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Lee Y, Kwon S, Balaraju K, Jeon Y. Influence of phenotypic variation of Paenibacillus polymyxa E681 on growth promotion in cucumbers. Front Microbiol 2024; 15:1427265. [PMID: 39144205 PMCID: PMC11322358 DOI: 10.3389/fmicb.2024.1427265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/10/2024] [Indexed: 08/16/2024] Open
Abstract
The goal of the current study is to better understand how bacteria may adapt to survive under adverse environmental conditions by altering and improving their phenotypes. In this study, we report the consequences of phenotypic variation in Paenibacillus polymyxa E681 (E681), a plant growth-promoting rhizobacterium (PGPR), isolated from winter barley root that has a variety of advantageous effects on crop plants. In our previous study, two different types of bacterial cells in E681 were distinguished. We used the term F-type for the variant that doesn't produce endospores and B-type for the endospore-producing wild type. Under the circumstances of our experiment, the cucumber rhizosphere soil and the surface of the seeds produced phenotypic variance. On tryptic soy agar (TSA) plates, the B-type spontaneously converted into the F-type, but the reverse was not reversible. Intriguingly, the plant growth promotion test displayed that cucumber seedlings treated with F-type cells had characteristics resembling those of the untreated control. Whereas, growth promotion of cucumber seedlings treated with B-type depends on temperature conditions. In particular, an increased growth promotion was observed at a low temperature of 20°C. The phenotypic change from B-type to F-type did not occur at 20°C for 6 days in the growth curve analysis of E681, but it did occur on the fourth and second days at 30 and 37°C, respectively. Therefore, before using PGPR strains as a bacterial inoculant for sustainable agriculture, it is imperative to resolve phenotypic variance in these strains.
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Affiliation(s)
- Younmi Lee
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
| | - Sungmoon Kwon
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
| | - Kotnala Balaraju
- Agricultural Science and Technology Research Institute, Andong National University, Andong, Republic of Korea
| | - Yongho Jeon
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
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2
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Hartmann A, Binder T, Rothballer M. Quorum sensing-related activities of beneficial and pathogenic bacteria have important implications for plant and human health. FEMS Microbiol Ecol 2024; 100:fiae076. [PMID: 38744663 PMCID: PMC11149725 DOI: 10.1093/femsec/fiae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 05/16/2024] Open
Abstract
Eukaryotic organisms coevolved with microbes from the environment forming holobiotic meta-genomic units. Members of host-associated microbiomes have commensalic, beneficial/symbiotic, or pathogenic phenotypes. More than 100 years ago, Lorenz Hiltner, pioneer of soil microbiology, introduced the term 'Rhizosphere' to characterize the observation that a high density of saprophytic, beneficial, and pathogenic microbes are attracted by root exudates. The balance between these types of microbes decide about the health of the host. Nowadays we know, that for the interaction of microbes with all eukaryotic hosts similar principles and processes of cooperative and competitive functions are in action. Small diffusible molecules like (phyto)hormones, volatiles and quorum sensing signals are examples for mediators of interspecies and cross-kingdom interactions. Quorum sensing of bacteria is mediated by different autoinducible metabolites in a density-dependent manner. In this perspective publication, the role of QS-related activities for the health of hosts will be discussed focussing mostly on N-acyl-homoserine lactones (AHL). It is also considered that in some cases very close phylogenetic relations exist between plant beneficial and opportunistic human pathogenic bacteria. Based on a genome and system-targeted new understanding, sociomicrobiological solutions are possible for the biocontrol of diseases and the health improvement of eukaryotic hosts.
