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Vats M, Cillero-Pastor B, Cuypers E, Heeren RMA. Mass spectrometry imaging in plants, microbes, and food: a review. Analyst 2024. [PMID: 39196541 DOI: 10.1039/d4an00644e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024]
Abstract
Plant health, which affects the nutritional quality and safety of derivative food products, is influenced by symbiotic interactions with microorganisms. These interactions influence the local molecular profile at the tissue level. Therefore, studying the distribution of molecules within plants, microbes, and plant-based food is crucial to assess plant health, ensure the safety and quality of the agricultural products that become part of our food supply, and plan agricultural management practices. Within this framework, the molecular distribution within plant-based samples can be visualized with mass spectrometry imaging (MSI). This review describes key MSI methodologies, highlighting the role they play in unraveling the localization of metabolites, lipids, proteins, pigments, and elemental components across plants, microbes, and food products. Furthermore, investigations that involve multimodal molecular imaging approaches combining MSI with other imaging techniques are described. The advantages and limitations of the different MSI techniques that influence their applicability in diverse agro-food studies are described to enable informed choices for tailored analyses. For example, some MSI technologies involve meticulous sample preparation while others compromise spatial resolution to gain throughput. Key parameters such as sensitivity, ionization bias and fragmentation, reference database and compound class specificity are described and discussed in this review. With the ongoing refinements in instrumentation, data analysis, and integration of complementary techniques, MSI deepens our insight into the molecular biology of the agricultural ecosystem. This in turn empowers the quest for sustainable and productive agricultural practices.
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Affiliation(s)
- Mudita Vats
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
| | - Berta Cillero-Pastor
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
- MERLN Institute for Technology-inspired Regenerative Medicine, Department of Cell Biology-Inspired Tissue Engineering (cBITE), Maastricht University, Maastricht, the Netherlands
| | - Eva Cuypers
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4i), Division of Imaging Mass Spectrometry, Maastricht University, Maastricht, the Netherlands.
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2
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Nimbeshaho F, Nihorimbere G, Arias AA, Liénard C, Steels S, Nibasumba A, Nihorimbere V, Legrève A, Ongena M. Unravelling the secondary metabolome and biocontrol potential of the recently described species Bacillus nakamurai. Microbiol Res 2024; 288:127841. [PMID: 39153465 DOI: 10.1016/j.micres.2024.127841] [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: 05/22/2024] [Revised: 07/02/2024] [Accepted: 07/14/2024] [Indexed: 08/19/2024]
Abstract
In the prospect of novel potential biocontrol agents, a new strain BDI-IS1 belonging to the recently described Bacillus nakamurai was selected for its strong in vitro antimicrobial activities against a range of bacterial and fungal phytopathogens. Genome mining coupled with metabolomics revealed that BDI-IS1 produces multiple non-ribosomal secondary metabolites including surfactin, iturin A, bacillaene, bacillibactin and bacilysin, together with some some ribosomally-synthesized and post-translationally modified peptides (RiPPs) such as plantazolicin, and potentially amylocyclicin, bacinapeptin and LCI. Reverse genetics further showed the specific involvement of some of these compounds in the antagonistic activity of the strain. Comparative genomics between the five already sequenced B. nakamurai strains showed that non-ribosomal products constitute the core metabolome of the species while RiPPs are more strain-specific. Although the secondary metabolome lacks some key bioactive metabolites found in B. velezensis, greenhouse experiments show that B. nakamurai BDI-IS1 is able to protect tomato and maize plants against early blight and northern leaf blight caused by Alternaria solani and Exserohilum turcicum, respectively, at levels similar to or better than B. velezensis QST713. The reduction of these foliar diseases, following root or leaf application of the bacterial suspension demonstrates that BDI-IS1 can act by direct antibiosis and by inducing plant defence mechanisms. These findings indicate that B. nakamurai BDI-IS1 can be considered as a good candidate for biocontrol of plant diseases prevailing in tropical regions, and encourage further research into its spectrum of activity, its requirements and the conditions needed to ensure its efficacy.
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Affiliation(s)
- François Nimbeshaho
- Microbial Processes and Interactions (MiPI), Teaching and Research Centre (TERRA), Gembloux Agro-BioTech, University of Liège, Avenue de la Faculté 2B, Gembloux 5030, Belgium; Laboratoire de Nutrition-Phytochimie, d'Ecologie et d'Environnement Appliquée, Centre Universitaire de Recherche et de Pédagogie Appliquées aux Sciences, Institut de Pédagogie Appliquée, Université du Burundi, Avenue de l'Unesco 2, P.O Box 1550, Bujumbura, Burundi.
| | - Gaspard Nihorimbere
- Earth and Life Institute-Applied Microbiology, Université Catholique de Louvain, Croix du Sud 2, Louvain-la-Neuve 1348, Belgium; Research department, Institut des Sciences Agronomiques du Burundi (ISABU), Boulevard du Japon, Rohero 1, P.O Box 795, Bujumbura, Burundi.
| | - Anthony Argüelles Arias
- Microbial Processes and Interactions (MiPI), Teaching and Research Centre (TERRA), Gembloux Agro-BioTech, University of Liège, Avenue de la Faculté 2B, Gembloux 5030, Belgium.
| | - Charlotte Liénard
- Earth and Life Institute-Applied Microbiology, Université Catholique de Louvain, Croix du Sud 2, Louvain-la-Neuve 1348, Belgium.
| | - Sébastien Steels
- Microbial Processes and Interactions (MiPI), Teaching and Research Centre (TERRA), Gembloux Agro-BioTech, University of Liège, Avenue de la Faculté 2B, Gembloux 5030, Belgium.
| | - Anaclet Nibasumba
- Institut Supérieur de Formation Agricole, Université du Burundi, P.O Box 241, Gitega, Burundi.
| | - Venant Nihorimbere
- Laboratoire de Microbiologie, Faculté d'Agronomie et de BioIngéniérie (FABI), Université du Burundi, Avenue de l'Unesco 2, P.O Box 2940, Bujumbura, Burundi.
| | - Anne Legrève
- Earth and Life Institute-Applied Microbiology, Université Catholique de Louvain, Croix du Sud 2, Louvain-la-Neuve 1348, Belgium.
| | - Marc Ongena
- Microbial Processes and Interactions (MiPI), Teaching and Research Centre (TERRA), Gembloux Agro-BioTech, University of Liège, Avenue de la Faculté 2B, Gembloux 5030, Belgium.
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Yasmeen T, Arif MS, Tariq M, Akhtar S, Syrish A, Haidar W, Rizwan M, Hussain MI, Ahmad A, Ali S. Biofilm producing plant growth promoting bacteria in combination with glycine betaine uplift drought stress tolerance of maize plant. FRONTIERS IN PLANT SCIENCE 2024; 15:1327552. [PMID: 38405588 PMCID: PMC10884199 DOI: 10.3389/fpls.2024.1327552] [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: 10/25/2023] [Accepted: 01/05/2024] [Indexed: 02/27/2024]
Abstract
Introduction The escalating threat of drought poses a significant challenge to sustainable food production and human health, as water scarcity adversely impacts various aspects of plant physiology. Maize, a cornerstone in staple cereal crops, faces the formidable challenge of drought stress that triggers a series of transformative responses in the plant. Methods The present study was carried out in two sets of experiments. In first experiment, drought stress was applied after maintaining growth for 45 days and then irrigation was skipped, and plant samples were collected at 1st, 3rd and 6th day of drought interval for evaluation of changes in plant growth, water relation (relative water content) and antioxidants activity by inoculating indigenously isolated drought tolerant biofilm producing rhizobacterial isolates (Bacillus subtilis SRJ4, Curtobacterium citreum MJ1). In the second experiment, glycine betaine was applied as osmoregulator in addition to drought tolerant PGPR to perceive modulation in photosynthetic pigments (Chlorophyll a and b) and plant growth under varying moisture stress levels (100, 75 and 50% FC). Results and discussion Results of the study revealed upsurge in root and shoot length, fresh and dry biomass of root and shoot besides increasing chlorophyll contents in water stressed inoculated plants compared to uninoculated plants. Glycine betaine application resulted in an additional boost to plant growth and photosynthetic pigments, when applied in combination with bacterial inoculants. However, both bacterial inoculants behaved differently under drought stress as evident from their biochemical and physiological attributes. Isolate SRJ4 proved to be superior for its potential to express antioxidant activity, leaf water potential and relative water contents and drought responsive gene expression while isolate MJ1 showed exclusive increase in root dry biomass and plant P contents. Though it is quite difficult to isolate the bacterial isolates having both plant growth promoting traits and drought tolerance together yet, such biological resources could be an exceptional option to be applied for improving crop productivity and sustainable agriculture under abiotic stresses. By exploring the combined application of PGPR and glycine betaine, the study seeks to provide insights into potential strategies for developing sustainable agricultural practices aimed at improving crop resilience under challenging environmental conditions.
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Affiliation(s)
- Tahira Yasmeen
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Saleem Arif
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mohsin Tariq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Sadia Akhtar
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Afira Syrish
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Waqas Haidar
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Rizwan
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Ajaz Ahmad
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shafaqat Ali
- Department of Environmental Sciences, Government College University Faisalabad, Faisalabad, Pakistan
- Department of Biological Sciences and Technology, China Medical University, Taichung, Taiwan
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Stulanovic N, Kerdel Y, Rezende L, Deflandre B, Burguet P, Belde L, Denoel R, Tellatin D, Rigolet A, Hanikenne M, Quinton L, Ongena M, Rigali S. Nitrogen sources enhance siderophore-mediated competition for iron between potato common scab and late blight causative agents. Metallomics 2024; 16:mfae004. [PMID: 38244228 DOI: 10.1093/mtomcs/mfae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/18/2024] [Indexed: 01/22/2024]
Abstract
How do pathogens affecting the same host interact with each other? We evaluated here the types of microbe-microbe interactions taking place between Streptomyces scabiei and Phytophthora infestans, the causative agents of common scab and late blight diseases in potato crops, respectively. Under most laboratory culture conditions tested, S. scabiei impaired or completely inhibited the growth of P. infestans by producing either soluble and/or volatile compounds. Increasing peptone levels correlated with increased inhibition of P. infestans. Comparative metabolomics showed that production of S. scabiei siderophores (desferrioxamines, pyochelin, scabichelin, and turgichelin) increased with the quantity of peptone, thereby suggesting that they participate in the inhibition of the oomycete growth. Mass spectrometry imaging further uncovered that the zones of secreted siderophores and of P. infestans growth inhibition coincided. Moreover, either the repression of siderophore production or the neutralization of their iron-chelating activity led to a resumption of P. infestans growth. Replacement of peptone by natural nitrogen sources such as ammonium nitrate, sodium nitrate, ammonium sulfate, and urea also triggered siderophore production in S. scabiei. Interestingly, nitrogen source-induced siderophore production also inhibited the growth of Alternaria solani, the causative agent of the potato early blight. Overall, our work further emphasizes the importance of competition for iron between microorganisms that colonize the same niche. As common scab never alters the vegetative propagation of tubers, we propose that S. scabiei, under certain conditions, could play a protective role for its hosts against much more destructive pathogens through exploitative iron competition and volatile compound production.
