1
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Cianciotto NP. The type II secretion system as an underappreciated and understudied mediator of interbacterial antagonism. Infect Immun 2024; 92:e0020724. [PMID: 38980047 PMCID: PMC11320942 DOI: 10.1128/iai.00207-24] [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] [Indexed: 07/10/2024] Open
Abstract
Interbacterial antagonism involves all major phyla, occurs across the full range of ecological niches, and has great significance for the environment, clinical arena, and agricultural and industrial sectors. Though the earliest insight into interbacterial antagonism traces back to the discovery of antibiotics, a paradigm shift happened when it was learned that protein secretion systems (e.g., types VI and IV secretion systems) deliver toxic "effectors" against competitors. However, a link between interbacterial antagonism and the Gram-negative type II secretion system (T2SS), which exists in many pathogens and environmental species, is not evident in prior reviews on bacterial competition or T2SS function. A current examination of the literature revealed four examples of a T2SS or one of its known substrates having a bactericidal activity against a Gram-positive target or another Gram-negative. When further studied, the T2SS effectors proved to be peptidases that target the peptidoglycan of the competitor. There are also reports of various bacteriolytic enzymes occurring in the culture supernatants of some other Gram-negative species, and a link between these bactericidal activities and T2SS is suggested. Thus, a T2SS can be a mediator of interbacterial antagonism, and it is possible that many T2SSs have antibacterial outputs. Yet, at present, the T2SS remains relatively understudied for its role in interbacterial competition. Arguably, there is a need to analyze the T2SSs of a broader range of species for their role in interbacterial antagonism. Such investigation offers, among other things, a possible pathway toward developing new antimicrobials for treating disease.
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Affiliation(s)
- Nicholas P. Cianciotto
- Department of Microbiology-Immunology, Northwestern University School of Medicine, Chicago, Illinois, USA
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2
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Song T, Liu J, Han S, Li Y, Xu T, Xi J, Hou L, Lin Y. Effect of conventional and biodegradable microplastics on the soil-soybean system: A perspective on rhizosphere microbial community and soil element cycling. ENVIRONMENT INTERNATIONAL 2024; 190:108781. [PMID: 38880060 DOI: 10.1016/j.envint.2024.108781] [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: 02/04/2024] [Revised: 04/30/2024] [Accepted: 05/26/2024] [Indexed: 06/18/2024]
Abstract
As an exogenous carbon input, microplastics (MPs), especially biodegradable MPs, may significantly disrupt soil microbial communities and soil element cycling (CNPS cycling), but few studies have focused on this. Here, we focused on assessing the effects of conventional low-density polyethylene (LDPE), biodegradable polybutylene adipate terephthalate (PBAT), and polylactic acid (PLA) MPs on rhizosphere microbial communities and CNPS cycling in a soil-soybean system. The results showed that PBAT-MPs and PLA-MPs were more detrimental to soybean growth than LDPE-MPs, resulting in a reduction in shoot nitrogen (14.05% and 11.84%) and shoot biomass (33.80% and 28.09%) at the podding stage. In addition, dissolved organic carbon (DOC) increased by 20.91% and 66.59%, while nitrate nitrogen (NO3--N) significantly decreased by 56.91% and 69.65% in soils treated with PBAT-MPs and PLA-MPs, respectively. PBAT-MPs and PLA-MPs mainly enhanced copiotrophic bacteria (Proteobacteria) and suppressed oligotrophic bacteria (Verrucomicrobiota, Gemmatimonadota, etc.), increasing the abundance of CNPS cycling-related functional genes. LDPE-MPs tended to enrich oligotrophic bacteria (Verrucomicrobiota, etc.) and decrease the abundance of CNPS cycling-related functional genes. Correlation analysis revealed that MPs with different degradation properties selectively affected the composition and function of the bacterial community, resulting in changes in the availability of soil nutrients (especially NO3--N). Redundancy analysis further indicated that NO3--N was the primary constraining factor for soybean growth. This study provides a new perspective for revealing the underlying ecological effects of MPs on soil-plant systems.
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Affiliation(s)
- Tianjiao Song
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiaxi Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Siqi Han
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yan Li
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tengqi Xu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiao Xi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lijun Hou
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Quebec H9X 3V9, Canada
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Qiao Y, Tian F, Yu L, Zhao J, Zhai Q, Chen W. Imaging Mass Spectrometry and Genome Mining Reveal Antimicrobial Peptides of Novel Pediococcus acidilactici CCFM18. Foods 2024; 13:2213. [PMID: 39063297 PMCID: PMC11276274 DOI: 10.3390/foods13142213] [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: 05/29/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The mechanism of metabolites produced by lactic acid bacteria in mediating microbial interactions has been difficult to ascertain. This study comparatively evaluated the antimicrobial effect of the novel bacterium Pediococcus acidilactici CCFM18 and explored the global chemical view of its interactions with indicator bacteria. P. acidilactici CCFM18 had sufficiently strong antimicrobial activity to effectively inhibit the growth of the indicator bacteria and enhance their intracellular reactive oxygen species (ROS) level. The emerging technique of matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) imaging mass spectrometry indicated that P. acidilactici CCFM18 increased the production of pediocin PA-1 and the penocin A profile during its interaction with the indicator bacteria, thus differing from P. acidilactici CCFM28 (a commonly used laboratory strain). Strikingly, the production of coagulin A was triggered only by signaling molecules made by the competing strain L. thermophilus, suggesting an idiosyncratic response from P. acidilactici CCFM18. Bioinformatic mining of the P. acidilactici CCFM18 draft genome sequence revealed gene loci that code for the complex secondary metabolites analyzed via MSI. Taken together, these results illustrate that chemical interactions between P. acidilactici CCFM18 and indicator bacteria exhibit high complexity and specificity and can drive P. acidilactici CCFM18 to produce different secondary metabolites.
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Affiliation(s)
- Yiteng Qiao
- College of Food Science and Engineering, Shandong Agricultural University, Tai’an 271018, China;
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (F.T.); (L.Y.); (J.Z.); (Q.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (F.T.); (L.Y.); (J.Z.); (Q.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (F.T.); (L.Y.); (J.Z.); (Q.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (F.T.); (L.Y.); (J.Z.); (Q.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (F.T.); (L.Y.); (J.Z.); (Q.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (F.T.); (L.Y.); (J.Z.); (Q.Z.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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Zhou Z, Wang T, Pu X, Su Y, Shi T, Zhao P, Yang Z, Li G. Metabolites from Lysobacter gummosus YMF3.00690 Against Meloidogyne javanica. PHYTOPATHOLOGY 2024; 114:500-502. [PMID: 37750871 DOI: 10.1094/phyto-07-23-0261-le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The strains in Lysobacter spp. have the potential to control plant-parasitic nematodes. In our experiment, L. gummosus YMF3.00690 showed antagonistic effects against plant root-knot nematode. Nine metabolites were isolated and identified from cultures of L. gummosus YMF3.00690, of which compound 1 was identified as a new metabolite tetrahydro-4,4,6-trimethyl-6-[(tetrahydro-6,6-dimethyl-2-oxo-4(1H)-pyrimidinylidene) methyl]-2(1H)-pyrimidinone. The activity assay showed that two compounds, 5-(hydroxymethyl)-1H-pyrrole-2-carbaldehyde (2) and 1H-pyrrole-2-carboxylic acid (3), had nematicidal activities against Meloidogyne javanica with mortalities of 69.93 and 90.54% at 400 ppm for 96 h, respectively. These two compounds were further tested for the inhibition activity of eggs hatching, and compound 3 showed a significant inhibition rate of 63.36% at 50 ppm for 48 h. In the chemotactic activity assay, three compounds (1 to 3) were found to have concentration-dependent chemotactic activity, of which compound 1 showed attractive activity. This experiment explored the active metabolites of L. gummosus YMF3.00690 against M. javanica and laid the foundation for biopesticide development.
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Affiliation(s)
- Zhifan Zhou
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Ting Wang
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Xuejuan Pu
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Yinling Su
- Institute of Tropical Eco-Agricultural Sciences of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650091, China
| | - Tingting Shi
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Peiji Zhao
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
| | - Zixiang Yang
- Institute of Tropical Eco-Agricultural Sciences of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan 650091, China
| | - Guohong Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China
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Messer LF, Lee CE, Wattiez R, Matallana-Surget S. Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics. MICROBIOME 2024; 12:36. [PMID: 38389111 PMCID: PMC10882806 DOI: 10.1186/s40168-024-01751-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/03/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Microbial functioning on marine plastic surfaces has been poorly documented, especially within cold climates where temperature likely impacts microbial activity and the presence of hydrocarbonoclastic microorganisms. To date, only two studies have used metaproteomics to unravel microbial genotype-phenotype linkages in the marine 'plastisphere', and these have revealed the dominance of photosynthetic microorganisms within warm climates. Advancing the functional representation of the marine plastisphere is vital for the development of specific databases cataloging the functional diversity of the associated microorganisms and their peptide and protein sequences, to fuel biotechnological discoveries. Here, we provide a comprehensive assessment for plastisphere metaproteomics, using multi-omics and data mining on thin plastic biofilms to provide unique insights into plastisphere metabolism. Our robust experimental design assessed DNA/protein co-extraction and cell lysis strategies, proteomics workflows, and diverse protein search databases, to resolve the active plastisphere taxa and their expressed functions from an understudied cold environment. RESULTS For the first time, we demonstrate the predominance and activity of hydrocarbonoclastic genera (Psychrobacter, Flavobacterium, Pseudomonas) within a primarily heterotrophic plastisphere. Correspondingly, oxidative phosphorylation, the citrate cycle, and carbohydrate metabolism were the dominant pathways expressed. Quorum sensing and toxin-associated proteins of Streptomyces were indicative of inter-community interactions. Stress response proteins expressed by Psychrobacter, Planococcus, and Pseudoalteromonas and proteins mediating xenobiotics degradation in Psychrobacter and Pseudoalteromonas suggested phenotypic adaptations to the toxic chemical microenvironment of the plastisphere. Interestingly, a targeted search strategy identified plastic biodegradation enzymes, including polyamidase, hydrolase, and depolymerase, expressed by rare taxa. The expression of virulence factors and mechanisms of antimicrobial resistance suggested pathogenic genera were active, despite representing a minor component of the plastisphere community. CONCLUSION Our study addresses a critical gap in understanding the functioning of the marine plastisphere, contributing new insights into the function and ecology of an emerging and important microbial niche. Our comprehensive multi-omics and comparative metaproteomics experimental design enhances biological interpretations to provide new perspectives on microorganisms of potential biotechnological significance beyond biodegradation and to improve the assessment of the risks associated with microorganisms colonizing marine plastic pollution. Video Abstract.
