1
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Lee SI, Kim DR, Kwak YS. Genome analysis of Streptomyces recifensis SN1E1 to investigate mechanisms for inhibiting fire blight disease. J Appl Microbiol 2024; 135:lxae253. [PMID: 39363195 DOI: 10.1093/jambio/lxae253] [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: 07/12/2024] [Revised: 09/13/2024] [Accepted: 10/02/2024] [Indexed: 10/05/2024]
Abstract
AIM Fire blight, attributed to the bacterium Erwinia amylovora, significantly damages economically important crops, such as apples and pears. Conventional methods for managing fire blight involve the application of chemical pesticides, such as streptomycin and oxytetracycline. Nevertheless, apprehensions are increasing regarding developing antibiotic and pesticide-resistant strains, compounded by documented instances of plant toxicity. Here, we present that Streptomyces recifensis SN1E1 has exhibited remarkable efficacy in suppressing apple fire blight disease. This study aims to unravel the molecular-level antimicrobial mechanisms employed by the SN1E1 strain. METHODS AND RESULTS We identified four antimicrobial-associated biosynthetic gene clusters within the genomics of S. recifensis SN1E1. To validate antimicrobial activity against E. amylovora, knock-out mutants of biosynthetic genes linked to antimicrobial activity were generated using the CRISPR/Cas9 mutagenesis system. Notably, the whiE4 and phzB deficient mutants displayed statistically reduced antibacterial activity against E. amylovora. CONCLUSION This research establishes a foundation for environmental and biological control studies. The potential utilization of environmentally friendly microbial agents derived from the SN1E1 strain holds promise for the biological control of fire blight disease.
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Affiliation(s)
- Su In Lee
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Da-Ran Kim
- Department of Plant Medicine and RILS, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
- Department of Plant Medicine and RILS, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
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2
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Wang Z, Fan N, Li X, Yue L, Wang X, Liao H, Xiao Z. Trophic Transfer of Metal Oxide Nanoparticles in the Tomato- Helicoverpa armigera Food Chain: Effects on Phyllosphere Microbiota, Insect Oxidative Stress, and Gut Microbiome. ACS NANO 2024; 18:26631-26642. [PMID: 39297401 DOI: 10.1021/acsnano.4c05063] [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: 10/02/2024]
Abstract
Understanding the trophic transfer and ecological cascade effects of nanofertilizers and nanopesticides in terrestrial food chains is crucial for assessing their nanotoxicity and environmental risks. Herein, the trophic transfer of La2O3 (nLa2O3) and CuO (nCuO) nanoparticles from tomato leaves to Helicoverpa armigera (Lepidoptera: Noctuidae) caterpillars and their subsequent effects on caterpillar growth and intestinal health were investigated. We found that 50 mg/L foliar nLa2O3 and nCuO were transferred from tomato leaves to H. armigera, with particulate trophic transfer factors of 1.47 and 0.99, respectively. While nCuO exposure reduced larval weight gain more (34.7%) than nLa2O3 (11.3%), owing to higher oxidative stress (e.g., MDA and H2O2) and more serious intestinal pathological damage (i.e., crumpled columnar cell and disintegrated goblet cell) by nCuO. Moreover, nCuO exposure led to a more compact antagonism between the phyllosphere and gut microbiomes compared to nLa2O3. Specifically, nCuO exposure resulted in a greater increase in pathogenic bacteria (e.g., Mycobacterium, Bacillus, and Ralstonia) and a more significant decrease in probiotics (e.g., Streptomyces and Arthrobacter) than nLa2O3, ultimately destroying larval intestinal immunity. Altogether, our findings systematically revealed the cascade effect of metal oxide nanomaterials on higher trophic consumers through alteration in the phyllosphere and insect gut microbiome interaction, thus providing insights into nanotoxicity and environmental risk assessment of nanomaterials applied in agroecosystems.
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Affiliation(s)
- Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Ningke Fan
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Xiaona Li
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Le Yue
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Xie Wang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Huimin Liao
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
| | - Zhenggao Xiao
- Institute of Environmental Processes and Pollution Control, School of Environment and Ecology, Jiangnan University, Wuxi 214122, China
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3
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Spooren J, van Bentum S, Thomashow LS, Pieterse CMJ, Weller DM, Berendsen RL. Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:1-30. [PMID: 38857541 DOI: 10.1146/annurev-phyto-021622-100127] [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: 06/12/2024]
Abstract
Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.
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Affiliation(s)
- Jelle Spooren
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Sietske van Bentum
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Linda S Thomashow
- Wheat Health, Genetics and Quality Research Unit, US Department of Agriculture, Agricultural Research Service, Pullman, Washington, USA;
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - David M Weller
- Wheat Health, Genetics and Quality Research Unit, US Department of Agriculture, Agricultural Research Service, Pullman, Washington, USA;
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
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4
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Liu H, Li J, Singh BK. Harnessing co-evolutionary interactions between plants and Streptomyces to combat drought stress. NATURE PLANTS 2024; 10:1159-1171. [PMID: 39048724 DOI: 10.1038/s41477-024-01749-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/25/2024] [Indexed: 07/27/2024]
Abstract
Streptomyces is a drought-tolerant bacterial genus in soils, which forms close associations with plants to provide host resilience to drought stress. Here we synthesize the emerging research that illuminates the multifaceted interactions of Streptomyces spp. in both plant and soil environments. It also explores the potential co-evolutionary relationship between plants and Streptomyces spp. to forge mutualistic relationships, providing drought tolerance to plants. We propose that further advancement in fundamental knowledge of eco-evolutionary interactions between plants and Streptomyces spp. is crucial and holds substantial promise for developing effective strategies to combat drought stress, ensuring sustainable agriculture and environmental sustainability in the face of climate change.
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Affiliation(s)
- Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia.
| | - Jiayu Li
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, Australia.
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5
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Cuervo L, Méndez C, Salas JA, Olano C, Malmierca MG. Volatile communication in Actinobacteria: a language for secondary metabolism regulation. Microb Cell Fact 2024; 23:181. [PMID: 38890640 PMCID: PMC11186294 DOI: 10.1186/s12934-024-02456-4] [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: 04/02/2024] [Accepted: 06/08/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group. RESULTS We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities. CONCLUSIONS This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.
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Affiliation(s)
- Lorena Cuervo
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Carmen Méndez
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - José A Salas
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Carlos Olano
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain
| | - Mónica G Malmierca
- Department Functional Biology, University of Oviedo, 33006, Oviedo, Spain.
- University Institute of Oncology of Asturias (I.U.O.P.A), University of Oviedo, 33006, Oviedo, Spain.
- Health Research Institute of Asturias (ISPA), 33006, Oviedo, Spain.
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Kim DR, Jeon CW, Kwak YS. Antifungal Properties of Streptomyces bacillaris S8 for Biological Control Applications. THE PLANT PATHOLOGY JOURNAL 2024; 40:322-328. [PMID: 38835303 PMCID: PMC11162865 DOI: 10.5423/ppj.nt.01.2024.0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 06/06/2024]
Abstract
Soybean (Glycine max), a crucial global crop, experiences yearly yield reduction due to diseases such as anthracnose (Colletotrichum truncatum) and root rot (Fusarium spp.). The use of fungicides, which have traditionally been employed to control these phytopathogens, is now facing challenges due to the emergence of fungicide-resistant strains. Streptomyces bacillaris S8 strain S8 is previously known to produce valinomycin t through a nonribosomal peptide synthetase (NRPS) pathway. The objective of this study was to evaluate the antifungal activity of S. bacillaris S8 against C. truncatum and Fusarium sp., assessing its efficacy against soybean pathogens. The results indicate that strain S8 effectively controlled both above-ground and underground soybean diseases, using the NRPS and NRPS-related compound, suggesting its potential as a biological control in plant-microbe interactions. These findings underscore the pivotal role of the stain S8 in fostering healthy soybean microbial communities and emphasize the significance of microbiota structure studies in unveiling potent biocontrol agents.
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Affiliation(s)
- Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Chang-Wook Jeon
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Korea
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7
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Díaz-Cruz GA, Bignell DRD. Exploring the specialized metabolome of the plant pathogen Streptomyces sp. 11-1-2. Sci Rep 2024; 14:10414. [PMID: 38710735 DOI: 10.1038/s41598-024-60630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
Streptomyces bacteria are notable for producing chemically diverse specialized metabolites that exhibit various bioactivities and mediate interactions with different organisms. Streptomyces sp. 11-1-2 is a plant pathogen that produces nigericin and geldanamycin, both of which display toxic effects against various plants. Here, the 'One Strain Many Compounds' approach was used to characterize the metabolic potential of Streptomyces sp. 11-1-2. Organic extracts were prepared from 11-1-2 cultures grown on six different agar media, and the extracts were tested in antimicrobial and plant bioassays and were subjected to untargeted metabolomics and molecular networking. Most extracts displayed strong bioactivity against Gram-positive bacteria and yeast, and they exhibited phytotoxic activity against potato tuber tissue and radish seedlings. Several known specialized metabolites, including musacin D, galbonolide B, guanidylfungin A, meridamycins and elaiophylin, were predicted to be present in the extracts along with closely related compounds with unknown structure and bioactivity. Targeted detection confirmed the presence of elaiophylin in the extracts, and bioassays using pure elaiophylin revealed that it enhances the phytotoxic effects of geldanamycin and nigericin on potato tuber tissue. Overall, this study reveals novel insights into the specialized metabolites that may mediate interactions between Streptomyces sp. 11-1-2 and other bacteria and eukaryotic organisms.
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Affiliation(s)
- Gustavo A Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
- Phytopathology Department, Plant Protection Research Center (CIPROC), Agronomy School, Universidad de Costa Rica, San Jose, Costa Rica
| | - Dawn R D Bignell
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada.