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Affiliation(s)
- Nudzejma Stulanovic
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Yasmine Kerdel
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Lucas Rezende
- Hedera-22, Boulevard du Rectorat 27b, B-4000 Liège, Belgium
| | - Benoit Deflandre
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Pierre Burguet
- Molecular Systems (MolSys), Department of Chemistry, University of Liège, B-4000 Liège, Belgium
| | - Loïc Belde
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Romane Denoel
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Déborah Tellatin
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
| | - Augustin Rigolet
- Microbial Processes and Interactions, TERRA Teaching and Research Center, BioEcoAgro, Joint Research Unit/UMR transfrontalière 1158, University of Liège-Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, B-4000 Liège, Belgium
| | - Loïc Quinton
- Molecular Systems (MolSys), Department of Chemistry, University of Liège, B-4000 Liège, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions, TERRA Teaching and Research Center, BioEcoAgro, Joint Research Unit/UMR transfrontalière 1158, University of Liège-Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Sébastien Rigali
- InBioS-Center for Protein Engineering, Institut de Chimie, University of Liège, B-4000 Liège, Belgium
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Rigolet A, Argüelles Arias A, Anckaert A, Quinton L, Rigali S, Tellatin D, Burguet P, Ongena M. Lipopeptides as rhizosphere public goods for microbial cooperation. Microbiol Spectr 2024; 12:e0310623. [PMID: 38047676 PMCID: PMC10783051 DOI: 10.1128/spectrum.03106-23] [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: 08/16/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE Here, we provide new insights into the possible fate of cyclic lipopeptides as prominent specialized metabolites from beneficial bacilli and pseudomonads once released in the soil. Our data illustrate how the B. velezensis lipopeptidome may be enzymatically remodeled by Streptomyces as important members of the soil bacterial community. The enzymatic arsenal of S. venezuelae enables an unsuspected extensive degradation of these compounds, allowing the bacterium to feed on these exogenous products via a mechanism going beyond linearization, which was previously reported as a detoxification strategy. As soils are carbon-rich and nitrogen-poor environments, we propose a new role for cyclic lipopeptides in interspecies interactions, which is to fuel the nitrogen metabolism of a part of the rhizosphere microbial community. Streptomyces and other actinomycetes, producing numerous peptidases and displaying several traits of beneficial bacteria, should be at the front line to directly benefit from these metabolites as "public goods" for microbial cooperation.
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Affiliation(s)
- Augustin Rigolet
- Microbial Processes and Interactions laboratory, TERRA teaching and research centre, Gembloux Agro-Bio Tech,University of Liège, Gembloux, Belgium
| | - Anthony Argüelles Arias
- Microbial Processes and Interactions laboratory, TERRA teaching and research centre, Gembloux Agro-Bio Tech,University of Liège, Gembloux, Belgium
| | - Adrien Anckaert
- Microbial Processes and Interactions laboratory, TERRA teaching and research centre, Gembloux Agro-Bio Tech,University of Liège, Gembloux, Belgium
| | - Loïc Quinton
- Department of Chemistry, University of Liège, Liège, Belgium
| | - Sébastien Rigali
- InBioS—Centre for Protein Engineering,University of Liège, Liege, Belgium
- Hedera-22, Liege, Belgium
| | - Deborah Tellatin
- InBioS—Centre for Protein Engineering,University of Liège, Liege, Belgium
| | - Pierre Burguet
- Department of Chemistry, University of Liège, Liège, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions laboratory, TERRA teaching and research centre, Gembloux Agro-Bio Tech,University of Liège, Gembloux, Belgium
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Xia L, Wen J. Available strategies for improving the biosynthesis of surfactin: a review. Crit Rev Biotechnol 2023; 43:1111-1128. [PMID: 36001039 DOI: 10.1080/07388551.2022.2095252] [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: 01/04/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022]
Abstract
Surfactin is an excellent biosurfactant with a wide range of application prospects in many industrial fields. However, its low productivity and high cost have largely limited its commercial applications. In this review, the pathways for surfactin synthesis in Bacillus strains are summarized and discussed. Further, the latest strategies for improving surfactin production, including: medium optimization, genome engineering methods (rational genetic engineering, genome reduction, and genome shuffling), heterologous synthesis, and the use of synthetic biology combined with metabolic engineering approaches to construct high-quality artificial cells for surfactin production using xylose, are described. Finally, the prospects for improving surfactin synthesis are discussed in detail.
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Affiliation(s)
- Li Xia
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, People's Republic of China
- National Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, People's Republic of China
- Frontier Science Center of the Ministry of Education, Tianjin University, Tianjin, People's Republic of China
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7
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Boubsi F, Hoff G, Arguelles Arias A, Steels S, Andrić S, Anckaert A, Roulard R, Rigolet A, van Wuytswinkel O, Ongena M. Pectic homogalacturonan sensed by Bacillus acts as host associated cue to promote establishment and persistence in the rhizosphere. iScience 2023; 26:107925. [PMID: 37790276 PMCID: PMC10543691 DOI: 10.1016/j.isci.2023.107925] [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: 04/07/2023] [Revised: 07/19/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
Bacillus velezensis isolates are among the most promising plant-associated beneficial bacteria used as biocontrol agents. However, various aspects of the chemical communication between the plant and these beneficials, determining root colonization ability, remain poorly described. Here we investigated the molecular basis of such interkingdom interaction occurring upon contact between Bacillus velezensis and its host via the sensing of pectin backbone homogalacturonan (HG). We showed that B. velezensis stimulates key developmental traits via a dynamic process involving two conserved pectinolytic enzymes. This response integrates transcriptional changes leading to the switch from planktonic to sessile cells, a strong increase in biofilm formation, and an accelerated sporulation dynamics while conserving the potential to efficiently produce specialized secondary metabolites. As a whole, we anticipate that this response of Bacillus to cell wall-derived host cues contributes to its establishment and persistence in the competitive rhizosphere niche and ipso facto to its activity as biocontrol agent.
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Affiliation(s)
- Farah Boubsi
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Grégory Hoff
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Anthony Arguelles Arias
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Sébastien Steels
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Sofija Andrić
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Adrien Anckaert
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Romain Roulard
- UMRT INRAe 1158 Plant Biology and Innovation, University of Picardie Jules Verne, UFR des Sciences, 80039 Amiens, France
| | - Augustin Rigolet
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
| | - Olivier van Wuytswinkel
- UMRT INRAe 1158 Plant Biology and Innovation, University of Picardie Jules Verne, UFR des Sciences, 80039 Amiens, France
| | - Marc Ongena
- Microbial Processes and Interactions, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, 5030 Gembloux, Belgium
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8
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Zhang Y, Lin J, Chen S, Lu H, Liao C. The Influence of the Genotype and Planting Density on the Structure and Composition of Root and Rhizosphere Microbial Communities in Maize. Microorganisms 2023; 11:2443. [PMID: 37894100 PMCID: PMC10608840 DOI: 10.3390/microorganisms11102443] [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: 06/30/2023] [Revised: 08/18/2023] [Accepted: 09/15/2023] [Indexed: 10/29/2023] Open
Abstract
Maize has the largest cultivation area of any crop in the world and plays an important role in ensuring food security. High-density planting is essential for maintaining high maize yields in modern intensive agriculture. Nonetheless, how high-density planting and the tolerance of individual genotypes to such planting shape the root-associated microbiome of maize is still unknown. In this study, we analyzed the root and rhizosphere bacterial communities of two maize accessions with contrasting shoot architectures grown under high- and low-density planting conditions. Our results suggested that maize hosted specific, distinct bacterial communities in the root endocompartment and that the maize genotype had a significant effect on the selection of specific microbes from the rhizosphere. High-density planting also had significant effects on root-associated bacterial communities. Specifically, genotype and high-density planting coordinated to shape the structure, composition, and function of root and rhizosphere bacterial communities. Taken together, our results provide insights into how aboveground plant architecture and density may alter the belowground bacterial community in root-associated compartments of maize.
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Affiliation(s)
| | | | | | | | - Changjian Liao
- Technical Research Center of Dry Crop Variety Breeding in Fujian Province, Institute of Crops Research, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China; (Y.Z.); (J.L.); (S.C.); (H.L.)
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9
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Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [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: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
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Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
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10
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Dobrzyński J, Jakubowska Z, Kulkova I, Kowalczyk P, Kramkowski K. Biocontrol of fungal phytopathogens by Bacillus pumilus. Front Microbiol 2023; 14:1194606. [PMID: 37560520 PMCID: PMC10407110 DOI: 10.3389/fmicb.2023.1194606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Plant growth-promoting bacteria are one of the most interesting methods of controlling fungal phytopathogens. These bacteria can participate in biocontrol via a variety of mechanisms including lipopeptide production, hydrolytic enzymes (e.g., chitinase, cellulases, glucanase) production, microbial volatile organic compounds (mVOCs) production, and induced systemic resistance (ISR) triggering. Among the bacterial genera most frequently studied in this aspect are Bacillus spp. including Bacillus pumilus. Due to the range of biocontrol traits, B. pumilus is one of the most interesting members of Bacillus spp. that can be used in the biocontrol of fungal phytopathogens. So far, a number of B. pumilus strains that exhibit biocontrol properties against fungal phytopathogens have been described, e.g., B. pumilus HR10, PTB180, B. pumilus SS-10.7, B. pumilus MCB-7, B. pumilus INR7, B. pumilus SE52, SE34, SE49, B. pumilus RST25, B. pumilus JK-SX001, and B. pumilus KUDC1732. B. pumilus strains are capable of suppressing phytopathogens such as Arthrobotrys conoides, Fusarium solani, Fusarium oxysporum, Sclerotinia sclerotiorum, Rhizoctonia solani, and Fagopyrum esculentum. Importantly, B. pumilus can promote plant growth regardless of whether it alters the native microbiota or not. However, in order to increase its efficacy, research is still needed to clarify the relationship between the native microbiota and B. pumilus. Despite that, it can already be concluded that B. pumilus strains are good candidates to be environmentally friendly and commercially effective biocontrol agents.
