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Battu L, Ulaganathan K. Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls. Funct Integr Genomics 2019; 20:237-243. [PMID: 31482368 DOI: 10.1007/s10142-019-00713-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/11/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022]
Abstract
Leifsonia sp. ku-ls is an endophytic bacterial strain colonizing in high numbers the stem and leaf of the high-yielding and widely grown indica rice cultivar RP Bio-226. Whole genome sequencing of this strain using Illumina Hiseq-2500 system resulted in generation of 10,103,994 paired-end reads of 150 nucleotides length. De novo assembly of the reads with A5MySeq resulted in 51 scaffolds. Kmer analysis with KAT estimated the genome size as 3.83 Mbp with 70% GC content. Annotation of the genome resulted in identification of 3930 protein-coding genes, 45 tRNA genes, and 3 rRNA genes. Detailed analysis of the genes predicted resulted in identification of host beneficial genes which include genes associated with hormone production, nitrogen metabolism, and stress response. There is an elaborate defense against oxidative stress present in this bacterium which also can mitigate plant oxidative stress resulting from disease/abiotic stress. Comparison of this endophytic bacterial genome with non-endophytic Leifsonia sp. showed presence of additional genes, increase in copy number of some of the genes and regulators. Many genes with eukaryotic-like domains have also been identified in this bacterium.
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Affiliation(s)
- Latha Battu
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, Telangana, 500007, India
| | - Kandasamy Ulaganathan
- Centre for Plant Molecular Biology, Osmania University, Hyderabad, Telangana, 500007, India.
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Luo D, Langendries S, Mendez SG, De Ryck J, Liu D, Beirinckx S, Willems A, Russinova E, Debode J, Goormachtig S. Plant Growth Promotion Driven by a Novel Caulobacter Strain. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1162-1174. [PMID: 30933667 DOI: 10.1094/mpmi-12-18-0347-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Soil microbial communities hold great potential for sustainable and ecologically compatible agriculture. Although numerous plant-beneficial bacterial strains from a wide range of taxonomic groups have been reported, very little evidence is available on the plant-beneficial role of bacteria from the genus Caulobacter. Here, the mode of action of a Caulobacter strain, designated RHG1, which had originally been identified through a microbial screen for plant growth-promoting (PGP) bacteria in maize (Zea mays), is investigated in Arabidopsis thaliana. RHG1 colonized both roots and shoots of Arabidopsis, promoted lateral root formation in the root, and increased leaf number and leaf size in the shoot. The genome of RHG1 was sequenced and was utilized to look for PGP factors. Our data revealed that the bacterial production of nitric oxide, auxins, cytokinins, or 1-aminocyclopropane-1-carboxylate deaminase as PGP factors could be excluded. However, the analysis of brassinosteroid mutants suggests that an unknown PGP mechanism is involved that impinges directly or indirectly on the pathway of this growth hormone.
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Affiliation(s)
- Dexian Luo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sarah Langendries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sonia Garcia Mendez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Joren De Ryck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Derui Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Stien Beirinckx
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Anne Willems
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jane Debode
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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Kearl J, McNary C, Lowman JS, Mei C, Aanderud ZT, Smith ST, West J, Colton E, Hamson M, Nielsen BL. Salt-Tolerant Halophyte Rhizosphere Bacteria Stimulate Growth of Alfalfa in Salty Soil. Front Microbiol 2019; 10:1849. [PMID: 31474952 PMCID: PMC6702273 DOI: 10.3389/fmicb.2019.01849] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 07/26/2019] [Indexed: 11/16/2022] Open
Abstract
Halophytes are plants that are adapted to grow in saline soils, and have been widely studied for their physiological and molecular characteristics, but little is known about their associated microbiomes. Bacteria were isolated from the rhizosphere and as root endophytes of Salicornia rubra, Sarcocornia utahensis, and Allenrolfea occidentalis, three native Utah halophytes. A total of 41 independent isolates were identified by 16S rRNA gene sequencing analysis. Isolates were tested for maximum salt tolerance, and some were able to grow in the presence of up to 4 M NaCl. Pigmentation, Gram stain characteristics, optimal temperature for growth, and biofilm formation of each isolate aided in species identification. Some variation in the bacterial population was observed in samples collected at different times of the year, while most of the genera were present regardless of the sampling time. Halomonas, Bacillus, and Kushneria species were consistently isolated both from the soil and as endophytes from roots of all three plant species at all collection times. Non-culturable bacterial species were analyzed by Illumina DNA sequencing. The most commonly identified bacteria were from several phyla commonly found in soil or extreme environments: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Gamma- and Delta-Proteobacteria. Isolates were tested for the ability to stimulate growth of alfalfa under saline conditions. This screening led to the identification of one Halomonas and one Bacillus isolate that, when used to inoculate young alfalfa seedlings, stimulate plant growth in the presence of 1% NaCl, a level that significantly inhibits growth of uninoculated plants. The same bacteria used in the inoculation were recovered from surface sterilized alfalfa roots, indicating the ability of the inoculum to become established as an endophyte. The results with these isolates have exciting promise for enhancing the growth of inoculated alfalfa in salty soil.
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Affiliation(s)
- Jennifer Kearl
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Caitlyn McNary
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - J. Scott Lowman
- The Plant Endophyte Research Center, The Institute for Advanced Learning and Research, Danville, VA, United States
| | - Chuansheng Mei
- The Plant Endophyte Research Center, The Institute for Advanced Learning and Research, Danville, VA, United States
| | - Zachary T. Aanderud
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, United States
| | - Steven T. Smith
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Jason West
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Emily Colton
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Michelle Hamson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
| | - Brent L. Nielsen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, United States
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Sinnesael A, Leroux O, Janssens SB, Smets E, Panis B, Verstraete B. Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant. PLoS One 2019; 14:e0219863. [PMID: 31310638 PMCID: PMC6634412 DOI: 10.1371/journal.pone.0219863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND & AIMS The bacterial leaf nodule symbiosis is an interaction where bacteria are housed in specialised structures in the leaves of their plant host. In the Rubiaceae plant family, host plants interact with Burkholderia bacteria. This interaction might play a role in the host plant defence system. It is unique due to its high specificity; the vertical transmission of the endophyte to the next generation of the host plant; and its supposedly obligatory character. Although previous attempts have been made to investigate this obligatory character by developing Burkholderia-free plants, none have succeeded and nodulating plants were still produced. In order to investigate the obligatory character of this endosymbiosis, our aims were to develop Burkholderia-free Psychotria umbellata plants and to investigate the effect of the absence of the endophytes on the host in a controlled environment. METHODS The Burkholderia-free plants were obtained via embryo culture, a plant cultivation technique. In order to analyse the endophyte-free status, we screened the plants morphologically, microscopically and molecularly over a period of three years. To characterise the phenotype and growth of the in vitro aposymbiotic plants, we compared the growth of the Burkholderia-free plants to the nodulating plants under the same in vitro conditions. KEY RESULTS All the developed plants were Burkholderia-free and survived in a sterile in vitro environment. The growth analysis showed that plants without endophytes had a slower development. CONCLUSIONS Embryo culture is a cultivation technique with a high success rate for the development of Burkholderia-free plants of P. umbellata. The increased growth rate in vitro when the specific endophyte is present cannot be explained by possible benefits put forward in previous studies. This might indicate that the benefits of the endosymbiosis are not yet completely understood.
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Affiliation(s)
- Arne Sinnesael
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | | | - Steven B. Janssens
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Bart Panis
- Bioversity International, Leuven, Belgium
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Passera A, Compant S, Casati P, Maturo MG, Battelli G, Quaglino F, Antonielli L, Salerno D, Brasca M, Toffolatti SL, Mantegazza F, Delledonne M, Mitter B. Not Just a Pathogen? Description of a Plant-Beneficial Pseudomonas syringae Strain. Front Microbiol 2019; 10:1409. [PMID: 31293547 PMCID: PMC6598456 DOI: 10.3389/fmicb.2019.01409] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
Plants develop in a microbe-rich environment and must interact with a plethora of microorganisms, both pathogenic and beneficial. Indeed, such is the case of Pseudomonas, and its model organisms P. fluorescens and P. syringae, a bacterial genus that has received particular attention because of its beneficial effect on plants and its pathogenic strains. The present study aims to compare plant-beneficial and pathogenic strains belonging to the P. syringae species to get new insights into the distinction between the two types of plant–microbe interactions. In assays carried out under greenhouse conditions, P. syringae pv. syringae strain 260-02 was shown to promote plant-growth and to exert biocontrol of P. syringae pv. tomato strain DC3000, against the Botrytis cinerea fungus and the Cymbidium Ringspot Virus. This P. syringae strain also had a distinct volatile emission profile, as well as a different plant-colonization pattern, visualized by confocal microscopy and gfp labeled strains, compared to strain DC3000. Despite the different behavior, the P. syringae strain 260-02 showed great similarity to pathogenic strains at a genomic level. However, genome analyses highlighted a few differences that form the basis for the following hypotheses regarding strain 260-02. P. syringae strain 260-02: (i) possesses non-functional virulence genes, like the mangotoxin-producing operon Mbo; (ii) has different regulation pathways, suggested by the difference in the autoinducer system and the lack of a virulence activator gene; (iii) has genes encoding DNA methylases different from those found in other P. syringae strains, suggested by the presence of horizontal-gene-transfer-obtained methylases that could affect gene expression.
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Affiliation(s)
- Alessandro Passera
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Stéphane Compant
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Paola Casati
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Maria Giovanna Maturo
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Giovanna Battelli
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Fabio Quaglino
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Livio Antonielli
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Domenico Salerno
- Department Medicina e Chirurgia, Università degli Studi di Milano-Bicocca, Vedano al Lambro, Italy
| | - Milena Brasca
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Silvia Laura Toffolatti
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Francesco Mantegazza
- Department Medicina e Chirurgia, Università degli Studi di Milano-Bicocca, Vedano al Lambro, Italy
| | - Massimo Delledonne
- Functional Genomics Laboratory, Department of Biotechnology, University of Verona, Verona, Italy
| | - Birgit Mitter
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
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Biofilm-Constructing Variants of Paraburkholderia phytofirmans PsJN Outcompete the Wild-Type Form in Free-Living and Static Conditions but Not In Planta. Appl Environ Microbiol 2019; 85:AEM.02670-18. [PMID: 30902863 DOI: 10.1128/aem.02670-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/09/2019] [Indexed: 11/20/2022] Open
Abstract
Members of the genus Burkholderia colonize diverse ecological niches. Among the plant-associated strains, Paraburkholderia phytofirmans PsJN is an endophyte with a broad host range. In a spatially structured environment (unshaken broth cultures), biofilm-constructing specialists of P. phytofirmans PsJN colonizing the air-liquid interface arose at high frequency. In addition to forming a robust biofilm in vitro and in planta on Arabidopsis roots, those mucoid phenotypic variants display a reduced swimming ability and modulate the expression of several microbe-associated molecular patterns (MAMPs), including exopolysaccharides (EPS), flagellin, and GroEL. Interestingly, the variants induce low PR1 and PDF1.2 expression compared to that of the parental strain, suggesting a possible evasion of plant host immunity. We further demonstrated that switching from the planktonic to the sessile form did not involve quorum-sensing genes but arose from spontaneous mutations in two genes belonging to an iron-sulfur cluster: hscA (encoding a cochaperone protein) and iscS (encoding a cysteine desulfurase). A mutational approach validated the implication of these two genes in the appearance of variants. We showed for the first time that in a heterogeneous environment, P. phytofirmans strain PsJN is able to rapidly diversify and coexpress a variant that outcompete the wild-type form in free-living and static conditions but not in planta IMPORTANCE Paraburkholderia phytofirmans strain PsJN is a well-studied plant-associated bacterium known to induce resistance against biotic and abiotic stresses. In this work, we described the spontaneous appearance of mucoid variants in PsJN from static cultures. We showed that the conversion from the wild-type (WT) form to variants (V) correlates with an overproduction of EPS, an enhanced ability to form biofilm in vitro and in planta, and a reduced swimming motility. Our results revealed also that these phenotypes are in part associated with spontaneous mutations in an iron-sulfur cluster. Overall, the data provided here allow a better understanding of the adaptive mechanisms likely developed by P. phytofirmans PsJN in a heterogeneous environment.