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Affiliation(s)
- Anton Hartmann
- Faculty of Biology, Microbe-Host Interactions, Ludwig-Maximilian-University Munich, Grosshaderner Str. 2, D-82152 Planegg/Martinsried, Germany
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
| | - Tatiana Binder
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
| | - Michael Rothballer
- Department of Environmental Sciences, Helmholtz Zentrum Munich, German Research Center for Health and Environment, Research Unit Microbe-Plant Interactions, Ingolstädter Landstr. 1, D-85762 Neuherberg, Germany
- Helmholtz Zentrum Munich, German Research Center for Health and Environment, Institute of Network Biology, Ingolstädter Landstr. 1 D-85762 Neuherberg, Germany
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Velichko NS, Kokoulin MS, Dmitrenok PS, Grinev VS, Kuchur PD, Komissarov AS, Fedonenko YP. Lipopolysaccharides of Herbaspirillum species and their relevance for bacterium-host interactions. Int J Biol Macromol 2024; 261:129516. [PMID: 38278393 DOI: 10.1016/j.ijbiomac.2024.129516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/14/2023] [Accepted: 01/13/2024] [Indexed: 01/28/2024]
Abstract
The lipopolysaccharides of Herbaspirillum lusitanum P6-12T (HlP6-12T) and H. frisingense GSF30T (HfGSF30T) was isolated by phenol-water extraction from bacterial cells and was characterized using chemical analysis and SDS-PAGE. It was shown that these bacteria produce LPSs that differ in their physicochemical properties and macromolecular organization. In this paper, the lipid A structure of the HlP6-12T LPS, was characterized through chemical analyses and matrix-assisted laser desorption ionization (MALDI) mass spectrometry. To prove the effect of the size of micelles on their bioavailability, we examined the activity of both LPSs toward the morphology of wheat seedlings. Analysis of the HlP6-12T and HfGSF30T genomes showed no significant differences between the operons that encode proteins involved in the biosynthesis of the lipids A and core oligosaccharides. The difference may be due to the composition of the O-antigen operon. HfGSF30T has two copies of the rfb operon, with the main one divided into two fragments. In contrast, the HlP6-12T genome contains only a single rfb-containing operon, and the other O-antigen operons are not comparable at all. The integrity of O-antigen-related genes may also affect LPS variability of. Specifically, we have observed a hairpin structure in the middle of the O-antigen glycosyltransferase gene, which led to the division of the gene into two fragments, resulting in incorrect protein synthesis and potential abnormalities in O-antigen production.
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Affiliation(s)
- Natalya S Velichko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia.
| | - Maxim S Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospekt 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - Pavel S Dmitrenok
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospekt 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - Vyacheslav S Grinev
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia; Saratov State University, 83 Ulitsa Astrakhanskaya, Saratov 410012, Russia
| | - Polina D Kuchur
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 9 Ulitsa Lomonosova, St. Petersburg 191002, Russia
| | - Aleksey S Komissarov
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, 9 Ulitsa Lomonosova, St. Petersburg 191002, Russia
| | - Yulia P Fedonenko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), 13 Prospekt Entuziastov, Saratov 410049, Russia; G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospekt 100 Let Vladivostoku, Vladivostok 690022, Russia
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van Schaik J, Li Z, Cheadle J, Crook N. Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant-Microbe Interactions. ACS Synth Biol 2023; 12:3030-3040. [PMID: 37712562 DOI: 10.1021/acssynbio.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Sustainably enhancing crop production is a global necessity to meet the escalating demand for staple crops while sustainably managing their associated carbon/nitrogen inputs. Leveraging plant-associated microbiomes is a promising avenue for addressing this demand. However, studying these communities and engineering them for sustainable enhancement of crop production have remained a challenge due to limited genetic tools and methods. In this work, we detail the development of the Maize Root Microbiome ToolKit (MRMTK), a rapid Modular Cloning (MoClo) toolkit that only takes 2.5 h to generate desired constructs (5400 potential plasmids) that replicate and express heterologous genes in Enterobacter ludwigii strain AA4 (Elu), Pseudomonas putida strain AA7 (Ppu), Herbaspirillum robiniae strain AA6 (Hro), Stenotrophomonas maltophilia strain AA1 (Sma), and Brucella pituitosa strain AA2 (Bpi), which comprise a model maize root synthetic community (SynCom). In addition to these genetic tools, we describe a highly efficient transformation protocol (107-109 transformants/μg of DNA) 1 for each of these strains. Utilizing this highly efficient transformation protocol, we identified endogenous Expression Sequences (ES; promoter and ribosomal binding sites) for each strain via genomic promoter trapping. Overall, MRMTK is a scalable and adaptable platform that expands the genetic engineering toolbox while providing a standardized, high-efficiency transformation method across a diverse group of root commensals. These results unlock the ability to elucidate and engineer plant-microbe interactions promoting plant growth for each of the 5 bacterial strains in this study.