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Affiliation(s)
- Jakub Dobrzyński
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Zuzanna Jakubowska
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Iryna Kulkova
- Institute of Technology and Life Sciences—National Research Institute, Raszyn, Poland
| | - Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Jabłonna, Poland
| | - Karol Kramkowski
- Department of Physical Chemistry, Medical University of Białystok, Białystok, Poland
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Rosier A, Pomerleau M, Beauregard PB, Samac DA, Bais HP. Surfactin and Spo0A-Dependent Antagonism by Bacillus subtilis Strain UD1022 against Medicago sativa Phytopathogens. PLANTS (BASEL, SWITZERLAND) 2023; 12:1007. [PMID: 36903868 PMCID: PMC10005099 DOI: 10.3390/plants12051007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Plant growth-promoting rhizobacteria (PGPR) such as the root colonizers Bacillus spp. may be ideal alternatives to chemical crop treatments. This work sought to extend the application of the broadly active PGPR UD1022 to Medicago sativa (alfalfa). Alfalfa is susceptible to many phytopathogens resulting in losses of crop yield and nutrient value. UD1022 was cocultured with four alfalfa pathogen strains to test antagonism. We found UD1022 to be directly antagonistic toward Collectotrichum trifolii, Ascochyta medicaginicola (formerly Phoma medicaginis), and Phytophthora medicaginis, and not toward Fusarium oxysporum f. sp. medicaginis. Using mutant UD1022 strains lacking genes in the nonribosomal peptide (NRP) and biofilm pathways, we tested antagonism against A. medicaginicola StC 306-5 and P. medicaginis A2A1. The NRP surfactin may have a role in the antagonism toward the ascomycete StC 306-5. Antagonism toward A2A1 may be influenced by B. subtilis biofilm pathway components. The B. subtilis central regulator of both surfactin and biofilm pathways Spo0A was required for the antagonism of both phytopathogens. The results of this study indicate that the PGPR UD1022 would be a good candidate for further investigations into its antagonistic activities against C. trifolii, A. medicaginicola, and P. medicaginis in plant and field studies.
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Affiliation(s)
- Amanda Rosier
- Department of Plant and Soil Sciences, University of Delaware, 311 AP Biopharma, 590 Avenue 1743, Newark, DE 19713, USA
| | - Maude Pomerleau
- Département de Biologie, Bureau D8-1014, Université de Sherbrooke, 2500 boul. Université Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Pascale B. Beauregard
- Département de Biologie, Bureau D8-1014, Université de Sherbrooke, 2500 boul. Université Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Deborah A. Samac
- USDA-ARS Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Harsh P. Bais
- Department of Plant and Soil Sciences, University of Delaware, 311 AP Biopharma, 590 Avenue 1743, Newark, DE 19713, USA
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Korangi Alleluya V, Argüelles Arias A, Ribeiro B, De Coninck B, Helmus C, Delaplace P, Ongena M. Bacillus lipopeptide-mediated biocontrol of peanut stem rot caused by Athelia rolfsii. FRONTIERS IN PLANT SCIENCE 2023; 14:1069971. [PMID: 36890892 PMCID: PMC9986434 DOI: 10.3389/fpls.2023.1069971] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Peanut (Arachis hypogaea L.) is a widespread oilseed crop of high agricultural importance in tropical and subtropical areas. It plays a major role in the food supply in the Democratic Republic of Congo (DRC). However, one major constraint in the production of this plant is the stem rot (white mold or southern blight) disease caused by Athelia rolfsii which is so far controlled mainly using chemicals. Considering the harmful effect of chemical pesticides, the implementation of eco-friendly alternatives such as biological control is required for disease management in a more sustainable agriculture in the DRC as in the other developing countries concerned. Bacillus velezensis is among the rhizobacteria best described for its plant protective effect notably due to the production of a wide range of bioactive secondary metabolites. In this work, we wanted to evaluate the potential of B. velezensis strain GA1 at reducing A. rolfsii infection and to unravel the molecular basis of the protective effect. RESULTS AND DISCUSSION Upon growth under the nutritional conditions dictated by peanut root exudation, the bacterium efficiently produces the three types of lipopeptides surfactin, iturin and fengycin known for their antagonistic activities against a wide range of fungal phytopathogens. By testing a range of GA1 mutants specifically repressed in the production of those metabolites, we point out an important role for iturin and another unidentified compound in the antagonistic activity against the pathogen. Biocontrol experiments performed in greenhouse further revealed the efficacy of B. velezensis to reduce peanut disease caused by A. rolfsii both via direct antagonism against the fungus and by stimulating systemic resistance in the host plant. As treatment with pure surfactin yielded a similar level of protection, we postulate that this lipopeptide acts as main elicitor of peanut resistance against A. rolfsii infection.
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Affiliation(s)
- Virginie Korangi Alleluya
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Chemical and Agricultural Industries, Faculty of Agricultural Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Anthony Argüelles Arias
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Bianca Ribeiro
- Division of Plant Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Barbara De Coninck
- Division of Plant Biotechnics, Department of Biosystems, Faculty of Bioscience Engineering, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Catherine Helmus
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Pierre Delaplace
- Plant biology Unit, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Marc Ongena
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
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13
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Andrić S, Rigolet A, Argüelles Arias A, Steels S, Hoff G, Balleux G, Ongena L, Höfte M, Meyer T, Ongena M. Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor. THE ISME JOURNAL 2023; 17:263-275. [PMID: 36357782 PMCID: PMC9860033 DOI: 10.1038/s41396-022-01337-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022]
Abstract
Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.
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Affiliation(s)
- Sofija Andrić
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Augustin Rigolet
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Anthony Argüelles Arias
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Sébastien Steels
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Grégory Hoff
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.5477.10000000120346234Present Address: Ecology and Biodiversity, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Guillaume Balleux
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Loïc Ongena
- grid.4861.b0000 0001 0805 7253Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, Liège, Belgium
| | - Monica Höfte
- grid.5342.00000 0001 2069 7798Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thibault Meyer
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.7849.20000 0001 2150 7757Present Address: UMR Ecologie Microbienne, F-69622, University of Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
| | - Marc Ongena
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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14
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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15
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Cortés-Patiño S, Vargas CD, Alvarez-Flórez F, Estrada-Bonilla G. Co-Inoculation of Plant-Growth-Promoting Bacteria Modulates Physiological and Biochemical Responses of Perennial Ryegrass to Water Deficit. PLANTS (BASEL, SWITZERLAND) 2022; 11:2543. [PMID: 36235409 PMCID: PMC9570635 DOI: 10.3390/plants11192543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Perennial ryegrass is a forage commonly used in temperate regions for livestock feeding; however, its yield is affected by reduced biomass production under water deficit. In a previous study, three co-inoculations of beneficial bacteria were selected based on their ability to promote plant growth under reduced water availability. The aim of this work was to elucidate some mechanisms by which the selected bacteria can help improve the response of perennial ryegrass to water deficit. Ryegrass plants were inoculated with each of the co-inoculations (Herbaspirillum sp. AP02−Herbaspirillum sp. AP21; Herbaspirillum sp. AP02−Pseudomonas sp. N7; Herbaspirillum sp. AP21−Azospirillum brasilense D7) and subjected to water deficit for 10 days. Physiological and biochemical measurements were taken 10 days after stress and shortly after rehydration. The results showed that bacteria had a positive effect on shoot biomass production, dissipation of excess energy, and proline and chlorophyll pigments during the days of water deficit (p < 0.05). The leaf water status of the inoculated plants was 12% higher than that of the uninoculated control after rehydration. Two Herbaspirillum strains showed greater potential for use as biofertilizers that help ameliorate the effects of water deficit.
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Affiliation(s)
- Sandra Cortés-Patiño
- Rothamsted Research, Protection of Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK
- School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- Laboratorio de Fisiología y Bioquímica Vegetal, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 45 #26-85, Bogotá 111321, Colombia
| | - Christian D. Vargas
- Laboratorio de Fisiología y Bioquímica Vegetal, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 45 #26-85, Bogotá 111321, Colombia
| | - Fagua Alvarez-Flórez
- Laboratorio de Fisiología y Bioquímica Vegetal, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 45 #26-85, Bogotá 111321, Colombia
| | - German Estrada-Bonilla
- Corporación Colombiana de Investigación Agropecuaria-Agrosavia, Centro de Investigación Tibaitatá, Kilómetro 14 vía Mosquera-Bogotá, Mosquera 250047, Colombia
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16
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He C, Zheng L, Gao W, Ding J, Li C, Xu X, Han B, Li Q, Wang S. Diversity and functions of quorum sensing bacteria in the root environment of the Suaeda glauca and Phragmites australis coastal wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:54619-54631. [PMID: 35305219 DOI: 10.1007/s11356-022-19564-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
The quorum sensing (QS) system plays a significant role in the bacteria-bacteria or plant-bacteria relationships through signal molecules. However, little is known about the distribution and functional diversity of QS bacteria in the root environment of Suaeda glauca and Phragmites australis in coastal wetlands. We explored the bacterial community by amplicon sequencing and isolated 1050 strains from the rhizosphere soil and root tissues of S. glauca and P. australis in northern China to investigate the bacterial community and AHL producers. AHL activity was found in 76 isolates, and 22 distinct strains were confirmed by 16S rRNA gene sequencing. A substantial number of AHL producers clustered in rhizobiales and sphingomonadale, which derived from the root tissues. AHL producers in the rhizosphere soil mostly belonged to rhodobacterales. The different taxa of AHL producers in the rhizosphere soil and root tissues resulted in a variation of AHL profiles that C6-HSL dominated the AHL profiles in root bacteria compared to the C8-HSL in rhizobacteria, implying different ecological roles for AHL producers in the rhizosphere soil and root tissues. Many AHL producers may form biofilms, and some can degrade DMSP and oil, demonstrating that QS bacteria in the root environment have a wide ecological roles. In our study, for one of the first times here, we explore the distribution and functional variety of AHL producers in the root environment of S. glauca-P. australis. This study expands current knowledge of the relationship between QS bacteria and coastal plants (S. glauca and P. australis), and vital roles of QS bacterial in maintaining the health of coastal wetlands.
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Affiliation(s)
- Changfei He
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Li Zheng
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China.
| | - Wei Gao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Jinfeng Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Chengxuan Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Xiyuan Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Bin Han
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Qian Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shuai Wang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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Lipopeptide Biosurfactants from Bacillus spp.: Types, Production, Biological Activities, and Applications in Food. J FOOD QUALITY 2022. [DOI: 10.1155/2022/3930112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biosurfactants are a functionally and structurally heterogeneous group of biomolecules produced by multiple filamentous fungi, yeast, and bacteria, and characterized by their distinct surface and emulsifying ability. The genus Bacillus is well studied for biosurfactant production as it produces various types of lipopeptides, for example, lichenysins, bacillomycin, fengycins, and surfactins. Bacillus lipopeptides possess a broad spectrum of biological activities such as antimicrobial, antitumor, immunosuppressant, and antidiabetic, in addition to their use in skincare. Moreover, Bacillus lipopeptides are also involved in various food products to increase the antimicrobial, surfactant, and emulsification impact. From the previously published articles, it can be concluded that biosurfactants have strong potential to be used in food, healthcare, and agriculture. In this review article, we discuss the versatile functions of lipopeptide Bacillus species with particular emphasis on the biological activities and their applications in food.