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8
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Maritan E, Quagliariello A, Frago E, Patarnello T, Martino ME. The role of animal hosts in shaping gut microbiome variation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230071. [PMID: 38497257 PMCID: PMC10945410 DOI: 10.1098/rstb.2023.0071] [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: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
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Affiliation(s)
- Elisa Maritan
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Enric Frago
- CIRAD, UMR CBGP, INRAE, Institut Agro, IRD, Université Montpellier, 34398 Montpellier, France
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
| | - Maria Elena Martino
- Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Padova, Italy
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9
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Li X, Hu X, Zhao X, Wang F, Zhao Y. Modeling and optimization of triclosan biodegradation by the newly isolated Bacillus sp. DL4: kinetics and pathway speculation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:35567-35580. [PMID: 38730220 DOI: 10.1007/s11356-024-33096-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 03/22/2024] [Indexed: 05/12/2024]
Abstract
Triclosan is a widely used antibacterial agent and disinfectant, and its overuse endangered ecological safety and human health. Therefore, reducing residual TCS concentrations in the environment is an urgent issue. Bacillus sp. DL4, an aerobic bacterium with TCS biodegradability, was isolated from pharmaceutical wastewater samples. Response surface methodology (RSM) and artificial neural network (ANN) were carried out to optimize and verify the different condition variables, and the optimal growth conditions of strain DL4 were obtained (35 °C, initial pH 7.31, and 5% v/v). After 48 h of cultivation under the optimal conditions, the removal efficiency of strain DL4 on TCS was 95.89 ± 0.68%, which was consistent with the predicted values from RSM and ANN models. In addition, higher R2 value and lower MSE and ADD values indicated that the ANN model had a stronger predictive capability than the RSM model. Whole genome sequencing results showed that many functional genes were annotated in metabolic pathways related to TCS degradation (e.g., amino acid metabolism, xenobiotics biodegradation and metabolism, carbohydrate metabolism). Main intermediate metabolites were identified during the biodegradation process by liquid chromatography-mass spectrometry (LC-MS), and a possible pathway was hypothesized based on the metabolites. Overall, this study provides a theoretical foundation for the characterization and mechanism of TCS biodegradation in the environment by Bacillus sp. DL4.
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Affiliation(s)
- Xuejie Li
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, People's Republic of China
- School of Resource & Civil Engineering, Northeastern University, No. 11, Lane 3, Wenhua Road, P.O. Box 265, Shenyang, 110819, People's Republic of China
| | - Xiaomin Hu
- School of Resource & Civil Engineering, Northeastern University, No. 11, Lane 3, Wenhua Road, P.O. Box 265, Shenyang, 110819, People's Republic of China.
| | - Xin Zhao
- School of Resource & Civil Engineering, Northeastern University, No. 11, Lane 3, Wenhua Road, P.O. Box 265, Shenyang, 110819, People's Republic of China
| | - Fan Wang
- School of Resource & Civil Engineering, Northeastern University, No. 11, Lane 3, Wenhua Road, P.O. Box 265, Shenyang, 110819, People's Republic of China
| | - Yan Zhao
- School of Resource & Civil Engineering, Northeastern University, No. 11, Lane 3, Wenhua Road, P.O. Box 265, Shenyang, 110819, People's Republic of China
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10
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Park HS, Kang SH, Choi SS, Kim ES. Isolation of Streptomyces inhibiting multiple-phytopathogenic fungi and characterization of lucensomycin biosynthetic gene cluster. Sci Rep 2024; 14:7757. [PMID: 38565875 PMCID: PMC10987574 DOI: 10.1038/s41598-024-57888-0] [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: 12/07/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Soil microorganisms with diverse bioactive compounds such as Streptomyces are appreciated as valuable resources for the discovery of eco-friendly fungicides. This study isolated a novel Streptomyces from soil samples collected in the organic green tea fields in South Korea. The isolation process involved antifungal activity screening around 2400 culture extracts, revealing a strain designated as S. collinus Inha504 with remarkable antifungal activity against diverse phytopathogenic fungi. S. collinus Inha504 not only inhibited seven phytopathogenic fungi including Fusarium oxysporum and Aspergillus niger in bioassays and but also showed a control effect against F. oxysporum infected red pepper, strawberry, and tomato in the in vivo pot test. Genome mining of S. collinus Inha504 revealed the presence of the biosynthetic gene cluster (BGC) in the chromosome encoding a polyene macrolide which is highly homologous to the lucensomycin (LCM), a compound known for effective in crop disease control. Through genetic confirmation and bioassays, the antifungal activity of S. collinus Inha504 was attributed to the presence of LCM BGC in the chromosome. These results could serve as an effective strategy to select novel Streptomyces strains with valuable biological activity through bioassay-based screening and identify biosynthetic gene clusters responsible for the metabolites using genome mining approach.
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Affiliation(s)
- Heung-Soon Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Seung-Hoon Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Si-Sun Choi
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Eung-Soo Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
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11
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Guerrero-Egido G, Pintado A, Bretscher KM, Arias-Giraldo LM, Paulson JN, Spaink HP, Claessen D, Ramos C, Cazorla FM, Medema MH, Raaijmakers JM, Carrión VJ. bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria. Nat Commun 2024; 15:2072. [PMID: 38453959 PMCID: PMC10920822 DOI: 10.1038/s41467-024-46302-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE ( https://github.com/Carrion-lab/bacLIFE ) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.
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Affiliation(s)
- Guillermo Guerrero-Egido
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Adrian Pintado
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Kevin M Bretscher
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Luisa-Maria Arias-Giraldo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, N-Power Medicine, Redwood City, CA, 94063, USA
| | - Herman P Spaink
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Cayo Ramos
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
- Área de Genética, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Marnix H Medema
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Víctor J Carrión
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain.
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain.
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12
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Sakauchi K, Otaki JM. Soil Microbes and Plant-Associated Microbes in Response to Radioactive Pollution May Indirectly Affect Plants and Insect Herbivores: Evidence for Indirect Field Effects from Chernobyl and Fukushima. Microorganisms 2024; 12:364. [PMID: 38399767 PMCID: PMC10892324 DOI: 10.3390/microorganisms12020364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The biological impacts of the nuclear accidents in Chernobyl (1986) and Fukushima (2011) on wildlife have been studied in many organisms over decades, mainly from dosimetric perspectives based on laboratory experiments using indicator species. However, ecological perspectives are required to understand indirect field-specific effects among species, which are difficult to evaluate under dosimetric laboratory conditions. From the viewpoint that microbes play a fundamental role in ecosystem function as decomposers and symbionts for plants, we reviewed studies on microbes inhabiting soil and plants in Chernobyl and Fukushima in an attempt to find supporting evidence for indirect field-specific effects on plants and insect herbivores. Compositional changes in soil microbes associated with decreases in abundance and species diversity were reported, especially in heavily contaminated areas of both Chernobyl and Fukushima, which may accompany explosions of radioresistant species. In Chernobyl, the population size of soil microbes remained low for at least 20 years after the accident, and the abundance of plant-associated microbes, which are related to the growth and defense systems of plants, possibly decreased. These reported changes in microbes likely affect soil conditions and alter plant physiology. These microbe-mediated effects may then indirectly affect insect herbivores through food-mass-mediated, pollen-mediated, and metabolite-mediated interactions. Metabolite-mediated interactions may be a major pathway for ecological impacts at low pollution levels and could explain the decreases in insect herbivores in Fukushima. The present review highlights the importance of the indirect field effects of long-term low-dose radiation exposure under complex field circumstances.
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Affiliation(s)
| | - Joji M. Otaki
- The BCPH Unit of Molecular Physiology, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara 903-0213, Okinawa, Japan;
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13
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Nicolle C, Gayrard D, Noël A, Hortala M, Amiel A, Grat S, Le Ru A, Marti G, Pernodet JL, Lautru S, Dumas B, Rey T. Root-associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonization. THE ISME JOURNAL 2024; 18:wrae112. [PMID: 38896026 PMCID: PMC11463028 DOI: 10.1093/ismejo/wrae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/03/2024] [Accepted: 06/18/2024] [Indexed: 06/21/2024]
Abstract
The rhizosphere, which serves as the primary interface between plant roots and the soil, constitutes an ecological niche for a huge diversity of microbial communities. Currently, there is little knowledge on the nature and the function of the different metabolites released by rhizospheric microbes to facilitate colonization of this highly competitive environment. Here, we demonstrate how the production of galbonolides, a group of polyene macrolides that inhibit plant and fungal inositol phosphorylceramide synthase (IPCS), empowers the rhizospheric Streptomyces strain AgN23, to thrive in the rhizosphere by triggering the plant's defence mechanisms. Metabolomic analysis of AgN23-inoculated Arabidopsis roots revealed a strong induction in the production of an indole alkaloid, camalexin, which is a major phytoalexin in Arabidopsis. By using a plant mutant compromised in camalexin synthesis, we show that camalexin production is necessary for the successful colonization of the rhizosphere by AgN23. Conversely, hindering galbonolides biosynthesis in AgN23 knock-out mutant resulted in loss of inhibition of IPCS, a deficiency in plant defence activation, notably the production of camalexin, and a strongly reduced development of the mutant bacteria in the rhizosphere. Together, our results identified galbonolides as important metabolites mediating rhizosphere colonization by Streptomyces.
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Affiliation(s)
- Clément Nicolle
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Université Toulouse III, Toulouse INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
| | - Damien Gayrard
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Université Toulouse III, Toulouse INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
- DE SANGOSSE, 47480 Pont-Du-Casse, France
| | - Alba Noël
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marion Hortala
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Université Toulouse III, Toulouse INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
| | - Aurélien Amiel
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Université Toulouse III, Toulouse INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
- DE SANGOSSE, 47480 Pont-Du-Casse, France
| | - Sabine Grat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Université Toulouse III, Toulouse INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
| | - Aurélie Le Ru
- Plateforme d’Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane 31320, France
| | - Guillaume Marti
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Université Toulouse III, Toulouse INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
- Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UPS, Toulouse INP, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Jean-Luc Pernodet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sylvie Lautru
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Université Toulouse III, Toulouse INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
| | - Thomas Rey
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, Université Toulouse III, Toulouse INP, 24 Chemin de Borde Rouge, Auzeville, Auzeville-Tolosane 31320, France
- DE SANGOSSE, 47480 Pont-Du-Casse, France
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14
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Du X, Liu N, Yan B, Li Y, Liu M, Huang Y. Proximity-based defensive mutualism between Streptomyces and Mesorhizobium by sharing and sequestering iron. THE ISME JOURNAL 2024; 18:wrad041. [PMID: 38366066 PMCID: PMC10881299 DOI: 10.1093/ismejo/wrad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/25/2023] [Accepted: 12/26/2024] [Indexed: 02/18/2024]
Abstract
Microorganisms living in soil maintain intricate interactions among themselves, forming the soil microbiota that influences the rhizosphere microbiome and plant growth. However, the mechanisms underlying the soil microbial interactions remain unclear. Streptomyces and Mesorhizobium are commonly found in soil and serve as plant growth-promoting rhizobacteria (PGPR). Here, we identified an unprecedented interaction between the colonies of red-soil-derived Streptomyces sp. FXJ1.4098 and Mesorhizobium sp. BAC0120 and referred to it as "proximity-based defensive mutualism (PBDM)." We found that metabolite-mediated iron competition and sharing between the two microorganisms were responsible for PBDM. Streptomyces sp. FXJ1.4098 produced a highly diffusible siderophore, desferrioxamine, which made iron unavailable to co-cultured Mesorhizobium sp. BAC0120, thereby inhibiting its growth. Streptomyces sp. FXJ1.4098 also released poorly diffusible iron-porphyrin complexes, which could be utilized by Mesorhizobium sp. BAC0120, thereby restoring the growth of nearby Mesorhizobium sp. BAC0120. Furthermore, in ternary interactions, the PBDM strategy contributed to the protection of Mesorhizobium sp. BAC0120 close to Streptomyces sp. FXJ1.4098 from other microbial competitors, resulting in the coexistence of these two PGPR. A scale-up pairwise interaction screening suggested that the PBDM strategy may be common between Mesorhizobium and red-soil-derived Streptomyces. These results demonstrate the key role of iron in complex microbial interactions and provide novel insights into the coexistence of PGPR in soil.
