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Xiao Y, Ma J, Chen R, Xiang S, Yang B, Chen L, Fang J, Liu S. Two microbes assisting Miscanthus floridulus in remediating multi-metal(loid)s-contaminated soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:28922-28938. [PMID: 38565816 DOI: 10.1007/s11356-024-33032-3] [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: 09/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Miscanthus has good tolerance to multi-metal(loid)s and has received increasing attention in remediated studies of metal(loid)s-contaminated soil. In this study, we conducted phytoextraction techniques to investigate the synergic effects of remediation of multi-metal(loid)s-contaminated soil by Miscanthus floridulus (Lab.) and two plant growth-promoting bacteria (PGPB), TS8 and MR2, affiliated to Enterobacteriaceae. The results exhibited a decrease of arsenic (15.27-21.50%), cadmium (8.64-15.52%), plumbum (5.92-12.76%), and zinc (12.84-24.20%) except for copper contents in the soil in bacterial inoculation groups, indicating that MR2 and TS8 could enhance the remediation of metal(loid)s. Moreover, increased fresh/dry weight and height indicated that inoculated bacteria could promote Miscanthus growth. Although the activities of antioxidant enzymes and the content of chlorophyll in the overground tissues showed no significant increase or even decrease, the activities of antioxidant enzymes in the underground tissues and soil were elevated by 48.95-354.17%, available P by 19.07-23.02%, and available K by 15.34-17.79% (p < 0.05). Bacterial inoculants could also decrease the soil pH. High-throughput sequencing analysis showed that the bacterial inoculant affected the rhizosphere bacterial community and reduced community diversity, but the relative abundance of some PGPB was found to increase. Phylogenetic molecular ecological networks indicated that bacterial inoculants reduced interactions between rhizosphere bacteria and thereby led to a simpler network structure but increased the proportion of positive-correlation links and enhanced the metabiosis and symbiosis of those bacteria. Spearman's test showed that OTUs affiliated with Enterobacteriaceae and soil nutrients were critical for metal(loid) remediation and Miscanthus growth. The results of this study provide a basis for the synergic remediation of multi-metal(loid)s-contaminated soils by Miscanthus and PGPB and provide a reference for the subsequent regulation of Miscanthus remediation efficiency by the other PGPB or critical bacteria.
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Affiliation(s)
- Yunhua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jingjing Ma
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Rui Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Sha Xiang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Bo Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Liang Chen
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Shuming Liu
- School of Resources and Environment, Yili Normal University, Yining, 835000, China.
- Key Laboratory of Pollutant Chemistry and Environmental Treatment, Yili Normal University, Yining, 835000, China.
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Turck D, Bohn T, Castenmiller J, De Henauw S, Hirsch‐Ernst KI, Maciuk A, Mangelsdorf I, McArdle HJ, Naska A, Pentieva K, Siani A, Thies F, Tsabouri S, Vinceti M, Aguilera‐Gómez M, Cubadda F, Frenzel T, Heinonen M, Marchelli R, Neuhäuser‐Berthold M, Poulsen M, Prieto Maradona M, Schlatter JR, Siskos A, van Loveren H, Ferreira da Costa L, Albert O, Knutsen HK. Safety of isomaltulose syrup (dried) as a novel food pursuant to Regulation (EU) 2015/2283. EFSA J 2024; 22:e8491. [PMID: 38260771 PMCID: PMC10801438 DOI: 10.2903/j.efsa.2024.8491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Following a request from the European Commission, the EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA) was asked to deliver an opinion on isomaltulose syrup (dried) as a novel food (NF) pursuant to Regulation (EU) 2015/2283. The NF consists of a mixture of mono- and disaccharides in powder form, mainly composed of isomaltulose (≥ 75%) and trehalulose (< 13%). The applicant intends to use the NF as a replacement for sucrose already on the market. The information provided on the manufacturing process, composition and specifications of the NF is sufficient and does not raise safety concerns. No absorption, distribution, metabolism and excretion (ADME) or toxicological data were provided for the NF. Instead, the safety of the NF was assessed based on literature data available on isomaltulose and mixtures of isomaltulose and trehalulose. In addition, considering the nature, compositional characterisation and production process of the NF, the Panel considered that such data were sufficient to conclude that the NF is as safe as sucrose.