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Nephali L, Steenkamp P, Burgess K, Huyser J, Brand M, van der Hooft JJJ, Tugizimana F. Mass Spectral Molecular Networking to Profile the Metabolome of Biostimulant Bacillus Strains. FRONTIERS IN PLANT SCIENCE 2022; 13:920963. [PMID: 35755693 PMCID: PMC9218640 DOI: 10.3389/fpls.2022.920963] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/18/2022] [Indexed: 05/17/2023]
Abstract
Beneficial soil microbes like plant growth-promoting rhizobacteria (PGPR) significantly contribute to plant growth and development through various mechanisms activated by plant-PGPR interactions. However, a complete understanding of the biochemistry of the PGPR and microbial intraspecific interactions within the consortia is still enigmatic. Such complexities constrain the design and use of PGPR formulations for sustainable agriculture. Therefore, we report the application of mass spectrometry (MS)-based untargeted metabolomics and molecular networking (MN) to interrogate and profile the intracellular chemical space of PGPR Bacillus strains: B. laterosporus, B. amyloliquefaciens, B. licheniformis 1001, and B. licheniformis M017 and their consortium. The results revealed differential and diverse chemistries in the four Bacillus strains when grown separately, and also differing from when grown as a consortium. MolNetEnhancer networks revealed 11 differential molecular families that are comprised of lipids and lipid-like molecules, benzenoids, nucleotide-like molecules, and organic acids and derivatives. Consortium and B. amyloliquefaciens metabolite profiles were characterized by the high abundance of surfactins, whereas B. licheniformis strains were characterized by the unique presence of lichenysins. Thus, this work, applying metabolome mining tools, maps the microbial chemical space of isolates and their consortium, thus providing valuable insights into molecular information of microbial systems. Such fundamental knowledge is essential for the innovative design and use of PGPR-based biostimulants.
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Affiliation(s)
- Lerato Nephali
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Paul Steenkamp
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Karl Burgess
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, The University of Edinburgh, Edinburgh, United Kingdom
| | - Johan Huyser
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
| | - Margaretha Brand
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
| | - Justin J. J. van der Hooft
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
- *Correspondence: Justin J. J. van der Hooft,
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
- International Research and Development Division, Omnia Group, Ltd., Johannesburg, South Africa
- Fidele Tugizimana,
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Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Zehra A, Swapnil P. Role of Microbial Bioagents as Elicitors in Plant Defense Regulation. TRANSCRIPTION FACTORS FOR BIOTIC STRESS TOLERANCE IN PLANTS 2022:103-128. [DOI: 10.1007/978-3-031-12990-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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20
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Roychoudhury T, Ray B, Seal A. Metabolically dependent consortia in biofilm: A new horizon for green agriculture. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2021.102256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Abstract
Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera. IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.
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McCann A, Kune C, La Rocca R, Oetjen J, Arias AA, Ongena M, Far J, Eppe G, Quinton L, De Pauw E. Rapid visualization of lipopeptides and potential bioactive groups of compounds by combining ion mobility and MALDI imaging mass spectrometry. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:81-88. [PMID: 34906328 DOI: 10.1016/j.ddtec.2021.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 08/01/2021] [Accepted: 08/09/2021] [Indexed: 11/27/2022]
Abstract
Mass spectrometry imaging (MSI) has become a powerful method for mapping metabolite distribution in a tissue. Applied to bacterial colonies, MSI has a bright future, both for the discovery of new bioactive compounds and for a better understanding of bacterial antibiotic resistance mechanisms. Coupled with separation techniques such as ion mobility mass spectrometry (IM-MS), the identification of metabolites directly on the image is now possible and does not require additional analysis such as HPLC-MS/MS. In this article, we propose to apply a semi-targeted workflow for rapid IM-MSI data analysis focused on the search for bioactive compounds. First, chemically-related compounds showing a repetitive mass unit (i.e. lipids and lipopeptides) were targeted based on the Kendrick mass defect analysis. The detected groups of potentially bioactive compounds were then confirmed by fitting their measured ion moibilites to their measured m/z values. Using both their m/z and ion mobility values, the selected groups of compounds were identified using the available databases and finally their distribution was observed on the image. Using this workflow on a co-culture of bacteria, we were able to detect and localize bioactive compounds involved in the microbial interaction.
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Affiliation(s)
- Andréa McCann
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Raphael La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Janina Oetjen
- Bruker Daltonik GmbH, Fahrenheitsstr. 4, 28359 Bremen, Germany
| | | | - Marc Ongena
- Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Loic Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège, Belgium
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Moreno-Velandia CA, Ongena M, Cotes AM. Effects of Fengycins and Iturins on Fusarium oxysporum f. sp. physali and Root Colonization by Bacillus velezensis Bs006 Protect Golden Berry Against Vascular Wilt. PHYTOPATHOLOGY 2021; 111:2227-2237. [PMID: 34032523 DOI: 10.1094/phyto-01-21-0001-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacillus velezensis Bs006 has shown antagonistic activity on Fusarium oxysporum f. sp. physali and biocontrol activity against Fusarium wilt (FW) in golden berry (Physalis peruviana). We hypothesized that strain Bs006 has the ability to synthesize antimicrobial cyclic lipopeptides (CLPs) like other members of the same species. However, if so, the real effects of CLPs on F. oxysporum f. sp. physali and their potential as a biocontrol tool against Physalis-FW have not been elucidated. In this study the CLPs profile of Bs006 in liquid culture and antagonist-plant-pathogen interactions were characterized. Also, the potential effects of supernatant free of bacteria against F. oxysporum f. sp. physali and FW were explored and compared with the effects of pure CLPs. Ultraperformance liquid chromatography-electrospray ionization-mass spectrometry analysis revealed the capacity of Bs006 to synthesize homologous compounds of iturins, surfactins, and fengycins in liquid culture and on the inhibition zone against F. oxysporum f. sp. physali in dual confrontation tests. Bs006 supernatant reduced the germination and growth of F. oxysporum f. sp. physali and caused vacuolization, swelling, and lysis of F. oxysporum f. sp. physali cells in a concentration-dependent manner. Pure fengycins affected the development of F. oxysporum f. sp. physali from 11 mg/liter and iturins from 21 mg/liter. In a gnotobiotic system, Bs006 colonized the root surface of golden berry, inhibited the growth of F. oxysporum f. sp. physali, and produced CLPs. Individual application of Bs006 and supernatant protected the plants from F. oxysporum f. sp. physali infections by 37 to 53%, respectively. Meanwhile, fengycins reduced the disease progress by 39%. These results suggest further studies to select an optimum combination of Bs006 and supernatant or CLPs, which might be a good option as biofungicide against F. oxysporum f. sp. physali.
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Affiliation(s)
- Carlos Andrés Moreno-Velandia
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
| | - Marc Ongena
- Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Alba Marina Cotes
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Centro de Investigación Tibaitatá, Mosquera, Colombia
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Kumar A, Dubey A, Malla MA, Dames J. Pyrosequencing and phenotypic microarray to decipher bacterial community variation in Sorghum bicolor (L.) Moench rhizosphere. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100025. [PMID: 34841316 PMCID: PMC8610313 DOI: 10.1016/j.crmicr.2021.100025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 11/17/2022] Open
Abstract
Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities. This work, investigated the changes in bacterial community composition at taxonomic and functional level in rhizosphere soil of sweet sorghum under extensive cultivation practices at three different field sites of South Africa. 16S rRNA amplicon sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8% and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. Overall, this study showed that soil pH, nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in sorghum rhizosphere.
Different cultivation practices and climatic conditions play an important role in governing and modulating soil microbial communities as well as soil health. This study investigated, for the first time, keystone microbial taxa inhabiting the rhizosphere of sweet sorghum (Sorghum bicolor) under extensive cultivation practices at three different field sites of South Africa (North West-South (ASHSOIL1); Mpumalanga-West – (ASHSOIL2); and Free State-North West – (ASHSOIL3)). Soil analysis of these sites revealed differences in P, K, Mg, and pH. 16S rRNA amplicon sequencing data revealed that the rhizosphere bacterial microbiome differed significantly both in the structure and composition across the samples. The sequencing data revealed that at the phylum level, the dominant group was Cyanobacteria with a relative abundance of 63.3%, 71.8%, and 81.6% from ASHSOIL1, ASHSOIL2, and ASHSOIL3, respectively. Putative metabolic requirements analyzed by METAGENassist software revealed the ASHSOIL1 sample as the prominent ammonia degrader (21.1%), followed by ASHSOIL3 (17.3%) and ASHSOIL2 (11.1%). The majority of core-microbiome taxa were found to be from Cyanobacteria, Bacteroidetes, and Proteobacteria. Functionally, community-level physiological profiling (CLPP) analysis revealed that the metabolic activity of the bacterial community in ASHSOIL3 was the highest, followed by ASHSOIL1 and ASHSOIL2. This study showed that soil pH and nutrient availability and cultivation practices played significant roles in governing the bacterial community composition in the sorghum rhizosphere across the different sites.
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Affiliation(s)
- Ashwani Kumar
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
- Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
- Corresponding author at: Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India.
| | - Anamika Dubey
- Metagenomics and Secretomics Research laboratory, Department of Botany, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
| | - Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour University (Central University), Sagar 470003, MP, India
| | - Joanna Dames
- Mycorrhizal Research Laboratory, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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Surfactin Stimulated by Pectin Molecular Patterns and Root Exudates Acts as a Key Driver of the Bacillus-Plant Mutualistic Interaction. mBio 2021; 12:e0177421. [PMID: 34724831 PMCID: PMC8561381 DOI: 10.1128/mbio.01774-21] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Bacillus velezensis is considered as a model species belonging to the so-called Bacillus subtilis complex that evolved typically to dwell in the soil rhizosphere niche and establish an intimate association with plant roots. This bacterium provides protection to its natural host against diseases and represents one of the most promising biocontrol agents. However, the molecular basis of the cross talk that this bacterium establishes with its natural host has been poorly investigated. We show here that these plant-associated bacteria have evolved a polymer-sensing system to perceive their host and that, in response, they increase the production of the surfactin-type lipopeptide. Furthermore, we demonstrate that surfactin synthesis is favored upon growth on root exudates and that this lipopeptide is a key component used by the bacterium to optimize biofilm formation, motility, and early root colonization. In this specific nutritional context, the bacterium also modulates qualitatively the pattern of surfactin homologues coproduced in planta and forms mainly variants that are the most active at triggering plant immunity. Surfactin represents a shared good as it reinforces the defensive capacity of the host. IMPORTANCE Within the plant-associated microbiome, some bacterial species are of particular interest due to the disease protective effect they provide via direct pathogen suppression and/or stimulation of host immunity. While these biocontrol mechanisms are quite well characterized, we still poorly understand the molecular basis of the cross talk these beneficial bacteria initiate with their host. Here, we show that the model species Bacillus velezensis stimulates the production of the surfactin lipopeptide upon sensing pectin as a cell surface molecular pattern and upon feeding on root exudates. Surfactin favors bacterial rhizosphere fitness on one hand and primes the plant immune system on the other hand. Our data therefore illustrate how both partners use this multifunctional compound as a unique shared good to sustain a mutualistic interaction.