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Affiliation(s)
- Xueyuan Du
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
- National Engineering Laboratory for Site Remediation Technologies, BCEG Environmental Remediation Co., Ltd., Beijing 100015, P. R. China
| | - Ning Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
| | - Bingfa Yan
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
| | - Yisong Li
- School of Public Health, Qingdao University, Qingdao 266071, P. R. China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Institute of Microbiology, Beijing 100101, P. R. China
- College of Life Sciences, University of Chinese Academy of Sciences , Beijing 101408, P. R. China
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15
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Serrano-Mislata A, Brumós J. Clearing of Vascular Tissue in Arabidopsis thaliana for Reporter Analysis of Gene Expression. Methods Mol Biol 2024; 2722:227-239. [PMID: 37897610 DOI: 10.1007/978-1-0716-3477-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
To study the gene regulatory mechanisms modulating development is essential to visualize gene expression patterns at cellular resolution. However, this kind of analysis has been limited as a consequence of the plant tissues' opacity. In the last years, ClearSee has been increasingly used to obtain high-quality imaging of plant tissue anatomy combined with the visualization of gene expression patterns. ClearSee is established as a major tissue clearing technique due to its simplicity and versatility.In this chapter, we outline an easy-to-follow ClearSee protocol to analyze gene expression of reporters using either β-glucuronidase (GUS) or fluorescent protein (FP) tags, compatible with different dyes to stain cell walls. We detail materials, equipment, solutions, and procedures to easily implement ClearSee for the study of vascular development in Arabidopsis thaliana, but the protocol can be easily adapted to a variety of plant tissues in a wide range of plant species.
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Affiliation(s)
- Antonio Serrano-Mislata
- Instituto de Biología Molecular y Celular de Plantas, (CSIC-Universitat Politècnica de València), Valencia, Spain.
| | - Javier Brumós
- Instituto de Biología Molecular y Celular de Plantas, (CSIC-Universitat Politècnica de València), Valencia, Spain.
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16
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Park JW, Braswell WE, Kunta M. Co-Occurrence Analysis of Citrus Root Bacterial Microbiota under Citrus Greening Disease. PLANTS (BASEL, SWITZERLAND) 2023; 13:80. [PMID: 38202388 PMCID: PMC10781011 DOI: 10.3390/plants13010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
Candidatus Liberibacter asiaticus (CLas) is associated with Citrus Huanglongbing (HLB), a devastating disease in the US. Previously, we conducted a two-year-long monthly HLB survey by quantitative real-time PCR using root DNA fractions prepared from 112 field grapefruit trees grafted on sour orange rootstock. Approximately 10% of the trees remained CLas-free during the entire survey period. This study conducted 16S metagenomics using the time-series root DNA fractions, monthly prepared during twenty-four consecutive months, followed by microbial co-occurrence network analysis to investigate the microbial factors contributing to the CLas-free phenotype of the aforementioned trees. Based on the HLB status and the time when the trees were first diagnosed as CLas-positive during the survey, the samples were divided into four groups, Stage H (healthy), Stage I (early), II (mid), and III (late) samples. The 16S metagenomics data using Silva 16S database v132 revealed that HLB compromised the diversity of rhizosphere microbiota. At the phylum level, Actinobacteria and Proteobacteria were the predominant bacterial phyla, comprising >93% of total bacterial phyla, irrespective of HLB status. In addition, a temporal change in the rhizosphere microbe population was observed during a two-year-long survey, from which we confirmed that some bacterial families differently responded to HLB disease status. The clustering of the bacterial co-occurrence network data revealed the presence of a subnetwork composed of Streptomycetaceae and bacterial families with plant growth-promoting activity in Stage H and III samples. These data implicated that the Streptomycetaceae subnetwork may act as a functional unit against HLB.
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Affiliation(s)
- Jong-Won Park
- Citrus Center, Texas A&M University-Kingsville, 312 N. International Blvd., Weslaco, TX 78599, USA
| | - W. Evan Braswell
- Insect Management and Molecular Diagnostic Laboratory, USDA APHIS PPQ S&T, Edinburg, TX 78541, USA
| | - Madhurababu Kunta
- Citrus Center, Texas A&M University-Kingsville, 312 N. International Blvd., Weslaco, TX 78599, USA
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17
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Wippel K. Plant and microbial features governing an endophytic lifestyle. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102483. [PMID: 37939457 DOI: 10.1016/j.pbi.2023.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress alleviation. Their efficient application in agriculture requires the understanding of the molecular mechanisms and environmental conditions that facilitate in planta accommodation. Accumulating evidence reveals that commensal microorganisms employ similar colonization strategies as their pathogenic counterparts. Fine-tuning of immune response, motility, and metabolic crosstalk accounts for their differentiation. For a holistic perspective, in planta experiments with microbial collections and comprehensive genome data exploration are crucial. This review describes the most recent findings on factors involved in endophytic colonization processes, focusing on bacteria and fungi, and discusses required methodological approaches to unravel their relevance within a community context.
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Affiliation(s)
- Kathrin Wippel
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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18
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Kim DR, Lee SI, Kwak YS. Unraveling the Role of Cytochrome P450 as a Key Regulator Lantipeptide Production in Streptomyces globisporus. THE PLANT PATHOLOGY JOURNAL 2023; 39:566-574. [PMID: 38081316 PMCID: PMC10721394 DOI: 10.5423/ppj.oa.08.2023.0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 12/17/2023]
Abstract
The aim of this study was to investigate the regulation of lantipeptide production in Streptomyces globisporus SP6C4, which produces the novel antifungal lantipeptides conprimycin and grisin, and to identify the role of cytochrome P450 (P450) in tis regulation. To investigate the regulation of lantipeptide production, we created gene deletion mutants, including ΔP450, ΔtsrD, ΔlanM, ΔP450ΔtsrD, and ΔP450ΔlanM. These mutants were characterized in terms of their morphology, sporulation, attachment, and antifungal activity against Fusarium oxysporum. The gene deletion mutants showed distinct characteristics compared to the wild-type strain. Among them, the ΔP450ΔlanM double mutant exhibited a recovery of antifungal activity against F. oxysporum, indicating that P450 plays a significant role in regulating lantipeptide production in S. globisporus SP6C4. Our findings highlight the significant role of P450 in the regulation of lantipeptide production and morphological processes in S. globisporus. The results suggest a potential link between P450-mediated metabolic pathways and the regulation of growth and secondary metabolism in SP6C4, thereby highlighting P450 as a putative target for the development of new antifungal agents.
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Affiliation(s)
- Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Su In Lee
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Korea
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Sun K, Jiang HJ, Pan YT, Lu F, Zhu Q, Ma CY, Zhang AY, Zhou JY, Zhang W, Dai CC. Hyphosphere microorganisms facilitate hyphal spreading and root colonization of plant symbiotic fungus in ammonium-enriched soil. THE ISME JOURNAL 2023; 17:1626-1638. [PMID: 37443341 PMCID: PMC10504341 DOI: 10.1038/s41396-023-01476-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Anthropogenic nitrogen inputs lead to a high ammonium (NH4+)/nitrate (NO3-) ratio in the soil, which restricts hyphal spreading of soil fungi. Access of symbiotic fungi to roots is a prerequisite for plant-fungal interactions. Hyphosphere bacteria protect fungi from environmental stress, yet the impact of hyphosphere bacteria on adaptation of host fungi to NH4+-enriched conditions remains unclear. By developing soil microcosm assays, we report that a plant-symbiotic fungus, Phomopsis liquidambaris, harbors specific hyphosphere bacteria that facilitate hyphal spreading and assist in the root colonization in NH4+-enriched soil. Genetic manipulation, 16S rRNA gene analysis and coinoculation assays revealed that the genus Enterobacter was enriched in the hyphosphere of NH4+-sensitive wild-type compared to NH4+-preferring nitrite reductase-deficient strain. The representative Enterobacter sp. SZ2-promoted hyphal spreading is only evident in nonsterilized soil. We further identified an increased abundance and diversity of ammonia-oxidizing archaea (AOA) and a synchronously decreased NH4+:NO3- ratio following SZ2 inoculation. Microbial supplementation and inhibitor assays showed that AOA-mediated reduction in NH4+:NO3- ratio is responsible for SZ2-enhanced fungal adaptation to NH4+-enriched conditions. The Ph. liquidambaris-Enterobacter-AOA triple interaction promoted rice growth in NH4+-enriched soil. Our study reveals the essential role of hyphosphere microorganism-based hyphal spreading in plant-fungal symbiosis establishment within nitrogen-affected agroecosystems.
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Affiliation(s)
- Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Yi-Tong Pan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Fan Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Qiang Zhu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China
| | - Jia-Yu Zhou
- Jiangsu Key Laboratory for the Research and Uti1ization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China.
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu Province, China.
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20
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Lee HJ, Kim SH, Kim DR, Cho G, Kwak YS. Dynamics of Bacterial Communities by Apple Tissue: Implications for Apple Health. J Microbiol Biotechnol 2023; 33:1141-1148. [PMID: 37435872 PMCID: PMC10580880 DOI: 10.4014/jmb.2305.05003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/01/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023]
Abstract
Herein, we explored the potential of the apple's core microbiota for biological control of Erwinia amylovora, which causes fire blight disease, and analyzed the structure of the apple's bacterial community across different tissues and seasons. Network analysis results showed distinct differences in bacterial community composition between the endosphere and rhizosphere of healthy apples, and eight taxa were identified as negatively correlated with E. amylovora, indicating their potential key role in a new control strategy against the pathogen. This study highlights the critical role of the apple's bacterial community in disease control and provides a new direction for future research in apple production. In addition, the findings suggest that using the composition of the apple's core taxa as a biological control strategy could be an effective alternative to traditional chemical control methods, which have been proven futile and environmentally harmful.