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Kim HJ, Kim YC. Complete Genome Resource of Serratia plymuthica C-1 that Causes Root Rot Disease in Korean Ginseng. PLANT DISEASE 2021; 105:202-204. [PMID: 32697179 DOI: 10.1094/pdis-05-20-1154-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Serratia plymuthica C-1, a biocontrol agent, was isolated from soil collected from a mountain forest in Korea. Previous studies have shown that certain strains of S. plymuthica cause root rot disease in ginseng. To the best of our knowledge, this is the first report of the sequence of the circular chromosome of S. plymuthica C-1, which plays a dual role by causing root rot in ginseng and exhibiting biocontrol activity. The findings of this study will assist in analyzing the genes associated with the pathogenicity and biocontrol properties of S. plymuthica.
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Affiliation(s)
- Hyo Jeong Kim
- Environment-Friendly Agricultural Research Institute, Jeollanamdo Agricultural Research and Extension Services, Naju 58213, Korea
| | - Young Cheol Kim
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
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Genome Sequences of Serratia Strains Revealed Common Genes in Both Serratomolides Gene Clusters. BIOLOGY 2020; 9:biology9120482. [PMID: 33419369 PMCID: PMC7767323 DOI: 10.3390/biology9120482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/04/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023]
Abstract
Simple Summary Biosurfactants are amphiphilic molecules produced by microorganisms with a hydrophilic and a hydrophobic group, able to reduce surface tension. These molecules are largely used in the environmental, food, pharmaceutical, medical, and cleaning industries, among others. Serratia strains are ubiquitous microorganisms with the ability to produce biosurfactants, such as serrawettins. These extracellular lipopeptides are described as biocides against many bacteria and fungi. This work used comparative genomics to determine the distribution and organization of the serrawettins W1 and W2 biosynthetic gene clusters in all the 84 publicly available genomes of the Serratia genus. Here, the serrawettin W1 gene clusters’ organization is reported for the first time. The serrawettin W1 biosynthetic gene swrW and serrawettin W2 biosynthetic gene swrA were present in 17 and 11 Serratia genomes, respectively. The same genes in the biosynthetic clusters frame the swrW and swrA biosynthetic genes. This work identified four genes common to all serrawettin gene clusters, highlighting their key potential in the serrawettins biosynthetic process. Abstract Serratia strains are ubiquitous microorganisms with the ability to produce serratomolides, such as serrawettins. These extracellular lipopeptides are described as biocides against many bacteria and fungi and may have a nematicidal activity against phytopathogenic nematodes. Serrawettins W1 and W2 from different strains have different structures that might be correlated with distinct genomic organizations. This work used comparative genomics to determine the distribution and the organization of the serrawettins biosynthetic gene clusters in all the 84 publicly available genomes of the Serratia genus. The serrawettin W1 and W2 gene clusters’ organization was established using antiSMASH software and compared with single and short data previously described for YD25TSerratia. Here, the serrawettin W1 gene clusters’ organization is reported for the first time. The serrawettin W1 biosynthetic gene swrW was present in 17 Serratia genomes. Eighty different coding sequence (CDS) were assigned to the W1 gene cluster, 13 being common to all clusters. The serrawettin W2 swrA gene was present in 11 Serratia genomes. The W2 gene clusters included 68 CDS with 24 present in all the clusters. The genomic analysis showed the swrA gene constitutes five modules, four with three domains and one with four domains, while the swrW gene constitutes one module with four domains. This work identified four genes common to all serrawettin gene clusters, highlighting their essential potential in the serrawettins biosynthetic process.