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Affiliation(s)
- Lauren F Messer
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland
| | - Charlotte E Lee
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland
| | - Ruddy Wattiez
- Proteomics and Microbiology Department, University of Mons, Mons, 7000, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland.
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Kudryakova I, Afoshin A, Tarlachkov S, Leontyevskaya E, Suzina N, (Vasilyeva) NL. Lysobacter gummosus 10.1.1, a Producer of Antimicrobial Agents. Microorganisms 2023; 11:2853. [PMID: 38137997 PMCID: PMC10745450 DOI: 10.3390/microorganisms11122853] [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: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
This work investigated the antimicrobial potential of Lysobacter gummosus 10.1.1. The culture fluid of the strain was found to contain antimicrobial agents active against Staphylococcus aureus, Micrococcus luteus, and Bacillus cereus. L. gummosus was first shown to be capable of forming outer membrane vesicles, which have a bacteriolytic effect against not only Gram-positive bacteria but also against the Gram-negative pathogen Pseudomonas aeruginosa. Transcriptomic analysis revealed the genes of almost all known bacteriolytic enzymes of Lysobacter, as well as the genes of enzymes with putative bacteriolytic activity. Also identified were genes involved in the biosynthesis of a number of secondary metabolites for which antimicrobial activities are known. This research is indicative of the relevance of isolating and studying L. gummosus antimicrobial agents.
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Affiliation(s)
| | | | | | | | | | - Natalia Leontyevskaya (Vasilyeva)
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, FRC PSCBR, Russian Academy of Sciences, 5 Prosp. Nauki, Pushchino 142290, Russia; (I.K.); (A.A.); (S.T.); (E.L.); (N.S.)
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7
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Gagnon JC, Beauregard-Tousignant S, Marcil JS, Lazar CS. Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada. Genes (Basel) 2023; 14:1529. [PMID: 37628582 PMCID: PMC10454208 DOI: 10.3390/genes14081529] [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: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.
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Affiliation(s)
- Jean-Christophe Gagnon
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
- Interuniversity Research Group in Limnology/Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montréal, QC H3C 3P8, Canada
| | - Samuel Beauregard-Tousignant
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
| | - Jean-Sébastien Marcil
- Derena Geosciences, Quebec, QC G7A 3Y5, Canada;
- Ressources Utica Inc., Quebec, QC G1V 4M7, Canada
| | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
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Wagner N, Ben-Meir D, Teper D, Pupko T. Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. pelargonii strain 305 and novel type III effectors identified in Xanthomonas. FRONTIERS IN PLANT SCIENCE 2023; 14:1155341. [PMID: 37332699 PMCID: PMC10275491 DOI: 10.3389/fpls.2023.1155341] [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] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Xanthomonas hortorum pv. pelargonii is the causative agent of bacterial blight in geranium ornamental plants, the most threatening bacterial disease of this plant worldwide. Xanthomonas fragariae is the causative agent of angular leaf spot in strawberries, where it poses a significant threat to the strawberry industry. Both pathogens rely on the type III secretion system and the translocation of effector proteins into the plant cells for their pathogenicity. Effectidor is a freely available web server we have previously developed for the prediction of type III effectors in bacterial genomes. Following a complete genome sequencing and assembly of an Israeli isolate of Xanthomonas hortorum pv. pelargonii - strain 305, we used Effectidor to predict effector encoding genes both in this newly sequenced genome, and in X. fragariae strain Fap21, and validated its predictions experimentally. Four and two genes in X. hortorum and X. fragariae, respectively, contained an active translocation signal that allowed the translocation of the reporter AvrBs2 that induced the hypersensitive response in pepper leaves, and are thus considered validated novel effectors. These newly validated effectors are XopBB, XopBC, XopBD, XopBE, XopBF, and XopBG.
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Affiliation(s)
- Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Daniella Ben-Meir
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Doron Teper
- Department of Plant Pathology and Weed Research, Institute of Plant Protection Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZion, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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Xu Q, Zou H, Pan C, Wang H, Shen Y, Li Y. Lysohexaenetides A and B, linear lipopeptides from Lysobacter sp. DSM 3655 identified by heterologous expression in Streptomyces. Chin J Nat Med 2023; 21:454-458. [PMID: 37407176 DOI: 10.1016/s1875-5364(23)60473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Indexed: 07/07/2023]
Abstract
Lysobacter harbors a plethora of cryptic biosynthetic gene clusters (BGCs), albeit only a limited number have been analyzed to date. In this study, we described the activation of a cryptic polyketide synthase (PKS)/nonribosomal peptide synthetase (NRPS) gene cluster (lsh) in Lysobacter sp. DSM 3655 through promoter engineering and heterologous expression in Streptomyces sp. S001. As a result of this methodology, we were able to isolate two novel linear lipopeptides, lysohexaenetides A (1) and B (2), from the recombinant strain S001-lsh. Furthermore, we proposed the biosynthetic pathway for lysohexaenetides and identified LshA as another example of entirely iterative bacterial PKSs. This study highlights the potential of heterologous expression systems in uncovering cryptic biosynthetic pathways in Lysobacter genomes, particularly in the absence of genetic manipulation tools.
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Affiliation(s)
- Qiushuang Xu
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Haochen Zou
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Chen Pan
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Haoxin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Yaoyao Li
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China.
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Tu CK, Wang PH, Lee MH. Endophytic Bacterium Lysobacter firmicutimachus Strain 5-7 Is a Promising Biocontrol Agent Against Rice Seedling Disease Caused by Pythium arrhenomanes in Nursery Trays. PLANT DISEASE 2023; 107:1075-1086. [PMID: 36096100 DOI: 10.1094/pdis-05-22-1195-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Rice root rot disease caused by Pythium spp. is a highly destructive disease in rice nurseries. Biocontrol with endophytic bacteria was developed in this study to control rice seedling diseases. An in planta screening assay revealed that two bacterial endophytes, strains 5-7 and 6-4, displayed strong protection of rice seedlings from attack by Pythium arrhenomanes. Phylogenetic analysis indicated that strain 5-7 is Lysobacter firmicutimachus, while strain 6-4 belongs to the Kitasatospora genus. To quickly evaluate the disease severity of the root system damaged by Pythium spp. in nursery trays, a root surface area measurement assay was developed. By using this measurement, the control efficacy in nursery trays was evaluated, and L. firmicutimachus 5-7 showed promising biocontrol activity against Pythium disease. In a field trial, the two endophytes exhibited significant disease control efficacy on rice brown spot disease caused by Bipolaris oryzae naturally occurring in a commercial nursery field. The two endophytes exhibited multiple enzymatic activities and broad-spectrum antagonistic activities against multiple rice pathogens. The two endophytes colonized the root surface and inside of the root. L. firmicutimachus 5-7 primarily colonized the intercellular space and aerenchyma. Antibiosis is the major mechanism used by strain 5-7 to cause Bipolaris hyphal swelling and inhibit Pythium zoospore germination and sporangium formation, while a hyperparasitism-like phenomenon was found in the interaction of strain 6-4 with Pythium and Bipolaris hyphae. In conclusion, we report the promising biocontrol agent L. firmicutimachus 5-7 and the potential biocontrol agent Kitasatospora sp. 6-4 for disease control of rice seedlings in commercial nursery trays and their possible mechanisms of action.
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Affiliation(s)
- Chi-Kuan Tu
- Department of Plant Pathology and Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40277, Taiwan
| | - Pei-Han Wang
- Department of Plant Pathology and Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40277, Taiwan
| | - Miin-Huey Lee
- Department of Plant Pathology and Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40277, Taiwan
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Feucherolles M, Frache G. MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology. Cells 2022; 11:cells11233900. [PMID: 36497158 PMCID: PMC9738593 DOI: 10.3390/cells11233900] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022] Open
Abstract
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.
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12
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Clements-Decker T, Kode M, Khan S, Khan W. Underexplored bacteria as reservoirs of novel antimicrobial lipopeptides. Front Chem 2022; 10:1025979. [PMID: 36277345 PMCID: PMC9581180 DOI: 10.3389/fchem.2022.1025979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Natural products derived from microorganisms play a prominent role in drug discovery as potential anti-infective agents. Over the past few decades, lipopeptides produced by particularly Bacillus, Pseudomonas, Streptomyces, Paenibacillus, and cyanobacteria species, have been extensively studied for their antimicrobial potential. Subsequently, daptomycin and polymyxin B were approved by the Food and Drug Administration as lipopeptide antibiotics. Recent studies have however, indicated that Serratia, Brevibacillus, and Burkholderia, as well as predatory bacteria such as Myxococcus, Lysobacter, and Cystobacter, hold promise as relatively underexplored sources of novel classes of lipopeptides. This review will thus highlight the structures and the newly discovered scaffolds of lipopeptide families produced by these bacterial genera, with potential antimicrobial activities. Additionally, insight into the mode of action and biosynthesis of these lipopeptides will be provided and the application of a genome mining approach, to ascertain the biosynthetic gene cluster potential of these bacterial genera (genomes available on the National Center for Biotechnology Information) for their future pharmaceutical exploitation, will be discussed.
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Affiliation(s)
| | - Megan Kode
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, Doornfontein, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Stellenbosch, South Africa
- *Correspondence: Wesaal Khan,
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13
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Papadopoulou ES, Bachtsevani E, Papazlatani CV, Rousidou C, Brouziotis A, Lampronikou E, Tsiknia M, Vasileiadis S, Ipsilantis I, Menkissoglu-Spiroudi U, Ehaliotis C, Philippot L, Nicol GW, Karpouzas DG. The Effects of Quinone Imine, a New Potent Nitrification Inhibitor, Dicyandiamide, and Nitrapyrin on Target and Off-Target Soil Microbiota. Microbiol Spectr 2022; 10:e0240321. [PMID: 35856708 PMCID: PMC9431271 DOI: 10.1128/spectrum.02403-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/24/2022] [Indexed: 11/26/2022] Open
Abstract
Dicyandiamide (DCD) and nitrapyrin (NP) are nitrification inhibitors (NIs) used in agriculture for over 40 years. Recently, ethoxyquin (EQ) was proposed as a novel potential NI, acting through its derivative quinone imine (QI). Still, the specific activity of these NIs on the different groups of ammonia-oxidizing microorganisms (AOM), and mostly their effects on other soil microbiota remain unknown. We determined the impact of QI, and comparatively of DCD and NP, applied at two doses (regular versus high), on the function, diversity, and dynamics of target (AOM), functionally associated (nitrite-oxidizing bacteria-NOB), and off-target prokaryotic and fungal communities in two soils mainly differing in pH (5.4 versus 7.9). QI was equally effective to DCD but more effective than NP in inhibiting nitrification in the acidic soil, while in the alkaline soil QI was less efficient than DCD and NP. This was attributed to the higher activity of QI toward AOA prevailing in the acidic soil. All NIs induced significant effects on the composition of the AOB community in both soils, unlike AOA, which were less responsive. Beyond on-target effects, we noted an inhibitory effect of all NIs on the abundance of NOB in the alkaline soil, with Nitrobacter being more sensitive than Nitrospira. QI, unlike the other NIs, induced significant changes in the composition of the bacterial and fungal communities in both soils. Our findings have serious implications for the efficiency and future use of NIs on agriculture and provide unprecedented evidence for the potential off-target effects of NIs on soil microbiota. IMPORTANCE NIs could improve N use efficiency and decelerate N cycling. Still, we know little about their activity on the distinct AOM groups and about their effects on off-target soil microorganisms. Here, we studied the behavior of a new potent NI, QI, compared to established NIs. We show that (i) the variable efficacy of NIs across soils with different pH reflects differences in the inherent specific activity of the NIs to AOA and AOB; (ii) beyond AOM, NIs exhibit negative effects on other nitrifiers, like NOB; (iii) QI was the sole NI that significantly affected prokaryotic and fungal diversity. Our findings (i) highlight the need for novel NI strategies that consider the variable sensitivity of AOM groups to the different NIs (ii) identify QI as a potent AOA inhibitor, and (iii) stress the need for monitoring NIs' impact on off-target soil microorganisms to ensure sustainable N fertilizers use and soil ecosystem functioning.