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Affiliation(s)
- Hwa-Jung Lee
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Su-Hyeon Kim
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Da-Ran Kim
- Department of Plant Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeongjun Cho
- Division of Agricultural Microbiology, National Institute of Agriculture Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
- Department of Plant Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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21
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Lee SI, Cho G, Kim SH, Kim DR, Kwak YS. Mycobiota community and fungal species response to development stage and fire blight disease in apples. AIMS Microbiol 2023; 9:554-569. [PMID: 37649796 PMCID: PMC10462452 DOI: 10.3934/microbiol.2023029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/29/2023] [Accepted: 07/12/2023] [Indexed: 09/01/2023] Open
Abstract
Fire blight disease, caused by the bacterial pathogen Erwinia amylovora, has been a significant concern for over 50 countries worldwide. The efficacy of chemical pesticides currently available for disease control is limited. To address this issue, research is being conducted to explore environmentally friendly control methods, particularly biological control using beneficial microorganisms. However, there is limited research on the apple microbiota community and minimal research has been conducted on fungal communities that may exhibit reliable performance in apple trees. Therefore, our objective was to analyze the fungal communities present in apples at different developmental stages and in different tissues, aiming to identify potential biological control agents for fire blight disease. Our findings indicate that the fungal communities present in apple buds, flowers and leaves play an important role in inhibiting the invasion of E. amylovora. Specifically, we propose GS11 and Lipomyces starkeyi as potential keystone taxa that respond to fire blight disease. These findings provide insights into the continuity and discontinuity of fungal community structure in different developmental stages of apples and offer predictions for potential biological control agents for fire blight disease.
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Affiliation(s)
- Su In Lee
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeongjun Cho
- Division of Agricultural Microbiology, National Institute of Agriculture Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Su-Hyeon Kim
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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22
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Kim DR, Kwak YS. Endophytic Streptomyces population induced by L-glutamic acid enhances plant resilience to abiotic stresses in tomato. Front Microbiol 2023; 14:1180538. [PMID: 37362924 PMCID: PMC10288847 DOI: 10.3389/fmicb.2023.1180538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Endophyte bacteria, which colonize plants including roots, stem, flower, and fruit, it can derive their nutrients from the host, are recognized for their mutualistic relationship with the host plant. They play a critical role in promoting host growth and modulating abiotic stress. Carbon and nitrogen have a significant impact on bacterial population and secondary metabolite production, which are highly specific in various categories such as bacterial growth regulation, anti-compounds production. Application of L-glutamic acid can significantly enhance Streptomyces globisporus population buildup in plants. However, the effectiveness of this population buildup against abiotic stresses such as salinity and drought has not been investigated. Therefore, in this study, we tested the bacteria and their prebiotic activity against salinity and drought stress in tomato plants. Three different amino acids were treated on the tomato plants, and it was observed that L-asparagine and L-proline had a negative effect on plant growth and phenotype, while L-glutamic acid promoted plant growth and increased bacteria population density. The bacteria were found to colonize the rhizosphere and root endosphere, with colonization being promoted by L-glutamic acid. Additionally, Streptomyces was found to have plant growth promotion effects and provided protection against abiotic stresses. Interestingly, L-glutamic acid reduced the damage caused by salinity stress, but not drought stress. These findings suggest that L-glutamic acid plays a role in providing tolerance to salinity stress with the core microbiota, thus the current study demonstrated their prebiotic activity in the agriculture system.
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Affiliation(s)
- Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Youn-Sig Kwak
- Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Plus), Research Institute of Life Science, Gyeongsang National University, Jinju, Republic of Korea
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23
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Scarano F, Deivarajan Suresh M, Tiraboschi E, Cabirol A, Nouvian M, Nowotny T, Haase A. Geosmin suppresses defensive behaviour and elicits unusual neural responses in honey bees. Sci Rep 2023; 13:3851. [PMID: 36890201 PMCID: PMC9995521 DOI: 10.1038/s41598-023-30796-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 03/01/2023] [Indexed: 03/10/2023] Open
Abstract
Geosmin is an odorant produced by bacteria in moist soil. It has been found to be extraordinarily relevant to some insects, but the reasons for this are not yet fully understood. Here we report the first tests of the effect of geosmin on honey bees. A stinging assay showed that the defensive behaviour elicited by the bee's alarm pheromone component isoamyl acetate (IAA) is strongly suppressed by geosmin. Surprisingly, the suppression is, however, only present at very low geosmin concentrations, and disappears at higher concentrations. We investigated the underlying mechanisms at the level of the olfactory receptor neurons by means of electroantennography, finding the responses to mixtures of geosmin and IAA to be lower than to pure IAA, suggesting an interaction of both compounds at the olfactory receptor level. Calcium imaging of the antennal lobe (AL) revealed that neuronal responses to geosmin decreased with increasing concentration, correlating well with the observed behaviour. Computational modelling of odour transduction and coding in the AL suggests that a broader activation of olfactory receptor types by geosmin in combination with lateral inhibition could lead to the observed non-monotonic increasing-decreasing responses to geosmin and thus underlie the specificity of the behavioural response to low geosmin concentrations.
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Affiliation(s)
- Florencia Scarano
- Department of Physics, University of Trento, 38120, Trento, Italy.,Center for Mind/Brain Sciences (CIMeC), University of Trento, 38068, Rovereto, Italy
| | | | - Ettore Tiraboschi
- Center for Mind/Brain Sciences (CIMeC), University of Trento, 38068, Rovereto, Italy
| | - Amélie Cabirol
- Center for Mind/Brain Sciences (CIMeC), University of Trento, 38068, Rovereto, Italy.,Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Morgane Nouvian
- Department of Biology, University of Konstanz, 78457, Konstanz, Germany.,Zukunftskolleg, University of Konstanz, 78464, Konstanz, Germany
| | - Thomas Nowotny
- School of Engineering and Informatics, University of Sussex, Brighton, BN1 9QJ, UK.
| | - Albrecht Haase
- Department of Physics, University of Trento, 38120, Trento, Italy. .,Center for Mind/Brain Sciences (CIMeC), University of Trento, 38068, Rovereto, Italy.
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24
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Malla MA, Dubey A, Kumar A, Yadav S, Kumari S. Modeling and optimization of chlorpyrifos and glyphosate biodegradation using RSM and ANN: Elucidating their degradation pathways by GC-MS based metabolomics. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 252:114628. [PMID: 36774796 DOI: 10.1016/j.ecoenv.2023.114628] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 01/28/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Ongoing and extensive use of pesticides negatively impact the environment and human health. Microbe-based remediation bears importance as it is an eco-friendly and cost-effective technique. The present study investigated chlorpyrifos (CHL) and glyphosate (GLY) degrading potential of Bacillus cereus AKAD 3-1, isolated from the soybean rhizosphere. Optimization and validation of different process variables were carried out by response surface methodology (RSM) and artificial neural network (ANN). Critical parameters which affect the degradation process are initial pesticide concentration, pH, and inoculum size. At optimum conditions, the bacterial strain demonstrated 94.52% and 83.58% removal of chlorpyrifos and glyphosate, respectively. Both Central-composite design (CCD-RSM) and ANN approaches proved to perform well in modeling and optimizing the growth conditions. The optimum ANN-GA model resulted in R2 ≥ 0.99 for chlorpyrifos and glyphosate, while in the case of RSM, the obtained R2 value was 0.96 and 0.95, respectively. Results indicated that the process variables significantly (p < 0.05) impact chlorpyrifos and glyphosate biodegradation. Moreover, the predicted RSM model had a "lack of fit p-value" of "0.8849" and "0.2502" for chlorpyrifos and glyphosate, respectively. GC-MS analysis revealed that the strain first converted chlorpyrifos into 3,5,6-trichloro pyridin-2-ol & O, O-diethyl O-hydrogen phosphorothiate. Later, these intermediate metabolites were broken and completely mineralized into non-toxic by-products. Similarly, glyphosate was first converted into 2-(methylamino) acetic acid and amino-oxyphosphonic acid, which were further mineralized without any toxic by-products. Taken together, the results of this study clarify the biodegradation pathways and highlights the promising potential of B. cereus AKAD 3-1 in the bioremediation of chlorpyrifos and glyphosate-polluted environments.
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Affiliation(s)
- Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar 470003, Madhya Pradesh, India; Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, Madhya Pradesh, India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, Madhya Pradesh, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, Madhya Pradesh, India; Metagenomics and Secretomics Research Laboratory, Department of Botany, University of Allahabad (A Central University), Prayagraj 211002, Uttar Pradesh, India.
| | - Shweta Yadav
- Department of Zoology, Dr. Harisingh Gour University (A Central University), Sagar 470003, Madhya Pradesh, India
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4001, South Africa
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25
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Shepherdson EM, Baglio CR, Elliot MA. Streptomyces behavior and competition in the natural environment. Curr Opin Microbiol 2023; 71:102257. [PMID: 36565538 DOI: 10.1016/j.mib.2022.102257] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
Streptomyces are ubiquitous terrestrial bacteria that are renowned for their robust metabolic capabilities and their behavioral flexibility. In competing for environmental niches, these bacteria can employ novel growth and dispersal behaviors. They also wield their diverse metabolic repertoire for everything from maximizing nutrient uptake, to preventing phage replication or inhibiting bacterial and fungal growth. Increasingly, they are found to live in association with plants and insects, often conferring protective benefits to their host courtesy of their ability to produce pathogen-inhibitory antimicrobial compounds. Here, we highlight recent advances in understanding the competitive and cooperative interactions between Streptomyces and phage, microbes, and higher organisms in their environment.
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Affiliation(s)
- Evan Mf Shepherdson
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada
| | - Christine R Baglio
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada
| | - Marie A Elliot
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada; M.G. DeGroote Institute for Infectious Disease Research, Canada.