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An Osmoregulatory Mechanism Operating through OmpR and LrhA Controls the Motile-Sessile Switch in the Plant Growth-Promoting Bacterium Pantoea alhagi. Appl Environ Microbiol 2019; 85:AEM.00077-19. [PMID: 30902852 DOI: 10.1128/aem.00077-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/14/2019] [Indexed: 11/20/2022] Open
Abstract
Adaptation to osmotic stress is crucial for bacterial growth and survival in changing environments. Although a large number of osmotic stress response genes have been identified in various bacterial species, how osmotic changes affect bacterial motility, biofilm formation, and colonization of host niches remains largely unknown. In this study, we report that the LrhA regulator is an osmoregulated transcription factor that directly binds to the promoters of the flhDC, eps, and opgGH operons and differentially regulates their expression, thus inhibiting motility and promoting exopolysaccharide (EPS) production, synthesis of osmoregulated periplasmic glucans (OPGs), biofilm formation, and root colonization of the plant growth-promoting bacterium Pantoea alhagi LTYR-11Z. Further, we observed that the LrhA-regulated OPGs control RcsCD-RcsB activation in a concentration-dependent manner, and a high concentration of OPGs induced by increased medium osmolarity is maintained to achieve the high level of activation of the Rcs phosphorelay, which results in enhanced EPS synthesis and decreased motility in P. alhagi Moreover, we showed that the osmosensing regulator OmpR directly binds to the promoter of lrhA and promotes its expression, while lrhA expression is feedback inhibited by the activated Rcs phosphorelay system. Overall, our data support a model whereby P. alhagi senses environmental osmolarity changes through the EnvZ-OmpR two-component system and LrhA to regulate the synthesis of OPGs, EPS production, and flagellum-dependent motility, thereby employing a hierarchical signaling cascade to control the transition between a motile lifestyle and a biofilm lifestyle.IMPORTANCE Many motile bacterial populations form surface-attached biofilms in response to specific environmental cues, including osmotic stress in a range of natural and host-related systems. However, cross talk between bacterial osmosensing, swimming, and biofilm formation regulatory networks is not fully understood. Here, we report that the pleiotropic regulator LrhA in Pantoea alhagi is involved in the regulation of flagellar motility, biofilm formation, and host colonization and responds to osmotic upshift. We further show that this sensing relies on the EnvZ-OmpR two-component system that was known to detect changes in external osmotic stress. The EnvZ-OmpR-LrhA osmosensing signal transduction cascade is proposed to increase bacterial fitness under hyperosmotic conditions inside the host. Our work proposes a novel regulatory mechanism that links osmosensing and motile-sessile lifestyle transitions, which may provide new approaches to prevent or promote the formation of biofilms and host colonization in P. alhagi and other bacteria possessing a similar osmoregulatory mechanism.
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Defining the Genetic Basis of Plant⁻Endophytic Bacteria Interactions. Int J Mol Sci 2019; 20:ijms20081947. [PMID: 31010043 PMCID: PMC6515357 DOI: 10.3390/ijms20081947] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 01/17/2023] Open
Abstract
Endophytic bacteria, which interact closely with their host, are an essential part of the plant microbiome. These interactions enhance plant tolerance to environmental changes as well as promote plant growth, thus they have become attractive targets for increasing crop production. Numerous studies have aimed to characterise how endophytic bacteria infect and colonise their hosts as well as conferring important traits to the plant. In this review, we summarise the current knowledge regarding endophytic colonisation and focus on the insights that have been obtained from the mutants of bacteria and plants as well as ‘omic analyses. These show how endophytic bacteria produce various molecules and have a range of activities related to chemotaxis, motility, adhesion, bacterial cell wall properties, secretion, regulating transcription and utilising a substrate in order to establish a successful interaction. Colonisation is mediated by plant receptors and is regulated by the signalling that is connected with phytohormones such as auxin and jasmonic (JA) and salicylic acids (SA). We also highlight changes in the expression of small RNAs and modifications of the cell wall properties. Moreover, in order to exploit the beneficial plant-endophytic bacteria interactions in agriculture successfully, we show that the key aspects that govern successful interactions remain to be defined.
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Raina JB, Fernandez V, Lambert B, Stocker R, Seymour JR. The role of microbial motility and chemotaxis in symbiosis. Nat Rev Microbiol 2019; 17:284-294. [DOI: 10.1038/s41579-019-0182-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Burygin GL, Kargapolova KY, Kryuchkova YV, Avdeeva ES, Gogoleva NE, Ponomaryova TS, Tkachenko OV. Ochrobactrum cytisi IPA7.2 promotes growth of potato microplants and is resistant to abiotic stress. World J Microbiol Biotechnol 2019; 35:55. [PMID: 30900049 DOI: 10.1007/s11274-019-2633-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/08/2019] [Indexed: 11/26/2022]
Abstract
Bacteria in natural associations with agricultural crops are promising for use in the improvement of clonal micropropagation of plants. We clarified the taxonomic position of Ochrobactrum cytisi strain IPA7.2 and investigated its tolerance for salinity, high temperature, and glyphosate pollution. We also tested the strain's potential to promote the growth of potato (Solanum tuberosum L.) microplants. Using the IPA7.2 draft genome (no. NZ_MOEC00000000), we searched for housekeeping genes and also for the target genes encoding glyphosate tolerance and plant-growth-promoting ability. A multilocus sequence analysis of the gap, rpoB, dnaK, trpE, aroC, and recA housekeeping genes led us to identify isolate IPA7.2 as O. cytisi. The strain tolerated temperatures up to 50 °C and NaCl concentrations up to 3-4%, and it produced 8 µg ml-1 of indole-3-acetic acid. It also tolerated 6 mM glyphosate owing to the presence of type II 5-enolpyruvylshikimate-3-phosphate synthase. Finally, it was able to colonize the roots and tissues of potato microplants, an ability preserved by several generations after subculturing. We identified the development phase of potato microplants that was optimal for inoculation with O. cytisi IPA7.2. Inoculation of in vitro-grown 15-day-old microplants increased the mitotic index of root meristem cells (by 50%), the length of shoots (by 34%), the number of leaves (by 7%), and the number of roots (by 16%). Under ex vitro conditions, the inoculated plants had a greater leaf area (by 77%) and greater shoot and root dry weight (by 84 and 61%, respectively) than did the control plants. We recommend O. cytisi IPA 7.2 for use in the growing of potato microplants to improve the production of elite seed material.
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Affiliation(s)
- Gennady L Burygin
- Vavilov Saratov State Agrarian University, 1 Teatralnaya Ploshchad, Saratov, Russia, 410012.
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, Russia, 410049.
| | | | - Yelena V Kryuchkova
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, Russia, 410049
| | - Elena S Avdeeva
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, Russia, 410049
| | - Natalia E Gogoleva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky Street, Kazan, Russia, 420111
- Kazan Federal University, 18 Ulitsa Kremlyovskaya, Kazan, Russia, 420111
| | | | - Oksana V Tkachenko
- Vavilov Saratov State Agrarian University, 1 Teatralnaya Ploshchad, Saratov, Russia, 410012
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Bulgari D, Montagna M, Gobbi E, Faoro F. Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe⁻Plant⁻Animal Interactions. Microorganisms 2019; 7:microorganisms7020044. [PMID: 30736387 PMCID: PMC6406919 DOI: 10.3390/microorganisms7020044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/23/2019] [Accepted: 02/02/2019] [Indexed: 12/16/2022] Open
Abstract
The recent and massive revival of green strategies to control plant diseases, mainly as a consequence of the Integrated Pest Management (IPM) rules issued in 2009 by the European Community and the increased consumer awareness of organic products, poses new challenges for human health and food security that need to be addressed in the near future. One of the most important green technologies is biocontrol. This approach is based on living organisms and how these biocontrol agents (BCAs) directly or indirectly interact as a community to control plant pathogens and pest. Although most BCAs have been isolated from plant microbiomes, they share some genomic features, virulence factors, and trans-kingdom infection abilities with human pathogenic microorganisms, thus, their potential impact on human health should be addressed. This evidence, in combination with the outbreaks of human infections associated with consumption of raw fruits and vegetables, opens new questions regarding the role of plants in the human pathogen infection cycle. Moreover, whether BCAs could alter the endophytic bacterial community, thereby leading to the development of new potential human pathogens, is still unclear. In this review, all these issues are debated, highlighting that the research on BCAs and their formulation should include these possible long-lasting consequences of their massive spread in the environment.
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Affiliation(s)
- Daniela Bulgari
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Italy, via Celoria 2, 20133 Milan, Italy.
- Piattaforma di Microbiologia Agroalimentare ed Ambientale (Pi.Mi.A.A.), AgroFood Lab, Department ofMolecular and Translational Medicine, University of Brescia; 25121 Brescia, Italy.
| | - Matteo Montagna
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Italy, via Celoria 2, 20133 Milan, Italy.
| | - Emanuela Gobbi
- Piattaforma di Microbiologia Agroalimentare ed Ambientale (Pi.Mi.A.A.), AgroFood Lab, Department ofMolecular and Translational Medicine, University of Brescia; 25121 Brescia, Italy.
| | - Franco Faoro
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Italy, via Celoria 2, 20133 Milan, Italy.