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Affiliation(s)
- Evangelia S. Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
- Laboratory of Environmental Microbiology, Department of Environmental Sciences, University of Thessaly, Larissa, Greece
| | - Eleftheria Bachtsevani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Christina V. Papazlatani
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Constantina Rousidou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Antonios Brouziotis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Eleni Lampronikou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Myrto Tsiknia
- Laboratory of Soils and Agricultural Chemistry, Agricultural University of Athens, Athens, Greece
| | - Sotirios Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Ioannis Ipsilantis
- Laboratory of Soil Sciences, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Urania Menkissoglu-Spiroudi
- Pesticide Science Laboratory, School of Agriculture, Forestry and Environment, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Constantinos Ehaliotis
- Laboratory of Soils and Agricultural Chemistry, Agricultural University of Athens, Athens, Greece
| | - Laurent Philippot
- Université Bourgogne Franche-Comté, INRAE, AgroSup Dijon, Agroécologie, Dijon, France
| | - Graeme W. Nicol
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, CNRS UMR 5005, Université de Lyon, Lyon, France
| | - Dimitrios G. Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
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14
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Yu M, Zhao Y. Spectinomycin resistance in Lysobacter enzymogenes is due to its rRNA target but also relies on cell-wall recycling and purine biosynthesis. Front Microbiol 2022; 13:988110. [PMID: 36118211 PMCID: PMC9471086 DOI: 10.3389/fmicb.2022.988110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Resistance to spectinomycin emerged after widely used for treatment of gonorrhea. Previous studies revealed that Lysobacter enzymogenes strain C3 (LeC3) exhibited elevated level of intrinsic resistance to spectinomycin. In this study, we screened a Tn5 transposon mutant library of LeC3 to elucidate the underlying molecular mechanisms of spectinomycin resistance. Insertion sites in 15 out of 19 mutants recovered with decreased spectinomycin resistance were located on two ribosomal RNA operons at different loci, indicating the pivotal role of ribosomal RNAs in conferring spectinomycin resistance in L. enzymogenes. The other mutants harbored mutations in the tuf, rpoD, mltB, and purB genes. Among them, the tuf and rpoD genes, respectively, encode a translation elongation factor Tu and an RNA polymerase primary sigma factor. They both contribute to protein biosynthesis, where ribosomal RNAs play essential roles. The mltB gene, whose product is involved in cell-wall recycling, was not only associated with resistance against spectinomycin, but also conferred resistance to osmotic stress and ampicillin. In addition, mutation of the purB gene, for which its product is involved in the biosynthesis of inosine and adenosine monophosphates, led to decreased spectinomycin resistance. Addition of exogenous adenine at lower concentration in medium restored the growth deficiency in the purB mutant and increased bacterial resistance to spectinomycin. These results suggest that while cell-wall recycling and purine biosynthesis might contribute to spectinomycin resistance, target rRNAs play critical role in spectinomycin resistance in L. enzymogenes.
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Affiliation(s)
- Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Plant Pathology, WSU-IAREC, Prosser, WA, United States
- *Correspondence: Youfu Zhao,
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15
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“Omic” Approaches to Bacteria and Antibiotic Resistance Identification. Int J Mol Sci 2022; 23:ijms23179601. [PMID: 36077000 PMCID: PMC9455953 DOI: 10.3390/ijms23179601] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.
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16
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Xu S, Zhang Z, Xie X, Shi Y, Chai A, Fan T, Li B, Li L. Comparative genomics provides insights into the potential biocontrol mechanism of two Lysobacter enzymogenes strains with distinct antagonistic activities. Front Microbiol 2022; 13:966986. [PMID: 36033849 PMCID: PMC9410377 DOI: 10.3389/fmicb.2022.966986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022] Open
Abstract
Lysobacter enzymogenes has been applied as an abundant beneficial microorganism to control plant disease; however, most L. enzymogenes strains have been mainly reported to control fungal diseases, not bacterial diseases. In this study, two L. enzymogenes strains were characterized, of which CX03 displayed a broad spectrum of antagonistic activities toward multiple bacteria, while CX06 exhibited a broad spectrum of antagonistic activities toward diverse fungi and oomycete, and the whole genomes of the two strains were sequenced and compared. The genome annotation showed that the CX03 genome comprised a 5,947,018 bp circular chromosome, while strain CX06 comprised a circular 6,206,196 bp chromosome. Phylogenetic analysis revealed that CX03 had a closer genetic relationship with L. enzymogenes ATCC29487T and M497-1, while CX06 was highly similar to L. enzymogenes C3. Functional gene annotation analyses of the two L. enzymogenes strains showed that many genes or gene clusters associated with the biosynthesis of different secondary metabolites were found in strains CX03 and CX06, which may be responsible for the different antagonistic activities against diverse plant pathogens. Moreover, comparative genomic analysis revealed the difference in bacterial secretory systems between L. enzymogenes strains CX03 and CX06. In addition, numerous conserved genes related to siderophore biosynthesis, quorum sensing, two-component systems, flagellar biosynthesis and chemotaxis were also identified in the genomes of strains CX03 and CX06. Most reported L. enzymogenes strains were proven mainly to suppress fungi, while CX03 exhibited direct inhibitory activities toward plant bacterial pathogens and showed an obvious role in managing bacterial disease. This study provides a novel understanding of the biocontrol mechanisms of L. enzymogenes, and reveals great potential for its application in plant disease control.
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Affiliation(s)
| | | | | | | | | | | | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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17
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Cheng X, Bi LW, Li SN, Lu YJ, Wang J, Xu SC, Gu Y, Zhao ZD, Chen YX. Succession of endophytic bacterial community and its contribution to cinnamon oil production during cinnamon shade-drying process. FOOD CHEMISTRY. MOLECULAR SCIENCES 2022; 4:100094. [PMID: 35415681 PMCID: PMC8991592 DOI: 10.1016/j.fochms.2022.100094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/27/2022] [Accepted: 03/04/2022] [Indexed: 11/20/2022]
Abstract
Cinnamon oil is a blend of secondary metabolites and is widely used as spice. Endophytic bacteria are always related to the secondary metabolites production. However, the potential of endophytic bacteria communities for cinnamon oil production during cinnamon shade-drying process is still not clear. In this study, we investigated the composition and metabolic function of endophytic bacterial community during 80-day shade-drying process. The temporal dynamics of essential oil content and its dominant constituents were analyzed. The succession of endophytic bacterial community from d0 to d80 was identified. The influence of endophytic bacterial community evolution on cinnamon oil is significant positive. Predictive functional analysis indicated that shade-drying process was rich in Saccharopolyspora that produce enzymes for the conversion of phenylalanine to cinnamaldehyde. These findings enhance our understanding of the functional bacterial genera and functional genes involved in the production of cinnamon oil during cinnamon shade-drying process.
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Affiliation(s)
- Xian Cheng
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Liang-Wu Bi
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Sheng-Nan Li
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Yan-Ju Lu
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Jing Wang
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Shi-Chao Xu
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Yan Gu
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Zhen-Dong Zhao
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
| | - Yu-Xiang Chen
- Institute of Chemical Industry of Forest Products, CAF, China
- National Engineering Lab. for Biomass Chemical Utilization, China
- Key Lab. of Chemical Engineering of Forest Products, National Forestry and Grassland Administration, China
- Key Lab. of Biomass Energy and Material, Jiangsu Province, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing 210042, China
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18
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Hernández-Guzmán M, Pérez-Hernández V, Gómez-Acata S, Jiménez-Bueno N, Verhulst N, Muñoz-Arenas LC, Navarro-Noya YE, Luna-Guido ML, Dendooven L. Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study. Arch Microbiol 2022; 204:458. [PMID: 35788780 DOI: 10.1007/s00203-022-03060-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/01/2022] [Accepted: 06/07/2022] [Indexed: 12/24/2022]
Abstract
To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.
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Affiliation(s)
| | | | - Selene Gómez-Acata
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | | | - Nele Verhulst
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, Mexico
| | | | | | - Marco L Luna-Guido
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico
| | - Luc Dendooven
- Laboratory of Soil Ecology, ABACUS, CINVESTAV, 07360, Mexico City, Mexico.
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19
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Lysobacter chinensis sp. nov., a cellulose-degrading strain isolated from cow dung compost. Antonie Van Leeuwenhoek 2022; 115:1031-1040. [PMID: 35699855 DOI: 10.1007/s10482-022-01755-3] [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: 02/02/2022] [Accepted: 05/21/2022] [Indexed: 10/18/2022]
Abstract
A novel bacterial strain, TLK-CK17T, was isolated from cow dung compost sample. The strain was Gram-staining negative, non-gliding rods, aerobic, and displayed growth at 15-40 °C (optimally, 35 °C), with 0-5.0% (w/v) NaCl (optimally, 0.5) and at pH 6.5-8.5 (optimally, 7.0-7.5). The assembled genome of strain TLK-CK17T has a total length of 4.3 Mb with a G + C content of 68.2%. According to the genome analysis, strain TLK-CK17T encodes quite a few glycoside hydrolases that may play a role in the degradation of accumulated plant biomass in compost. On the basis 16S rRNA gene sequence analysis, strain TLK-CK17T showed the highest sequence similarity (98.9%) with L. penaei GDMCC 1.1817 T, followed by L. maris KCTC 42381 T (98.3%). Cells contained iso-C16:0, iso-C15:0, and summed feature 9 (comprising C17:1 ω9c and/or 10-methyl C16:0), as its major cellular fatty acids (> 10.0%) and ubiquinone-8 as the exclusively respiratory quinone. Diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol prevailed among phospholipids. Based on the phenotypic, genomic and phylogenetic data, strain TLK-CK17T represents a novel species of the genus Lysobacter, for which the name Lysobacter chinensis sp. nov. is proposed, and the type strain is TLK-CK17T (= CCTCC AB2021257T = KCTC 92122 T).