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Nadarajah K, Abdul Rahman NSN. Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad. Int J Mol Sci 2021; 22:ijms221910388. [PMID: 34638728 PMCID: PMC8508622 DOI: 10.3390/ijms221910388] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 02/06/2023] Open
Abstract
Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.
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Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions. Microorganisms 2021; 9:microorganisms9102030. [PMID: 34683351 PMCID: PMC8540375 DOI: 10.3390/microorganisms9102030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria.
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McCann A, Rappe S, La Rocca R, Tiquet M, Quinton L, Eppe G, Far J, De Pauw E, Kune C. Mass shift in mass spectrometry imaging: comprehensive analysis and practical corrective workflow. Anal Bioanal Chem 2021; 413:2831-2844. [PMID: 33517478 DOI: 10.1007/s00216-021-03174-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/22/2020] [Accepted: 01/13/2021] [Indexed: 12/19/2022]
Abstract
MALDI mass spectrometry imaging (MSI) allows the mapping and the tentative identification of compounds based on their m/z value. In typical MSI, a spectrum is taken at incremental 2D coordinates (pixels) across a sample surface. Single pixel mass spectra show the resolving power of the mass analyzer. Mass shift, i.e., variations of the m/z of the same ion(s), may occur from one pixel to another. The superposition of shifted masses from individual pixels peaks apparently degrades the resolution and the mass accuracy in the average spectrum. This leads to low confidence annotations and biased localization in the image. Besides the intrinsic performances of the analyzer, the sample properties (local composition, thickness, matrix deposition) and the calibration method are sources of mass shift. Here, we report a critical analysis and recommendations to mitigate these sources of mass shift. Mass shift 2D distributions were mapped to illustrate its effect and explore systematically its origin. Adapting the sample preparation, carefully selecting the data acquisition settings, and wisely applying post-processing methods (i.e., m/z realignment or individual m/z recalibration pixel by pixel) are key factors to lower the mass shift and to improve image quality and annotations. A recommended workflow, resulting from a comprehensive analysis, was successfully applied to several complex samples acquired on both MALDI ToF and MALDI FT-ICR instruments.
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Affiliation(s)
- Andréa McCann
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Sophie Rappe
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Raphaël La Rocca
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Mathieu Tiquet
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Johann Far
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium
| | - Christopher Kune
- Mass Spectrometry Laboratory, MolSys Research Unit, Department of Chemistry, University of Liège, Allée du Six Août, 11 - Quartier Agora, 4000, Liège, Belgium.
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Feng WM, Liu P, Yan H, Zhang S, Shang EX, Yu G, Jiang S, Qian DW, Ma JW, Duan JA. Impact of Bacillus on Phthalides Accumulation in Angelica sinensis (Oliv.) by Stoichiometry and Microbial Diversity Analysis. Front Microbiol 2021; 11:611143. [PMID: 33488552 PMCID: PMC7819887 DOI: 10.3389/fmicb.2020.611143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Plant-microorganism interaction in the rhizosphere is thought to play an important role in the formation of soil fertility, transformation and absorption of nutrients, growth and development of medicinal plants, and accumulation of medicinal ingredients. Yet, the role that they play in the phthalides accumulation of Angelica sinensis (Oliv.) Diels remains unclear. In the present study, we report a correlative analysis between rhizosphere microorganisms and phthalides accumulation in A. sinensis from Gansu, China where was the major production areas. Meanwhile, Bacillus was explored the potential functions in the plant growth and phthalide accumulation. Results revealed that the common bacterial species detected in six samples comprised 1150 OTUs which were involved in 368 genera, and predominant taxa include Actinobacteria, Acidobacteria, and Proteobacteria. The average contents of the six phthalides were 4.0329 mg/g. The correlation analysis indicated that 20 high abundance strains showed positive or negative correlations with phthalides accumulation. Flavobacterium, Nitrospira, Gaiella, Bradyrhizobium, Mycobacterium, Bacillus, RB41, Blastococcus, Nocardioides, and Solirubrobacter may be the key strains that affect phthalides accumulation on the genus level. By the plant-bacterial co-culture and fermentation, Bacillus which were isolated from rhizosphere soils can promote the plant growth, biomass accumulation and increased the contents of the butylidenephthalide (36∼415%) while the ligustilide (12∼67%) was decreased. Altogether, there is an interaction between rhizosphere microorganisms and phthalides accumulation in A. sinensis, Bacillus could promote butylidenephthalide accumulation while inhibiting ligustilide accumulation.
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Affiliation(s)
- Wei-Meng Feng
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Pei Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Yan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Sen Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Er-Xin Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guang Yu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Da-Wei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun-Wei Ma
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
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Cortés-Patiño S, Vargas C, Álvarez-Flórez F, Bonilla R, Estrada-Bonilla G. Potential of Herbaspirillum and Azospirillum Consortium to Promote Growth of Perennial Ryegrass under Water Deficit. Microorganisms 2021; 9:E91. [PMID: 33401477 PMCID: PMC7824676 DOI: 10.3390/microorganisms9010091] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 11/16/2022] Open
Abstract
Plant growth-promoting bacteria (PGPB) can mitigate the effect of abiotic stresses on plant growth and development; however, the degree of plant response is host-specific. The present study aimed to assess the growth-promoting effect of Herbaspirillum (AP21, AP02), Azospirillum (D7), and Pseudomonas (N7) strains (single and co-inoculated) in perennial ryegrass plants subjected to drought. The plants were grown under controlled conditions and subjected to water deficit for 10 days. A significant increase of approximately 30% in dry biomass production was observed using three co-inoculation combinations (p < 0.01). Genomic analysis enabled the detection of representative genes associated with plant colonization and growth promotion. In vitro tests revealed that all the strains could produce indolic compounds and exopolysaccharides and suggested that they could promote plant growth via volatile organic compounds. Co-inoculations mostly decreased the in vitro-tested growth-promoting traits; however, the co-inoculation of Herbaspirillum sp. AP21 and Azospirillum brasilense D7 resulted in the highest indolic compound production (p < 0.05). Although the Azospirillum strain showed the highest potential in the in vitro and in silico tests, the plants responded better when PGPB were co-inoculated, demonstrating the importance of integrating in silico, in vitro, and in vivo assessment results when selecting PGPB to mitigate drought stress.
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Affiliation(s)
- Sandra Cortés-Patiño
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), C.I. Tibaitatá, Km 14 Via Mosquera-Bogotá, Mosquera, Cundinamarca 250047, Colombia; (S.C.-P.); (R.B.)
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (C.V.); (F.Á.-F.)
| | - Christian Vargas
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (C.V.); (F.Á.-F.)
| | - Fagua Álvarez-Flórez
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (C.V.); (F.Á.-F.)
| | - Ruth Bonilla
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), C.I. Tibaitatá, Km 14 Via Mosquera-Bogotá, Mosquera, Cundinamarca 250047, Colombia; (S.C.-P.); (R.B.)
| | - German Estrada-Bonilla
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), C.I. Tibaitatá, Km 14 Via Mosquera-Bogotá, Mosquera, Cundinamarca 250047, Colombia; (S.C.-P.); (R.B.)
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Vishwakarma K, Kumar N, Shandilya C, Mohapatra S, Bhayana S, Varma A. Revisiting Plant-Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review. Front Microbiol 2020; 11:560406. [PMID: 33408698 PMCID: PMC7779480 DOI: 10.3389/fmicb.2020.560406] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.
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Affiliation(s)
| | - Nitin Kumar
- Department of Biotechnology, Periyar Maniammai Institute of Science and Technology, Thanjavur, India
| | | | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Sahil Bhayana
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, India
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Li J, Philp J, Li J, Wei Y, Li H, Yang K, Ryder M, Toh R, Zhou Y, Denton MD, Hu J, Wang Y. Trichoderma harzianum Inoculation Reduces the Incidence of Clubroot Disease in Chinese Cabbage by Regulating the Rhizosphere Microbial Community. Microorganisms 2020; 8:microorganisms8091325. [PMID: 32878079 PMCID: PMC7563613 DOI: 10.3390/microorganisms8091325] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/14/2020] [Accepted: 08/26/2020] [Indexed: 11/30/2022] Open
Abstract
Clubroot is a disease of cruciferous crops that causes significant economic losses to vegetable production worldwide. We applied high-throughput amplicon sequencing technology to quantify the effect of Trichodermaharzianum LTR-2 inoculation on the rhizosphere community of Chinese cabbage (Brassica rapa subsp. pekinensis cv. Jiaozhou) in a commercial production area. T. harzianum inoculation of cabbage reduced the incidence of clubroot disease by 45.4% (p < 0.05). The disease control efficacy (PDIDS) was 63%. This reduction in disease incidence and severity coincided with a drastic reduction in both the relative abundance of Plasmodiaphora brassicae, the causative pathogen of cabbage clubroot disease, and its copy number in rhizosphere soil. Pathogenic fungi Alternaria and Fusarium were also negatively associated with Trichoderma inoculation according to co-occurrence network analysis. Inoculation drastically reduced the relative abundance of the dominant bacterial genera Delftia and Pseudomonas, whilst increasing others including Bacillus. Our results demonstrate that T. harzianum LTR-2 is an effective biological control agent for cabbage clubroot, which acts through modulation of the soil and rhizosphere microbial community.
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Affiliation(s)
- Junhui Li
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China;
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.L.); (Y.W.); (H.L.); (K.Y.)
| | - Joshua Philp
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae 5064, Australia
| | - Jishun Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.L.); (Y.W.); (H.L.); (K.Y.)
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
| | - Yanli Wei
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.L.); (Y.W.); (H.L.); (K.Y.)
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
| | - Hongmei Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.L.); (Y.W.); (H.L.); (K.Y.)
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
| | - Kai Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.L.); (Y.W.); (H.L.); (K.Y.)
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
| | - Maarten Ryder
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae 5064, Australia
| | - Ruey Toh
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae 5064, Australia
| | - Yi Zhou
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae 5064, Australia
| | - Matthew D. Denton
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae 5064, Australia
| | - Jindong Hu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.L.); (Y.W.); (H.L.); (K.Y.)