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Muñoz PA, Arismendi MJ, Cárdenas SF, Cifuentes Bachmann DE, Venegas FA, Sepúlveda-Chavera GF. Diversity of culturable bacteria isolated from ancestral crops of Arica and Parinacota Region, Atacama Desert. Antonie van Leeuwenhoek 2020; 113:2123-2137. [PMID: 33136285 DOI: 10.1007/s10482-020-01482-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/13/2020] [Indexed: 11/30/2022]
Abstract
Arica and Parinacota Region is located at the extreme north of the Atacama Desert, where the high levels of salts and boron, lack of rain, high UV radiation, among other conditions, make this zone an extreme environment. Despite these characteristics, in the transversal valleys, different types of crops are cultivated in this region, which are associated to beneficial microorganisms with specific traits that allow plants surviving and developing under extreme conditions. However, there is incomplete information related to these microorganisms. In this work, bacteria associated with ancestral crops were isolated from oregano, alfalfa, maize, potato, and grapevine samples from Belén, Codpa, Molinos, Poconchile and Socoroma localities, representing the first report of these microorganisms in those sites. Bacteria were identified, being γ-Proteobacteria, the most frequent class (~ 74.4%), with members of Pseudomonas genus the most common isolated genus. All bacteria were functionally characterized for plant growth-promoting activities, including siderophores and auxins production, phosphate solubilization, and nitrogen fixation, revealing an extraordinary potential from these microorganisms for agricultural applications under arid and semiarid conditions.
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Affiliation(s)
- Patricio A Muñoz
- Laboratorio de Patología Vegetal Y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Chile. .,UC Davis Chile Life Sciences Innovation Center, Santiago, Chile.
| | - Mabel J Arismendi
- Laboratorio de Patología Vegetal Y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Chile.,UC Davis Chile Life Sciences Innovation Center, Santiago, Chile
| | - Steffany F Cárdenas
- Laboratorio de Patología Vegetal Y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Chile
| | | | | | - Germán F Sepúlveda-Chavera
- Laboratorio de Patología Vegetal Y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Arica, Chile.
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Douriet-Gámez NR, Maldonado-Mendoza IE, Ibarra-Laclette E, Blom J, Calderón-Vázquez CL. Genomic Analysis of Bacillus sp. Strain B25, a Biocontrol Agent of Maize Pathogen Fusarium verticillioides. Curr Microbiol 2017; 75:247-255. [DOI: 10.1007/s00284-017-1372-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/10/2017] [Indexed: 11/24/2022]
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Quorum sensing activity of the plant growth-promoting rhizobacterium Serratia glossinae GS2 isolated from the sesame (Sesamum indicum L.) rhizosphere. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1291-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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8
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Proença DN, Grass G, Morais PV. Understanding pine wilt disease: roles of the pine endophytic bacteria and of the bacteria carried by the disease-causing pinewood nematode. Microbiologyopen 2017; 6:e00415. [PMID: 27785885 PMCID: PMC5387314 DOI: 10.1002/mbo3.415] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 12/03/2022] Open
Abstract
Pine wilt disease (PWD) is one of the most destructive diseases in trees of the genus Pinus and is responsible for environmental and economic losses around the world. The only known causal agent of the disease is the pinewood nematode (PWN) Bursaphelenchus xylophilus. Despite that, bacteria belonging to several different genera have been found associated with PWN and their roles in the development of PWD have been suggested. Molecular methodologies and the new era of genomics have revealed different perspectives to the problem, recognizing the manifold interactions between different organisms involved in the disease. Here, we reviewed the possible roles of nematode-carried bacteria in PWD, what could be the definition of this group of microorganisms and questioned their origin as possible endophytes, discussing their relation within the endophytic community of pine trees. The diversity of the nematode-carried bacteria and the diversity of pine tree endophytes, reported until now, is revised in detail in this review. What could signify a synergetic effect with PWN harming the plant, or what could equip bacteria with functions to control the presence of nematodes inside the tree, is outlined as two possible roles of the microbial community in the etiology of this disease. An emphasis is put on the potential revealed by the genomic data of isolated organisms in their potential activities as effective tools in PWD management.
