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Shan Y, Wang D, Zhao FH, Song J, Zhu H, Li Y, Zhang XJ, Dai XF, Han D, Chen JY. Insights into the biocontrol and plant growth promotion functions of Bacillus altitudinis strain KRS010 against Verticillium dahliae. BMC Biol 2024; 22:116. [PMID: 38764012 PMCID: PMC11103837 DOI: 10.1186/s12915-024-01913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Verticillium wilt, caused by the fungus Verticillium dahliae, is a soil-borne vascular fungal disease, which has caused great losses to cotton yield and quality worldwide. The strain KRS010 was isolated from the seed of Verticillium wilt-resistant Gossypium hirsutum cultivar "Zhongzhimian No. 2." RESULTS The strain KRS010 has a broad-spectrum antifungal activity to various pathogenic fungi as Verticillium dahliae, Botrytis cinerea, Fusarium spp., Colletotrichum spp., and Magnaporthe oryzae, of which the inhibition rate of V. dahliae mycelial growth was 73.97% and 84.39% respectively through confrontation test and volatile organic compounds (VOCs) treatments. The strain was identified as Bacillus altitudinis by phylogenetic analysis based on complete genome sequences, and the strain physio-biochemical characteristics were detected, including growth-promoting ability and active enzymes. Moreover, the control efficiency of KRS010 against Verticillium wilt of cotton was 93.59%. After treatment with KRS010 culture, the biomass of V. dahliae was reduced. The biomass of V. dahliae in the control group (Vd991 alone) was 30.76-folds higher than that in the treatment group (KRS010+Vd991). From a molecular biological aspect, KRS010 could trigger plant immunity by inducing systemic resistance (ISR) activated by salicylic acid (SA) and jasmonic acid (JA) signaling pathways. Its extracellular metabolites and VOCs inhibited the melanin biosynthesis of V. dahliae. In addition, KRS010 had been characterized as the ability to promote plant growth. CONCLUSIONS This study indicated that B. altitudinis KRS010 is a beneficial microbe with a potential for controlling Verticillium wilt of cotton, as well as promoting plant growth.
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Affiliation(s)
- Yujia Shan
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157012, China
| | - Dan Wang
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Fu-Hua Zhao
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157012, China
| | - Jian Song
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - He Zhu
- The Cotton Research Center of Liaoning Academy of Agricultural Sciences, National Cotton Industry Technology System Liaohe Comprehensive Experimental Station, Liaoning Provincial Institute of Economic Crops, Liaoyang, 111000, China
| | - Yue Li
- The Cotton Research Center of Liaoning Academy of Agricultural Sciences, National Cotton Industry Technology System Liaohe Comprehensive Experimental Station, Liaoning Provincial Institute of Economic Crops, Liaoyang, 111000, China
| | - Xiao-Jun Zhang
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157012, China
| | - Xiao-Feng Dai
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China
| | - Dongfei Han
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, 100081, China.
| | - Jie-Yin Chen
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100, China.
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Yang Y, Wang H, Tu J, Li Y, Guan H. Comprehensive genomic analysis of Burkholderia arboris PN-1 reveals its biocontrol potential against Fusarium solani-induced root rot in Panax notoginseng. Curr Genet 2024; 70:4. [PMID: 38555312 DOI: 10.1007/s00294-024-01288-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Panax notoginseng (Burkill) F.H. Chen, a valuable traditional Chinese medicine, faces significant yield and quality challenges stemming from root rot primarily caused by Fusarium solani. Burkholderia arboris PN-1, isolated from the rhizosphere soil of P. notoginseng, demonstrated a remarkable ability to inhibit the growth of F. solani. This study integrates phenotypic, phylogenetic, and genomic analyses to enhance our understanding of the biocontrol mechanisms employed by B. arboris PN-1. Phenotype analysis reveals that B. arboris PN-1 effectively suppresses P. notoginseng root rot both in vitro and in vivo. The genome of B. arboris PN-1 comprises three circular chromosomes (contig 1: 3,651,544 bp, contig 2: 1,355,460 bp, and contig 3: 3,471,056 bp), with a 66.81% GC content, housing 7,550 protein-coding genes. Notably, no plasmids were detected. Phylogenetic analysis places PN-1 in close relation to B. arboris AU14372, B. arboris LMG24066, and B. arboris MEC_B345. Average nucleotide identity (ANI) values confirm the PN-1 classification as B. arboris. Comparative analysis with seven other B. arboris strains identified 4,628 core genes in B. arboris PN-1. The pan-genome of B. arboris appears open but may approach closure. Whole-genome sequencing revealed 265 carbohydrate-active enzymes and identified 9 gene clusters encoding secondary metabolites. This comprehensive investigation enhances our understanding of B. arboris genomes, paving the way for their potential as effective biocontrol agents against fungal plant pathogens in the future.