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26
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Santorelli LA, Wilkinson T, Abdulmalik R, Rai Y, Creevey CJ, Huws S, Gutierrez-Merino J. Beehives possess their own distinct microbiomes. ENVIRONMENTAL MICROBIOME 2023; 18:1. [PMID: 36624518 PMCID: PMC9830898 DOI: 10.1186/s40793-023-00460-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 01/03/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Honeybees use plant material to manufacture their own food. These insect pollinators visit flowers repeatedly to collect nectar and pollen, which are shared with other hive bees to produce honey and beebread. While producing these products, beehives accumulate a considerable number of microbes, including bacteria that derive from plants and different parts of the honeybees' body. Whether bacteria form similar communities amongst beehives, even if located in close proximity, is an ecologically important question that has been addressed in this study. Specific ecological factors such as the surrounding environment and the beekeeping methods used can shape the microbiome of the beehive as a whole, and eventually influence the health of the honeybees and their ecosystem. RESULTS We conducted 16S rRNA meta-taxonomic analysis on honey and beebread samples that were collected from 15 apiaries in the southeast of England to quantify the bacteria associated with different beehives. We observed that honeybee products carry a significant variety of bacterial groups that comprise bee commensals, environmental bacteria and symbionts and pathogens of plants and animals. Remarkably, this bacterial diversity differs not only amongst apiaries, but also between the beehives of the same apiary. In particular, the levels of the bee commensals varied significantly, and their fluctuations correlated with the presence of different environmental bacteria and various apiculture practices. CONCLUSIONS Our results show that every hive possesses their own distinct microbiome and that this very defined fingerprint is affected by multiple factors such as the nectar and pollen gathered from local plants, the management of the apiaries and the bacterial communities living around the beehives. Based on our findings, we suggest that the microbiome of beehives could be used as a valuable biosensor informing of the health of the honeybees and their surrounding environment.
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Affiliation(s)
| | - Toby Wilkinson
- The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Ronke Abdulmalik
- School of Biosciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Yuma Rai
- School of Biosciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Christopher J Creevey
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Sharon Huws
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, BT9 5DL, UK
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27
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Xi M, Deyett E, Stajich JE, El-Kereamy A, Roper MC, Rolshausen PE. Microbiome diversity, composition and assembly in a California citrus orchard. Front Microbiol 2023; 14:1100590. [PMID: 36910183 PMCID: PMC9992537 DOI: 10.3389/fmicb.2023.1100590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
The citrus root and rhizosphere microbiomes have been relatively well described in the literature, especially in the context of Huanglonbing disease. Yet questions addressing the assembly of root microbial endophytes have remained unanswered. In the above ground tree tissues, leaves and stems have been the research focus point, while flush and flower microbiomes, two important tissues in the vegetative and reproductive cycles of the tree, are not well described. In this study, the fungal and bacterial taxa in five biocompartments (bulk soil, rhizosphere, root endosphere, flower and flush) of citrus trees grown in a single California orchard were profiled using an amplicon-based metagenomic Illumina sequencing approach. Trees with no observable signs of abiotic or biotic stresses were sampled for two consecutive years during the floral development phase. The rhizosphere was the most biodiverse compartment compared to bulk soil, root endosphere, flower and flush microbiomes. In addition, the belowground bacteriome was more diverse than the mycobiome. Microbial richness decreased significantly from the root exosphere to the endosphere and was overall low in the above ground tissues. Root endophytic microbial community composition shared strong similarities to the rhizosphere but also contained few taxa from above ground tissues. Our data indicated compartmentalization of the microbiome with distinct profiles between above and below ground microbial communities. However, several taxa were present across all compartments suggesting the existence of a core citrus microbiota. These findings highlight key microbial taxa that could be engineered as biopesticides and biofertilizers for citriculture.
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Affiliation(s)
- MengYuan Xi
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Elizabeth Deyett
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Ashraf El-Kereamy
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
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28
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Cui P, Wu H, Jiang T, Tao J, Zhu Z, Liu P, Yu L, Zhang Y. Diversity and antibacterial potential of the Actinobacteria associated with Apis mellifera ligustica. Front Microbiol 2022; 13:1056176. [PMID: 36590398 PMCID: PMC9800615 DOI: 10.3389/fmicb.2022.1056176] [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: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Insect-associated Actinobacteria are a potentially rich source of novel natural products with antibacterial activity. Here, the community composition of Actinobacteria associated with Apis mellifera ligustica was investigated by integrated culture-dependent and independent methods. A total of 61 strains of Streptomyces genera were isolated from the honeycomb, larva, and different anatomical parts of the honeybee's body using the culture-dependent method. Amplicon sequencing analyses revealed that the actinobacterial communities were dominated by the family of Bifidobacteriaceae and Microbacteriaceae in the honeybee gut, and Nocardiaceae and Pseudonocardiaceae in the honeycomb, whereas only Streptomyces genera were isolated by the culture-dependent method. Culture-independent analyses showed more diverse actinobacterial communities than those of culture-dependent methods. The antibacterial bioassay showed that most crude extracts of representative isolates exhibited antibacterial activities. Among them, the crude extract of Streptomyces sp. FCF01 showed the best antibacterial activities against Staphylococcus aureus, Micrococcus tetragenus, and Pseudomonas syringae pv. actinidiae (Psa) with the disc diameter of inhibition zone diameter (IZD) of 23.00, 15.00, and 13.33 mm, respectively. Chemical analysis of Streptomyces sp. FCF01 led to the isolation of three secondary metabolites, including mayamycin (1), mayamycin B (2), and N-(2-Hydroxyphenyl) acetamide (3). Among them, compound 1 displayed strong antibacterial activity against S. aureus, M. tetragenus, and Psa with minimum inhibitory concentrations (MIC) values of 6.25, 12.5, and 6.25 μg/ml, respectively. In addition, two novel derivative compounds 1a and 1b were synthesized by acetylation of compound 1. Both compounds 1a and 1b displayed similar antibacterial activities with those of metabolite 1. These results indicated that Streptomyces species associated with honeybees had great potential in finding antibiotics.
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Affiliation(s)
- Pu Cui
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Haoyang Wu
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Taoshan Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Jian Tao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Zhiwei Zhu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Peng Liu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Linsheng Yu
- School of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yinglao Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei, China,*Correspondence: Yinglao Zhang,
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29
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Bobek J, Filipová E, Bergman N, Čihák M, Petříček M, Lara AC, Kristufek V, Megyes M, Wurzer T, Chroňáková A, Petříčková K. Polyenic Antibiotics and Other Antifungal Compounds Produced by Hemolytic Streptomyces Species. Int J Mol Sci 2022; 23:15045. [PMID: 36499372 PMCID: PMC9740855 DOI: 10.3390/ijms232315045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/14/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
Streptomyces are of great interest in the pharmaceutical industry as they produce a plethora of secondary metabolites that act as antibacterial and antifungal agents. They may thrive on their own in the soil, or associate with other organisms, such as plants or invertebrates. Some soil-derived strains exhibit hemolytic properties when cultivated on blood agar, raising the question of whether hemolysis could be a virulence factor of the bacteria. In this work we examined hemolytic compound production in 23 β-hemolytic Streptomyces isolates; of these 12 were soil-derived, 10 were arthropod-associated, and 1 was plant-associated. An additional human-associated S. sp. TR1341 served as a control. Mass spectrometry analysis suggested synthesis of polyene molecules responsible for the hemolysis: candicidins, filipins, strevertene A, tetrafungin, and tetrin A, as well as four novel polyene compounds (denoted here as polyene A, B, C, and D) in individual liquid cultures or paired co-cultures. The non-polyene antifungal compounds actiphenol and surugamide A were also identified. The findings indicate that the ability of Streptomyces to produce cytolytic compounds (here manifested by hemolysis on blood agar) is an intrinsic feature of the bacteria in the soil environment and could even serve as a virulence factor when colonizing available host organisms. Additionally, a literature review of polyenes and non-polyene hemolytic metabolites produced by Streptomyces is presented.
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Affiliation(s)
- Jan Bobek
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studničkova 7, 128 00 Prague, Czech Republic
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 400 96 Ústí nad Labem, Czech Republic
| | - Eliška Filipová
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studničkova 7, 128 00 Prague, Czech Republic
| | - Natalie Bergman
- Faculty of Science, Jan Evangelista Purkyně University in Ústí nad Labem, České mládeže 8, 400 96 Ústí nad Labem, Czech Republic
| | - Matouš Čihák
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studničkova 7, 128 00 Prague, Czech Republic
- Contipro a.s., Dolní Dobrouč 401, 561 02 Dolní Dobrouč, Czech Republic
| | - Miroslav Petříček
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studničkova 7, 128 00 Prague, Czech Republic
| | - Ana Catalina Lara
- Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Vaclav Kristufek
- Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Melinda Megyes
- Doctoral School of Environmental Sciences, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Theresa Wurzer
- Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Alica Chroňáková
- Institute of Soil Biology and Biogeochemistry, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
| | - Kateřina Petříčková
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studničkova 7, 128 00 Prague, Czech Republic
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30
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Zakalyukina YV, Pavlov NA, Lukianov DA, Marina VI, Belozerova OA, Tashlitsky VN, Guglya EB, Osterman IA, Biryukov MV. A New Albomycin-Producing Strain of Streptomyces globisporus subsp. globisporus May Provide Protection for Ants Messor structor. INSECTS 2022; 13:1042. [PMID: 36421945 PMCID: PMC9693239 DOI: 10.3390/insects13111042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
There are several well-studied examples of protective symbiosis between insect host and symbiotic actinobacteria, producing antimicrobial metabolites to inhibit host pathogens. These mutualistic relationships are best described for some wasps and leaf-cutting ants, while a huge variety of insect species still remain poorly explored. For the first time, we isolated actinobacteria from the harvester ant Messor structor and evaluated the isolates' potential as antimicrobial producers. All isolates could be divided into two morphotypes of single and mycelial cells. We found that the most common mycelial morphotype was observed among soldiers and least common among larvae in the studied laboratory colony. The representative of this morphotype was identified as Streptomyces globisporus subsp. globisporus 4-3 by a polyphasic approach. It was established using a E. coli JW5503 pDualRep2 system that crude broths of mycelial isolates inhibited protein synthesis in reporter strains, but it did not disrupt the in vitro synthesis of proteins in cell-free extracts. An active compound was extracted, purified and identified as albomycin δ2. The pronounced ability of albomycin to inhibit the growth of entomopathogens suggests that Streptomyces globisporus subsp. globisporus may be involved in defensive symbiosis with the Messor structor ant against infections.