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20
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Leitão F, Pinto G, Amaral J, Monteiro P, Henriques I. New insights into the role of constitutive bacterial rhizobiome and phenolic compounds in two Pinus spp. with contrasting susceptibility to pine pitch canker. TREE PHYSIOLOGY 2022; 42:600-615. [PMID: 34508603 DOI: 10.1093/treephys/tpab119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/06/2021] [Accepted: 09/01/2021] [Indexed: 05/24/2023]
Abstract
The rhizobiome is being increasingly acknowledged as a key player in plant health and breeding strategies. The pine pitch canker (PPC), caused by the fungus Fusarium circinatum, affects pine species with varying susceptibility degrees. Our aims were to explore the bacterial rhizobiome of a susceptible (Pinus radiata) and a resistant (Pinus pinea) species together with other physiological traits, and to analyze shifts upon F. circinatum inoculation. Pinus seedlings were stem inoculated with F. circinatum spores and needle gas exchange and antioxidant-related parameters were analyzed in non-inoculated and inoculated plants. Rhizobiome structure was evaluated through 16S rRNA gene massive parallel sequencing. Species (non-inoculated plants) harbored distinct rhizobiomes (<40% similarity), where P. pinea displayed a rhizobiome with increased abundance of taxa described in suppressive soils, displaying plant growth promoting (PGP) traits and/or anti-fungal activity. Plants of this species also displayed higher levels of phenolic compounds. F. circinatum induced slight changes in the rhizobiome of both species and a negative impact in photosynthetic-related parameters in P. radiata. We concluded that the rhizobiome of each pine species is distinct and higher abundance of bacterial taxa associated to disease protection was registered for the PPC-resistant species. Furthermore, differences in the rhizobiome are paralleled by a distinct content in phenolic compounds, which are also linked to plants' resistance against PPC. This study unveils a species-specific rhizobiome and provides insights to exploit the rhizobiome for plant selection in nurseries and for rhizobiome-based plant-growth-promoting strategies, boosting environmentally friendly disease control strategies.
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Affiliation(s)
- Frederico Leitão
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Glória Pinto
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Joana Amaral
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Pedro Monteiro
- Biology Department, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Isabel Henriques
- Faculty of Science and Technology, Department of Life Sciences and CESAM, University of Coimbra, Coimbra, Portugal
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21
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Liu Z, Jiang P, Niu G, Wang W, Li J. Lysobacter antarcticus sp. nov., an SUF-system-containing bacterium from Antarctic coastal sediment. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A Gram-stain-negative, heterotrophic, aerobic, non-motile, rod-shaped bacterial strain (GW1-59T) belonging to the genus
Lysobacter
was isolated from coastal sediment collected from the Chinese Great Wall Station, Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew well on Reasoner's 2A media and could grow in the presence of 0–4 % (w/v) NaCl (optimum, 1 %), at pH 9.0–11.0 and at 15–37 °C (optimum, 30 °C). Strain GW1-59T possessed ubiquinone-8 as the sole respiratory quinone. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1
ω9c), iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, C16 : 0 and iso-C11 : 0 3-OH. DNA–DNA relatedness with
Lysobacter concretionis
Ko07T, the nearest phylogenetic relative (98.5 % 16S rRNA gene sequence similarity) was 23.4 % (21.1–25.9 %). The average nucleotide identity value between strain GW1-59T and
L. concretionis
Ko07T was 80.1 %. The physiological and biochemical results and low level of DNA–DNA relatedness suggested the phenotypic and genotypic differentiation of strain GW1-59T from other
Lysobacter
species. On the basis of phenotypic, phylogenetic and genotypic data, a novel species, Lysobacter antarcticus sp. nov., is proposed. The type strain is GW1-59T (=CCTCC AB 2019390T=KCTC 72831T).
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Affiliation(s)
- Zuoyang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Peiqiang Jiang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Guojiang Niu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
| | - Wenjing Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, PR China
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Zhang L, Guan Y. Microbial investigations of new hydrogel-biochar composites as soil amendments for simultaneous nitrogen-use improvement and heavy metal immobilization. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127154. [PMID: 34600389 DOI: 10.1016/j.jhazmat.2021.127154] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/08/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Agricultural sustainability is challenging because of increasingly serious and co-existing issues, e.g., poor nitrogen-fertilizer use and heavy metal pollution. Herein, we introduced a new poly(acrylic acid)-grafted chitosan and biochar composite (PAA/CTS/BC) for soil amendment, and provided a first microbial insight into how PAA/CTS/BC amendment simultaneously improved nitrogen cycling and immobilized heavy metals. Our results suggest that the PAA/CTS/BC amendment significantly promoted soil ammonium retention, and reduced nitrate accumulation, nitrous oxide emission and ammonia volatilization during the rice cultivation. The availability of various heavy metals (Fe, Mn, Cu, Zn, Ni, Pb, Cr, and As) markedly decreased in the PAA/CTS/BC amended soil, thereby reducing their accumulation in rice root. The PAA/CTS/BC amendment significantly altered the structure and function of soil microbial communities. Importantly, the co-occurrence networks of microbial communities became more complex and function-specific after PAA/CTS/BC addition. For example, the keystone species related to organic matter degradation, denitrification, and plant resistance to pathogen or stresses were enriched within the network. In addition to direct adsorption, the effects of PAA/CTS/BC on shaping microbial communities played dominant roles in the soil amendment. Our findings provide a promising strategy of simultaneous nitrogen-use improvement and heavy metal immobilization for achieving crop production improvement, pollution control, and climate change mitigation.
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Affiliation(s)
- Lixun Zhang
- Guangdong Provincial Engineering Technology Research Center for Urban Water Cycle and Water Environment Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China; Department of Civil and Environmental Engineering, University of California, Irvine, CA 92612, United States
| | - Yuntao Guan
- Guangdong Provincial Engineering Technology Research Center for Urban Water Cycle and Water Environment Safety, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, PR China.
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23
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Yue H, Miller AL, Khetrapal V, Jayaseker V, Wright S, Du L. Biosynthesis, regulation, and engineering of natural products from Lysobacter. Nat Prod Rep 2022; 39:842-874. [PMID: 35067688 DOI: 10.1039/d1np00063b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: up to August 2021Lysobacter is a genus of Gram-negative bacteria that was classified in 1987. Several Lysobacter species are emerging as new biocontrol agents for crop protection in agriculture. Lysobacter are prolific producers of new bioactive natural products that are largely underexplored. So far, several classes of structurally interesting and biologically active natural products have been isolated from Lysobacter. This article reviews the progress in Lysobacter natural product research over the past ten years, including molecular mechanisms for biosynthesis, regulation and mode of action, genome mining of cryptic biosynthetic gene clusters, and metabolic engineering using synthetic biology tools.
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Affiliation(s)
- Huan Yue
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Amanda Lynn Miller
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vimmy Khetrapal
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Vishakha Jayaseker
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Stephen Wright
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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24
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Naureen Z, Gilani SA, Benny BK, Sadia H, Hafeez FY, Khanum A. Metabolomic Profiling of Plant Growth-Promoting Rhizobacteria for Biological Control of Phytopathogens. Fungal Biol 2022. [DOI: 10.1007/978-3-031-04805-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Chammem H, Antonielli L, Nesler A, Pindo M, Pertot I. Effect of a Wood-Based Carrier of Trichoderma atroviride SC1 on the Microorganisms of the Soil. J Fungi (Basel) 2021; 7:751. [PMID: 34575789 PMCID: PMC8467423 DOI: 10.3390/jof7090751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 01/04/2023] Open
Abstract
Wood pellets can sustain the growth of Trichoderma spp. in soil; however, little is known about their side effects on the microbiota. The aims of this study were to evaluate the effect of wood pellets on the growth of Trichoderma spp. in bulk soil and on the soil microbial population's composition and diversity. Trichoderma atroviride SC1 coated wood pellets and non-coated pellets were applied at the level of 10 g∙kg-1 of soil and at the final concentration of 5 × 103 conidia∙g-1 of soil and compared to a conidial suspension applied at the same concentration without the wood carrier. Untreated bulk soil served as a control. The non-coated wood pellets increased the total Trichoderma spp. population throughout the experiment (estimated as colony-forming unit g-1 of soil), while wood pellets coated with T. atroviride SC1 did not. The wood carrier increased the richness, and temporarily decreased the diversity, of the bacterial population, with Massilia being the most abundant bacterial genus, while it decreased both the richness and diversity of the fungal community. Wood pellets selectively increased fungal species having biocontrol potential, such as Mortierella, Cladorrhinum, and Stachybotrys, which confirms the suitability of such carriers of Trichoderma spp. for soil application.