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Affiliation(s)
- Diogo N. Proença
- CEMUCUniversity of CoimbraCoimbraPortugal
- Department of Biology and CESAMUniversity of AveiroAveiroPortugal
| | - Gregor Grass
- Bundeswehr Institute of MicrobiologyMunichGermany
| | - Paula V. Morais
- CEMUCUniversity of CoimbraCoimbraPortugal
- Department of Life SciencesUniversity of CoimbraCoimbraPortugal
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Khan AR, Park GS, Asaf S, Hong SJ, Jung BK, Shin JH. Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants. PLoS One 2017; 12:e0171534. [PMID: 28187139 PMCID: PMC5302809 DOI: 10.1371/journal.pone.0171534] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 01/22/2017] [Indexed: 11/28/2022] Open
Abstract
Serratia marcescens RSC-14 is a Gram-negative bacterium that was previously isolated from the surface-sterilized roots of the Cd-hyperaccumulator Solanum nigrum. The strain stimulates plant growth and alleviates Cd stress in host plants. To investigate the genetic basis for these traits, the complete genome of RSC-14 was obtained by single-molecule real-time sequencing. The genome of S. marcescens RSC-14 comprised a 5.12-Mbp-long circular chromosome containing 4,593 predicted protein-coding genes, 22 rRNA genes, 88 tRNA genes, and 41 pseudogenes. It contained genes with potential functions in plant growth promotion, including genes involved in indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis, and phosphate solubilization. Moreover, annotation using NCBI and Rapid Annotation using Subsystem Technology identified several genes that encode antioxidant enzymes as well as genes involved in antioxidant production, supporting the observed resistance towards heavy metals, such as Cd. The presence of IAA pathway-related genes and oxidative stress-responsive enzyme genes may explain the plant growth-promoting potential and Cd tolerance, respectively. This is the first report of a complete genome sequence of Cd-tolerant S. marcescens and its plant growth promotion pathway. The whole-genome analysis of this strain clarified the genetic basis underlying its phenotypic and biochemical characteristics, underpinning the beneficial interactions between RSC-14 and plants.
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Affiliation(s)
- Abdur Rahim Khan
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Gun-Seok Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sajjad Asaf
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Byung Kwon Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
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Tian JH, Pourcher AM, Klingelschmitt F, Le Roux S, Peu P. Class P dye-decolorizing peroxidase gene: Degenerated primers design and phylogenetic analysis. J Microbiol Methods 2016; 130:148-153. [PMID: 27686379 DOI: 10.1016/j.mimet.2016.09.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) were classified as a new family of heme peroxidase in 2007. Produced by various bacteria, they are the first bacterial enzymes known able to degrade lignin and dyes, for which their application in waste treatment and pretreatment of lignocellulosic biomass could be envisaged. In this work, a PCR primer pair was created and tested that enabled the detection and quantification of a wide range of bacterial genes of P class DyP in complex matrices. In addition, a phylogenetic tree was built with all available sequences of DyP genes available, offering a first overview of their presence in the bacteria kingdom.
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Affiliation(s)
- J-H Tian
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Européenne de Bretagne, France
| | - A-M Pourcher
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Européenne de Bretagne, France.
| | - F Klingelschmitt
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Européenne de Bretagne, France
| | - S Le Roux
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Européenne de Bretagne, France
| | - P Peu
- IRSTEA, UR GERE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes, France; Université Européenne de Bretagne, France
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11
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Genome Sequence of Serratia plymuthica A153, a Model Rhizobacterium for the Investigation of the Synthesis and Regulation of Haterumalides, Zeamine, and Andrimid. GENOME ANNOUNCEMENTS 2016; 4:4/3/e00373-16. [PMID: 27198016 PMCID: PMC4888998 DOI: 10.1128/genomea.00373-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The rhizobacterium Serratia plymuthica A153 is a Gram-negative bacterium belonging to the family Enterobacteriaceae. Here, we present the genome sequence of this strain, which produces multiple bioactive secondary metabolites, including the halogenated macrolide oocydin A, the polyamino antibiotic zeamine, and the bacterial acetyl-CoA carboxylase inhibitor andrimid.