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Affiliation(s)
- Yuliya V. Zakalyukina
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Department of Soil Science, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Nikolay A. Pavlov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
| | - Dmitrii A. Lukianov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Valeria I. Marina
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russia
| | - Vadim N. Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Elena B. Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova st. 1, 117997 Moscow, Russia
| | - Ilya A. Osterman
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
| | - Mikhail V. Biryukov
- Center for Translational Medicine, Sirius University of Science and Technology, Olympic Avenue 1, 354340 Sochi, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Bld. 1, 121205 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
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31
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A dual-stimuli responsive electrochemiluminescence biosensor for pathogenic bacterial sensing and killing in foods. Talanta 2022. [DOI: 10.1016/j.talanta.2022.124074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Kim DR, Kwak YS. Roads to Construct and Re-build Plant Microbiota Community. THE PLANT PATHOLOGY JOURNAL 2022; 38:425-431. [PMID: 36221915 PMCID: PMC9561157 DOI: 10.5423/ppj.rw.05.2022.0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/19/2022] [Indexed: 05/12/2023]
Abstract
Plant microbiota has influenced plant growth and physiology significantly. Plant and plant-associated microbes have flexible interactions that respond to changes in environmental conditions. These interactions can be adjusted to suit the requirements of the microbial community or the host physiology. In addition, it can be modified to suit microbiota structure or fixed by the host condition. However, no technology is realized yet to control mechanically manipulated plant microbiota structure. Here, we review step-by-step plant-associated microbial partnership from plant growth-promoting rhizobacteria to the microbiota structural modulation. Glutamic acid enriched the population of Streptomyces, a specific taxon in anthosphere microbiota community. Additionally, the population density of the microbes in the rhizosphere was also a positive response to glutamic acid treatment. Although many types of research are conducted on the structural revealing of plant microbiota, these concepts need to be further understood as to how the plant microbiota clusters are controlled or modulated at the community level. This review suggests that the intrinsic level of glutamic acid in planta is associated with the microbiota composition that the external supply of the biostimulant can modulate.
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Affiliation(s)
- Da-Ran Kim
- Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Research Institute of Life Sciences (RILS), Gyeongsang National University, Jinju 52828, Korea
- Division of Applied Life Science (BK 21 Plus), Gyeongsang National University, Jinju 52828, Korea
- Corresponding author. Phone) +82-55-772-1922, FAX) +82-55-772-1929, E-mail)
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Haider T, Soni V. “Response surface methodology and artificial neural network-based modeling and optimization of phosphatidylserine targeted nanocarriers for effective treatment of cancer: In vitro and in silico studies”. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Burgess EC, Schaeffer RN. The Floral Microbiome and Its Management in Agroecosystems: A Perspective. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9819-9825. [PMID: 35917340 DOI: 10.1021/acs.jafc.2c02037] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Disease management is critical to ensuring healthy crop yields and is often targeted at flowers because of their susceptibility to pathogens and direct link to reproduction. Many disease management strategies are unsustainable however because of the potential for pathogens to evolve resistance, or nontarget effects on beneficial insects. Manipulating the floral microbiome holds some promise as a sustainable alternative to chemical means of disease control. In this perspective, we discuss the current state of research concerning floral microbiome assembly and management in agroecosystems as well as future directions aimed at improving the sustainability of disease control and insect-mediated ecosystem services.
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Affiliation(s)
- Emily C Burgess
- Department of Biology, Utah State University, Logan, Utah 84322, United States
| | - Robert N Schaeffer
- Department of Biology, Utah State University, Logan, Utah 84322, United States
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Park HS, Park JH, Kim HJ, Kang SH, Choi SS, Kim ES. BAC cloning and heterologous expression of a giant biosynthetic gene cluster encoding antifungal neotetrafibricin in streptomyces rubrisoli. Front Bioeng Biotechnol 2022; 10:964765. [PMID: 36046673 PMCID: PMC9421130 DOI: 10.3389/fbioe.2022.964765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Polyene natural products including nystatin A1, amphotericin B, ECO-02301, and mediomycin belong to a large family of valuable antifungal polyketide compounds typically produced by soil actinomycetes. A previous study (Park et al., Front. Bioeng. Biotechnol., 2021, 9, 692340) isolated Streptomyces rubrisoli Inha501 with strong antifungal activity and analyzed a large-sized biosynthetic gene cluster (BGC) of a linear polyene compound named Inha-neotetrafibricin (I-NTF) using whole genome sequencing and bioinformatics. In the present study, an entire I-NTF BGC (∼167 kb) was isolated through construction and screening of Streptomyces BAC library. Overexpression of the cloned I-NTF BGC in the wild-type S. rubrisoli Inha501 and its heterologous expression in S. lividans led to 2.6-fold and 2.8-fold increase in I-NTF yields, respectively. The qRT-PCR confirmed that the transcription levels of I-NTF BGC were significantly increased in both homologous and heterologous hosts containing the BAC integration of I-NTF BGC. In addition, the I-NTF aglycone-producing strains were constructed by a target-specific deletion of glycosyltransferase gene present in I-NTF BGC. A comparison of the in vitro biological activities of I-NTF and I-NTF aglycone confirmed that the rhamnose sugar motif of I-NTF plays a critical role in both antifungal and antibacterial activities. These results suggest that the Streptomyces BAC cloning of a large-sized natural product BGC is a valuable approach for natural product titer improvement and biological activity screening of natural product in actinomycetes.
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Pronk LJU, Bakker PAHM, Keel C, Maurhofer M, Flury P. The secret life of plant-beneficial rhizosphere bacteria: insects as alternative hosts. Environ Microbiol 2022; 24:3273-3289. [PMID: 35315557 PMCID: PMC9542179 DOI: 10.1111/1462-2920.15968] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/15/2022]
Abstract
Root-colonizing bacteria have been intensively investigated for their intimate relationship with plants and their manifold plant-beneficial activities. They can inhibit growth and activity of pathogens or induce defence responses. In recent years, evidence has emerged that several plant-beneficial rhizosphere bacteria do not only associate with plants but also with insects. Their relationships with insects range from pathogenic to mutualistic and some rhizobacteria can use insects as vectors for dispersal to new host plants. Thus, the interactions of these bacteria with their environment are even more complex than previously thought and can extend far beyond the rhizosphere. The discovery of this secret life of rhizobacteria represents an exciting new field of research that should link the fields of plant-microbe and insect-microbe interactions. In this review, we provide examples of plant-beneficial rhizosphere bacteria that use insects as alternative hosts, and of potentially rhizosphere-competent insect symbionts. We discuss the bacterial traits that may enable a host-switch between plants and insects and further set the multi-host lifestyle of rhizobacteria into an evolutionary and ecological context. Finally, we identify important open research questions and discuss perspectives on the use of these rhizobacteria in agriculture.
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Affiliation(s)
| | | | - Christoph Keel
- Department of Fundamental MicrobiologyUniversity of LausanneLausanneSwitzerland
| | - Monika Maurhofer
- Plant Pathology, Institute of Integrative BiologyETH ZürichZürichSwitzerland
| | - Pascale Flury
- Crop Protection – Phytopathology, Department of Crop SciencesResearch Institute of Organic Agriculture FiBLFrickSwitzerland
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Kim DR, Kim SH, Lee SI, Kwak YS. Microbiota Communities of Healthy and Bacterial Pustule Diseased Soybean. THE PLANT PATHOLOGY JOURNAL 2022; 38:372-382. [PMID: 35953057 PMCID: PMC9372108 DOI: 10.5423/ppj.oa.05.2022.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Soybean is an important source of protein and for a wide range of agricultural, food, and industrial applications. Soybean is being affected by Xanthomonas citri pv. glycines, a causal pathogen of bacterial pustule disease, result in a reduction in yield and quality. Diverse microbial communities of plants are involved in various plant stresses is known. Therefore, we designed to investigate the microbial community differentiation depending on the infection of X. citri pv. glycines. The microbial community's abundance, diversity, and similarity showed a difference between infected and non-infected soybean. Microbiota community analysis, excluding X. citri pv. glycines, revealed that Pseudomonas spp. would increase the population of the infected soybean. Results of DESeq analyses suggested that energy metabolism, secondary metabolite, and TCA cycle metabolism were actively diverse in the non-infected soybeans. Additionally, Streptomyces bacillaris S8, an endophyte microbiota member, was nominated as a key microbe in the healthy soybeans. Genome analysis of S. bacillaris S8 presented that salinomycin may be the critical antibacterial metabolite. Our findings on the composition of soybean microbiota communities and the key strain information will contribute to developing biological control strategies against X. citri pv. glycines.
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Affiliation(s)
- Da-Ran Kim
- Resarch Institute of Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | - Su-Hyeon Kim
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828,
Korea
| | - Su In Lee
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828,
Korea
| | - Youn-Sig Kwak
- Resarch Institute of Life Science, Gyeongsang National University, Jinju 52828,
Korea
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828,
Korea
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Cho G, Jo GS, Lee Y, Kwak YS. Effect of Scenedesmus sp. CHK0059 on Strawberry Microbiota Community. J Microbiol Biotechnol 2022; 32:862-868. [PMID: 35880478 PMCID: PMC9628918 DOI: 10.4014/jmb.2205.05016] [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: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/27/2022] [Indexed: 12/15/2022]
Abstract
Microalgae are photosynthetic cyanobacteria and eukaryotic microorganisms, mainly living in the water. In agriculture, numerous studies have been conducted to utilize microalgae as a biostimulant resource. Scenedesmus has been known to be one such microalga that can promote plant growth by secretion of auxin or cytokinin hormone analogs. However, no research has been performed on the effect of microalgae treatment on plant microbiota communities. This study was conducted to investigate the mode of action of microalgae as biostimulants in a plant microbiota perspective by using Scenedesmus sp. CHK0059 (also known as species Chlorella fusca), which has been well documented as a biostimulant for strawberries. The strawberry cultivar Keumsil was bred with Seolhyang and Maehyang as the parent cultivars. Using these three cultivars, microbiota communities were evaluated for changes in structural composition according to the CHK0059 treatment. CHK0059-treated Seolhyang, and CHK0059-untreated Maehyang were similar in microbial diversity in the endosphere. From a microbiota community perspective, the diversity change showed that CHK0059 was affected by the characteristics of the host. Conversely, when CHK0059 treatment was applied, populations of Streptomyces and Actinospica were observed in the crown endosphere.