- China-Australia Joint Laboratory for Soil Ecological Health and Remediation, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, China; (J.P.); (M.R.); (R.T.); (Y.Z.); (M.D.D.)
- Correspondence: (J.H.); (Y.W.)
| | - Yan Wang
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China;
- Correspondence: (J.H.); (Y.W.)
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Hansen BL, Pessotti RDC, Fischer MS, Collins A, El-Hifnawi L, Liu MD, Traxler MF. Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome. mBio 2020; 11:e01917-20. [PMID: 32843548 PMCID: PMC7448283 DOI: 10.1128/mbio.01917-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 01/01/2023] Open
Abstract
Microbiomes associated with various plant structures often contain members with the potential to make specialized metabolites, e.g., molecules with antibacterial, antifungal, or siderophore activities. However, when and where microbes associated with plants produce specialized metabolites, and the potential role of these molecules in mediating intramicrobiome interactions, is not well understood. Root nodules of legume plants are organs devoted to hosting symbiotic bacteria that fix atmospheric nitrogen and have recently been shown to harbor a relatively simple accessory microbiome containing members with the ability to produce specialized metabolites in vitro On the basis of these observations, we sought to develop a model nodule microbiome system for evaluating specialized microbial metabolism in planta Starting with an inoculum derived from field-grown Medicago sativa nodules, serial passaging through gnotobiotic nodules yielded a simplified accessory community composed of four members: Brevibacillus brevis, Paenibacillus sp., Pantoea agglomerans, and Pseudomonas sp. Some members of this community exhibited clear cooperation in planta, while others were antagonistic and capable of disrupting cooperation between other partners. Using matrix-assisted laser desorption ionization-imaging mass spectrometry, we found that metabolites associated with individual taxa had unique distributions, indicating that some members of the nodule community were spatially segregated. Finally, we identified two families of molecules produced by B. brevisin planta as the antibacterial tyrocidines and a novel set of gramicidin-type molecules, which we term the britacidins. Collectively, these results indicate that in addition to nitrogen fixation, legume root nodules are likely also sites of active antimicrobial production.
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Affiliation(s)
- Bridget L Hansen
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Rita de Cassia Pessotti
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Monika S Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Alyssa Collins
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, USA
| | - Laila El-Hifnawi
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, USA
| | - Mira D Liu
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
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Pandit A, Adholeya A, Cahill D, Brau L, Kochar M. Microbial biofilms in nature: unlocking their potential for agricultural applications. J Appl Microbiol 2020; 129:199-211. [PMID: 32034822 DOI: 10.1111/jam.14609] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 12/17/2022]
Abstract
Soil environments are dynamic and the plant rhizosphere harbours a phenomenal diversity of micro-organisms which exchange signals and beneficial nutrients. Bipartite beneficial or symbiotic interactions with host roots, such as mycorrhizae and various bacteria, are relatively well characterized. In addition, a tripartite interaction also exists between plant roots, arbuscular mycorrhizal fungi (AMF) and associated bacteria. Bacterial biofilms exist as a sheet of bacterial cells in association with AMF structures, embedded within a self-produced exopolysaccharide matrix. Such biofilms may play important functional roles within these tripartite interactions. However, the details about such interactions in the rhizosphere and their relevant functional relationships have not been elucidated. This review explores the current understanding of naturally occurring microbial biofilms, and their interaction with biotic surfaces, especially AMF. The possible roles played by bacterial biofilms and the potential for their application for a more productive and sustainable agriculture is discussed in this review.
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Affiliation(s)
- A Pandit
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - A Adholeya
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
| | - D Cahill
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - L Brau
- School of Life and Environmental Sciences, Deakin University, Geelong, Vic, Australia
| | - M Kochar
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, TERI Gram, Gwal Pahari, Gurugram, Haryana, India
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Abdallah DB, Krier F, Jacques P, Tounsi S, Frikha-Gargouri O. Agrobacterium tumefaciens C58 presence affects Bacillus velezensis 32a ecological fitness in the tomato rhizosphere. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:28429-28437. [PMID: 32415456 DOI: 10.1007/s11356-020-09124-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
The persistence of pathogenic Agrobacterium strains as soil-associated saprophytes may cause an inconsistency in the efficacy of the biocontrol inoculants under field condition. The study of the interaction occurring in the rhizosphere between the beneficial and the pathogenic microbes is thus interesting for the development of effective biopesticides for the management of crown gall disease. However, very little is still known about the influence of these complex interactions on the biocontrol determinants of beneficial bacteria, especially Bacillus strains. This study aimed to evaluate the effect of the soil borne pathogen Agrobacterium tumefaciens C58 on root colonization and lipopeptide production by Bacillus velezensis strain 32a during interaction with tomato plants. Results show that the presence of A. tumefaciens C58 positively impacted the root colonization level of the Bacillus strain. However, negative impact on surfactin production was observed in Agrobacterium-treated seedling, compared with control. Further investigation suggests that these modulations are due to a modified tomato root exudate composition during the tripartite interaction. Thus, this work contributes to enhance the knowledge on the impact of interspecies interaction on the ecological fitness of Bacillus cells living in the rhizosphere.
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Affiliation(s)
- Dorra Ben Abdallah
- Biopesticides Laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box 1177, 3018, Sfax, Tunisia
| | - François Krier
- Université de Lille, INRA, Université d'Artois, Université du Littoral-Côte d'Opale, EA 7394 - ICV-Institut Charles Viollette, F-59000, Lille, France
| | - Philippe Jacques
- Microbial Processes and Interactions (MiPI), TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech University of Liege, B-5030, Gembloux, Belgium
| | - Slim Tounsi
- Biopesticides Laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box 1177, 3018, Sfax, Tunisia
| | - Olfa Frikha-Gargouri
- Biopesticides Laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box 1177, 3018, Sfax, Tunisia.
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Yang X, Zhang L, Xiang Y, Du L, Huang X, Liu Y. Comparative transcriptome analysis of Sclerotinia sclerotiorum revealed its response mechanisms to the biological control agent, Bacillus amyloliquefaciens. Sci Rep 2020; 10:12576. [PMID: 32724140 PMCID: PMC7387486 DOI: 10.1038/s41598-020-69434-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/12/2020] [Indexed: 11/08/2022] Open
Abstract
Biological control mechanisms of plant diseases have been intensively studied. However, how plant pathogens respond to and resist or alleviate biocontrol agents remains largely unknown. In this study, a comparative transcriptome analysis was performed to elucidate how the pathogen of sclerotinia stem rot, Sclerotinia sclerotiorum, responds and resists to the biocontrol agent, Bacillus amyloliquefaciens. Results revealed that a total of 2,373 genes were differentially expressed in S. sclerotiorum samples treated with B. amyloliquefaciens fermentation broth (TS) when compared to control samples (CS). Among these genes, 2,017 were upregulated and 356 were downregulated. Further analyses indicated that various genes related to fungal cell wall and cell membrane synthesis, antioxidants, and the autophagy pathway were significantly upregulated, including glucan synthesis, ergosterol biosynthesis pathway, fatty acid synthase, heme-binding peroxidase related to oxidative stress, glutathione S-transferase, ABC transporter, and autophagy-related genes. These results suggest that S. sclerotiorum recruits numerous genes to respond to or resist the biocontrol of B. amyloliquefaciens. Thus, this study serves as a valuable resource regarding the mechanisms of fungal pathogen resistance to biocontrol agents.
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Affiliation(s)
- Xiaoxiang Yang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu, 610066, Sichuan, People's Republic of China
| | - Lei Zhang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu, 610066, Sichuan, People's Republic of China
| | - Yunjia Xiang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China
| | - Lei Du
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China
| | - Xiaoqin Huang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China.
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu, 610066, Sichuan, People's Republic of China.
| | - Yong Liu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China.
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu, 610066, Sichuan, People's Republic of China.
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Chen M, Wang J, Liu B, Zhu Y, Xiao R, Yang W, Ge C, Chen Z. Biocontrol of tomato bacterial wilt by the new strain Bacillus velezensis FJAT-46737 and its lipopeptides. BMC Microbiol 2020; 20:160. [PMID: 32539679 PMCID: PMC7296739 DOI: 10.1186/s12866-020-01851-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 06/09/2020] [Indexed: 01/25/2023] Open
Abstract
Background There is an urgent need to discover biocontrol agents to control bacterial wilt. This study reports on a new lipopeptide-producing biocontrol strain FJAT-46737 and explores its lipopeptidic compounds, and this study investigates the antagonistic effects of these compounds. Results Based on a whole genome sequence analysis, the new strain FJAT-46737 was identified as Bacillus velezensis, and seven gene clusters responsible for the synthesis of bioactive secondary metabolites in FJAT-46737 were predicted. The antimicrobial results demonstrated that FJAT-46737 exhibited broad-spectrum antimicrobial activities in vitro against three bacteria and three fungi. Pot experiments showed that the control efficiencies for tomato bacterial wilt of the whole cultures, the 2-fold diluted supernatants and the crude lipopeptide of FJAT-46737 were 66.2%, 82.0%, and 96.2%, respectively. The above results suggested that one of the antagonistic mechanisms of FJAT-46737 was the secretion of lipopeptides consisting of iturins, fengycins and surfactins. The crude lipopeptides had significant antagonistic activities against several pathogens (including Ralstonia solanacearum, Escherichia coli and Fusarium oxysporum) and fengycins were the major antibacterial components of the lipopeptides against R. solanacearum in vitro. Furthermore, the rich organic nitrogen sources (especially yeast extracts) in the media promoted the production of fengycin and surfactin by FJAT-46737. The secretion of these two lipopeptides was related to temperature fluctuations, with the fengycin content decreasing by 96.6% and the surfactins content increasing by 59.9% from 20 °C to 40 °C. The optimal temperature for lipopeptide production by FJAT-46737 varied between 20 °C and 25 °C. Conclusions The B. velezensis strain FJAT-46737 and its secreted lipopeptides could be used as new sources of potential biocontrol agents against several plant pathogens, and especially the bacterial wilt pathogen R. solanacearum.