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Affiliation(s)
- Hamza Chammem
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano, 20, 38123 Trento, TN, Italy;
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria;
| | - Andrea Nesler
- Bi-PA nv (Biological Products for Agriculture), Technologielaan, 7, B-1840 Londerzeel, Belgium;
- Reserch and Innovation Center, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, TN, Italy;
| | - Massimo Pindo
- Reserch and Innovation Center, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, TN, Italy;
| | - Ilaria Pertot
- Reserch and Innovation Center, Fondazione Edmund Mach (FEM), Via E. Mach 1, 38010 San Michele all’Adige, TN, Italy;
- Center Agriculture Food Environment, University of Trento, Via E. Mach 1, 38010 San Michele all’Adige, TN, Italy
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26
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Bejarano A, Perazzolli M, Pertot I, Puopolo G. The Perception of Rhizosphere Bacterial Communication Signals Leads to Transcriptome Reprogramming in Lysobacter capsici AZ78, a Plant Beneficial Bacterium. Front Microbiol 2021; 12:725403. [PMID: 34489914 PMCID: PMC8416617 DOI: 10.3389/fmicb.2021.725403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/21/2021] [Indexed: 12/13/2022] Open
Abstract
The rhizosphere is a dynamic region governed by complex microbial interactions where diffusible communication signals produced by bacteria continuously shape the gene expression patterns of individual species and regulate fundamental traits for adaptation to the rhizosphere environment. Lysobacter spp. are common bacterial inhabitants of the rhizosphere and have been frequently associated with soil disease suppressiveness. However, little is known about their ecology and how diffusible communication signals might affect their behavior in the rhizosphere. To shed light on the aspects determining rhizosphere competence and functioning of Lysobacter spp., we carried out a functional and transcriptome analysis on the plant beneficial bacterium Lysobacter capsici AZ78 (AZ78) grown in the presence of the most common diffusible communication signals released by rhizosphere bacteria. Mining the genome of AZ78 and other Lysobacter spp. showed that Lysobacter spp. share genes involved in the production and perception of diffusible signal factors, indole, diffusible factors, and N-acyl-homoserine lactones. Most of the tested diffusible communication signals (i.e., indole and glyoxylic acid) influenced the ability of AZ78 to inhibit the growth of the phytopathogenic oomycete Pythium ultimum and the Gram-positive bacterium Rhodococcus fascians. Moreover, RNA-Seq analysis revealed that nearly 21% of all genes in AZ78 genome were modulated by diffusible communication signals. 13-Methyltetradecanoic acid, glyoxylic acid, and 2,3-butanedione positively influenced the expression of genes related to type IV pilus, which might enable AZ78 to rapidly colonize the rhizosphere. Moreover, glyoxylic acid and 2,3-butanedione downregulated tRNA genes, possibly as a result of the elicitation of biological stress responses. On its behalf, indole downregulated genes related to type IV pilus and the heat-stable antifungal factor, which might result in impairment of twitching motility and antibiotic production in AZ78. These results show that diffusible communication signals may affect the ecology of Lysobacter spp. in the rhizosphere and suggest that diffusible communication signals might be used to foster rhizosphere colonization and functioning of plant beneficial bacteria belonging to the genus Lysobacter.
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Affiliation(s)
- Ana Bejarano
- Center of Agriculture, Food, Environment, University of Trento, San Michele all'Adige, Italy.,Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Michele Perazzolli
- Center of Agriculture, Food, Environment, University of Trento, San Michele all'Adige, Italy.,Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Ilaria Pertot
- Center of Agriculture, Food, Environment, University of Trento, San Michele all'Adige, Italy.,Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Gerardo Puopolo
- Center of Agriculture, Food, Environment, University of Trento, San Michele all'Adige, Italy.,Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
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27
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Leinberger J, Holste J, Bunk B, Freese HM, Spröer C, Dlugosch L, Kück AC, Schulz S, Brinkhoff T. High Potential for Secondary Metabolite Production of Paracoccus marcusii CP157, Isolated From the Crustacean Cancer pagurus. Front Microbiol 2021; 12:688754. [PMID: 34262548 PMCID: PMC8273931 DOI: 10.3389/fmicb.2021.688754] [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: 03/31/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Secondary metabolites are key components in microbial ecology by mediating interactions between bacteria and their environment, neighboring species or host organisms. Bioactivities can be beneficial for both interaction partners or provide a competitive advantage only for the producer. Colonizers of confined habitats such as biofilms are known as prolific producers of a great number of bioactive secondary metabolites and are a potential source for novel compounds. We investigated the strain Paracoccus marcusii CP157, which originates from the biofilm on the carapace of a shell disease-affected Cancer pagurus specimen, for its potential to produce bioactive secondary metabolites. Its closed genome contains 22 extrachromosomal elements and several gene clusters potentially involved in biosynthesis of bioactive polyketides, bacteriocins, and non-ribosomal peptides. Culture extracts of CP157 showed antagonistic activities against bacteria from different phyla, but also against microalgae and crustacean larvae. Different HPLC-fractions of CP157 culture extracts had antibacterial properties, indicating that several bioactive compounds are produced by CP157. The bioactive extract contains several small, antibacterial compounds that partially withstand elevated temperatures, extreme pH values and exposure to proteolytic enzymes, providing high stability toward environmental conditions in the natural habitat of CP157. Further, screening of 17 Paracoccus spp. revealed that antimicrobial activity, hemolysis and production of N-acyl homoserine lactones are common features within the genus. Taking into account the large habitat diversity and phylogenetic distance of the tested strains, we hypothesize that bioactive secondary metabolites play a central role in the ecology of Paracoccus spp. in their natural environments.
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Affiliation(s)
- Janina Leinberger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jonas Holste
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Heike M. Freese
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Leon Dlugosch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Anna-Carlotta Kück
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Stefan Schulz
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
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28
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Zhu L, Yan H, Zhou GS, Jiang CH, Liu P, Yu G, Guo S, Wu QN, Duan JA. Insights into the mechanism of the effects of rhizosphere microorganisms on the quality of authentic Angelica sinensis under different soil microenvironments. BMC PLANT BIOLOGY 2021; 21:285. [PMID: 34157988 PMCID: PMC8220839 DOI: 10.1186/s12870-021-03047-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/11/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Angelica sinensis (Oliv.) Diels (A. sinensis) is a Chinese herb grown in different geographical locations. It contains numerous active components with therapeutic value. Rhizosphere microbiomes affect various aspects of plant performance, such as nutrient acquisition, growth and development and plant diseases resistance. So far, few studies have investigated how the microbiome effects level of active components of A. sinensis. This study investigated whether changes in rhizosphere microbial communities and metabolites of A. sinensis vary with the soil microenvironment. Soils from the two main A. sinensis-producing areas, Gansu and Yunnan Province, were used to conduct pot experiments. The soil samples were divided into two parts, one part was sterilized and the other was unsterilized planting with the seedling variety of Gansu danggui 90-01. All seedlings were allowed to grow for 180 days. At the end of the experiment, radix A. sinensis were collected and used to characterize growth targets and chemical compositions. Rhizosphere soils were subjected to microbial analyses. RESULTS Changes in metabolic profiles and rhizosphere microbial communities of A. sinensis grown under different soil microenvironments were similar. The GN (Gansu non-sterilized), YN (Yunnan non-sterilized), GS (Gansu sterilized), and YS (Yunnan sterilized) groups were significantly separated. Notably, antagonistic bacteria such as Sphingomonas, Pseudomonas, Lysobacter, Pseudoxanthomonas, etc. were significantly (p < 0.05) enriched in Gansu soil compared with Yunnan soil. Moreover, senkyunolide I and ligustilide dimers which were enriched in GS group were strongly positively correlated with Pseudomonas parafulva; organic acids (including chlorogenic acid, dicaffeoylquinic acid and 5-feruloylquinic acid) and their ester coniferyl ferulate which were enriched in YS Group were positively associated with Gemmatimonadetes bacterium WY71 and Mucilaginibater sp., respectively. CONCLUSIONS The soil microenvironment influences growth and level/type of active components in A. sinensis. Further studies should explore the functional features of quality-related bacteria, identify the key response genes and clarify the interactions between genes and soil environments. This will reveal the mechanisms that determine the quality formation of genuine A. sinensis.
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Affiliation(s)
- Lei Zhu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Yan
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Gui-Sheng Zhou
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chun-Hao Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Pei Liu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guang Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Sheng Guo
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qi-Nan Wu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Ao Duan
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, State Administration of Traditional Chinese Medicine Key Laboratory of Chinese Medicinal Resources Recycling Utilization, Nanjing University of Chinese Medicine, Nanjing, China.
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Xu K, Lin L, Shen D, Chou SH, Qian G. Clp is a "busy" transcription factor in the bacterial warrior, Lysobacter enzymogenes. Comput Struct Biotechnol J 2021; 19:3564-3572. [PMID: 34257836 PMCID: PMC8246147 DOI: 10.1016/j.csbj.2021.06.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/13/2021] [Accepted: 06/13/2021] [Indexed: 02/06/2023] Open
Abstract
Cyclic AMP receptor protein (CRP) is a well-characterized group of global transcription factors in bacteria. They are known to regulate numerous cellular processes by binding DNA and/or cAMP (a ligand called bacterial second messenger) to control target gene expression. Gram-negative Lysobacter enzymogenes is a soilborne, plant-beneficial bacterium without flagella that can fight against filamentous fungi and oomycete. Driven by the type IV pilus (T4P) system, this bacterium moves to nearby pathogens and uses a “mobile-attack” antifungal strategy to kill them via heat-stable antifungal factor (HSAF) and abundant lyases. This strategy is controlled by a unique “busy” transcription factor Clp, which is a CRP-like protein that is inactivated by binding of c-di-GMP, another ubiquitous second messenger of bacteria. In this review, we summarize the current progress in how Clp initiates a “mobile-attack” strategy through a series of previously uncharacterized mechanisms, including binding to DNA in a unique pattern, directly interacting with or responding to various small molecules, and interacting specifically with proteins adopting distinct structure. Together, these characteristics highlight the multifunctional roles of Clp in L. enzymogenes, a powerful bacterial warrior against fungal pathogens.
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Affiliation(s)
- Kangwen Xu
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Long Lin
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Danyu Shen
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
| | - Shan-Ho Chou
- Institute of Biochemistry, and NCHU Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Guoliang Qian
- College of Plant Protection, Laboratory of Plant Immunity, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, PR China
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30
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Liu Q, Yang J, Wang X, Wei L, Ji G. Effect of culture medium optimization on the secondary metabolites activity of Lysobacter antibioticus 13-6. Prep Biochem Biotechnol 2021; 51:1008-1017. [PMID: 33656401 DOI: 10.1080/10826068.2021.1888298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Fermentation products of Lysobacter antibioticus 13-6 have antagonistic activity against devastating phytopathogenic bacerium Xanthomonas oryzae pv. oryzicola. The production of Lysobacter antibioticus 13-6 secondary metabolites was increased by optimizing the fermentation medium; using a single-factor screening test, Plackett-Burman Design, and Box-Behnken Design. The medium's final formulation for active secondary metabolites high-yield included peptone 5 g/L, glucose 4.73 g/L, MgSO4·7H2O 2.33 g/L, and K2HPO4 2.21 g/L. We compared phenazine-1-carboxylic acid (PCA) contents of L. antibioticus 13-6 in the initial and optimized mediums through HPLC. It was found PCA contents of the optimized medium are two folds more than in the initial medium. We also detected the relative expression of five phenazine genes of L. antibioticus 13-6 via RT-qPCR, and it was found that genes: phzB, C, S, and NO1 have more significant expression compared with the initial medium, while gene phzD has found just significant. Further, we revealed that the optimal fermentation conditions for secondary metabolites were: fermentation time 60 hours, shaking speed 160 rpm, inoculum size 3%, and the initial pH = 7.0. In the end, it was determined that the antimicrobial activity and quality of L. antibioticus 13-6 secondary metabolites were increased by about 41.75% and 2-times, respectively, after the optimization of the fermentation medium.