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12
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Gkarmiri K, Finlay RD, Alström S, Thomas E, Cubeta MA, Högberg N. Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica. BMC Genomics 2015; 16:630. [PMID: 26296338 PMCID: PMC4546130 DOI: 10.1186/s12864-015-1758-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/07/2015] [Indexed: 11/23/2022] Open
Abstract
Background Improved understanding of bacterial-fungal interactions in the rhizosphere should assist in the successful application of bacteria as biological control agents against fungal pathogens of plants, providing alternatives to chemicals in sustainable agriculture. Rhizoctonia solani is an important soil-associated fungal pathogen and its chemical treatment is not feasible or economic. The genomes of the plant-associated bacteria Serratia proteamaculans S4 and Serratia plymuthica AS13 have been sequenced, revealing genetic traits that may explain their diverse plant growth promoting activities and antagonistic interactions with R. solani. To understand the functional response of this pathogen to different bacteria and to elucidate whether the molecular mechanisms that the fungus exploits involve general stress or more specific responses, we performed a global transcriptome profiling of R. solani Rhs1AP anastomosis group 3 (AG-3) during interaction with the S4 and AS13 species of Serratia using RNA-seq. Results Approximately 104,504 million clean 75-100 bp paired-end reads were obtained from three libraries, each in triplicate (AG3-Control, AG3-S4 and AG3-AS13). Transcriptome analysis revealed that approximately 10 % of the fungal transcriptome was differentially expressed during challenge with Serratia. The numbers of S4- and AS13-specific differentially expressed genes (DEG) were 866 and 292 respectively, while there were 1035 common DEGs in the two treatment groups. Four hundred and sixty and 242 genes respectively had values of log2 fold-change > 3 and for further analyses this cut-off value was used. Functional classification of DEGs based on Gene Ontology enrichment analysis and on KEGG pathway annotations revealed a general shift in fungal gene expression in which genes related to xenobiotic degradation, toxin and antioxidant production, energy, carbohydrate and lipid metabolism and hyphal rearrangements were subjected to transcriptional regulation. Conclusions This RNA-seq profiling generated a novel dataset describing the functional response of the phytopathogen R. solani AG3 to the plant-associated Serratia bacteria S4 and AS13. Most genes were regulated in the same way in the presence of both bacterial isolates, but there were also some strain-specific responses. The findings in this study will be beneficial for further research on biological control and in depth exploration of bacterial-fungal interactions in the rhizosphere. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1758-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konstantia Gkarmiri
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Roger D Finlay
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Sadhna Alström
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
| | - Elizabeth Thomas
- Department of Plant Pathology, Center for Integrated Fungal Research, Fungal Disease Ecology, Genetics and Population Biology, North Carolina State University, 851 Main Campus Drive, Suite 233, 225 Partners III, Raleigh, NC, 27606, USA.
| | - Marc A Cubeta
- Department of Plant Pathology, Center for Integrated Fungal Research, Fungal Disease Ecology, Genetics and Population Biology, North Carolina State University, 851 Main Campus Drive, Suite 233, 225 Partners III, Raleigh, NC, 27606, USA.
| | - Nils Högberg
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7026, SE-75007, Uppsala, Sweden.
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13
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Li P, Kwok AHY, Jiang J, Ran T, Xu D, Wang W, Leung FC. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential. PLoS One 2015; 10:e0123061. [PMID: 25856195 PMCID: PMC4391916 DOI: 10.1371/journal.pone.0123061] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/16/2015] [Indexed: 11/19/2022] Open
Abstract
S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.