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Affiliation(s)
- Meichun Chen
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Jieping Wang
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China.
| | - Bo Liu
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Yujing Zhu
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Rongfeng Xiao
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Wenjing Yang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350001, China
| | - Cibin Ge
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Zheng Chen
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
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Izquierdo-García LF, González-Almario A, Cotes AM, Moreno-Velandia CA. Trichoderma virens Gl006 and Bacillus velezensis Bs006: a compatible interaction controlling Fusarium wilt of cape gooseberry. Sci Rep 2020; 10:6857. [PMID: 32321998 PMCID: PMC7176702 DOI: 10.1038/s41598-020-63689-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
The combination of Trichoderma virens Gl006 and B. velezensis Bs006 as a consortium has high potential to control Fusarium wilt (FW) of cape gooseberry (Physalis peruviana) caused by Fusarium oxysporum f. sp. physali (Foph). However, the interactions between these two microorganisms that influence the biocontrol activity as a consortium have not been studied. Here, we studied the interactions between Gl006 and Bs006 that keep their compatibility under in vitro and greenhouse conditions. Antagonism tests between Gl006 and Bs006 inoculated both individually and in consortium against Foph strain Map5 was carried out on several solid media. The effect of supernatant of each selected microorganism on growth, conidia germination, biofilm formation and antagonistic activity on its partner was also studied. Biocontrol activity by different combinations of cells and supernatants from both microorganisms against Fusarium wilt was evaluated under greenhouse conditions. In vitro antagonism of the consortium against Foph showed a differential response among culture media and showed compatibility among BCA under nutritional conditions close to those of the rhizosphere. The supernatant of Bs006 did not affect the antagonistic activity of Gl006 and vice versa. However, the supernatant of Bs006 promoted the biocontrol activity of Gl006 in a synergistic way under greenhouse, reducing the disease severity by 71%. These results prove the compatibility between T. virens Gl006 and B. velezensis Bs006 as a potential tool to control Fusarium wilt of cape gooseberry.
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Affiliation(s)
- L F Izquierdo-García
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Km 14 vía Mosquera - Bogotá, Mosquera, Colombia
| | - A González-Almario
- Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - A M Cotes
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Km 14 vía Mosquera - Bogotá, Mosquera, Colombia
| | - C A Moreno-Velandia
- Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Centro de Investigación Tibaitatá, Km 14 vía Mosquera - Bogotá, Mosquera, Colombia.
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Thérien M, Kiesewalter HT, Auria E, Charron-Lamoureux V, Wibowo M, Maróti G, Kovács ÁT, Beauregard PB. Surfactin production is not essential for pellicle and root-associated biofilm development of Bacillus subtilis. Biofilm 2020; 2:100021. [PMID: 33447807 PMCID: PMC7798449 DOI: 10.1016/j.bioflm.2020.100021] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/11/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
Secondary metabolites have an important impact on the biocontrol potential of soil-derived microbes. In addition, various microbe-produced chemicals have been suggested to impact the development and phenotypic differentiation of bacteria, including biofilms. The non-ribosomal synthesized lipopeptide of Bacillus subtilis, surfactin, has been described to impact the plant promoting capacity of the bacterium. Here, we investigated the impact of surfactin production on biofilm formation of B. subtilis using the laboratory model systems; pellicle formation at the air-medium interface and architecturally complex colony development, in addition to plant root-associated biofilms. We found that the production of surfactin by B. subtilis is not essential for pellicle biofilm formation neither in the well-studied strain, NCIB 3610, nor in the newly isolated environmental strains, but lack of surfactin reduces colony expansion. Further, plant root colonization was comparable both in the presence or absence of surfactin synthesis. Our results suggest that surfactin-related biocontrol and plant promotion in B. subtilis strains are independent of biofilm formation.
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Affiliation(s)
- Maude Thérien
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Emile Auria
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada.,Biology Department, Ecole Normale Supérieure Paris-Saclay, Paris-Saclay University, Cachan, France
| | - Vincent Charron-Lamoureux
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Mario Wibowo
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Pascale B Beauregard
- Centre SÈVE, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada
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Lesson from Ecotoxicity: Revisiting the Microbial Lipopeptides for the Management of Emerging Diseases for Crop Protection. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17041434. [PMID: 32102264 PMCID: PMC7068399 DOI: 10.3390/ijerph17041434] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 11/17/2022]
Abstract
Microorganisms area treasure in terms of theproduction of various bioactive compounds which are being explored in different arenas of applied sciences. In agriculture, microbes and their bioactive compounds are being utilized in growth promotion and health promotion withnutrient fortification and its acquisition. Exhaustive explorations are unraveling the vast diversity of microbialcompounds with their potential usage in solving multiferous problems incrop production. Lipopeptides are one of such microbial compounds which havestrong antimicrobial properties against different plant pathogens. These compounds are reported to be produced by bacteria, cyanobacteria, fungi, and few other microorganisms; however, genus Bacillus alone produces a majority of diverse lipopeptides. Lipopeptides are low molecular weight compounds which havemultiple industrial roles apart from being usedas biosurfactants and antimicrobials. In plant protection, lipopeptides have wide prospects owing totheirpore-forming ability in pathogens, siderophore activity, biofilm inhibition, and dislodging activity, preventing colonization bypathogens, antiviral activity, etc. Microbes with lipopeptides that haveall these actions are good biocontrol agents. Exploring these antimicrobial compounds could widen the vistasof biological pest control for existing and emerging plant pathogens. The broader diversity and strong antimicrobial behavior of lipopeptides could be a boon for dealing withcomplex pathosystems and controlling diseases of greater economic importance. Understanding which and how these compounds modulate the synthesis and production of defense-related biomolecules in the plants is a key question—the answer of whichneeds in-depth investigation. The present reviewprovides a comprehensive picture of important lipopeptides produced by plant microbiome, their isolation, characterization, mechanisms of disease control, behavior against phytopathogens to understand different aspects of antagonism, and potential prospects for future explorations as antimicrobial agents. Understanding and exploring the antimicrobial lipopeptides from bacteria and fungi could also open upan entire new arena of biopesticides for effective control of devastating plant diseases.
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Farzand A, Moosa A, Zubair M, Khan AR, Ayaz M, Massawe VC, Gao X. Transcriptional Profiling of Diffusible Lipopeptides and Fungal Virulence Genes During Bacillus amyloliquefaciens EZ1509-Mediated Suppression of Sclerotinia sclerotiorum. PHYTOPATHOLOGY 2020; 110:317-326. [PMID: 31322486 DOI: 10.1094/phyto-05-19-0156-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Sclerotinia sclerotiorum is a devastating necrotrophic pathogen that infects multiple crops, and its control is an unremitting challenge. In this work, we attempted to gain insights into the pivotal role of lipopeptides (LPs) in the antifungal activity of Bacillus amyloliquefaciens EZ1509. In a comparative study involving five Bacillus strains, B. amyloliquefaciens EZ1509 harboring four LPs biosynthetic genes (viz. surfactin, iturin, fengycin, and bacilysin) exhibited promising antifungal activity against S. sclerotiorum in a dual-culture assay. Our data demonstrated a remarkable upsurge in LPs biosynthetic gene expression through quantitative reverse transcription PCR during in vitro interaction assay with S. sclerotiorum. Maximum upregulation in LPs biosynthetic genes was observed on the second and third days of in vitro interaction, with iturin and fengycin being the highly expressed genes. Subsequently, Matrix-assisted laser desorption/ionization-time of flight-mass spectrometry analysis confirmed the presence of LPs in the inhibition zone. Scanning electron microscope analysis showed disintegration, shrinkage, plasmolysis, and breakdown of fungal hyphae. During in planta evaluation, S. sclerotiorum previously challenged with EZ1509 showed significant suppression in pathogenicity on detached leaves of tobacco and rapeseed. The oxalic acid synthesis was also significantly reduced in S. sclerotiorum previously confronted with antagonistic bacterium. The expression of major virulence genes of S. sclerotiorum, including endopolygalacturonase-3, oxalic acid hydrolase, and endopolygalacturonase-6, was significantly downregulated during in vitro confrontation with EZ1509.
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Affiliation(s)
- Ayaz Farzand
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Anam Moosa
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Zubair
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
| | - Abdur Rashid Khan
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
| | - Muhammad Ayaz
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
| | - Venance Colman Massawe
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
| | - Xuewen Gao
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
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42
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Brescia F, Marchetti-Deschmann M, Musetti R, Perazzolli M, Pertot I, Puopolo G. The rhizosphere signature on the cell motility, biofilm formation and secondary metabolite production of a plant-associated Lysobacter strain. Microbiol Res 2020; 234:126424. [PMID: 32036275 DOI: 10.1016/j.micres.2020.126424] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/10/2020] [Accepted: 01/26/2020] [Indexed: 12/15/2022]
Abstract
Lysobacter spp. are common bacterial inhabitants of the rhizosphere of diverse plant species. However, the impact of the rhizosphere conditions on their physiology is still relatively understudied. To provide clues on the behaviour of Lysobacter spp. in this ecological niche, we investigated the physiology of L. capsici AZ78 (AZ78), a biocontrol strain isolated from tobacco rhizosphere, on a common synthetic growth medium (LBA) and on a growth medium containing components of the plant rhizosphere (RMA). The presence of a halo surrounding the AZ78 colony on RMA was a first visible effect related to differences in growth medium composition and it corresponded to the formation of a large outer ring. The lower quantity of nutrients available in RMA as compared with LBA was associated to a higher expression of a gene encoding cAMP-receptor-like protein (Clp), responsible for cell motility and biofilm formation regulation. AZ78 cells on RMA were motile, equipped with cell surface appendages and organised in small groups embedded in a dense layer of fibrils. Metabolic profiling by mass spectrometry imaging revealed increased diversity of analytes produced by AZ78 on RMA as compared with LBA. In particular, putative cyclic lipodepsipeptides, polycyclic tetramate macrolactams, cyclic macrolactams and other putative secondary metabolites with antibiotic activity were identified. Overall, the results obtained in this study shed a light on AZ78 potential to thrive in the rhizosphere by its ability to move, form biofilm and release secondary metabolites.
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Affiliation(s)
- Francesca Brescia
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; PhD school in Agricultural Science and Biotechnology, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Martina Marchetti-Deschmann
- Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Vienna, 1060, Austria
| | - Rita Musetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, 33100, Italy
| | - Michele Perazzolli
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Ilaria Pertot
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy; Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38010, San Michele all'Adige, Italy.
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43
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Antimicrobial secondary metabolites from agriculturally important bacteria as next-generation pesticides. Appl Microbiol Biotechnol 2019; 104:1013-1034. [PMID: 31858191 DOI: 10.1007/s00253-019-10300-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
The whole organisms can be packaged as biopesticides, but secondary metabolites secreted by microorganisms can also have a wide range of biological activities that either protect the plant against pests and pathogens or act as plant growth promotors which can be beneficial for the agricultural crops. In this review, we have compiled information about the most important secondary metabolites of three important bacterial genera currently used in agriculture pest and disease management.