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Rehman K, Imran A, Amin I, Afzal M. Enhancement of oil field-produced wastewater remediation by bacterially-augmented floating treatment wetlands. CHEMOSPHERE 2019; 217:576-583. [PMID: 30445402 DOI: 10.1016/j.chemosphere.2018.11.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/24/2018] [Accepted: 11/04/2018] [Indexed: 06/09/2023]
Abstract
Plants and bacteria individually as well as in synergism with each other hold a great potential to degrade a wide range of environmental pollutants. Floating treatment wetlands (FTWs) is an efficient and low-cost technology that uses the synergistic interaction between plant roots and microbes for in situ remediation of wastewater. The present study aims to assess the feasibility of FTW-based remediation of oil field-produced wastewater using an interaction between two plant species, Typha domingensis and Leptochloa fusca, in partnership with a consortium of crude oil-degrading bacterial species, Bacillus subtilis LORI66, Klebsiella sp. LCRI87, Acinetobacter Junii TYRH47, and Acinetobacter sp. BRSI56. All the treatments reduced contaminant levels, but T. domingensis, in combination with bacterial inoculation, exhibited the highest reduction in hydrocarbon (95%), COD (90%), and BOD content (93%) as compared to L. fusca. This combination maximally promoted increases in fresh biomass (31%), dry biomass (52%), and length (25%) of plants as well. This effect was further signified by the persistence of bacteria (40%) and considerable abundance (27%) and expression (28.5%) of the alkB gene in the rhizoplane of T. domingensis in comparison to that of L. fusca. The study, therefore, suggests that T. domingensis, in combination with bacterial consortium, has significant potential for treatment of oil field-produced water and can be exploited on large scale in FTWs.
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Affiliation(s)
- Khadeeja Rehman
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Asma Imran
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Imran Amin
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Afzal
- Soil and Environmental Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
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63
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Baccari C, Antonova E, Lindow S. Biological Control of Pierce's Disease of Grape by an Endophytic Bacterium. PHYTOPATHOLOGY 2019; 109:248-256. [PMID: 30540526 DOI: 10.1094/phyto-07-18-0245-fi] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Effective preventive measures and therapies are lacking for control of Pierce's disease of grape caused by the xylem-colonizing bacterium Xylella fastidiosa responsible for serious losses in grape production. In this study we explored the potential for endophytic bacteria to alter the disease process. While most endophytic bacteria found within grape did not grow or multiply when inoculated into mature grape vines, Paraburkholderia phytofirmans strain PsJN achieved population sizes as large as 106 cells/g and moved 1 m or more within 4 weeks after inoculation into vines. While X. fastidiosa achieved large population sizes and moved extensively in grape when inoculated alone, few viable cells were recovered from plants in which it was co-inoculated with strain PsJN and the incidence of leaves exhibiting scorching symptoms typical of Pierce's disease was consistently greatly reduced from that in control plants. Suppression of disease symptoms occurred not only when strain PsJN was co-inoculated with the pathogen by puncturing stems in the same site in plants, but also when inoculated at the same time but at different sites in the plant. Large population sizes of strain PsJN could be established in both leaf lamina and petioles by topical application of cell suspensions in 0.2% of an organo-silicon surfactant conferring low surface tension, and such treatments were as effective as direct puncture inoculations of this biocontrol strain in reducing disease severity. While inoculation of strain PsJN into plants by either method at the same time as or even 4 weeks after that of the pathogen resulted in large reductions in disease severity, much less disease control was conferred by inoculation of PsJN 4 weeks prior to that of the pathogen. The expression of grapevine PR1 and ETR1 within 3 weeks of inoculation was substantially higher in plants inoculated with both X. fastidiosa and strain PsJN compared with that in plants inoculated only with the pathogen or strain PsJN, suggesting that this biological control agent reduces disease by priming expression of innate disease resistance pathways in plants that otherwise would have exhibited minimal responses to the pathogen. Strain PsJN thus appears highly efficacious for the control of Pierce's disease when used as an eradicant treatment that can be easily made even by spray application.
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Affiliation(s)
- Clelia Baccari
- Department of Plant and Microbial Biology, University of California, Berkeley 94720
| | - Elena Antonova
- Department of Plant and Microbial Biology, University of California, Berkeley 94720
| | - Steven Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley 94720
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64
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Lee Y, Lee Y, Jeon CO. Biodegradation of naphthalene, BTEX, and aliphatic hydrocarbons by Paraburkholderia aromaticivorans BN5 isolated from petroleum-contaminated soil. Sci Rep 2019; 9:860. [PMID: 30696831 PMCID: PMC6351602 DOI: 10.1038/s41598-018-36165-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 11/16/2018] [Indexed: 11/09/2022] Open
Abstract
To isolate bacteria responsible for the biodegradation of naphthalene, BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene), and aliphatic hydrocarbons in petroleum-contaminated soil, three enrichment cultures were established using soil extract as the medium supplemented with naphthalene, BTEX, or n-hexadecane. Community analyses showed that Paraburkholderia species were predominant in naphthalene and BTEX, but relatively minor in n-hexadecane. Paraburkholderia aromaticivorans BN5 was able to degrade naphthalene and all BTEX compounds, but not n-hexadecane. The genome of strain BN5 harbors genes encoding 29 monooxygenases including two alkane 1-monooxygenases and 54 dioxygenases, indicating that strain BN5 has versatile metabolic capabilities, for diverse organic compounds: the ability of strain BN5 to degrade short chain aliphatic hydrocarbons was verified experimentally. The biodegradation pathways of naphthalene and BTEX compounds were bioinformatically predicted and verified experimentally through the analysis of their metabolic intermediates. Some genomic features including the encoding of the biodegradation genes on a plasmid and the low sequence homologies of biodegradation-related genes suggest that biodegradation potentials of strain BN5 may have been acquired via horizontal gene transfers and/or gene duplication, resulting in enhanced ecological fitness by enabling strain BN5 to degrade all compounds including naphthalene, BTEX, and short aliphatic hydrocarbons in contaminated soil.
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Affiliation(s)
- Yunho Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Yunhee Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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65
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Hussain Z, Arslan M, Malik MH, Mohsin M, Iqbal S, Afzal M. Treatment of the textile industry effluent in a pilot-scale vertical flow constructed wetland system augmented with bacterial endophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:966-973. [PMID: 30032091 DOI: 10.1016/j.scitotenv.2018.07.163] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 07/01/2018] [Accepted: 07/13/2018] [Indexed: 05/18/2023]
Abstract
A pilot-scale vertical flow constructed wetland (VFCWs) system was designed, implemented and operated for one year for the treatment of dye-rich real textile effluent. Brachiaria mutica was vegetated to develop VFCWs in which five different textile effluent degrading endophytic bacteria were inoculated. These bacteria were screened based on their dye degrading and plant growth promoting capabilities. The system's performance was evaluated by monitoring physicochemical parameters, nutrients removal, heavy metals reduction, detoxification potential, and persistence of endophytic bacteria in the plant rhizo- and endosphere. Although VFCWs were able to remove a majority of the pollutants from the wastewater, bacterial augmentation further enhanced the remediation efficiency. The system promoted an increase in dissolved oxygen up to 188% and, concomitantly, a substantial decrease in the chemical oxygen demand (81%), biochemical oxygen demand (72%), total dissolved solids (32%), color (74%), nitrogen (84%), phosphorous (79%), and heavy metals [Cr(97%), Fe(89%), Ni(88%), Cd(72%)] was recorded. Wastewater treated with VFCWs augmented with bacteria was found to be non-toxic and inoculated bacteria showed persistence in the root and shoot interior of B. mutica. Conclusively, VFCWs proved to be an effective methodology for treatment of textile effluent whereas its smaller size with high efficiency is an advantage for field-scale applications.
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Affiliation(s)
- Zahid Hussain
- University of Management and Technology, Lahore, Pakistan; Interloop Limited, Khurrianwala, Faisalabad, Pakistan
| | - Muhammad Arslan
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan; Environmental Biotechnology Department, Helmholtz Centre for Environmental Research, Leipzig, Germany.
| | | | | | - Samina Iqbal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Muhammad Afzal
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
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66
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Baliyan N, Dheeman S, Maheshwari DK, Dubey RC, Vishnoi VK. Rhizobacteria isolated under field first strategy improved chickpea growth and productivity. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s42398-018-00042-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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67
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Nigris S, Baldan E, Tondello A, Zanella F, Vitulo N, Favaro G, Guidolin V, Bordin N, Telatin A, Barizza E, Marcato S, Zottini M, Squartini A, Valle G, Baldan B. Biocontrol traits of Bacillus licheniformis GL174, a culturable endophyte of Vitis vinifera cv. Glera. BMC Microbiol 2018; 18:133. [PMID: 30326838 PMCID: PMC6192205 DOI: 10.1186/s12866-018-1306-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/07/2018] [Indexed: 12/14/2022] Open
Abstract
Background Bacillus licheniformis GL174 is a culturable endophytic strain isolated from Vitis vinifera cultivar Glera, the grapevine mainly cultivated for the Prosecco wine production. This strain was previously demonstrated to possess some specific plant growth promoting traits but its endophytic attitude and its role in biocontrol was only partially explored. In this study, the potential biocontrol action of the strain was investigated in vitro and in vivo and, by genome sequence analyses, putative functions involved in biocontrol and plant-bacteria interaction were assessed. Results Firstly, to confirm the endophytic behavior of the strain, its ability to colonize grapevine tissues was demonstrated and its biocontrol properties were analyzed. Antagonism test results showed that the strain could reduce and inhibit the mycelium growth of diverse plant pathogens in vitro and in vivo. The strain was demonstrated to produce different molecules of the lipopeptide class; moreover, its genome was sequenced, and analysis of the sequences revealed the presence of many protein-coding genes involved in the biocontrol process, such as transporters, plant-cell lytic enzymes, siderophores and other secondary metabolites. Conclusions This step-by-step analysis shows that Bacillus licheniformis GL174 may be a good biocontrol agent candidate, and describes some distinguished traits and possible key elements involved in this process. The use of this strain could potentially help grapevine plants to cope with pathogen attacks and reduce the amount of chemicals used in the vineyard. Electronic supplementary material The online version of this article (10.1186/s12866-018-1306-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastiano Nigris
- Botanical Garden and Department of Biology, University of Padova, Padova, Italy
| | - Enrico Baldan
- Department of Biology, University of Padova, Padova, Italy
| | | | | | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Gabriella Favaro
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | | | - Nicola Bordin
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | | | - Andrea Squartini
- DAFNAE Department of Agronomy Food Natural Resources Animals and Environment, Legnaro, PD, Italy
| | - Giorgio Valle
- Department of Biology, University of Padova, Padova, Italy
| | - Barbara Baldan
- Botanical Garden and Department of Biology, University of Padova, Padova, Italy.
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68
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Esmaeel Q, Miotto L, Rondeau M, Leclère V, Clément C, Jacquard C, Sanchez L, Barka EA. Paraburkholderia phytofirmans PsJN-Plants Interaction: From Perception to the Induced Mechanisms. Front Microbiol 2018; 9:2093. [PMID: 30214441 PMCID: PMC6125355 DOI: 10.3389/fmicb.2018.02093] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022] Open
Abstract
The use of plant-associated bacteria has received many scientific and economic attention as an effective and alternative method to reduce the chemical pesticides use in agriculture. The genus Burkholderia includes at least 90 species including pathogenic strains, plant pathogens, as well as plant beneficial species as those related to Paraburkholderia, which has been reported to be associated with plants and exerts a positive effect on plant growth and fitness. Paraburkholderia phytofirmans PsJN, a beneficial endophyte able to colonize a wide range of plants, is an established model for plant-associated endophytic bacteria. Indeed, in addition to its plant growth promoting ability, it can also induce plant resistance against biotic as well as abiotic stresses. Here, we summarized an inventory of knowledge on PsJN-plant interaction, from the perception to the resistance mechanisms induced in the plant by a way of the atypical colonization mode of this endophyte. We also have carried out an extensive genome analysis to identify all gene clusters which contribute to the adaptive mechanisms under different environments and partly explaining the high ecological competence of P. phytofirmans PsJN.