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Affiliation(s)
- Qi Liu
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jun Yang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xing Wang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lanfang Wei
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Guanghai Ji
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management, College of Plant Protection, Yunnan Agricultural University, Kunming, Yunnan, China
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31
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Colored Microbial Coatings in Show Caves from the Galapagos Islands (Ecuador): First Microbiological Approach. COATINGS 2020. [DOI: 10.3390/coatings10111134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Galapagos Islands (Ecuador) have a unique ecosystem on Earth due to their outstanding biodiversity and geological features. This also extends to their subterranean heritage, such as volcanic caves, with plenty of secondary mineral deposits, including coralloid-type speleothems and moonmilk deposits. In this study, the bacterial communities associated with speleothems from two lava tubes of Santa Cruz Island were investigated. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features associated with moonmilk and coralloid speleothems from Bellavista and Royal Palm Caves. Microbial cells, especially filamentous bacteria in close association with extracellular polymeric substances (EPS), were abundant in both types of speleothems. Furthermore, reticulated filaments and Actinobacteria-like cells were observed by FESEM. The analysis of 16S rDNA revealed the presence of different bacterial phylotypes, many of them associated with the carbon, nitrogen, iron and sulfur cycles, and some others with pollutants. This study gives insights into subsurface microbial diversity of the Galapagos Islands and further shows the interest of the conservation of these subterranean geoheritage sites used as show caves.
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32
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Fulano AM, Shen D, Zhang EH, Shen X, Chou SH, Minamino T, Puopolo G, Qian G. Functional divergence of flagellar type III secretion system: A case study in a non-flagellated, predatory bacterium. Comput Struct Biotechnol J 2020; 18:3368-3376. [PMID: 33294133 PMCID: PMC7688988 DOI: 10.1016/j.csbj.2020.10.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/19/2023] Open
Abstract
The lack of functional flagella and the ability to prey upon other microorganisms are well-known traits of Lysobacter enzymogenes, a plant beneficial bacterial species. Here, we report a possible link between these two traits in the model strain L. enzymogenes OH11 (OH11). The genome of OH11 encompasses several homologous genes involved in the flagellum formation but it lacks a functional fliC, encoding the flagellin. Despite the lack of the main component of the flagellum, OH11 genome includes genes involved in the flagellar type III secretion system (FT3SS), which is commonly deployed by flagellated bacteria to transport flagellar subunit proteins. To understand the role played by FT3SS in OH11, we showed that the remaining FT3SS genes were expressed under laboratory conditions. Subsequently, we showed that the identified FT3SS genes involved in the secretion of the hook-capping protein FlgD, suggesting OH11 likely possessed a functional FT3SS system. Blocking FT3SS in OH11 via inactivation of the ATPase FliI impaired the secretion of the proteins Le3970 (protease), Le4493 (ß-1,3-glucanase A) and Le1659 (halo acid dehalogenase family), that showed a toxic activity against the yeast Saccharomyces cerevisiae. The possible link between FT3SS and OH11 antagonism towards S. cerevisiae was also confirmed by loss of toxicity in both mutants of ΔfliI and ΔflhB that lacks the FT3SS structural gene flhB when co-cultured with the yeast strain. The design of synthetic proteins toxic against the Gram-negative bacterium Ralstonia solanacearum further supported the involvement of FT3SS in the ability of OH11 to parasitize other microorganisms. Overall, these results revealed a possible cooption of components of FT3SS system in the competition with other microorganisms in the plant beneficial bacterium OH11 and highlighted a functional divergence of FT3SS between flagellated and non-flagellated bacteria.
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Affiliation(s)
- Alex M. Fulano
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, PR China
| | - Danyu Shen
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, PR China
| | - En-Hui Zhang
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xi Shen
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shan-Ho Chou
- Institute of Biochemistry, and NCHU Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - 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
| | - Guoliang Qian
- College of Plant Protection (Laboratory of Plant Immunity; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing 210095, PR China
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Zhao Y, Jiang T, Xu H, Xu G, Qian G, Liu F. Characterization of Lysobacter spp. strains and their potential use as biocontrol agents against pear anthracnose. Microbiol Res 2020; 242:126624. [PMID: 33189074 DOI: 10.1016/j.micres.2020.126624] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 10/09/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022]
Abstract
Colletotrichum fructicola, is an important fungal pathogen that has been reported to cause pear (Pyrus) anthracnose in China, resulting in substantial economic losses due to severe defoliation and decreased fruit quality and yield. In the search for novel strategies to control pear anthracnose, Lysobacter strains have drawn a great deal of attention due to their high-level production of extracellular enzymes and bioactive metabolites. In the present study, we compared four Lysobacter strains including Lysobacter enzymogenes OH11, Lysobacter antibioticus OH13, Lysobacter gummosus OH17 and Lysobacter brunescens OH23 with respect to their characteristics and activity against pear anthracnose caused by C. fructicola. The results showed that the evaluated Lysobacter species presented various colony morphologies when cultured on different media and were proficient in producing protease, chitinase, cellulase and glucanase, with L. enzymogenes OH11 showing typical twitching motility. L. enzymogenes OH11 and L. gummosus OH17 showed potent activity against the tested fungi and oomycetes. L. gummosus OH17 produced HSAF (heat-stable antifungal factor) which was demonstrated to be a major antifungal factor in L. enzymogenes OH11 and C3. Furthermore, L. antibioticus OH13 and L. brunescens OH23 exhibited strong antibacterial activity, especially against Xanthomonas species. Cultures of L. enzymogenes OH11 protected pear against anthracnose caused by C. fructicola, and the in vivo results indicated that treatment with an L. enzymogenes OH11 culture could decrease the diameter of lesions in pears by 35 % and reduce the severity of rot symptoms compared to that observed in the control. In the present study, we systemically compared four Lysobacter strains and demonstrated that they have strong antagonistic activity against a range of pathogens, demonstrating their promise in the development of biological control agents.
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Affiliation(s)
- Yangyang Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, PR China
| | - Tianping Jiang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, PR China; College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Huiyong Xu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, PR China
| | - Gaoge Xu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, PR China
| | - Guoliang Qian
- College of Plant Protection (Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, 210014, PR China; Institute of Life Sciences, Jiangsu University, Zhenjiang, 212013, PR China.
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Lee JC, Whang KS. Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil. Arch Microbiol 2020; 203:287-293. [PMID: 32920671 DOI: 10.1007/s00203-020-02032-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/04/2020] [Accepted: 09/02/2020] [Indexed: 11/28/2022]
Abstract
A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15T, was isolated from soil at Bigeum island in Korea. Growth was observed at 10-37 °C (optimum, 28 °C), at pH 6.0-7.5 (optimum, pH 7.0) and in the absence of NaCl. Based on 16S rRNA gene sequence analysis, strain YJ15T was closely related to 'Lysobacter tongrenensis' YS037T (97.8%), Lysobacter pocheonensis Gsoil193T (96.5%) and Lysobacter daecheongensis Dae08T (95.8%) and phylogenetically grouped together with 'Lysobacter tongrenensis' YS037T, Lysobacter dokdonensis DS-58T and Lysobacter pocheonensis Gsoil 193T. The DNA-DNA relatedness between strain YJ15T and 'Lysobacter tongrenensis' KCTC 52206T was 12% and the phylogenomic analysis based on the whole genome sequence demonstrated that strain YJ20T formed a distinct phyletic line with Lysobacterlter dokdonensis DS-58T showing average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of 76.3 and 21.3%, respectively. The predominant ubiquinone was identified as Q-8, and polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unidentified aminolipids. The major fatty acids were iso-C17:1 ω9c, iso-C15:0, iso-C16:0 and iso-C17:0. The genomic DNA G + C content was 68.2 mol %. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ15T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter telluris sp. nov. is proposed. The type strain is YJ15T (= KACC 19552T = NBRC 113197T).
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea.,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea. .,Department of Microbiology & Resources, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea.
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Song C, Zhu F, Carrión VJ, Cordovez V. Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches. Front Bioeng Biotechnol 2020; 8:896. [PMID: 32850744 PMCID: PMC7426627 DOI: 10.3389/fbioe.2020.00896] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/13/2020] [Indexed: 12/12/2022] Open
Abstract
Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant–microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current -omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.
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Affiliation(s)
- Chunxu Song
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China.,National Academy of Agriculture Green Development, China Agricultural University, Beijing, China.,Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Víctor J Carrión
- Institute of Biology, Leiden University, Leiden, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Viviane Cordovez
- Institute of Biology, Leiden University, Leiden, Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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Afoshin AS, Kudryakova IV, Borovikova AO, Suzina NE, Toropygin IY, Shishkova NA, Vasilyeva NV. Lytic potential of Lysobacter capsici VKM B-2533 T: bacteriolytic enzymes and outer membrane vesicles. Sci Rep 2020; 10:9944. [PMID: 32561806 PMCID: PMC7305183 DOI: 10.1038/s41598-020-67122-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/03/2020] [Indexed: 11/10/2022] Open
Abstract
Recent recurrent outbreaks of bacterial resistance to antibiotics have shown the critical need to identify new lytic agents to combat them. The species Lysobacter capsici VKM B-2533T possesses a potent antimicrobial action against a number of bacteria, fungi and yeasts. Its activity can be due to the impact of bacteriolytic enzymes, antibiotics and peptides. This work isolated four homogeneous bacteriolytic enzymes and a mixture of two proteins, which also had a bacteriolytic activity. The isolates included proteins identical to L. enzymogenes α- and β-lytic proteases and lysine-specific protease. The proteases of 26 kDa and 29 kDa and a protein identified as N-acetylglycosaminidase had not been isolated in Lysobacter earlier. The isolated β-lytic protease digested live methicillin-resistant staphylococcal cells with high efficiency (minimal inhibitory concentration, 2.85 μg/mL). This property makes the enzyme deserving special attention. A recombinant β-lytic protease was produced. The antimicrobial potential of the bacterium was contributed to by outer membrane vesicles (OMVs). L. capsici cells were found to form a group of OMVs responsible for antifungal activity. The data are indicative of a significant antimicrobial potential of this bacterium that requires thorough research.
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Affiliation(s)
- A S Afoshin
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia
| | - I V Kudryakova
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia
| | - A O Borovikova
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia
| | - N E Suzina
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia
| | - I Yu Toropygin
- Department of Proteomics, V.N. Orekhovich Research Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, 10 Pogodinskaja Str., Moscow, 119832, Russia
| | - N A Shishkova
- Laboratory of Anthrax Microbiology, FBIS State Research Center for Applied Microbiology and Biotechnology, Obolensk, Serpukhov District, Moscow Region, 142279, Russia
| | - N V Vasilyeva
- Laboratory of Microbial Cell Surface Biochemistry, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, PSCBR RAS, 5 Prosp. Nauki, Pushchino, Moscow Region, 142290, Russia.
