial Phytophthotra by Bv-SM1.
IsolateGrowth of Isolate NKST002 (cm) Growth of Isolate CP002 (cm)
Day 7Day 14Day 7Day 14
Bv-SM1 0.88 ± 0.091.06 ± 0.061.06 ± 0.061.20 ± 0.05
Control3.01 ± 0.03 5.02 ± 0.07 3.00 ± 0.045.00 ± 0.12
Table 2. Growth inhibition of mycelial Phytophthora by volatile organic compounds from Bv-SM1 at day 6.
Table 2. Growth inhibition of mycelial Phytophthora by volatile organic compounds from Bv-SM1 at day 6.
IsolateGrowth of Isolate NKST002 (cm)Growth of Isolate CP002 (cm)
Bv-SM12.20 ± 0.202.11 ± 0.09
Control5.00 ± 0.005.00 ± 0.00
Table 3. Growth inhibition of Phytophthora by Bv-SM1 on durian leaves.
Table 3. Growth inhibition of Phytophthora by Bv-SM1 on durian leaves.
IsolateGrowth of Isolate NKST002 (cm)Growth of Isolate CP002 (cm)
Day 3Day 5Day 7Day 3Day 5Day 7
Bv-SM1 0.00 ± 0.00 0.62 ± 0.17 3.78 ± 0.41 0.03 ± 0.02 0.36 ± 0.18 2.16 ± 0.32
Control 0.09 ± 0.09 1.32 ± 0.16 5.06 ± 0.59 0.30 ± 0.021.37 ± 0.24 4.73 ± 0.29
Table 4. Summary of draft genome and annotation statistics for Bv-SM1.
Table 4. Summary of draft genome and annotation statistics for Bv-SM1.
Contigs20 (https://www.bv-brc.org/view/Genome/2.14291#view_tab=sequences, accessed on 5 January 2025)
Genome Length3,964,444
GC Content46.19
Contig N502,988,422
tRNA86
rRNA27
CDS4100
Hypothetical CDS1129
Table 5. Summary of biosynthetic gene clusters (BGCs) identified by antiSMASH.
Table 5. Summary of biosynthetic gene clusters (BGCs) identified by antiSMASH.
Metabolite% Similarity with a Bacterium
fengycin93% Bacillus velezensis FZB42
bacillaene100% Bacillus velezensis FZB42
macrolactin H100% Bacillus velezensis FZB42
butirosin A7% Bacillus circulans
surfactin82% Bacillus velezensis FZB42
bacilysin100% Bacillus velezensis FZB42
bacillibactin100% Bacillus subtilis subsp. subtilis str. 168
type III polyketide synthase (T3PKS)No known cluster
plipastatin30% Bacillus subtilis subsp. subtilis
terpeneNo known cluster identified
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Pengnoo, A.; Lohlaeh, U.; Maduerehand, F.; Kaewmano, C.; Krualee, S.; Wongpisal, P.; Homhaul, W.; Boonyapipat, P.; Saeng-ngam, S.; Äkbärjan, A.; et al. Bacillus velezensis SM1: A Promising Biocontrol Solution for Phytophthora Durian Root Rot. Appl. Microbiol. 2025, 5, 21. https://doi.org/10.3390/applmicrobiol5010021

AMA Style

Pengnoo A, Lohlaeh U, Maduerehand F, Kaewmano C, Krualee S, Wongpisal P, Homhaul W, Boonyapipat P, Saeng-ngam S, Äkbärjan A, et al. Bacillus velezensis SM1: A Promising Biocontrol Solution for Phytophthora Durian Root Rot. Applied Microbiology. 2025; 5(1):21. https://doi.org/10.3390/applmicrobiol5010021

Chicago/Turabian Style

Pengnoo, Ashara, Usman Lohlaeh, Fadila Maduerehand, Chuthamard Kaewmano, Sudanai Krualee, Pimchana Wongpisal, Wipa Homhaul, Pawika Boonyapipat, Sukhumaporn Saeng-ngam, Abbas Äkbärjan, and et al. 2025. "Bacillus velezensis SM1: A Promising Biocontrol Solution for Phytophthora Durian Root Rot" Applied Microbiology 5, no. 1: 21. https://doi.org/10.3390/applmicrobiol5010021

APA Style

Pengnoo, A., Lohlaeh, U., Maduerehand, F., Kaewmano, C., Krualee, S., Wongpisal, P., Homhaul, W., Boonyapipat, P., Saeng-ngam, S., Äkbärjan, A., & Phuntumart, V. (2025). Bacillus velezensis SM1: A Promising Biocontrol Solution for Phytophthora Durian Root Rot. Applied Microbiology, 5(1), 21. https://doi.org/10.3390/applmicrobiol5010021

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