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Affiliation(s)
- Yun Yang
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Wenshan Academy of Agricultural Sciences, Wenshan, 663000, Yunnan, China
| | - Haoji Wang
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Jielei Tu
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Yan Li
- Yunnan Provincial Rural Energy Management Station, Kunming, 650233, Yunnan, China
| | - Huilin Guan
- Yunnan Provincial Observation and Research Station of Soil Degradation and Restoration for Cultivating Plateau Traditional Chinese Medicinal Plants, Yunnan Normal University, Kunming, 650500, Yunnan, China.
- Yunnan Provincial Renewable Energy Engineering Key Laboratory, Yunnan Normal University, Kunming, 650500, Yunnan, China.
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Shi C, Zeng S, Gao X, Hussain M, He M, Niu X, Wei C, Yang R, Lan M, Xie Y, Wang Z, Wu G, Tang P. Complete Genome Sequence Analysis of Bacillus subtilis MC4-2 Strain That against Tobacco Black Shank Disease. Int J Genomics 2024; 2024:8846747. [PMID: 38567257 PMCID: PMC10985647 DOI: 10.1155/2024/8846747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 02/18/2024] [Accepted: 02/21/2024] [Indexed: 04/04/2024] Open
Abstract
The MC4-2 bacterium strain was isolated and purified from the Periplaneta americana intestine as a biocontrol agent with good antagonistic effect against the pathogens of a soil-borne disease called tobacco black shank. The MC4-2 strain was found to have good broad-spectrum inhibition by plate stand-off test. Based on 16S rRNA and gyrB genes, ANI analysis, and other comparative genomics methods, it was determined that the MC4-2 strain was Bacillus subtilis. The complete genome sequence showed that the genome size was 4,076,630 bp, the average GC content was 43.78%, and the total number of CDSs was 4,207. Genomic prediction analysis revealed that a total of 145 genes were annotated by the CAZy, containing mainly GH and CE enzymes that break down carbohydrates such as glucose, chitin, starch, and alginate, and a large number of enzymes involved in glycosylation were present. A total of ten secondary metabolite clusters were predicted, six clusters of which were annotated as surfactin, bacillaene, fengycin, bacillibactin, subtilosin A, and bacilysin. The present investigation found the biological control mechanism of B. subtilis MC4-2, which provides a strong theoretical basis for the best use of this strain in biological control methods and provides a reference for the subsequent development of agents of this bacterium.
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Affiliation(s)
- Chunlan Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Shuquan Zeng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Xi Gao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Mehboob Hussain
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Mingchuan He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Xurong Niu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Congcong Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Rui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Mingxian Lan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Yonghui Xie
- Yunnan Tobacco Company Kunming Company, Kunming 650201, China
| | - Zhijiang Wang
- Yunnan Tobacco Company Kunming Company, Kunming 650201, China
| | - Guoxing Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
| | - Ping Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China
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Ma XH, Shen S, Li W, Wang J. Bioherbicidal potential of Bacillus altitudinis D30202 on Avena fatua L.: a whole-genome sequencing analysis. J Appl Genet 2023; 64:809-817. [PMID: 37752317 DOI: 10.1007/s13353-023-00788-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023]
Abstract
Avena fatua L. (wild oat) is one of the most harmful gramineous weeds that can affect the yield and quality of infiltrating crops. Bacillus altitudinis D30202 exhibits an excellent biocontrol activity against wild oat. To elucidate the biocontrol mechanisms of B. altitudinis D30202, the genome structure of this strain was assessed via whole-genome sequencing analysis. We predicted and analyzed secondary metabolite synthesis gene clusters to elucidate the mechanisms underlying the biocontrol of weeds. The whole-genome sequencing data indicated that B. altitudinis D30202 had the genome size and GC content of 3,777,154 bp and 41.32%, respectively, and 3809 coding genes were identified. Moreover, this strain could generate several compounds with bioherbicidal activity, including 4-hydroxy-3-methoxycinnamic acid and two indole derivatives. Bioinformatics prediction and comparative genomic analysis revealed that the strain had 6 secondary metabolite gene clusters. Furthermore, the taxonomic position of B. altitudinis D30202 was assessed, confirming its uniqueness and novelty within the Bacillus genus. Comparative genomic analysis showed differences in gene distribution, suggesting potential adaptations to different environments. In conclusion, B. altitudinis D30202 possesses a genome with unique characteristics, encoding enzymes and pathways related to herbicidal potential and biocontrol. This study provides a reference basis for understanding the molecular mechanisms of weed inhibition.
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Affiliation(s)
- Xiu-Hua Ma
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, 810016, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining, 810016, Qinghai, China
| | - Shuo Shen
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China.
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, 810016, Qinghai, China.
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China.