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Affiliation(s)
- Qassim Esmaeel
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Lidiane Miotto
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Marine Rondeau
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV- Institut Charles Viollette, SFR Condorcet FR CNRS 3417, Lille, France
| | - Christophe Clément
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Cédric Jacquard
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Lisa Sanchez
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
| | - Essaid A Barka
- Unité de Résistance Induite et Bioprotection des Plantes EA 4707, SFR Condorcet FR CNRS 3417, University of Reims Champagne-Ardenne, Reims, France
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69
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Singh R, Dubey AK. Diversity and Applications of Endophytic Actinobacteria of Plants in Special and Other Ecological Niches. Front Microbiol 2018; 9:1767. [PMID: 30135681 PMCID: PMC6092505 DOI: 10.3389/fmicb.2018.01767] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/16/2018] [Indexed: 12/19/2022] Open
Abstract
Actinobacteria are wide spread in nature and represent the largest taxonomic group within the domain Bacteria. They are abundant in soil and have been extensively explored for their therapeutic applications. This versatile group of bacteria has adapted to diverse ecological habitats, which has drawn considerable attention of the scientific community in recent times as it has opened up new possibilities for novel metabolites that may help in solving some of the most challenging problems of the day, for example, novel drugs for drug-resistant human pathogens, affordable means to maintain ecological balance in various habitats, and alternative practices for sustainable agriculture. Traditionally, free dwelling soil actinobacteria have been the subject of intensive research. Of late, symbiotic actinobacteria residing as endophytes within the plant tissues have generated immense interest as potential source of novel compounds, which may find applications in medicine, agriculture, and environment. In the light of these possibilities, this review focuses on the diversity of endophytic actinobacteria isolated from the plants of extreme habitats and specific ecological niches. Furthermore, an attempt has been made to assign chemical class to the compounds obtained from endophytic actinobacteria. Potential therapeutic applications of these compounds and the utility of endophytic actinobacteria in agriculture and environment are discussed.
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Affiliation(s)
| | - Ashok K. Dubey
- Division of Biological Sciences and Engineering, Netaji Subhas Institute of Technology, New Delhi, India
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70
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Pinto-Carbó M, Gademann K, Eberl L, Carlier A. Leaf nodule symbiosis: function and transmission of obligate bacterial endophytes. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:23-31. [PMID: 29452904 DOI: 10.1016/j.pbi.2018.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 06/08/2023]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves, and have been used as taxonomic marker since the early 20th century. These structures are present in very diverse taxa, including dicots (Rubiaceae and Primulaceae) and monocots (Dioscorea). The symbionts colonize the plants throughout their life cycles and contribute bioactive secondary metabolites to the association. In this review, we present recent progress in the understanding of these plant-bacteria symbioses, including the modes of transmission, distribution and roles of the symbionts.
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Affiliation(s)
- Marta Pinto-Carbó
- Department of Microbiology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Leo Eberl
- Department of Microbiology, University of Zurich, CH-8008 Zurich, Switzerland
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71
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Trovero MF, Scavone P, Platero R, de Souza EM, Fabiano E, Rosconi F. Herbaspirillum seropedicae Differentially Expressed Genes in Response to Iron Availability. Front Microbiol 2018; 9:1430. [PMID: 30018605 PMCID: PMC6037834 DOI: 10.3389/fmicb.2018.01430] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 06/11/2018] [Indexed: 01/20/2023] Open
Abstract
Herbaspirillum seropedicae Z67 is a nitrogen-fixing endophyte that colonizes many important crops. Like in almost all organisms, vital cellular processes of this endophyte are iron dependent. In order to efficiently acquire iron to fulfill its requirements, this bacterium produces the siderophores serobactins. However, the presence in its genome of many others iron acquisition genes suggests that serobactins are not the only strategy used by H. seropedicae to overcome metal deficiency. The aim of this work was to identify genes and proteins differentially expressed by cells growing in low iron conditions in order to describe H. seropedicae response to iron limitation stress. For this purpose, and by using a transcriptomic approach, we searched and identified a set of genes up-regulated when iron was scarce. One of them, Hsero_2337, codes for a TonB-dependent transporter/transducer present in the serobactins biosynthesis genomic locus, with an unknown function. Another TonB-dependent receptor, the one encoded by Hsero_1277, and an inner membrane ferrous iron permease, coded by Hsero_2720, were also detected. By using a proteomic approach focused in membrane proteins, we identified the specific receptor for iron-serobactin internalization SbtR and two non-characterized TonB-dependent receptors (coded by genes Hsero_1277 and Hsero_3255). We constructed mutants on some of the identified genes and characterized them by in vitro growth, biofilm formation, and interaction with rice plants. Characterization of mutants in gene Hsero_2337 showed that the TonB-dependent receptor coded by this gene has a regulatory role in the biosynthesis of serobactins, probably by interacting with the alternative sigma factor PfrI, coded by gene Hsero_2338. Plant colonization of the mutant strains was not affected, since the mutant strain normally colonize the root and aerial part of rice plants. These results suggest that the strategies used by H. seropedicae to acquire iron inside plants are far more diverse than the ones characterized in this work. In vivo expression studies or colonization competition experiments between the different mutant strains could help us in future works to determine the relative importance of the different iron acquisition systems in the interaction of H. seropedicae with rice plants.
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Affiliation(s)
- María F Trovero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Paola Scavone
- Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Raúl Platero
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Emanuel M de Souza
- Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, Brazil
| | - Elena Fabiano
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Federico Rosconi
- Departamento de Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
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Kotoky R, Rajkumari J, Pandey P. The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2018; 217:858-870. [PMID: 29660711 DOI: 10.1016/j.jenvman.2018.04.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/22/2018] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation. Although the importance of the rhizosphere microbiome for plant growth has been widely recognized, the interactions between microbiome and plant roots in the process of rhizosphere mediated remediation of PAH still needs attention. Most of the current researches target PAH degradation by plant or single microorganism, separately, whereas the interactions between plants and whole microbiome are overlooked and its role has been ignored. This review summarizes recent knowledge of PAH degradation in the rhizosphere in the process of plant-microbiome interactions based on emerging omics approaches such as metagenomics, metatranscriptomics, metabolomics and metaproteomics. These omics approaches with combinations to bioinformatics tools provide us a better understanding in integrated activity patterns between plants and rhizosphere microbes, and insight into the biochemical and molecular modification of the meta-organisms (plant-microbiome) to maximize rhizoremediation activity. Moreover, a better understanding of the interactions could lead to the development of techniques to engineer rhizosphere microbiome for better hydrocarbon degradation.
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Affiliation(s)
- Rhitu Kotoky
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, 788011, India.
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73
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Dent D. Non-nodular Endophytic Bacterial Symbiosis and the Nitrogen Fixation of Gluconacetobacter diazotrophicus. Symbiosis 2018. [DOI: 10.5772/intechopen.75813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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74
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Schwab S, Terra LA, Baldani JI. Genomic characterization of Nitrospirillum amazonense strain CBAmC, a nitrogen-fixing bacterium isolated from surface-sterilized sugarcane stems. Mol Genet Genomics 2018; 293:997-1016. [PMID: 29696375 DOI: 10.1007/s00438-018-1439-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 04/18/2018] [Indexed: 02/07/2023]
Abstract
Nitrospirillum amazonense is a nitrogen-fixing bacterium that shows potential to promote plant growth when inoculated into sugarcane and rice plants. This microorganism has been the subject of biochemical and genetic characterization to elucidate important functions related to host plant interaction and growth promotion, including the determination of draft genome sequences of two strains, Y2 and CBAmC, the second of which is the aim of the present study. CBAmC has been isolated from sugarcane (Saccharum spp.), and is currently used in a sugarcane consortium inoculant with four other nitrogen-fixing bacterial strains. The present paper describes a significant improvement in the genome sequence and assembly for the N. amazonense strain CBAmC, and determination for the first time of a complete genome sequence for this bacterial species, using PacBio technology. The analysis of the genomic data obtained allowed the discovery of genes coding for metabolic pathways and cellular structures that may be determinant for the success of the bacterial establishment and colonization into the host sugarcane plant, besides conferring important characteristics to the inoculant. These include genes for the use of sucrose and N-glycans, biosynthesis of autoinducer molecules, siderophore production and acquisition, auxin and polyamine biosynthesis, flagellum, σ-fimbriae, a variety of secretion systems, and a complete denitrification system. Concerning genes for nitrogenase and auxiliary proteins, it was possible to corroborate literature data that in N. amazonense these probably had originated from horizontal gene transfer, from bacteria of the Rhizobiales order. The complete genomic sequence of the CBAmC strain of N. amazonense revealed that the bacterium harbors four replicons, including three chromosomes and one chromid, a profile that coincides with that of other two strains, according to literature data, suggesting that as a replicon pattern for the species. Finally, results of phylogenomic analyses in this work support the recent reclassification of the species, separating it from the Azospirillum genus. More importantly, results of the present work shall guide subsequent studies on strain CBAmC as well as the development of a sugarcane inoculant.
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Affiliation(s)
- Stefan Schwab
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, CNPq, Curitiba, Brazil.
- Embrapa Agrobiologia, Rodovia BR 465, km 7, Seropédica, RJ, 23891-000, Brazil.
| | - Leonardo Araujo Terra
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, CNPq, Curitiba, Brazil
- Embrapa Agrobiologia, Rodovia BR 465, km 7, Seropédica, RJ, 23891-000, Brazil
- Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, km 7, Seropédica, RJ, 23890-000, Brazil
| | - José Ivo Baldani
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, CNPq, Curitiba, Brazil
- Embrapa Agrobiologia, Rodovia BR 465, km 7, Seropédica, RJ, 23891-000, Brazil
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Chagas FO, Pessotti RDC, Caraballo-Rodríguez AM, Pupo MT. Chemical signaling involved in plant-microbe interactions. Chem Soc Rev 2018; 47:1652-1704. [PMID: 29218336 DOI: 10.1039/c7cs00343a] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.
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Affiliation(s)
- Fernanda Oliveira Chagas
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo (FCFRP-USP), Avenida do Café, s/n, 14040-903, Ribeirão Preto-SP, Brazil.