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Affiliation(s)
- Gyeongjun Cho
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeong Seo Jo
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yejin Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Youn-Sig Kwak
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea,Department of Plant Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea,Corresponding author Phone: +82-55-772-1922 Fax: +82-55-772-1929 E-mail:
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Microbial Turnover and Dispersal Events Occur in Synchrony with Plant Phenology in the Perennial Evergreen Tree Crop Citrus sinensis. mBio 2022; 13:e0034322. [PMID: 35642946 PMCID: PMC9239260 DOI: 10.1128/mbio.00343-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Emerging research indicates that plant-associated microbes can alter plant developmental timing. However, it is unclear if host phenology affects microbial community assembly. Microbiome studies in annual or deciduous perennial plants face challenges in separating effects of tissue age from phenological driven effects on the microbiome. In contrast, evergreen perennial trees, like Citrus sinensis, retain leaves for years, allowing for uniform sampling of similarly aged leaves from the same developmental cohort. This aids in separating phenological effects on the microbiome from impacts due to annual leaf maturation/senescence. Here, we used this system to test the hypothesis that host phenology acts as a driver of microbiome composition. Citrus sinensis leaves and roots were sampled during seven phenological stages. Using amplicon-based sequencing, followed by diversity, phylogenetic, differential abundance, and network analyses, we examined changes in bacterial and fungal communities. Host phenological stage is the main determinant of microbiome composition, particularly within the foliar bacteriome. Microbial enrichment/depletion patterns suggest that microbial turnover and dispersal were driving these shifts. Moreover, a subset of community shifts were phylogenetically conserved across bacterial clades, suggesting that inherited traits contribute to microbe-microbe and/or plant-microbe interactions during specific phenophases. Plant phenology influences microbial community composition. These findings enhance understanding of microbiome assembly and identify microbes that potentially influence plant development and reproduction. IMPORTANCE Research at the forefront of plant microbiome studies indicates that plant-associated microbes can alter the timing of plant development (phenology). However, it is unclear if host phenological stage affects microbial community assembly. Microbiome studies in annual or deciduous perennial plants can face difficulty in separating effects of tissue age from phenological driven effects on the microbiome. Evergreen perennial plants, like sweet orange, maintain mature leaves for multiple years, allowing for uniform sampling of similarly aged tissue across host reproductive stages. Using this system, multiyear sampling, and high-throughput sequencing, we identified plant phenology as a major driver of microbiome composition, particularly within the leaf-associated bacterial communities. Distinct changes in microbial patterns suggest that microbial turnover and dispersal are mechanisms driving these community shifts. Additionally, closely related bacteria have similar abundance patterns across plant stages, indicating that inherited microbial traits may influence how bacteria respond to host developmental changes. Overall, this study illustrates that plant phenology does indeed govern microbiome seasonal shifts and identifies microbial candidates that may affect plant reproduction and development.
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Takeda K, Sakai S. Idea paper: Extended benefits of pollinator‐mediated microbial dispersal among flowers. Ecol Res 2022. [DOI: 10.1111/1440-1703.12326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kazuya Takeda
- Center for Ecological Research Kyoto University Otsu Shiga Japan
- Research Institute for Food and Agriculture Ryukoku University Shiga Japan
| | - Shoko Sakai
- Center for Ecological Research Kyoto University Otsu Shiga Japan
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Li S, Tang R, Yi H, Cao Z, Sun S, Liu TX, Zhang S, Jing X. Neutral Processes Provide an Insight Into the Structure and Function of Gut Microbiota in the Cotton Bollworm. Front Microbiol 2022; 13:849637. [PMID: 35591990 PMCID: PMC9113526 DOI: 10.3389/fmicb.2022.849637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/29/2022] [Indexed: 11/30/2022] Open
Abstract
Gut-associated microbes can influence insect health and fitness. Understanding the structure of bacterial communities provides valuable insights on how different species may be selected and their functional characteristics in their hosts. The neutral model is powerful in predicting the structure of microbial communities, but its application in insects remains rare. Here, we examined the contribution of neutral processes to the gut-associated bacterial communities in Helicoverpa armigera caterpillars collected from different maize varieties at four locations. The gut-associated bacteria can be assigned to 37 Phyla, 119 orders, and 515 genera, with each individual gut containing 17–75% of the OTUs and 19–79% of the genera in the pooled samples of each population. The distribution patterns of most (75.59–83.74%) bacterial taxa were in good agreement with the neutral expectations. Of the remaining OTUs, some were detected in more individual hosts than would be predicted by the neutral model (i.e., above-partition), and others were detected in fewer individual hosts than predicted by the neutral model (i.e., below-partition). The bacterial taxa in the above-partitions were potentially selected by the caterpillar hosts, while the bacteria in the below-partitions may be preferentially eliminated by the hosts. Moreover, the gut-associated microbiota seemed to vary between maize varieties and locations, so ecological parameters outside hosts can affect the bacterial communities. Therefore, the structure of gut microbiota in the H. armigera caterpillar was mainly determined by stochastic processes, and the bacteria in the above-partition warrant further investigation for their potential roles in the caterpillar host.
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Affiliation(s)
- Sali Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China.,Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Rui Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China.,Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Hao Yi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China.,Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Zhichao Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China.,Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Shaolei Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China.,Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Tong-Xian Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China.,Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Sicong Zhang
- Shandong Academy of Pesticide Sciences, Jinan, China
| | - Xiangfeng Jing
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China.,Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Xianyang, China
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Santos-Beneit F, Ceniceros A, Nikolaou A, Salas JA, Gutierrez-Merino J. Identification of Antimicrobial Compounds in Two Streptomyces sp. Strains Isolated From Beehives. Front Microbiol 2022; 13:742168. [PMID: 35185841 PMCID: PMC8851239 DOI: 10.3389/fmicb.2022.742168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/12/2022] [Indexed: 01/22/2023] Open
Abstract
The World Health Organization warns that the alarming increase in antibiotic resistant bacteria will lead to 2.7 million deaths annually due to the lack of effective antibiotic therapies. Clearly, there is an urgent need for short-term alternatives that help to alleviate these alarming figures. In this respect, the scientific community is exploring neglected ecological niches from which the prototypical antibiotic-producing bacteria Streptomycetes are expected to be present. Recent studies have reported that honeybees and their products carry Streptomyces species that possess strong antibacterial activity. In this study, we have investigated the antibiotic profile of two Streptomycetes strains that were isolated from beehives. One of the isolates is the strain Streptomyces albus AN1, which derives from pollen, and shows potent antimicrobial activity against Candida albicans. The other isolate is the strain Streptomyces griseoaurantiacus AD2, which was isolated from honey, and displays a broad range of antimicrobial activity against different Gram-positive bacteria, including pathogens such as Staphylococcus aureus and Enterococus faecalis. Cultures of S. griseoaurantiacus AD2 have the capacity to produce the antibacterial compounds undecylprodigiosin and manumycin, while those of S. albus AN1 accumulate antifungal compounds such as candicidins and antimycins. Furthermore, genome and dereplication analyses suggest that the number of putative bioactive metabolites produced by AD2 and AN1 is considerably high, including compounds with anti-microbial and anti-cancer properties. Our results postulate that beehives are a promising source for the discovery of novel bioactive compounds that might be of interest to the agri-food sector and healthcare pharmaceuticals.
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Affiliation(s)
- Fernando Santos-Beneit
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid, Spain
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Ana Ceniceros
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Athanasios Nikolaou
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - José A. Salas
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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Kim DR, Jeon CW, Cho G, Thomashow LS, Weller DM, Paik MJ, Lee YB, Kwak YS. Glutamic acid reshapes the plant microbiota to protect plants against pathogens. MICROBIOME 2021; 9:244. [PMID: 34930485 PMCID: PMC8691028 DOI: 10.1186/s40168-021-01186-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/27/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Plants in nature interact with other species, among which are mutualistic microorganisms that affect plant health. The co-existence of microbial symbionts with the host contributes to host fitness in a natural context. In turn, the composition of the plant microbiota responds to the environment and the state of the host, raising the possibility that it can be engineered to benefit the plant. However, technology for engineering the structure of the plant microbiome is not yet available. RESULTS The loss of diversity and reduction in population density of Streptomyces globisporus SP6C4, a core microbe, was observed coincident with the aging of strawberry plants. Here, we show that glutamic acid reshapes the plant microbial community and enriches populations of Streptomyces, a functional core microbe in the strawberry anthosphere. Similarly, in the tomato rhizosphere, treatment with glutamic acid increased the population sizes of Streptomyces as well as those of Bacillaceae and Burkholderiaceae. At the same time, diseases caused by species of Botrytis and Fusarium were significantly reduced in both habitats. We suggest that glutamic acid directly modulates the composition of the microbiome community. CONCLUSIONS Much is known about the structure of plant-associated microbial communities, but less is understood about how the community composition and complexity are controlled. Our results demonstrate that the intrinsic level of glutamic acid in planta is associated with the composition of the microbiota, which can be modulated by an external supply of a biostimulant. Video Abstract.
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Affiliation(s)
- Da-Ran Kim
- RILS, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Chang-Wook Jeon
- Division of Applied Life Science (BK 21 plus) and IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Gyeongjun Cho
- Division of Applied Life Science (BK 21 plus) and IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Linda S Thomashow
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, 99164-6430, USA
| | - David M Weller
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, 99164-6430, USA
| | - Man-Jeong Paik
- College of Pharmacy, Sunchon National University, Suncheon, 65980, Republic of Korea
| | - Yong Bok Lee
- Division of Applied Life Science (BK 21 plus) and IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Youn-Sig Kwak
- RILS, Gyeongsang National University, Jinju, 52828, Republic of Korea.
- Division of Applied Life Science (BK 21 plus) and IALS, Gyeongsang National University, Jinju, 52828, Republic of Korea.
- Department of Plant Medicine, Gyeongsang National University, Jinju, 52828, Republic of Korea.
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Kurihara D, Mizuta Y, Nagahara S, Higashiyama T. ClearSeeAlpha: Advanced Optical Clearing for Whole-Plant Imaging. PLANT & CELL PHYSIOLOGY 2021; 62:1302-1310. [PMID: 33638989 PMCID: PMC8579160 DOI: 10.1093/pcp/pcab033] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/16/2021] [Accepted: 02/24/2021] [Indexed: 05/10/2023]
Abstract
To understand how the body of plants is made, it is essential to observe the morphology, structure and arrangement of constituent cells. However, the opaque nature of the plant body makes it difficult to observe the internal structures directly under a microscope. To overcome this problem, we developed a reagent, ClearSee, that makes plants transparent, allowing direct observation of the inside of a plant body without inflicting damage on it, e.g. through physical cutting. However, because ClearSee is not effective in making some plant species and tissues transparent, in this study, we further improved its composition to prevent oxidation, and have developed ClearSeeAlpha, which can be applied to a broader range of plant species and tissues. Sodium sulfite, one of the reductants, prevented brown pigmentation due to oxidation during clearing treatment. Using ClearSeeAlpha, we show that it is possible to obtain clear chrysanthemum leaves, tobacco and Torenia pistils and fertilized Arabidopsis thaliana fruits-tissues that have hitherto been challenging to clear. Moreover, we show that the fluorescence intensity of purified fluorescent proteins emitting light of various colors was unaffected in the ClearSeeAlpha solution; only the fluorescence intensity of TagRFP was reduced by about half. ClearSeeAlpha should be useful in the discovery and analysis of biological phenomena occurring deep inside the plant tissues.