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44
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Matilla MA, Daddaoua A, Chini A, Morel B, Krell T. An auxin controls bacterial antibiotics production. Nucleic Acids Res 2019; 46:11229-11238. [PMID: 30500953 PMCID: PMC6265452 DOI: 10.1093/nar/gky766] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/21/2018] [Indexed: 01/02/2023] Open
Abstract
The majority of clinically used antibiotics originate from bacteria. As the need for new antibiotics grows, large-scale genome sequencing and mining approaches are being used to identify novel antibiotics. However, this task is hampered by the fact that many antibiotic biosynthetic clusters are not expressed under laboratory conditions. One strategy to overcome this limitation is the identification of signals that activate the expression of silent biosynthetic pathways. Here, we report the use of high-throughput screening to identify signals that control the biosynthesis of the acetyl-CoA carboxylase inhibitor antibiotic andrimid in the broad-range antibiotic-producing rhizobacterium Serratia plymuthica A153. We reveal that the pathway-specific transcriptional activator AdmX recognizes the auxin indole-3-acetic acid (IAA). IAA binding causes conformational changes in AdmX that result in the inhibition of the expression of the andrimid cluster and the suppression of antibiotic production. We also show that IAA synthesis by pathogenic and beneficial plant-associated bacteria inhibits andrimid production in A153. Because IAA is a signalling molecule that is present across all domains of life, this study highlights the importance of intra- and inter-kingdom signalling in the regulation of antibiotic synthesis. Our discovery unravels, for the first time, an IAA-dependent molecular mechanism for the regulation of antibiotic synthesis.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | | | - Andrea Chini
- Department of Plant Molecular Genetics, National Centre for Biotechnology, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Bertrand Morel
- Departament of Physical Chemistry and Institute for Biotechnology, Science Faculty, Granada University, 18071 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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45
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Zhong Y, Yang Y, Liu P, Xu R, Rensing C, Fu X, Liao H. Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities. PLANT, CELL & ENVIRONMENT 2019; 42:2028-2044. [PMID: 30646427 DOI: 10.1111/pce.13519] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 12/29/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities and resulted in dramatically different co-occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype-dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents.
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Affiliation(s)
- Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongqing Yang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Peng Liu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruineng Xu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resource and Environmental Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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46
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Chen M, Wang J, Zhu Y, Liu B, Yang W, Ruan C. Antibacterial activity against
Ralstonia solanacearum
of the lipopeptides secreted from the
Bacillus amyloliquefaciens
strain
FJAT
‐2349. J Appl Microbiol 2019; 126:1519-1529. [DOI: 10.1111/jam.14213] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 01/19/2023]
Affiliation(s)
- M.C. Chen
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences Fuzhou China
| | - J.P. Wang
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences Fuzhou China
| | - Y.J. Zhu
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences Fuzhou China
| | - B. Liu
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences Fuzhou China
| | - W.J. Yang
- College of Biological Science and Engineering Fuzhou University Fuzhou China
| | - C.Q. Ruan
- Agricultural Bioresources Research Institute, Fujian Academy of Agricultural Sciences Fuzhou China
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47
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Wang J, Guo R, Wang W, Ma G, Li S. Insight into the surfactin production of Bacillus velezensis B006 through metabolomics analysis. ACTA ACUST UNITED AC 2018; 45:1033-1044. [PMID: 30203399 DOI: 10.1007/s10295-018-2076-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/30/2018] [Indexed: 11/25/2022]
Abstract
Abstract
Bacillus velezensis B006 is a biocontrol agent which functions through effective colonization and surfactin production. To reveal the surfactin-producing mechanism, gas chromatography–mass spectrometry based untargeted metabolomics was performed to compare the metabolite profiles of strain B006 grown in industrial media M3 and M4. Based on the statistical and pathway topology analyses, a total of 31 metabolites with a fold change of less than − 1.0 were screened as the significantly altered metabolites, which distributed in 15 metabolic pathways. Fourteen amino acids involving in the metabolisms of alanine/aspartate/glutamate, glycine/serine/threonine, arginine/proline, glutathione/cysteine/methionine and valine/leucine/isoleucine as well as succinic acid in TCA cycle were identified to be the hub metabolites. Aminoacyl-tRNA biosynthesis, glycerolipid metabolism, and pantothenate/CoA biosynthesis also contributed to surfactin production. To the best of our knowledge, this study is the first to investigate the metabolic pathways of B. velezensis on surfactin production, and will benefit the optimization of commercial fermentation for higher surfactin yield.
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Affiliation(s)
- Junqiang Wang
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
- Jiangsu Frey Agrochemicals Co. Ltd 222005 Lianyungang Jiangsu China
| | - Rongjun Guo
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
| | - Wenchao Wang
- Shanghai ProfLeader Biotech Co. Ltd 200231 Shanghai China
| | - Guizhen Ma
- 0000 0004 1800 0658 grid.443480.f School of Chemical Engineering Huaihai Institute of Technology 222005 Lianyungang Jiangsu China
| | - Shidong Li
- grid.464356.6 Institute of Plant Protection, Chinese Academy of Agricultural Sciences No. 2 Yuanmingyuan West Road 100193 Beijing China
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48
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Abdallah DB, Tounsi S, Gharsallah H, Hammami A, Frikha-Gargouri O. Lipopeptides from Bacillus amyloliquefaciens strain 32a as promising biocontrol compounds against the plant pathogen Agrobacterium tumefaciens. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:36518-36529. [PMID: 30374716 DOI: 10.1007/s11356-018-3570-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Despite the potential biological importance of lipopeptides from Bacillus amyloliquefaciens as antimicrobial compounds, their effects on Agrobacterium tumefaciens biofilms have not been previously studied. These latter are important virulence factors for the development and re-occurrence of crown gall disease. As part of the development of a new biopesticide acting as anti-biofilm and biocontrol agent, we investigated for the first time the ability of a mixture of lipopeptides produced by B. amyloliquefaciens strain 32a to inhibit the tumor formation on plants and to reduce the formation of biofilms by the phytopathogenic A. tumefaciens strains C58 and B6. The mixture was found to display a strong biosurfactant activity as well as bactericidal activity against planktonic Agrobacterium cells. Moreover, the lipopeptide treatment inhibited biofilm formation in the range of 79.58 ± 0.60-100.00 ± 0.00% and dislodged 43.42 ± 0.91-93.89 ± 2.70% of preformed biofilm. For these assays, fluorescence microscopy did not show any adherent cell in the anti-adhesive assay and only few ones in the cell-dislodging assay. More importantly, lipopeptide-enriched extract inhibits tumor formation on tomato stem when treatments were applied after pathogen adhesion to wounded tissues. By virtue of its ability to inhibit biofilms formed on biotic and abiotic surfaces and to control efficiently tumor development, the 32a lipopeptide mixture may represent an excellent new tool for an efficient biocontrol of crown gall disease.
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Affiliation(s)
- Dorra Ben Abdallah
- Biopesticides laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box "1177", 3018, Sfax, Tunisia
| | - Slim Tounsi
- Biopesticides laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box "1177", 3018, Sfax, Tunisia
| | - Houda Gharsallah
- Laboratory of Microbiology, Research Laboratory "MPH," Habib Bourguiba University Hospital of Sfax, Sfax University, Sfax, Tunisia
| | - Adnane Hammami
- Laboratory of Microbiology, Research Laboratory "MPH," Habib Bourguiba University Hospital of Sfax, Sfax University, Sfax, Tunisia
| | - Olfa Frikha-Gargouri
- Biopesticides laboratory, Centre of Biotechnology of Sfax, Sfax University, P.O. Box "1177", 3018, Sfax, Tunisia.
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49
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Zeng M, Zhong Y, Cai S, Diao Y. Deciphering the bacterial composition in the rhizosphere of Baphicacanthus cusia (NeeS) Bremek. Sci Rep 2018; 8:15831. [PMID: 30361644 PMCID: PMC6202335 DOI: 10.1038/s41598-018-34177-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 10/12/2018] [Indexed: 02/06/2023] Open
Abstract
Rhizobacteria is an important ingredient for growth and health of medicinal herbs, and synthesis of pharmacological effective substances from it. In this study, we investigated the community structure and composition of rhizobacteria in Baphicacanthus cusia (NeeS) Bremek via 16S rRNA amplicon sequencing. We obtained an average of 3,371 and 3,730 OTUs for bulk soil and rhizosphere soil samples respectively. Beta diversity analysis suggested that the bacterial community in the rhizosphere was distinctive from that in the bulk soil, which indicates that B.cusia can specifically recruit microbes from bulk soil and host in the rhizosphere. Burkholderia was significantly enriched in the rhizosphere. Burkholderia is a potentially beneficial bacteria that has been reported to play a major role in the synthesis of indigo, which was a major effective substances in B. cusia. In addition, we found that Bacilli were depleted in the rhizosphere, which are useful for biocontrol of soil-borne diseases, and this may explain the continuous cropping obstacles in B. cusia. Our results revealed the structure and composition of bacterial diversity in B. cusia rhizosphere, and provided clues for improving the medicinal value of B. cusia in the future.
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Affiliation(s)
- Meijuan Zeng
- School of Biomedical Sciences, Huaqiao University, 362021, Quanzhou, China.,Zhangzhou Health Vocational College, 363000, Zhangzhou, China
| | - Yongjia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.,Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Shijie Cai
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
| | - Yong Diao
- School of Biomedical Sciences, Huaqiao University, 362021, Quanzhou, China.
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50
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Cao Y, Pi H, Chandrangsu P, Li Y, Wang Y, Zhou H, Xiong H, Helmann JD, Cai Y. Antagonism of Two Plant-Growth Promoting Bacillus velezensis Isolates Against Ralstonia solanacearum and Fusarium oxysporum. Sci Rep 2018. [PMID: 29531357 PMCID: PMC5847583 DOI: 10.1038/s41598-018-22782-z] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Plant growth promoting rhizobacteria (PGPR) provide an effective and environmentally sustainable method to protect crops against pathogens. The spore-forming Bacilli are attractive PGPR due to their ease of storage and application. Here, we characterized two rhizosphere-associated Bacillus velezensis isolates (Y6 and F7) that possess strong antagonistic activity against Ralstonia solanacearum and Fusarium oxysporum under both laboratory and greenhouse conditions. We identified three lipopeptide (LP) compounds (surfactin, iturin and fengycin) as responsible for the antimicrobial activity of these two strains. We further dissected the contribution of LPs to various biological processes important for rhizosphere colonization. Although either iturin or fengycin is sufficient for antibacterial activity, cell motility and biofilm formation, only iturin plays a primary role in defense against the fungal pathogen F. oxysporum. Additionally, we found that LP production is significantly stimulated during interaction with R. solanacearum. These results demonstrate the different roles of LPs in the biology of B. velezensis and highlight the potential of these two isolates as biocontrol agents against phytopathogens.
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Affiliation(s)
- Yu Cao
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Hualiang Pi
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA
| | - Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Yuqi Wang
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China.,College of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, PR China
| | - Han Zhou
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China
| | - Hanqin Xiong
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China.,Guangzhou Daodong New Energy Co. Ltd, Guangzhou, 510670, PR China
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA.
| | - Yanfei Cai
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, PR China. .,Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101, USA.
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