- Northwest Potato Engineering Research Center, Ministry of Education, Xining, 810016, Qinghai, China.
| | - Wei Li
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, 810016, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining, 810016, Qinghai, China
| | - Jian Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, 810016, Qinghai, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining, 810016, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining, 810016, Qinghai, China
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Asif M, Li-Qun Z, Zeng Q, Atiq M, Ahmad K, Tariq A, Al-Ansari N, Blom J, Fenske L, Alodaini HA, Hatamleh AA. Comprehensive genomic analysis of Bacillus paralicheniformis strain BP9, pan-genomic and genetic basis of biocontrol mechanism. Comput Struct Biotechnol J 2023; 21:4647-4662. [PMID: 37841331 PMCID: PMC10568305 DOI: 10.1016/j.csbj.2023.09.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
Many Bacillus species are essential antibacterial agents, but their antibiosis potential still needs to be elucidated to its full extent. Here, we isolated a soil bacterium, BP9, which has significant antibiosis activity against fungal and bacterial pathogens. BP9 improved the growth of wheat seedlings via active colonization and demonstrated effective biofilm and swarming activity. BP9 sequenced genome contains 4282 genes with a mean G-C content of 45.94% of the whole genome. A single copy concatenated 802 core genes of 28 genomes, and their calculated average nucleotide identity (ANI) discriminated the strain BP9 from Bacillus licheniformis and classified it as Bacillus paralicheniformis. Furthermore, a comparative pan-genome analysis of 40 B. paralicheniformis strains suggested that the genetic repertoire of BP9 belongs to open-type genome species. A comparative analysis of a pan-genome dataset using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Gene groups (COG) revealed the diversity of secondary metabolic pathways, where BP9 distinguishes itself by exhibiting a greater prevalence of loci associated with the metabolism and transportation of organic and inorganic substances, carbohydrate and amino acid for effective inhabitation in diverse environments. The primary secondary metabolites and their genes involved in synthesizing bacillibactin, fencing, bacitracin, and lantibiotics were identified as acquired through a recent Horizontal gene transfer (HGT) event, which contributes to a significant part of the strain`s antimicrobial potential. Finally, we report some genes essential for plant-host interaction identified in BP9, which reduce spore germination and virulence of multiple fungal and bacterial species. The effective colonization, diverse predicted metabolic pathways and secondary metabolites (antibiotics) suggest testing the suitability of strain BP9 as a potential bio-preparation in agricultural fields.
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Affiliation(s)
- Muhammad Asif
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhang Li-Qun
- Department of Plant Pathology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Khalil Ahmad
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China
| | - Aqil Tariq
- Department of Wildlife, Fisheries, and Aquaculture, College of Forest Resources, Mississippi State, University, MS 39762-9690, USA
| | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Linda Fenske
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen 35392, Germany
| | - Hissah Abdulrahman Alodaini
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Pei X, Liu X, Zang C, Yu S, Xie J, Lin Y, Liang B, Wu X, Liang C. Genome Resource of Streptomyces atratus PY-1, a Broad-Spectrum Antimicrobial Strain in Particular Antagonistic Against Plasmopara viticola. PLANT DISEASE 2023; 107:2506-2508. [PMID: 36774571 DOI: 10.1094/pdis-09-22-2093-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Streptomyces atratus PY-1 exhibited promising antimicrobial properties; in particular, it is highly inhibitory to Plasmopara viticola, which causes downy mildew of grape. It is very necessary to carry out systematic and in-depth research on the PY-1 strain for the improvement, application, and promotion of biocontrol agents. The PY-1 genome was fully sequenced and assembled. We present the draft genome sequence of PY-1, with a size of 9, 254, and 781 bp. Preliminary analysis on the PY-1 genome sequence shows that at least 35 gene clusters are involved in the biosynthesis of polyketides, terpenes, and nonribosomally synthesized peptides.
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Affiliation(s)
- Xue Pei
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xiaozhou Liu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Chaoqun Zang
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Shuyi Yu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Jinhui Xie
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Ying Lin
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Bingbing Liang
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chunhao Liang
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
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Suppression of Grape White Rot Caused by Coniella vitis Using the Potential Biocontrol Agent Bacillus velezensis GSBZ09. Pathogens 2022; 11:pathogens11020248. [PMID: 35215191 PMCID: PMC8876275 DOI: 10.3390/pathogens11020248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/10/2022] Open
Abstract
Grape white rot caused by Coniella vitis is prevalent in almost all grapevines worldwide and results in a yield loss of 10–20% annually. Bacillus velezensis is a reputable plant growth-promoting bacterial. Strain GSBZ09 was isolated from grapevine cv. Red Globe (Vitis vinifera) and identified as B. velezensis according to morphological, physiological, biochemical characteristics and a multilocus gene sequence analysis (MLSA) based on six housekeeping genes (16S rRNA, gyrB, rpoD, atpD, rho and pgk). B. velezensis GSBZ09 was screened for antifungal activity against C. vitis under in vitro and in vivo conditions. GSBZ09 presented broad spectrum antifungal activity and produced many extracellular enzymes that remarkably inhibited the mycelial growth and spore germination of C. vitis. Furthermore, GSBZ09 had a high capacity for indole-3-acetic acid (IAA) production, siderophore production, and mineral phosphate solubilization. Pot experiments showed that the application of GSBZ09 significantly decreased the disease index of the grape white rot, directly promoted the growth of grapes, and upregulated defense-related enzymes. Overall, the features of B. velezensis GSBZ09 make it a potential strain for application as a biological control agent against C. vitis.
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