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Affiliation(s)
| | - Yoko Mizuta
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601 Japan
- Institute for Advanced Research (IAR), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601 Japan
| | - Shiori Nagahara
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601 Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601 Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602 Japan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bukyo-ku, Tokyo, 113-0033 Japan
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El-Baky NA, Amara AAAF. Recent Approaches towards Control of Fungal Diseases in Plants: An Updated Review. J Fungi (Basel) 2021; 7:jof7110900. [PMID: 34829188 PMCID: PMC8621679 DOI: 10.3390/jof7110900] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Recent research demonstrates that the number of virulent phytopathogenic fungi continually grows, which leads to significant economic losses worldwide. Various procedures are currently available for the rapid detection and control of phytopathogenic fungi. Since 1940, chemical and synthetic fungicides were typically used to control phytopathogenic fungi. However, the substantial increase in development of fungal resistance to these fungicides in addition to negative effects caused by synthetic fungicides on the health of animals, human beings, and the environment results in the exploration of various new approaches and green strategies of fungal control by scientists from all over the world. In this review, the development of new approaches for controlling fungal diseases in plants is discussed. We argue that an effort should be made to bring these recent technologies to the farmer level.
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O'Brien AM, Ginnan NA, Rebolleda-Gómez M, Wagner MR. Microbial effects on plant phenology and fitness. AMERICAN JOURNAL OF BOTANY 2021; 108:1824-1837. [PMID: 34655479 DOI: 10.1002/ajb2.1743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Plant development and the timing of developmental events (phenology) are tightly coupled with plant fitness. A variety of internal and external factors determine the timing and fitness consequences of these life-history transitions. Microbes interact with plants throughout their life history and impact host phenology. This review summarizes current mechanistic and theoretical knowledge surrounding microbe-driven changes in plant phenology. Overall, there are examples of microbes impacting every phenological transition. While most studies have focused on flowering time, microbial effects remain important for host survival and fitness across all phenological phases. Microbe-mediated changes in nutrient acquisition and phytohormone signaling can release plants from stressful conditions and alter plant stress responses inducing shifts in developmental events. The frequency and direction of phenological effects appear to be partly determined by the lifestyle and the underlying nature of a plant-microbe interaction (i.e., mutualistic or pathogenic), in addition to the taxonomic group of the microbe (fungi vs. bacteria). Finally, we highlight biases, gaps in knowledge, and future directions. This biotic source of plasticity for plant adaptation will serve an important role in sustaining plant biodiversity and managing agriculture under the pressures of climate change.
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Affiliation(s)
- Anna M O'Brien
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nichole A Ginnan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | - María Rebolleda-Gómez
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, CA, USA
| | - Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, USA
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Kim SH, Cho G, Lee SI, Kim DR, Kwak YS. Comparison of Bacterial Community of Healthy and Erwinia amylovora Infected Apples. THE PLANT PATHOLOGY JOURNAL 2021; 37:396-403. [PMID: 34365751 PMCID: PMC8357565 DOI: 10.5423/ppj.nt.04.2021.0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/17/2021] [Indexed: 06/01/2023]
Abstract
Fire blight disease, caused by Erwinia amylovora, could damage rosaceous plants such as apples, pears, and raspberries. In this study, we designed to understand how E. amylovora affected other bacterial communities on apple rhizosphere; twig and fruit endosphere; and leaf, and fruit episphere. Limited studies on the understanding of the microbial community of apples and changes the community structure by occurrence of the fire blight disease were conducted. As result of these experiments, the infected trees had low species richness and operational taxonomic unit diversity when compared to healthy trees. Rhizospheric bacterial communities were stable regardless of infection. But the communities in endosphere and episphere were significanlty affected by E. amylovora infection. We also found that several metabolic pathways differ significantly between infected and healthy trees. In particular, we observed differences in sugar metabolites. The finding provides that sucrose metabolites are important for colonization of E. amylovora in host tissue. Our results provide fundamental information on the microbial community structures between E. amylovora infected and uninfected trees, which will contribute to developing novel control strategies for the fire blight disease.
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Affiliation(s)
- Su-Hyeon Kim
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Gyoengjun Cho
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Su In Lee
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Da-Ran Kim
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science (BK21Plus) and Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828, Korea
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Kim DR, Kwak YS. A Genome-Wide Analysis of Antibiotic Producing Genes in Streptomyces globisporus SP6C4. THE PLANT PATHOLOGY JOURNAL 2021; 37:389-395. [PMID: 34365750 PMCID: PMC8357572 DOI: 10.5423/ppj.nt.03.2021.0047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 06/13/2023]
Abstract
Soil is the major source of plant-associated microbes. Several fungal and bacterial species live within plant tissues. Actinomycetes are well known for producing a variety of antibiotics, and they contribute to improving plant health. In our previous report, Streptomyces globisporus SP6C4 colonized plant tissues and was able to move to other tissues from the initially colonized ones. This strain has excellent antifungal and antibacterial activities and provides a suppressive effect upon various plant diseases. Here, we report the genome-wide analysis of antibiotic producing genes in S. globisporus SP6C4. A total of 15 secondary metabolite biosynthetic gene clusters were predicted using antiSMASH. We used the CRISPR/Cas9 mutagenesis system, and each biosynthetic gene was predicted via protein basic local alignment search tool (BLAST) and rapid annotation using subsystems technology (RAST) server. Three gene clusters were shown to exhibit antifungal or antibacterial activity, viz. cluster 16 (lasso peptide), cluster 17 (thiopeptide-lantipeptide), and cluster 20 (lantipeptide). The results of the current study showed that SP6C4 has a variety of antimicrobial activities, and this strain is beneficial in agriculture.
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Affiliation(s)
- Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
- Division of Applied Life Science (BK21Plus) and IALS, Gyeongsang National University, Jinju 52828, Korea
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Lara AC, Corretto E, Kotrbová L, Lorenc F, Petříčková K, Grabic R, Chroňáková A. The Genome Analysis of the Human Lung-Associated Streptomyces sp. TR1341 Revealed the Presence of Beneficial Genes for Opportunistic Colonization of Human Tissues. Microorganisms 2021; 9:1547. [PMID: 34442631 PMCID: PMC8401907 DOI: 10.3390/microorganisms9081547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/12/2021] [Accepted: 07/17/2021] [Indexed: 12/16/2022] Open
Abstract
Streptomyces sp. TR1341 was isolated from the sputum of a man with a history of lung and kidney tuberculosis, recurrent respiratory infections, and COPD. It produces secondary metabolites associated with cytotoxicity and immune response modulation. In this study, we complement our previous results by identifying the genetic features associated with the production of these secondary metabolites and other characteristics that could benefit the strain during its colonization of human tissues (virulence factors, modification of the host immune response, or the production of siderophores). We performed a comparative phylogenetic analysis to identify the genetic features that are shared by environmental isolates and human respiratory pathogens. The results showed a high genomic similarity of Streptomyces sp. TR1341 to the plant-associated Streptomyces sp. endophyte_N2, inferring a soil origin of the strain. Putative virulence genes, such as mammalian cell entry (mce) genes were not detected in the TR1341's genome. The presence of a type VII secretion system, distinct from the ones found in Mycobacterium species, suggests a different colonization strategy than the one used by other actinomycete lung pathogens. We identified a higher diversity of genes related to iron acquisition and demonstrated that the strain produces ferrioxamine B in vitro. These results indicate that TR1341 may have an advantage in colonizing environments that are low in iron, such as human tissue.
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Affiliation(s)
- Ana Catalina Lara
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Erika Corretto
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Lucie Kotrbová
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - František Lorenc
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
| | - Kateřina Petříčková
- Institute of Immunology and Microbiology, 1st Faculty of Medicine, Charles University, Studničkova 7, 12800 Prague 2, Czech Republic;
- Faculty of Science, University of South Bohemia, Branišovská 1645/31a, 37005 České Budějovice, Czech Republic
| | - Roman Grabic
- Faculty of Fisheries and Protection of Waters, University of South Bohemia, Zátiší 728/II, 38925 Vodňany, Czech Republic;
| | - Alica Chroňáková
- Institute of Soil Biology, Biology Centre Academy of Sciences of The Czech Republic, Na Sádkách 702/7, 37005 České Budějovice, Czech Republic; (A.C.L.); (E.C.); (L.K.); (F.L.)
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Park HS, Nah HJ, Kang SH, Choi SS, Kim ES. Screening and Isolation of a Novel Polyene-Producing Streptomyces Strain Inhibiting Phytopathogenic Fungi in the Soil Environment. Front Bioeng Biotechnol 2021; 9:692340. [PMID: 34322478 PMCID: PMC8312574 DOI: 10.3389/fbioe.2021.692340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/01/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial-based eco-friendly biological substances are needed to protect crops from phytopathogenic fungi and replace toxic chemical fungicides that cause serious environmental issues. This study screened for soil antifungal Streptomyces strains, which produce rich, diverse, and valuable bioactive metabolites in the soil environment. Bioassay-based antifungal screening of approximately 2,400 Streptomyces strains led to the isolation of 149 strains as tentative antifungal producers. One Streptomyces strain showing the most potent antifungal activities against Candida albicans and Fusarium oxysporum was identified as a putative anti-phytopathogenic soil isolate that is highly homologous to Streptomyces rubrisoli (named S. rubrisoli Inha 501). An in vitro antifungal assay, pot-test, and field-test against various phytopathogenic fungi confirmed that S. rubrisoli Inha 501 is a potential novel phytopathogenic fungicide producer to protect various crops in the soil environment. Whole-genome sequencing of S. rubrisoli Inha 501 and an anti-SMASH genome mining approach revealed an approximately 150-kb polyene biosynthetic gene cluster (BGC) in the chromosome. The target compound isolation and its BGC analysis confirmed that the giant linear polyene compound exhibiting the anti-phytopathogenic activity in S. rubrisoli Inha 501 was highly homologous to the previously reported compound, neotetrafibricin A. These results suggest that a bioassay-based screening of a novel antifungal Streptomyces strain followed by its genome mining for target compound BGC characterization would be an efficient approach to isolating a novel candidate phytopathogenic fungicide that can protect crops in the soil environment.
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Affiliation(s)
- Heung-Soon Park
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Hee-Ju Nah
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Seung-Hoon Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Si-Sun Choi
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea
| | - Eung-Soo Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, South Korea.,Department of Biological Engineering, Inha University, Incheon, South Korea
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