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76
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Lidor O, Dror O, Hamershlak D, Shoshana N, Belausov E, Zahavi T, Mozes-Daube N, Naor V, Zchori-Fein E, Iasur-Kruh L, Bahar O. Introduction of a putative biocontrol agent into a range of phytoplasma- and liberibacter-susceptible crop plants. PEST MANAGEMENT SCIENCE 2018; 74:811-819. [PMID: 29072824 DOI: 10.1002/ps.4775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/03/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Phytoplasma, the causative agent of Bois Noir disease of grapevines, are vectored by the planthopper Hyalesthes obsoletus (Hemiptera: Cixiidae). A Dyella-like bacterium (DLB) isolated from H. obsoletus inhibits the growth of Spiroplasma melliferum, a cultivable relative of phytoplasma. Additional evidence suggests that DLB can reduce the symptoms of yellows disease in grapevine plantlets. The aim of this study was to test whether DLB could colonize a range of phytoplasma- and liberibacter-sensitive crop plants, and thus assess its potential agricultural use. RESULTS Vitex agnus-castus, the preferred host plant of H. obsoletus was found to be a natural host of DLB, which was successfully introduced into a range of crop plants belonging to seven families. The most effective DLB application method was foliar spraying. Microscopy observation revealed that DLB aggregated on the leaf surface and around the stomata, suggesting that this is its route of entry. DLB was also present in the vascular tissues of plants, indicating that it moved systemically through the plant. CONCLUSIONS DLB is a potential biocontrol agent and its broad spectrum of host plants indicates the possibility of its future use against a range of diseases caused by phloem-limited bacteria. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Ofir Lidor
- Department of Entomology, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, Israel
| | - Orit Dror
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Dor Hamershlak
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, Israel
| | - Nofar Shoshana
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Eduard Belausov
- Microscopy Unit, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | | | - Netta Mozes-Daube
- Department of Entomology, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, Israel
| | - Vered Naor
- Shamir Research Institute, Katzrin, Israel
- Ohallo College, Katzrin, Israel
| | - Einat Zchori-Fein
- Department of Entomology, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, Israel
| | - Lilach Iasur-Kruh
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel, Israel
| | - Ofir Bahar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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77
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Nafees M, Ali S, Naveed M, Rizwan M. Efficiency of biogas slurry and Burkholderia phytofirmans PsJN to improve growth, physiology, and antioxidant activity of Brassica napus L. in chromium-contaminated soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:6387-6397. [PMID: 29249026 DOI: 10.1007/s11356-017-0924-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 12/03/2017] [Indexed: 06/07/2023]
Abstract
Contamination of soil is a major problem globally with colligated danger for ecosystem and human health. Chromium (Cr) is a toxic heavy metal and caused harmful effect on growth and development of plants. Phytostabilization reduced the mobility of heavy metals with addition of amendments which can significantly decrease metal solubility in soil. Phytostabilization can be achieved by application of biogas slurry (BGS) and endophytic bacteria as amendments in the contaminated soils. The present study revealed that the Burkholderia phytofirmans PsJN and BGS improved the growth, physiology, and antioxidant activity and reduced Cr uptake under a pot experiment spiked with Cr (20 mg kg-1 soil). The experiment was designed under completely randomized design, four treatments with three replications in normal and Cr-contaminated soil. The inoculation of endophytic bacteria improved the growth and physiology of Brassica. This study showed that the inoculation of endophytic bacteria stabilized the Cr levels in soil and minimized the uptake by the plant shoots and roots in BGS-amended soil. Similarly, activity of antioxidants such as catalase (CAT), reduced glutathione (GSH), glutathione peroxidase (GSH-Px), and glutathione s-transferase (GST) was decreased to normal with combined treatment of BGS and endophytic bacteria in Cr-stressed soil. Overall, the best results were analyzed by combined treatment of BGS and endophytic bacteria to improve growth, physiology, and antioxidant activity of Brassica and immobilize Cr in soil. Moreover, results emphasized the need to use BGS alone or in combination with endophytic bacteria to optimize crop performance, stabilize Cr concentration, and improve environmental efficiency.
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Affiliation(s)
- Muhammad Nafees
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Allama Iqbal Road, Faisalabad, 38000, Pakistan.
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Muhammad Naveed
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Muhammad Rizwan
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Allama Iqbal Road, Faisalabad, 38000, Pakistan
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Nguyen TT, Lee HH, Park I, Seo YS. Genome-Wide Analysis of Type VI System Clusters and Effectors in Burkholderia Species. THE PLANT PATHOLOGY JOURNAL 2018; 34:11-22. [PMID: 29422784 PMCID: PMC5796746 DOI: 10.5423/ppj.ft.11.2017.0231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/28/2017] [Accepted: 12/04/2017] [Indexed: 05/18/2023]
Abstract
Type VI secretion system (T6SS) has been discovered in a variety of gram-negative bacteria as a versatile weapon to stimulate the killing of eukaryotic cells or prokaryotic competitors. Type VI secretion effectors (T6SEs) are well known as key virulence factors for important pathogenic bacteria. In many Burkholderia species, T6SS has evolved as the most complicated secretion pathway with distinguished types to translocate diverse T6SEs, suggesting their essential roles in this genus. Here we attempted to detect and characterize T6SSs and potential T6SEs in target genomes of plant-associated and environmental Burkholderia species based on computational analyses. In total, 66 potential functional T6SS clusters were found in 30 target Burkholderia bacterial genomes, of which 33% possess three or four clusters. The core proteins in each cluster were specified and phylogenetic trees of three components (i.e., TssC, TssD, TssL) were constructed to elucidate the relationship among the identified T6SS clusters. Next, we identified 322 potential T6SEs in the target genomes based on homology searches and explored the important domains conserved in effector candidates. In addition, using the screening approach based on the profile hidden Markov model (pHMM) of T6SEs that possess markers for type VI effectors (MIX motif) (MIX T6SEs), 57 revealed proteins that were not included in training datasets were recognized as novel MIX T6SE candidates from the Burkholderia species. This approach could be useful to identify potential T6SEs from other bacterial genomes.
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Affiliation(s)
- Thao Thi Nguyen
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Inmyoung Park
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
- Department of Asian Food and Culinary Arts, Youngsan University, Busan 48015,
Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
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Klonowska A, Melkonian R, Miché L, Tisseyre P, Moulin L. Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history. BMC Genomics 2018; 19:105. [PMID: 29378510 PMCID: PMC5789663 DOI: 10.1186/s12864-018-4487-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Rhizobial symbionts belong to the classes Alphaproteobacteria and Betaproteobacteria (called "alpha" and "beta"-rhizobia). Most knowledge on the genetic basis of symbiosis is based on model strains belonging to alpha-rhizobia. Mimosa pudica is a legume that offers an excellent opportunity to study the adaptation toward symbiotic nitrogen fixation in beta-rhizobia compared to alpha-rhizobia. In a previous study (Melkonian et al., Environ Microbiol 16:2099-111, 2014) we described the symbiotic competitiveness of M. pudica symbionts belonging to Burkholderia, Cupriavidus and Rhizobium species. RESULTS In this article we present a comparative analysis of the transcriptomes (by RNAseq) of B. phymatum STM815 (BP), C. taiwanensis LMG19424 (CT) and R. mesoamericanum STM3625 (RM) in conditions mimicking the early steps of symbiosis (i.e. perception of root exudates). BP exhibited the strongest transcriptome shift both quantitatively and qualitatively, which mirrors its high competitiveness in the early steps of symbiosis and its ancient evolutionary history as a symbiont, while CT had a minimal response which correlates with its status as a younger symbiont (probably via acquisition of symbiotic genes from a Burkholderia ancestor) and RM had a typical response of Alphaproteobacterial rhizospheric bacteria. Interestingly, the upregulation of nodulation genes was the only common response among the three strains; the exception was an up-regulated gene encoding a putative fatty acid hydroxylase, which appears to be a novel symbiotic gene specific to Mimosa symbionts. CONCLUSION The transcriptional response to root exudates was correlated to each strain nodulation competitiveness, with Burkholderia phymatum appearing as the best specialised symbiont of Mimosa pudica.
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Affiliation(s)
| | - Rémy Melkonian
- IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France
| | - Lucie Miché
- IRD, UMR LSTM, Campus de Baillarguet, Montpellier, France.,Present address: Aix Marseille University, University of Avignon, CNRS, IRD, IMBE, Marseille, France
| | | | - Lionel Moulin
- IRD, Cirad, University of Montpellier, IPME, Montpellier, France.
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Passera A, Marcolungo L, Casati P, Brasca M, Quaglino F, Cantaloni C, Delledonne M. Hybrid genome assembly and annotation of Paenibacillus pasadenensis strain R16 reveals insights on endophytic life style and antifungal activity. PLoS One 2018; 13:e0189993. [PMID: 29351296 PMCID: PMC5774705 DOI: 10.1371/journal.pone.0189993] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/06/2017] [Indexed: 01/27/2023] Open
Abstract
Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one. In this study, we have characterized the genome of Paenibacillus pasadenensis, strain R16, recently investigated for its antifungal activities and plant-associated features. An hybrid assembly approach was used integrating the very precise reads obtained by Illumina technology and long fragments acquired with Oxford Nanopore Technology (ONT) sequencing. De novo genome assembly based solely on Illumina reads generated a relatively fragmented assembly of 5.72 Mbp in 99 ungapped sequences with an N50 length of 544 Kbp; hybrid assembly, integrating Illumina and ONT reads, improved the assembly quality, generating a genome of 5.75 Mbp, organized in 6 contigs with an N50 length of 3.4 Mbp. Annotation of the latter genome identified 4987 coding sequences, of which 1610 are hypothetical proteins. Enrichment analysis identified pathways of particular interest for the endophyte biology, including the chitin-utilization pathway and the incomplete siderophore pathway which hints at siderophore parasitism. In addition the analysis led to the identification of genes for the production of terpenes, as for example farnesol, that was hypothesized as the main antifungal molecule produced by the strain. The functional analysis on the genome confirmed several plant-associated, plant-growth promotion, and biocontrol traits of strain R16, thus adding insights in the genetic bases of these complex features, and of the Paenibacillus genus in general.
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Affiliation(s)
- Alessandro Passera
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Luca Marcolungo
- Department of Biotechnologies, Università degli Studi di Verona, Verona, Italy
| | - Paola Casati
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
- * E-mail:
| | - Milena Brasca
- Institute of Sciences of Food Production, Italian National Research Council, Milan, Italy
| | - Fabio Quaglino
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Chiara Cantaloni
- Department of Biotechnologies, Università degli Studi di Verona, Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnologies, Università degli Studi di Verona, Verona, Italy
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81
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Joshi R, Singla-Pareek SL, Pareek A. Engineering abiotic stress response in plants for biomass production. J Biol Chem 2018; 293:5035-5043. [PMID: 29339553 DOI: 10.1074/jbc.tm117.000232] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
One of the major challenges in today's agriculture is to achieve enhanced plant growth and biomass even under adverse environmental conditions. Recent advancements in genetics and molecular biology have enabled the identification of a complex signaling network contributing toward plant growth and development on the one hand and abiotic stress response on the other hand. As an outcome of these studies, three major approaches have been identified as having the potential to improve biomass production in plants under abiotic stress conditions. These approaches deal with having changes in the following: (i) plant-microbe interactions; (ii) cell wall biosynthesis; and (iii) phytohormone levels. At the same time, employing functional genomics and genetics-based approaches, a very large number of genes have been identified that play a key role in abiotic stress tolerance. Our Minireview is an attempt to unveil the cross-talk that has just started to emerge between the transcriptional circuitries for biomass production and abiotic stress response. This knowledge may serve as a valuable resource to eventually custom design the crop plants for higher biomass production, in a more sustainable manner, in marginal lands under variable climatic conditions.