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The Homologous Components of Flagellar Type III Protein Apparatus Have Acquired a Novel Function to Control Twitching Motility in a Non-Flagellated Biocontrol Bacterium. Biomolecules 2020; 10:biom10050733. [PMID: 32392834 PMCID: PMC7277350 DOI: 10.3390/biom10050733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 01/07/2023] Open
Abstract
The bacterial flagellum is one of the best-studied surface-attached appendages in bacteria. Flagellar assembly in vivo is promoted by its own protein export apparatus, a type III secretion system (T3SS) in pathogenic bacteria. Lysobacter enzymogenes OH11 is a non-flagellated soil bacterium that utilizes type IV pilus (T4P)-driven twitching motility to prey upon nearby fungi for food. Interestingly, the strain OH11 encodes components homologous to the flagellar type III protein apparatus (FT3SS) on its genome, but it remains unknown whether this FT3SS-like system is functional. Here, we report that, despite the absence of flagella, the FT3SS homologous genes are responsible not only for the export of the heterologous flagellin in strain OH11 but also for twitching motility. Blocking the FT3SS-like system by in-frame deletion mutations in either flhB or fliI abolished the secretion of heterologous flagellin molecules into the culture medium, indicating that the FT3SS is functional in strain OH11. A deletion of flhA, flhB, fliI, or fliR inhibited T4P-driven twitching motility, whereas neither that of fliP nor fliQ did, suggesting that FlhA, FlhB, FliI, and FliR may obtain a novel function to modulate the twitching motility. The flagellar FliI ATPase was required for the secretion of the major pilus subunit, PilA, suggesting that FliI would have evolved to act as a PilB-like pilus ATPase. These observations lead to a plausible hypothesis that the non-flagellated L. enzymogenes OH11 could preserve FT3SS-like genes for acquiring a distinct function to regulate twitching motility associated with its predatory behavior.
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Daura-Pich O, Hernández I, Pinyol-Escala L, Lara JM, Martínez-Servat S, Fernández C, López-García B. No antibiotic and toxic metabolites produced by the biocontrol agent Pseudomonas putida strain B2017. FEMS Microbiol Lett 2020; 367:5826813. [DOI: 10.1093/femsle/fnaa075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
ABSTRACTPseudomonas putida and closely-related species such as Pseudomonas fluorescens and Pseudomonas brassicacearum have been reported as potential biocontrol agents and plant growth-promoters. Recently, we have described the biocontrol activity of P. putida B2017 against several phytopathogens of agricultural relevance. In this study, its ability to produce potential antibiotic / toxic metabolites was assessed by functional, chromatography-mass spectrometry and genomic analysis. Our results show that B2017 is not able to synthesize surfactants and common antibiotics produced by Pseudomonas spp., i.e. pyrrolnitrin, 2,4-diacetylphloroglucinol, pyoluteorin and pyocyanin, but it produces pyoverdine, a siderophore which is involved in its biocontrol activity. The non-production of other metabolites, such as cyanide, safracin, promysalin and lipopeptides between others, is also discussed. Our data suggest that the mode of action of B2017 is not mainly due to the production of antimicrobial / toxic metabolites. Moreover, these features make P. putida B2017 a promising biocontrol microorganism for plant protection without side effects on environment, non-target organisms and human health.
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Affiliation(s)
- Oriol Daura-Pich
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Iker Hernández
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Lola Pinyol-Escala
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Jose M Lara
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Sonia Martínez-Servat
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Carolina Fernández
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
| | - Belén López-García
- Futureco Bioscience S. A., Avinguda del Cadí 19–23, 08799 Olérdola (Barcelona), Spain
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Yu M, Zhang G, Jiang J, Du L, Zhao Y. Lysobacter enzymogenes Employs Diverse Genes for Inhibiting Hypha Growth and Spore Germination of Soybean Fungal Pathogens. PHYTOPATHOLOGY 2020; 110:593-602. [PMID: 31774360 DOI: 10.1094/phyto-09-19-0356-r] [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] [Indexed: 06/10/2023]
Abstract
Lysobacter enzymogenes strain C3 (LeC3) is a potential biocontrol agent for plant diseases caused by fungi and oomycetes. Understanding the interaction between LeC3 and soybean pathogens at the molecular level could help improve its biocontrol efficacy. In this study, we obtained mutants with decreased abilities in inhibiting hypha growth of the white mold pathogen Sclerotinia sclerotiorum. Insertion sites for 50 mutants, which no longer inhibited S. sclerotiorum hypha growth in dual cultural assay, were determined and seven mutants were selected for further characterization. These seven mutants also completely lost their abilities in suppressing spore germination of Fusarium virguliforme, the causal agent of soybean sudden death syndrome. Furthermore, mutation of the seven genes, which encode diguanylate cyclase, transcriptional regulators from the TetR family, hemolysin III family channel protein, type IV secretion system VirB10 protein, phenol hydroxylase, and phosphoadenosine phosphosulfate reductase, respectively, led to reduced production or secretion of four extracellular enzymes and heat-stable antifungal factor (HSAF). These results suggest that these seven genes play important roles in L. enzymogenes in suppressing hypha growth and spore germination of fungal pathogens, probably by influencing production or secretion of extracellular enzymes and HSAF.
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Affiliation(s)
- Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
| | - Guiying Zhang
- Department of Plant Protection, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, People's Republic of China
| | - Jiasong Jiang
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, U.S.A
| | - Liangcheng Du
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588, U.S.A
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, U.S.A
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Lysobacter prati sp. nov., isolated from a plateau meadow sample. Antonie van Leeuwenhoek 2020; 113:763-772. [PMID: 31980979 DOI: 10.1007/s10482-020-01386-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/09/2020] [Indexed: 10/25/2022]
Abstract
A novel proteobacterial strain designated SYSU H10001T was isolated from a soil sample collected from plateau meadow in Hongyuan county, Sichuan province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and phylogenetic analysis, strain SYSU H10001T was most closely related to Lysobacter soli KCTC 22011T (98.6%, sequence similarity) and Lysobacter panacisoli JCM 19212T (98.2%). The prediction result of secondary metabolites based on genome shown that the strain SYSU H10001T contained 3 clusters of bacteriocins, 1 cluster of non-ribosomal peptide synthetase, 1 cluster of type 1 polyketide synthase and 1 cluster of arylpolyene. In addition, the major isoprenoid quinone was Q-8 and the major fatty acids were identified as iso-C15:0, iso-C17:0 and Summed feature 9. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and three unidentified phospholipids. The genomic DNA G + C content of strain SYSU H10001T was 66.5% (genome). On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU H10001T represents a novel species of the genus Lysobacter, for which the name Lysobacter prati sp. nov. is proposed. The type strain is SYSU H10001T (= KCTC 72062T = CGMCC 1.16662T).
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Yu M, Zhao Y. Cell permeability, β-lactamase activity, and transport contribute to high level of resistance to ampicillin in Lysobacter enzymogenes. Appl Microbiol Biotechnol 2019; 104:1149-1161. [PMID: 31822985 DOI: 10.1007/s00253-019-10266-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/12/2019] [Accepted: 11/22/2019] [Indexed: 11/26/2022]
Abstract
Discovery of multidrug resistance (MDR) in environmental microorganisms provides unique resources for uncovering antibiotic resistomes, which could be vital to predict future emergence of MDR pathogens. Our previous studies indicated that Lysobacter sp. conferred intrinsic resistance to multiple antibiotics at high levels, especially ampicillin, the first broad-spectrum β-lactam antibiotics against both Gram-positive and Gram-negative bacteria. However, the underlying molecular mechanisms for resistance to ampicillin in Lysobacter enzymogenes strain C3 (LeC3) remain unknown. In this study, screening a Tn5 transposon mutant library of LeC3 recovered 12 mutants with decreased ampicillin resistance, and three mutants (i.e., tatC, lebla, and lpp) were selected for further characterization. Our results revealed that genes encoding β-lactamase (lebla) and twin-arginine translocation (tatC) system for β-lactamase transport played a pivotal role in conferring ampicillin resistance in L. enzymogenes. It was also demonstrated that the lpp gene was not only involved in resistance against β-lactams but also conferred resistance to multiple antibiotics in L. enzymogenes. Permeability assay results indicated that decreased MDR in the lpp mutant was in part due to its higher cellular permeability. Furthermore, our results showed that the difference of LeC3 and L. antibioticus strain LaATCC29479 in ampicillin susceptibility was partly due to their differences in cellular permeability, but not due to β-lactamase activities.
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Affiliation(s)
- Menghao Yu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Yu M, Zhao Y. Comparative resistomic analyses of Lysobacter species with high intrinsic multidrug resistance. J Glob Antimicrob Resist 2019; 19:320-327. [DOI: 10.1016/j.jgar.2019.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/24/2019] [Accepted: 05/04/2019] [Indexed: 01/01/2023] Open
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Genome Mining of Marine-Derived Streptomyces sp. SCSIO 40010 Leads to Cytotoxic New Polycyclic Tetramate Macrolactams. Mar Drugs 2019; 17:md17120663. [PMID: 31775228 PMCID: PMC6950151 DOI: 10.3390/md17120663] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/10/2019] [Accepted: 11/16/2019] [Indexed: 01/09/2023] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) biosynthetic gene cluster are widely distributed in different bacterial types, especially in Streptomyces species. The mining of the genomic data of marine-derived Streptomyces sp. SCSIO 40010 reveals the presence of a putative PTM-encoding biosynthetic gene cluster (ptm′ BGC) that features a genetic organization for potentially producing 5/5/6 type of carbocyclic ring-containing PTMs. A fermentation of Streptomyces sp. SCSIO 40010 led to the isolation and characterization of six new PTMs 1–6. Comprehensive spectroscopic analysis assigned their planar structures and relative configurations, and their absolute configurations were deduced by comparing the experimental electronic circular dichroism (ECD) spectra with the reported spectra of the known PTMs. Intriguingly, compounds 1–6 were determined to have a trans-orientation of H-10/H-11 at the first 5-membered ring, being distinct from the cis-orientation in their known PTM congeners. PTMs 1–5 displayed cytotoxicity against several cancer cell lines, with IC50 values that ranged from 2.47 to 17.68 µM.