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Affiliation(s)
- Pengpeng Li
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
| | - Amy H. Y. Kwok
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
| | - Jingwei Jiang
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
- School of Biological Sciences, University of Hong Kong, Hong Kong Special Administration Region, China
| | - Tingting Ran
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dongqing Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Weiwu Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Frederick C. Leung
- Bioinformatics Center, Nanjing Agricultural University, Nanjing, China
- School of Biological Sciences, University of Hong Kong, Hong Kong Special Administration Region, China
- * E-mail:
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Hellberg JEEU, Matilla MA, Salmond GPC. The broad-spectrum antibiotic, zeamine, kills the nematode worm Caenorhabditis elegans. Front Microbiol 2015; 6:137. [PMID: 25767467 PMCID: PMC4341552 DOI: 10.3389/fmicb.2015.00137] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/05/2015] [Indexed: 12/02/2022] Open
Abstract
Soil bacteria can be prolific producers of secondary metabolites and other biologically active compounds of economic and clinical importance. These natural products are often synthesized by large multi-enzyme complexes such as polyketide synthases (PKSs) or non-ribosomal peptide synthases (NRPSs). The plant-associated Gram-negative bacterium, Serratia plymuthica A153, produces several secondary metabolites and is capable of killing the nematode worm Caenorhabditis elegans; a commonly used model for the study of bacterial virulence. In this study, we show that disruption of the hybrid PKS/NRPS zeamine (zmn) gene cluster results in the attenuation of “fast-killing” of C. elegans, indicating that zeamine has nematicidal activity. C. elegans also exhibits age-dependent susceptibility to zeamine, with younger worms being most sensitive to the bioactive molecule. The zmn gene cluster is widely distributed within Serratia and phytopathogenic Dickeya species and investigation of strains harboring the zmn gene cluster showed that several of them are highly virulent in C. elegans. Zeamine was described previously as a phytotoxin and broad-spectrum antibacterial compound. In addition to its nematicidal properties, we show here that zeamine can also kill Saccharomyces cerevisiae and Schizosaccharomyces pombe. The expression of the zmn gene cluster and regulation of zeamine production were also investigated. Transcription of the cluster was growth phase-dependent, and was modulated by the post-transcriptional RNA chaperone, Hfq. The results of this study show that zeamine is a highly toxic molecule with little, or no, apparent host specificity in very diverse biological systems. In its current form, zeamine(s) may be useful as a lead compound suitable for chemical modification and structure-activity assays. However, because of widespread non-selective toxicity in multiple bioassays, unmodified zeamine(s) is unlikely to be suitable as a therapeutic antibiotic.
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Affiliation(s)
| | - Miguel A Matilla
- Department of Biochemistry, University of Cambridge Cambridge, UK ; Department of Environmental Protection, Estación Experimental del Zaidín - Consejo Superior de Investigaciones Científicas Granada, Spain
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Neupane S, Finlay RD, Alström S, Elfstrand M, Högberg N. Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:123-127. [PMID: 25139310 DOI: 10.1111/1758-2229.12203] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 08/14/2014] [Indexed: 06/03/2023]
Abstract
Rhizobacteria with biocontrol ability exploit a range of mechanisms to compete successfully with other microorganisms and to ensure their growth and survival in the rhizosphere, ultimately promoting plant growth. The rhizobacterium Serratia plymuthica AS13 is able to promote oilseed rape growth and improve seedling survival in the presence of the fungal pathogen, Rhizoctonia solani AG 2-1; however, our understanding of the mechanisms underlying the antagonism of Serratia is limited. To elucidate possible mechanisms, genome-wide gene expression profiling of S. plymuthica AS13 was carried out in the presence or absence of R. solani. We used RNA sequencing methodology to obtain a comprehensive overview of Serratia gene expression in response to R. solani. The differential gene expression profiles of S. plymuthica AS13 revealed significantly increased expression of genes related to the biosynthesis of the antibiotic pyrrolnitrin (prnABCD), protease production and transporters. The results presented here provide evidence that antibiosis is a major functional mechanism underlying the antagonistic behaviour of S. plymuthica AS13.
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Affiliation(s)
- Saraswoti Neupane
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, SE-750 07, Sweden
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