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Affiliation(s)
- Rohit Joshi
- From the Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India, and
| | - Ashwani Pareek
- From the Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India, .,the UWA Institute of Agriculture, School of Agriculture and Environment, University of Western Australia, Perth, Western Australia 6009, Australia
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83
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Liu H, Carvalhais LC, Crawford M, Singh E, Dennis PG, Pieterse CMJ, Schenk PM. Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria. Front Microbiol 2017; 8:2552. [PMID: 29312235 PMCID: PMC5742157 DOI: 10.3389/fmicb.2017.02552] [Citation(s) in RCA: 276] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/08/2017] [Indexed: 02/05/2023] Open
Abstract
One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.
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Affiliation(s)
- Hongwei Liu
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lilia C. Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Mark Crawford
- Department of Natural Resources and Mines, Toowoomba, QLD, Australia
| | - Eugenie Singh
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Paul G. Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Peer M. Schenk
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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84
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Kandel SL, Joubert PM, Doty SL. Bacterial Endophyte Colonization and Distribution within Plants. Microorganisms 2017; 5:E77. [PMID: 29186821 PMCID: PMC5748586 DOI: 10.3390/microorganisms5040077] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 11/16/2022] Open
Abstract
The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes.
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Affiliation(s)
| | | | - Sharon L. Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA; (S.L.K.); (P.M.J.)
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85
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Zhang W, Li J, Tang Y, Chen K, Shi X, Ohnishi K, Zhang Y. Involvement of NpdA, a Putative 2-Nitropropane Dioxygenase, in the T3SS Expression and Full Virulence in Ralstonia solanacearum OE1-1. Front Microbiol 2017; 8:1990. [PMID: 29075251 PMCID: PMC5641582 DOI: 10.3389/fmicb.2017.01990] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/27/2017] [Indexed: 01/16/2023] Open
Abstract
Previously, we isolated several genes that potentially affected the expression of type III secretion system (T3SS) in Ralstonia solanacearum OE1-1. Here, we focused on the rsp0316, which encodes a putative 2-nitropropane dioxygenase (hereafter designated NpdA). The deletion of npdA substantially reduced the T3SS expression and virulence in OE1-1, and the complementation with functional NpdA could completely restore its reduced T3SS expression and virulence to that of wild type. The NpdA was highly conserved among diverse R. solanacearum species and the NpdA-dependent expression of T3SS was not specific to OE1-1 strain, but not the virulence. The NpdA was important for the T3SS expression in planta, while it was not required for the bacterial growth in planta. Moreover, the NpdA was not required for the elicitation of hypersensitive response (HR) of R. solanacearum strains in tobacco leaves. The T3SS in R. solanacearum is directly controlled by the AraC-type transcriptional regulator HrpB and regulated by a complex regulation network. The NpdA affected the T3SS expression mediated with HrpB but through some novel pathway. All these results from genetic studies demonstrate that NpdA is a novel factor for the T3SS expression in diverse R. solanacearum species in medium, but specifically for the T3SS expression in strain OE1-1 in planta. And the NpdA-dependent expression of T3SS in planta plays an important role in pathogenicity of R. solanacearum OE1-1 in host plants.
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Affiliation(s)
- Weiqi Zhang
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Jing Li
- The Ninth People's Hospital of Chongqing, Chongqing, China
| | - Yu Tang
- Department of Pharmacognosy, College of Pharmacy, Third Military Medical University, Chongqing, China
| | - Kai Chen
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Xiaojun Shi
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Kochi, Japan
| | - Yong Zhang
- College of Resources and Environment, Southwest University, Chongqing, China
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86
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Dos-Santos CM, de Souza DG, Balsanelli E, Cruz LM, de Souza EM, Baldani JI, Schwab S. A Culture-Independent Approach to Enrich Endophytic Bacterial Cells from Sugarcane Stems for Community Characterization. MICROBIAL ECOLOGY 2017; 74:453-465. [PMID: 28160057 DOI: 10.1007/s00248-017-0941-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/19/2017] [Indexed: 05/16/2023]
Abstract
Bacterial endophytes constitute a very diverse community and they confer important benefits which help to improve agricultural yield. Some of these benefits remain underexplored or little understood, mainly due to the bottlenecks associated with the plant feature, a low number of endophytic bacterial cells in relation to the plant, and difficulties in accessing these bacteria using cultivation-independent methods. Enriching endophytic bacterial cells from plant tissues, based on a non-biased, cultivation-independent physical enrichment method, may help to circumvent those problems, especially in the case of sugarcane stems, which have a high degree of interfering factors, such as polysaccharides, phenolic compounds, nucleases, and fibers. In the present study, an enrichment approach for endophytic bacterial cells from sugarcane lower stems is described. The results demonstrate that the enriched bacterial cells are suitable for endophytic community characterization. A community analysis revealed the presence of previously well-described but also novel endophytic bacteria in sugarcane tissues which may exert functions such as plant growth promotion and biological control, with a predominance of the Proteobacterial phylum, but also Actinobacteria, Bacteroidetes, and Firmicutes, among others. In addition, by comparing the present and literature data, it was possible to list the most frequently detected bacterial endophyte genera in sugarcane tissues. The presented enrichment approach paves the way for improved future research toward the assessment of endophytic bacterial community in sugarcane and other biofuel crops.
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Affiliation(s)
- Carlos M Dos-Santos
- Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23897-000, Brazil
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil
| | - Daniel G de Souza
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil
- Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, Centro Politécnico, Jardim das Américas, Curitiba, PR, CEP 81531-980, Brazil
| | - Leonardo Magalhães Cruz
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, Centro Politécnico, Jardim das Américas, Curitiba, PR, CEP 81531-980, Brazil
| | - Emanuel M de Souza
- Departamento de Bioquímica e Biologia Molecular, Setor de Ciências Biológicas, Universidade Federal do Paraná, Centro Politécnico, Jardim das Américas, Curitiba, PR, CEP 81531-980, Brazil
| | - José I Baldani
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil
| | - Stefan Schwab
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, RJ, CEP 23891-000, Brazil.
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Faoro H, Rene Menegazzo R, Battistoni F, Gyaneshwar P, do Amaral FP, Taulé C, Rausch S, Gonçalves Galvão P, de Los Santos C, Mitra S, Heijo G, Sheu SY, Chen WM, Mareque C, Zibetti Tadra-Sfeir M, Ivo Baldani J, Maluk M, Paula Guimarães A, Stacey G, de Souza EM, Pedrosa FO, Magalhães Cruz L, James EK. The oil-contaminated soil diazotroph Azoarcus olearius DQS-4 T is genetically and phenotypically similar to the model grass endophyte Azoarcus sp. BH72. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:223-238. [PMID: 27893193 DOI: 10.1111/1758-2229.12502] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/24/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
The genome of Azoarcus olearius DQS-4T , a N2 -fixing Betaproteobacterium isolated from oil-contaminated soil in Taiwan, was sequenced and compared with other Azoarcus strains. The genome sequence showed high synteny with Azoarcus sp. BH72, a model endophytic diazotroph, but low synteny with five non-plant-associated strains (Azoarcus CIB, Azoarcus EBN1, Azoarcus KH32C, A. toluclasticus MF63T and Azoarcus PA01). Average Nucleotide Identity (ANI) revealed that DQS-4T shares 98.98% identity with Azoarcus BH72, which should now be included in the species A. olearius. The genome of DQS-4T contained several genes related to plant colonization and plant growth promotion, such as nitrogen fixation, plant adhesion and root surface colonization. In accordance with the presence of these genes, DQS-4T colonized rice (Oryza sativa) and Setaria viridis, where it was observed within the intercellular spaces and aerenchyma mainly of the roots. Although they promote the growth of grasses, the mechanism(s) of plant growth promotion by A. olearius strains is unknown, as the genomes of DQS-4T and BH72 do not contain genes for indole acetic acid (IAA) synthesis nor phosphate solubilization. In spite of its original source, both the genome and behaviour of DQS-4T suggest that it has the capacity to be an endophytic, nitrogen-fixing plant growth-promoting bacterium.
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Affiliation(s)
- Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
- Laboratory of Gene Expression Regulation, Instituto Carlos Chagas, Fiocruz-PR, Curitiba, Paraná, 81350-010, Brazil
| | - Rodrigo Rene Menegazzo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - Federico Battistoni
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Prasad Gyaneshwar
- Department of Biological Sciences, University of Wisconsin - Milwaukee, WI, 53211, USA
| | - Fernanda P do Amaral
- Division of Plant Science and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Cecilia Taulé
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Sydnee Rausch
- Department of Biological Sciences, University of Wisconsin - Milwaukee, WI, 53211, USA
| | | | - Cecilia de Los Santos
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Shubhajit Mitra
- Department of Biological Sciences, University of Wisconsin - Milwaukee, WI, 53211, USA
| | - Gabriela Heijo
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Shih-Yi Sheu
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung City, 811, Taiwan
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, Kaohsiung City, 811, Taiwan
| | - Cintia Mareque
- Department of Microbial Biochemistry and Genomics, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, 11600, Uruguay
| | - Michelle Zibetti Tadra-Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - J Ivo Baldani
- Embrapa Agrobiologia, Seropédica, Rio de Janeiro, 23891-000, Brazil
| | - Marta Maluk
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | | | - Gary Stacey
- Division of Plant Science and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA
| | - Emanuel M de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - Fabio O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - Leonardo Magalhães Cruz
- Department of Biochemistry and Molecular Biology, Universidade Federal do Parana, Curitiba, Parana, 81531-980, Brazil
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
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Nguyen TT, Lee HH, Park J, Park I, Seo YS. Computational Identification and Comparative Analysis of Secreted and Transmembrane Proteins in Six Burkholderia Species. THE PLANT PATHOLOGY JOURNAL 2017; 33:148-162. [PMID: 28381962 PMCID: PMC5378436 DOI: 10.5423/ppj.oa.11.2016.0252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/02/2017] [Accepted: 01/05/2017] [Indexed: 05/14/2023]
Abstract
As a step towards discovering novel pathogenesis-related proteins, we performed a genome scale computational identification and characterization of secreted and transmembrane (TM) proteins, which are mainly responsible for bacteria-host interactions and interactions with other bacteria, in the genomes of six representative Burkholderia species. The species comprised plant pathogens (B. glumae BGR1, B. gladioli BSR3), human pathogens (B. pseudomallei K96243, B. cepacia LO6), and plant-growth promoting endophytes (Burkholderia sp. KJ006, B. phytofirmans PsJN). The proportions of putative classically secreted proteins (CSPs) and TM proteins among the species were relatively high, up to approximately 20%. Lower proportions of putative type 3 non-classically secreted proteins (T3NCSPs) (~10%) and unclassified non-classically secreted proteins (NCSPs) (~5%) were observed. The numbers of TM proteins among the three clusters (plant pathogens, human pathogens, and endophytes) were different, while the distribution of these proteins according to the number of TM domains was conserved in which TM proteins possessing 1, 2, 4, or 12 TM domains were the dominant groups in all species. In addition, we observed conservation in the protein size distribution of the secreted protein groups among the species. There were species-specific differences in the functional characteristics of these proteins in the various groups of CSPs, T3NCSPs, and unclassified NCSPs. Furthermore, we assigned the complete sets of the conserved and unique NCSP candidates of the collected Burkholderia species using sequence similarity searching. This study could provide new insights into the relationship among plant-pathogenic, human-pathogenic, and endophytic bacteria.