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Lina F, Ting W, Lanfang W, Jun Y, Qi L, Yating W, Xing W, Guanghai J. Specific detection of Lysobacter antibioticus strains in agricultural soil using PCR and real-time PCR. FEMS Microbiol Lett 2019; 365:5094558. [PMID: 30202922 DOI: 10.1093/femsle/fny219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/07/2018] [Indexed: 11/13/2022] Open
Abstract
Lysobacter antibioticus is an important biocontrol bacteria against phytopathogens in soil, and with the ability to produce nonvolatile antimicrobial metabolites has been extensively characterised. It is important to establish applicable techniques to detect and monitor L. antibioticus directly and accurately in soil samples. We developed and tested 13 primer sets according to phenazine gene (phzA, phzB, phzD, phzF, phzS) and the cyclohexanone monooxygenase gene (phzNO1); a pair of primer phzNO1 F1/phzNO1 R1 based on the cyclohexanone monooxygenase (phzNO1) gene of L. antibioticus strain OH13 was selected and optimized polymerase chain reaction (PCR) amplification conditions for rapid and accurate detection. After screening eight strains of L. antibioticus, two strains of Lysobacter enzymogenes, one strain of Lysobacter capsici, Arthrobacterium, Bacillus, Microbacterium, Burkholderia, Pseudomonas and other bacterial strains isolated from different agricultural soils, the phzNO1 F1/phzNO1 R1 primers amplified a single PCR band of about 229 bp from L. antibioticus. The detection sensitivity with primers phzNO1 F1/phzNO1 R1 was 5.14 × 104 fg/25μL of genomic DNA and 2.254 × 1010 to 2.254 × 1011 colony-forming units/mL for the soil samples. Quantitative PCR assays were to develope as a specific method to monitor the L. antibioticus population in soil as well as guide soil micro-ecological management.
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Affiliation(s)
- Fu Lina
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Wang Ting
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Wei Lanfang
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Yang Jun
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Liu Qi
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Wang Yating
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Wang Xing
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, P. R. China
| | - Ji Guanghai
- Key Laboratory of Agriculture Biodiversity for Plant Disease Management under the Ministry of Education, Yunnan Agricultural University, Kunming 650201, P. R. China
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45
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Pérez-Jaramillo JE, de Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. MICROBIOME 2019; 7:114. [PMID: 31412927 PMCID: PMC6694607 DOI: 10.1186/s40168-019-0727-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/30/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood. RESULTS Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil. CONCLUSIONS Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.
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Affiliation(s)
- Juan E. Pérez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
| | - Camilo A. Ramírez
- Institute of Biology, University of Antioquia, Calle 67 #53-108, Medellín, Colombia
| | - Rodrigo Mendes
- Embrapa Meio Ambiente, Rodovia SP 340 - km 127.5, Jaguariúna, 13820-000 Brazil
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
| | - Víctor J. Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6708 PB The Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE The Netherlands
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46
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Xiao M, Zhou XK, Chen X, Duan YQ, Alkhalifah DHM, Im WT, Hozzein WN, Chen W, Li WJ. Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L. Int J Syst Evol Microbiol 2019; 69:1875-1880. [PMID: 30540245 DOI: 10.1099/ijsem.0.003164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
A Gram-stain-negative, aerobic, rod-shaped bacterium, designated strain C8-1T, was isolated from the rhizosphere soil of Nicotiana tabacum L. collected from Kunming, south-west China. The cells showed oxidase-positive and catalase-positive reactions. Growth was observed at 10-40 °C, at pH 6.0-8.0 and in the presence of up to 1 % (w/v) NaCl, with optimal growth at 30 °C and pH 7.0. The predominant isoprenoid quinone was Q-8. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. The cellular polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, five unidentified phospholipids and two unidentified aminophospholipids. The genomic DNA G+C content was 70.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C8-1T should be assigned to the genus Lysobacter. 16S rRNA gene sequence similarity analysis showed that strain C8-1T was closely related to Lysobacter cavernae YIM C01544T (98.6 %), Lysobacter soli DCY21T (97.6 %), Lysobacter panacisoli CJ29T (97.3 %), Lysobacter firmicutimachus PB-6250T (97.3 %), Lysobacter niastensis GH41-7T (97.3 %) and Lysobacter gummosus KCTC 12132T (97.1 %). DNA-DNA hybridization data indicated that the isolate may represent a novel genomic species belonging to the genus Lysobacter. Polyphasic taxonomic characteristics indicated that strain C8-1T represents a novel species of the genus Lysobacter, for which the name Lysobacter tabacisoli sp. nov. is proposed. The type strain is C8-1T (=KCTC 62034T=CGMCC 1.16271T) .
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Affiliation(s)
- Min Xiao
- 1State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xing-Kui Zhou
- 2China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PR China
- 3State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, PR China
| | - Xing Chen
- 2China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PR China
| | - Yan-Qing Duan
- 2China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PR China
| | - Dalal Hussien M Alkhalifah
- 4Biology Department, Faculty of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia
| | - Wan-Taek Im
- 5Department of Biotechnology, Hankyong National University, Kyonggi-do 456-749, Republic of Korea
| | - Wael N Hozzein
- 6Bioproducts Research Chair (BRC), College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Wei Chen
- 2China Tobacco Yunnan Industrial Co. Ltd, Kunming, 650231, PR China
| | - Wen-Jun Li
- 1State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
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47
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Qian G, Fei S, Galperin MY. Two forms of phosphomannomutase in gammaproteobacteria: The overlooked membrane-bound form of AlgC is required for twitching motility of Lysobacter enzymogenes. Environ Microbiol 2019; 21:3969-3978. [PMID: 30938049 DOI: 10.1111/1462-2920.14615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysobacter enzymogenes, a member of Xanthomonadaceae, is a promising tool to control crop-destroying fungal pathogens. One of its key antifungal virulence factors is the type IV pili that are required for twitching motility. Transposon mutagenesis of L. enzymogenes revealed that the production of type IV pili required the presence of the Le2152 gene, which encodes an AlgC-type phosphomannomutase/phosphoglucomutase (PMM). However, in addition to the cytoplasmic PMM domain, the Le2152 gene product contains a ~200-aa N-terminal periplasmic domain that is anchored in the membrane by two transmembrane segments and belongs to the dCache superfamily of periplasmic sensor domains. Sequence analysis identified similar membrane-anchored PMMs, encoded in conserved coaBC-dut-algC gene clusters, in a variety of gammaproteobacteria, either as the sole PMM gene in the entire genome or in addition to the gene encoding the stand-alone enzymatic domain. Previously overlooked N-terminal periplasmic sensor domains were detected in the well-characterized PMMs of Pseudomonas aeruginosa and Xanthomonas campestris, albeit not in the enzymes from Pseudomonas fluorescens, Pseudomonas putida or Azotobacter vinelandii. It appears that after the initial cloning of the enzymatically active soluble part of P. aeruginosa AlgC in 1991, all subsequent studies utilized N-terminally truncated open reading frames. The N-terminal dCache sensor domain of AlgC is predicted to modulate the PMM activity of the cytoplasmic domain in response to as yet unidentified environmental signal(s). AlgC-like membrane-bound PMMs appear to comprise yet another environmental signalling system that regulates the production of type IV pili and potentially other systems in certain gammaproteobacteria.
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Affiliation(s)
- Guoliang Qian
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Ministry of Education, Nanjing, 210014, China
| | - Shifang Fei
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.,Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Ministry of Education, Nanjing, 210014, China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
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Sgro GG, Oka GU, Souza DP, Cenens W, Bayer-Santos E, Matsuyama BY, Bueno NF, dos Santos TR, Alvarez-Martinez CE, Salinas RK, Farah CS. Bacteria-Killing Type IV Secretion Systems. Front Microbiol 2019; 10:1078. [PMID: 31164878 PMCID: PMC6536674 DOI: 10.3389/fmicb.2019.01078] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteria have been constantly competing for nutrients and space for billions of years. During this time, they have evolved many different molecular mechanisms by which to secrete proteinaceous effectors in order to manipulate and often kill rival bacterial and eukaryotic cells. These processes often employ large multimeric transmembrane nanomachines that have been classified as types I-IX secretion systems. One of the most evolutionarily versatile are the Type IV secretion systems (T4SSs), which have been shown to be able to secrete macromolecules directly into both eukaryotic and prokaryotic cells. Until recently, examples of T4SS-mediated macromolecule transfer from one bacterium to another was restricted to protein-DNA complexes during bacterial conjugation. This view changed when it was shown by our group that many Xanthomonas species carry a T4SS that is specialized to transfer toxic bacterial effectors into rival bacterial cells, resulting in cell death. This review will focus on this special subtype of T4SS by describing its distinguishing features, similar systems in other proteobacterial genomes, and the nature of the effectors secreted by these systems and their cognate inhibitors.
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Affiliation(s)
- Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel U. Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Diorge P. Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - William Cenens
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ethel Bayer-Santos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Y. Matsuyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Natalia F. Bueno
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Cristina E. Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, University of Campinas (UNICAMP), Campinas, Brazil
| | - Roberto K. Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Chuck S. Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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49
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Tang B, Laborda P, Sun C, Xu G, Zhao Y, Liu F. Improving the production of a novel antifungal alteramide B in Lysobacter enzymogenes OH11 by strengthening metabolic flux and precursor supply. BIORESOURCE TECHNOLOGY 2019; 273:196-202. [PMID: 30447620 DOI: 10.1016/j.biortech.2018.10.085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Lysobacter enzymogenes OH11 is currently considered to be a novel biocontrol agent for various plant fungi diseases. At present, only heat-stable antifungal factor (HSAF) has been isolated and identified in culture, although other active compounds also showed antifungal activity. In the present study, a novel active compound, alteramide B (ATB), which exhibits broad-spectrum antagonistic activity against phytopathogenic fungi and oomycetes, was isolated. The genes responsible for ATB biosynthesis were also determined. In addition, a strain producing ATB with minimal HSAF production was successfully generated by redirecting metabolic flux, namely L. enzymogenes OH57. Furthermore, ATB production increased to 893.32 ± 15.57 mg/L through medium optimization and precursor supply strategy, which was 24.36-fold higher than that of 10% tryptic soy broth (36.67 ± 1.63 mg/L). Taken together, this study indicates ATB has great development value as a biopesticide because of its bioactivity and high production.
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Affiliation(s)
- Bao Tang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Pedro Laborda
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Cheng Sun
- School of Medicine, Yangzhou Polytechnic College, Yangzhou 225009, China
| | - Gaoge Xu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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50
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Zhang XJ, Yao Q, Wang YH, Yang SZ, Feng GD, Zhu HH. Lysobacter silvisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:93-98. [DOI: 10.1099/ijsem.0.003105] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Xian-Jiao Zhang
- 1State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Qing Yao
- 2College of Horticulture, South China Agricultural University, Guangzhou 510642, PR China
| | - Yong-Hong Wang
- 1State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Song-Zhen Yang
- 1State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Guang-Da Feng
- 1State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
| | - Hong-Hui Zhu
- 1State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangzhou 510070, PR China
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