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Affiliation(s)
- Thao Thi Nguyen
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Hyun-Hee Lee
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Jungwook Park
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
| | - Inmyoung Park
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
- Department of Asian Food and Culinary Arts, Youngsan University, Busan 48015,
Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241,
Korea
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89
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Feng NX, Yu J, Zhao HM, Cheng YT, Mo CH, Cai QY, Li YW, Li H, Wong MH. Efficient phytoremediation of organic contaminants in soils using plant-endophyte partnerships. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 583:352-368. [PMID: 28117167 DOI: 10.1016/j.scitotenv.2017.01.075] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/11/2017] [Accepted: 01/12/2017] [Indexed: 05/20/2023]
Abstract
Soil pollution with organic contaminants is one of the most intractable environmental problems today, posing serious threats to humans and the environment. Innovative strategies for remediating organic-contaminated soils are critically needed. Phytoremediation, based on the synergistic actions of plants and their associated microorganisms, has been recognized as a powerful in situ approach to soil remediation. Suitable combinations of plants and their associated endophytes can improve plant growth and enhance the biodegradation of organic contaminants in the rhizosphere and/or endosphere, dramatically expediting the removal of organic pollutants from soils. However, for phytoremediation to become a more widely accepted and predictable alternative, a thorough understanding of plant-endophyte interactions is needed. Many studies have recently been conducted on the mechanisms of endophyte-assisted phytoremediation of organic contaminants in soils. In this review, we highlight the superiority of organic pollutant-degrading endophytes for practical applications in phytoremediation, summarize alternative strategies for improving phytoremediation, discuss the fundamental mechanisms of endophyte-assisted phytoremediation, and present updated information regarding the advances, challenges, and new directions in the field of endophyte-assisted phytoremediation technology.
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Affiliation(s)
- Nai-Xian Feng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Jiao Yu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yu-Ting Cheng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Quan-Ying Cai
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Hui Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China
| | - Ming-Hung Wong
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, School of Environment, Jinan University, Guangzhou 510632, China; Consortium on Health, Environment, Education and Research (CHEER), Department of Science and Environmental Studies, The Education University of Hong Kong, Tai Po, Hong Kong, China
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90
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Kandel SL, Firrincieli A, Joubert PM, Okubara PA, Leston ND, McGeorge KM, Mugnozza GS, Harfouche A, Kim SH, Doty SL. An In vitro Study of Bio-Control and Plant Growth Promotion Potential of Salicaceae Endophytes. Front Microbiol 2017; 8:386. [PMID: 28348550 PMCID: PMC5347143 DOI: 10.3389/fmicb.2017.00386] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/23/2017] [Indexed: 11/13/2022] Open
Abstract
Microbial communities in the endosphere of Salicaceae plants, poplar (Populus trichocarpa) and willow (Salix sitchensis), have been demonstrated to be important for plant growth promotion, protection from biotic and abiotic stresses, and degradation of toxic compounds. Our study aimed to investigate bio-control activities of Salicaceae endophytes against various soil borne plant pathogens including Rhizoctonia solani AG-8, Fusarium culmorum, Gaeumannomyces graminis var. tritici, and Pythium ultimum. Additionally, different plant growth promoting traits such as biological nitrogen fixation (BNF), indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, and siderophore production were assessed in all bio-control positive strains. Burkholderia, Rahnella, Pseudomonas, and Curtobacterium were major endophyte genera that showed bio-control activities in the in-vitro assays. The bio-control activities of Burkholderia strains were stronger across all tested plant pathogens as compared to other stains. Genomes of sequenced Burkholderia strains WP40 and WP42 were surveyed to identify the putative genes involved in the bio-control activities. The ocf and hcnABC gene clusters responsible for biosynthesis of the anti-fungal metabolites, occidiofungin and hydrogen cyanide, are present in the genomes of WP40 and WP42. Nearly all endophyte strains showing the bio-control activities produced IAA, solubilized tricalcium phosphate, and synthesized siderophores in the culture medium. Moreover, some strains reduced acetylene into ethylene in the acetylene reduction assay, a common assay used for BNF. Salicaceae endophytes could be useful for bio-control of various plant pathogens, and plant growth promotion possibly through the mechanisms of BNF, IAA production, and nutrient acquisition.
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Affiliation(s)
- Shyam L Kandel
- School of Environmental and Forest Sciences, College of the Environment, University of Washington Seattle, WA, USA
| | - Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia Viterbo, Italy
| | - Pierre M Joubert
- Department of Biology, University of Washington Seattle, WA, USA
| | - Patricia A Okubara
- Wheat Health, Genetics and Quality Research Unit, USDA-ARS Pullman, WA, USA
| | - Natalie D Leston
- Department of Plant Pathology, Washington State University Pullman, WA, USA
| | - Kendra M McGeorge
- Department of Plant Pathology, Washington State University Pullman, WA, USA
| | - Giuseppe S Mugnozza
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia Viterbo, Italy
| | - Antoine Harfouche
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia Viterbo, Italy
| | - Soo-Hyung Kim
- School of Environmental and Forest Sciences, College of the Environment, University of Washington Seattle, WA, USA
| | - Sharon L Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington Seattle, WA, USA
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91
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Timmermann T, Armijo G, Donoso R, Seguel A, Holuigue L, González B. Paraburkholderia phytofirmans PsJN Protects Arabidopsis thaliana Against a Virulent Strain of Pseudomonas syringae Through the Activation of Induced Resistance. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:215-230. [PMID: 28118091 DOI: 10.1094/mpmi-09-16-0192-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Paraburkholderia phytofirmans PsJN is a plant growth-promoting rhizobacterium (PGPR) that stimulates plant growth and improves tolerance to abiotic stresses. This study analyzed whether strain PsJN can reduce plant disease severity and proliferation of the virulent strain Pseudomonas syringae pv. tomato DC3000, in Arabidopsis plants, through the activation of induced resistance. Arabidopsis plants previously exposed to strain PsJN showed a reduction in disease severity and pathogen proliferation in leaves compared with noninoculated, infected plants. The plant defense-related genes WRKY54, PR1, ERF1, and PDF1.2 demonstrated increased and more rapid expression in strain PsJN-treated plants compared with noninoculated, infected plants. Transcriptional analyses and functional analysis using signaling mutant plants suggested that resistance to infection by DC3000 in plants treated with strain PsJN involves salicylic acid-, jasmonate-, and ethylene-signaling pathways to activate defense genes. Additionally, activation occurs through a specific PGPR-host recognition, being a necessary metabolically active state of the bacterium to trigger the resistance in Arabidopsis, with a strain PsJN-associated molecular pattern only partially involved in the resistance response. This study provides the first report on the mechanism used by the PGPR P. phytofirmans PsJN to protect A. thaliana against a widespread virulent pathogenic bacterium.
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Affiliation(s)
- Tania Timmermann
- 1 Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- 3 Millennium Nucleus Center for Plant Systems and Synthetic Biology, Santiago, Chile; and
- 4 Center of Applied Ecology and Sustainability, Santiago, Chile
| | - Grace Armijo
- 2 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- 3 Millennium Nucleus Center for Plant Systems and Synthetic Biology, Santiago, Chile; and
| | - Raúl Donoso
- 1 Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- 3 Millennium Nucleus Center for Plant Systems and Synthetic Biology, Santiago, Chile; and
- 4 Center of Applied Ecology and Sustainability, Santiago, Chile
| | - Aldo Seguel
- 2 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- 3 Millennium Nucleus Center for Plant Systems and Synthetic Biology, Santiago, Chile; and
| | - Loreto Holuigue
- 2 Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- 3 Millennium Nucleus Center for Plant Systems and Synthetic Biology, Santiago, Chile; and
| | - Bernardo González
- 1 Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile
- 3 Millennium Nucleus Center for Plant Systems and Synthetic Biology, Santiago, Chile; and
- 4 Center of Applied Ecology and Sustainability, Santiago, Chile
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92
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Bournaud C, Moulin L, Cnockaert M, Faria SD, Prin Y, Severac D, Vandamme P. Paraburkholderia piptadeniae sp. nov. and Paraburkholderia ribeironis sp. nov., two root-nodulating symbiotic species of Piptadenia gonoacantha in Brazil. Int J Syst Evol Microbiol 2017; 67:432-440. [DOI: 10.1099/ijsem.0.001648] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Caroline Bournaud
- Present address: Embrapa Genetic Resources and Biotechnology, Pest-Plant Molecular Interaction Laboratory, Brasilia, Distrito Federal, Brazil
- Cirad, IRD, Univ. Montpellier, SupAgro, Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier, France
| | - Lionel Moulin
- IRD, Cirad, Univ. Montpellier, Interactions Plantes Microorganismes Environnement (IPME), 34394 Montpellier, France
- Cirad, IRD, Univ. Montpellier, SupAgro, Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier, France
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Sergio de Faria
- EMBRAPA-Agrobiologia, Km 47 Seropedica, 23851-970 Rio de Janeiro, Brazil
| | - Yves Prin
- Cirad, IRD, Univ. Montpellier, SupAgro, Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398 Montpellier, France
| | - Dany Severac
- Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la Cardonille, 34094 Montpellier Cedex, France
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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93
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Thijs S, Sillen W, Weyens N, Vangronsveld J. Phytoremediation: State-of-the-art and a key role for the plant microbiome in future trends and research prospects. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2017; 19:23-38. [PMID: 27484694 DOI: 10.1080/15226514.2016.1216076] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Phytoremediation is increasingly adopted as a more sustainable approach for soil remediation. However, significant advances in efficiency are still necessary to attain higher levels of environmental and economic sustainability. Current interventions do not always give the expected outcomes in field settings due to an incomplete understanding of the multicomponent biological interactions. New advances in -omics are gradually implemented for studying microbial communities of polluted land in situ. This opens new perspectives for the discovery of biodegradative strains and provides us new ways of interfering with microbial communities to enhance bioremediation rates. This review presents retrospectives and future perspectives for plant microbiome studies relevant to phytoremediation, as well as some knowledge gaps in this promising research field. The implementation of phytoremediation in soil clean-up management systems is discussed, and an overview of the promoting factors that determine the growth of the phytoremediation market is given. Continuous growth is expected since elimination of contaminants from the environment is demanded. The evolution of scientific thought from a reductionist view to a more holistic approach will boost phytoremediation as an efficient and reliable phytotechnology. It is anticipated that phytoremediation will prove the most promising for organic contaminant degradation and bioenergy crop production on marginal land.
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Affiliation(s)
- Sofie Thijs
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Wouter Sillen
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Nele Weyens
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
| | - Jaco Vangronsveld
- a Centre for Environmental Sciences, Hasselt University , Diepenbeek , Belgium
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94
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Liu H, Carvalhais LC, Crawford M, Singh E, Dennis PG, Pieterse CMJ, Schenk PM. Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria. Front Microbiol 2017. [PMID: 29312235 DOI: 10.1016/j.apsoil.2011.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
One of the most exciting scientific advances in recent decades has been the realization that the diverse and immensely active microbial communities are not only 'passengers' with plants, but instead play an important role in plant growth, development and resistance to biotic and abiotic stresses. A picture is emerging where plant roots act as 'gatekeepers' to screen soil bacteria from the rhizosphere and rhizoplane. This typically results in root endophytic microbiome dominated by Proteobacteria, Actinobacteria and to a lesser extent Bacteroidetes and Firmicutes, but Acidobacteria and Gemmatimonadetes being almost depleted. A synthesis of available data suggest that motility, plant cell-wall degradation ability and reactive oxygen species scavenging seem to be crucial traits for successful endophytic colonization and establishment of bacteria. Recent studies provide solid evidence that these bacteria serve host functions such as improving of plant nutrients through acquisition of nutrients from soil and nitrogen fixation in leaves. Additionally, some endophytes can engage 'priming' plants which elicit a faster and stronger plant defense once pathogens attack. Due to these plant growth-promoting effects, endophytic bacteria are being widely explored for their use in the improvement of crop performance. Updating the insights into the mechanism of endophytic bacterial colonization and interactions with plants is an important step in potentially manipulating endophytic bacteria/microbiome for viable strategies to improve agricultural production.
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Affiliation(s)
- Hongwei Liu
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Lilia C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Mark Crawford
- Department of Natural Resources and Mines, Toowoomba, QLD, Australia
| | - Eugenie Singh
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Peer M Schenk
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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95
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96
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Puri A, Padda KP, Chanway CP. Plant Growth Promotion by Endophytic Bacteria in Nonnative Crop Hosts. ENDOPHYTES: CROP PRODUCTIVITY AND PROTECTION 2017. [DOI: 10.1007/978-3-319-66544-3_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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97
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Biochemical and Genetic Bases of Indole-3-Acetic Acid (Auxin Phytohormone) Degradation by the Plant-Growth-Promoting Rhizobacterium Paraburkholderia phytofirmans PsJN. Appl Environ Microbiol 2016; 83:AEM.01991-16. [PMID: 27795307 DOI: 10.1128/aem.01991-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/14/2016] [Indexed: 12/16/2022] Open
Abstract
Several bacteria use the plant hormone indole-3-acetic acid (IAA) as a sole carbon and energy source. A cluster of genes (named iac) encoding IAA degradation has been reported in Pseudomonas putida 1290, but the functions of these genes are not completely understood. The plant-growth-promoting rhizobacterium Paraburkholderia phytofirmans PsJN harbors iac gene homologues in its genome, but with a different gene organization and context than those of P. putida 1290. The iac gene functions enable P. phytofirmans to use IAA as a sole carbon and energy source. Employing a heterologous expression system approach, P. phytofirmans iac genes with previously undescribed functions were associated with specific biochemical steps. In addition, two uncharacterized genes, previously unreported in P. putida and found to be related to major facilitator and tautomerase superfamilies, are involved in removal of an IAA metabolite called dioxindole-3-acetate. Similar to the case in strain 1290, IAA degradation proceeds through catechol as intermediate, which is subsequently degraded by ortho-ring cleavage. A putative two-component regulatory system and a LysR-type regulator, which apparently respond to IAA and dioxindole-3-acetate, respectively, are involved in iac gene regulation in P. phytofirmans These results provide new insights about unknown gene functions and complex regulatory mechanisms in IAA bacterial catabolism. IMPORTANCE This study describes indole-3-acetic acid (auxin phytohormone) degradation in the well-known betaproteobacterium P. phytofirmans PsJN and comprises a complete description of genes, some of them with previously unreported functions, and the general basis of their gene regulation. This work contributes to the understanding of how beneficial bacteria interact with plants, helping them to grow and/or to resist environmental stresses, through a complex set of molecular signals, in this case through degradation of a highly relevant plant hormone.
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Ledger T, Rojas S, Timmermann T, Pinedo I, Poupin MJ, Garrido T, Richter P, Tamayo J, Donoso R. Volatile-Mediated Effects Predominate in Paraburkholderia phytofirmans Growth Promotion and Salt Stress Tolerance of Arabidopsis thaliana. Front Microbiol 2016; 7:1838. [PMID: 27909432 PMCID: PMC5112238 DOI: 10.3389/fmicb.2016.01838] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 11/01/2016] [Indexed: 01/09/2023] Open
Abstract
Abiotic stress has a growing impact on plant growth and agricultural activity worldwide. Specific plant growth promoting rhizobacteria have been reported to stimulate growth and tolerance to abiotic stress in plants, and molecular mechanisms like phytohormone synthesis and 1-aminocyclopropane-1-carboxylate deamination are usual candidates proposed to mediate these bacterial effects. Paraburkholderia phytofirmans PsJN is able to promote growth of several plant hosts, and improve their tolerance to chilling, drought and salinity. This work investigated bacterial determinants involved in PsJN stimulation of growth and salinity tolerance in Arabidopsis thaliana, showing bacteria enable plants to survive long-term salinity treatment, accumulating less sodium within leaf tissues relative to non-inoculated controls. Inactivation of specific bacterial genes encoding ACC deaminase, auxin catabolism, N-acyl-homoserine-lactone production, and flagellin synthesis showed these functions have little influence on bacterial induction of salinity tolerance. Volatile organic compound emission from strain PsJN was shown to reproduce the effects of direct bacterial inoculation of roots, increasing plant growth rate and tolerance to salinity evaluated both in vitro and in soil. Furthermore, early exposure to VOCs from P. phytofirmans was sufficient to stimulate long-term effects observed in Arabidopsis growth in the presence and absence of salinity. Organic compounds were analyzed in the headspace of PsJN cultures, showing production of 2-undecanone, 7-hexanol, 3-methylbutanol and dimethyl disulfide. Exposure of A. thaliana to different quantities of these molecules showed that they are able to influence growth in a wide range of added amounts. Exposure to a blend of the first three compounds was found to mimic the effects of PsJN on both general growth promotion and salinity tolerance. To our knowledge, this is the first report on volatile compound-mediated induction of plant abiotic stress tolerance by a Paraburkholderia species.
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Affiliation(s)
- Thomas Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
- Center of Applied Ecology and SustainabilitySantiago, Chile
- Millennium Nucleus Center for Plant Systems and Synthetic BiologySantiago, Chile
| | - Sandy Rojas
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
| | - Tania Timmermann
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
- Center of Applied Ecology and SustainabilitySantiago, Chile
- Millennium Nucleus Center for Plant Systems and Synthetic BiologySantiago, Chile
| | - Ignacio Pinedo
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
| | - María J. Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
- Center of Applied Ecology and SustainabilitySantiago, Chile
- Millennium Nucleus Center for Plant Systems and Synthetic BiologySantiago, Chile
| | - Tatiana Garrido
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de ChileSantiago, Chile
| | - Pablo Richter
- Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de ChileSantiago, Chile
| | - Javier Tamayo
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
| | - Raúl Donoso
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo IbáñezSantiago, Chile
- Center of Applied Ecology and SustainabilitySantiago, Chile
- Millennium Nucleus Center for Plant Systems and Synthetic BiologySantiago, Chile
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Essential Genes for In Vitro Growth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing. Appl Environ Microbiol 2016; 82:6664-6671. [PMID: 27590816 PMCID: PMC5086560 DOI: 10.1128/aem.02281-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 08/31/2016] [Indexed: 01/04/2023] Open
Abstract
The interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil. Herbaspirillum seropedicae strain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions of H. seropedicae with its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination of in vivo high-density mariner Tn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) in H. seropedicae SmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth of H. seropedicae SmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential in H. seropedicae SmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of the H. seropedicae endophytic lifestyle. IMPORTANCE A focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyte Herbaspirillum seropedicae SmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms of H. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.
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100
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Vicente CSL, Nascimento FX, Barbosa P, Ke HM, Tsai IJ, Hirao T, Cock PJA, Kikuchi T, Hasegawa K, Mota M. Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphelenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isolated from Wilting Pinus pinaster. MICROBIAL ECOLOGY 2016; 72:669-681. [PMID: 27461253 DOI: 10.1007/s00248-016-0820-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
Pine wilt disease (PWD) results from the interaction of three elements: the pathogenic nematode, Bursaphelenchus xylophilus; the insect-vector, Monochamus sp.; and the host tree, mostly Pinus species. Bacteria isolated from B. xylophilus may be a fourth element in this complex disease. However, the precise role of bacteria in this interaction is unclear as both plant-beneficial and as plant-pathogenic bacteria may be associated with PWD. Using whole genome sequencing and phenotypic characterization, we were able to investigate in more detail the genetic repertoire of Serratia marcescens PWN146, a bacterium associated with B. xylophilus. We show clear evidence that S. marcescens PWN146 is able to withstand and colonize the plant environment, without having any deleterious effects towards a susceptible host (Pinus thunbergii), B. xylophilus nor to the nematode model C. elegans. This bacterium is able to tolerate growth in presence of xenobiotic/organic compounds, and use phenylacetic acid as carbon source. Furthermore, we present a detailed list of S. marcescens PWN146 potentials to interfere with plant metabolism via hormonal pathways and/or nutritional acquisition, and to be competitive against other bacteria and/or fungi in terms of resource acquisition or production of antimicrobial compounds. Further investigation is required to understand the role of bacteria in PWD. We have now reinforced the theory that B. xylophilus-associated bacteria may have a plant origin.
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Affiliation(s)
- Cláudia S L Vicente
- NemaLab/ICAAM-Institute of Mediterranean Agricultural and Environmental Sciences, Biology Department, University of Évora, Évora, Portugal.
- Department of Environmental Biology, Chubu University, Kasugai, Japan.
| | - Francisco X Nascimento
- NemaLab/ICAAM-Institute of Mediterranean Agricultural and Environmental Sciences, Biology Department, University of Évora, Évora, Portugal
- Departamento de Microbiologia, Laboratório de Microbiologia do Solo, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Pedro Barbosa
- NemaLab/ICAAM-Institute of Mediterranean Agricultural and Environmental Sciences, Biology Department, University of Évora, Évora, Portugal
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung, Taiwan
| | - Isheng J Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Tomonori Hirao
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Ibaraki, Japan
| | - Peter J A Cock
- Information and Computer Sciences group, The James Hutton Institute, Invergowrie, DD2 5DA, Dundee, UK
| | - Taisei Kikuchi
- Division of Parasitology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Koichi Hasegawa
- Department of Environmental Biology, Chubu University, Kasugai, Japan
| | - Manuel Mota
- NemaLab/ICAAM-Institute of Mediterranean Agricultural and Environmental Sciences, Biology Department, University of Évora, Évora, Portugal
- Departamento de Ciências da Vida, Universidade Lusófona de Humanidades e Tecnologias, Lisbon, Portugal
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