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Affiliation(s)
- John van Schaik
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - Zidan Li
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - John Cheadle
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Room 2109, Partners II, 840 Main Campus Drive, Raleigh, North Carolina 27606, United States
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Pedrolo AM, Matteoli FP, Soares CRFS, Arisi ACM. Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02084-8. [PMID: 35932316 DOI: 10.1007/s00248-022-02084-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The genus Herbaspirillum gained the spotlight due to the several reports of diazotrophic strains and promising results in plant-growth field assays. However, as diversity exploration of Herbaspirillum species gained momentum, it became clearer that the plant beneficial lifestyle was not the only form of ecological interaction in this genus, due to reports of phytopathogenesis and nosocomial infections. Here we performed a deep search across all publicly available Herbaspirillum genomes. Using a robust core genome phylogeny, we have found that all described species are well delineated, being the only exception H. aquaticum and H. huttiense clade. We also uncovered that the nif genes are only highly prevalent in H. rubrisubalbicans; however, irrespective to the species, all nif genes share the same gene arrangement with high protein identity, and are present in only two main types, in inverted strands. By means of a NifHDKENB phylogenetic tree, we have further revealed that the Herbaspirillum nif sequences may have been acquired from the same last common ancestor belonging to the Nitrosomonadales order.
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Affiliation(s)
- Ana Marina Pedrolo
- CAL CCA UFSC, Food Science and Technology Department, Federal University of Santa Catarina, Rod. Admar Gonzaga, Florianopolis, SC, 1346, 88034-001, Brazil
| | - Filipe Pereira Matteoli
- ESALQ USP, Soil Science Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil.
| | - Cláudio Roberto Fônseca Sousa Soares
- MIP CCB UFSC, Microbiology, Immunology and Parasitology Department, Federal University of Santa Catarina, Av. Prof. Henrique da Silva Fontes, Florianopolis, SC, 2754, 88040-900, Brazil
| | - Ana Carolina Maisonnave Arisi
- CAL CCA UFSC, Food Science and Technology Department, Federal University of Santa Catarina, Rod. Admar Gonzaga, Florianopolis, SC, 1346, 88034-001, Brazil
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Amelioration in traditional farming system by exploring the different plant growth-promoting attributes of endophytes for sustainable agriculture. Arch Microbiol 2022; 204:151. [DOI: 10.1007/s00203-021-02637-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022]
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Hu X, Wei X, Ling J, Chen J. Cobalt: An Essential Micronutrient for Plant Growth? FRONTIERS IN PLANT SCIENCE 2021; 12:768523. [PMID: 34868165 PMCID: PMC8635114 DOI: 10.3389/fpls.2021.768523] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/29/2021] [Indexed: 05/19/2023]
Abstract
Cobalt is a transition metal located in the fourth row of the periodic table and is a neighbor of iron and nickel. It has been considered an essential element for prokaryotes, human beings, and other mammals, but its essentiality for plants remains obscure. In this article, we proposed that cobalt (Co) is a potentially essential micronutrient of plants. Co is essential for the growth of many lower plants, such as marine algal species including diatoms, chrysophytes, and dinoflagellates, as well as for higher plants in the family Fabaceae or Leguminosae. The essentiality to leguminous plants is attributed to its role in nitrogen (N) fixation by symbiotic microbes, primarily rhizobia. Co is an integral component of cobalamin or vitamin B12, which is required by several enzymes involved in N2 fixation. In addition to symbiosis, a group of N2 fixing bacteria known as diazotrophs is able to situate in plant tissue as endophytes or closely associated with roots of plants including economically important crops, such as barley, corn, rice, sugarcane, and wheat. Their action in N2 fixation provides crops with the macronutrient of N. Co is a component of several enzymes and proteins, participating in plant metabolism. Plants may exhibit Co deficiency if there is a severe limitation in Co supply. Conversely, Co is toxic to plants at higher concentrations. High levels of Co result in pale-colored leaves, discolored veins, and the loss of leaves and can also cause iron deficiency in plants. It is anticipated that with the advance of omics, Co as a constitute of enzymes and proteins and its specific role in plant metabolism will be exclusively revealed. The confirmation of Co as an essential micronutrient will enrich our understanding of plant mineral nutrition and improve our practice in crop production.
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Affiliation(s)
- Xiu Hu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Xiangying Wei
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Xiangying Wei
| | - Jie Ling
- He Xiangning College of Art and Design, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Jianjun Chen
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL, United States
- *Correspondence: Jianjun Chen
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Camelo A, Barreto CP, Vidal MS, Rouws JRC, da Silva Lédo FJ, Schwab S, Baldani JI. Field response of two seed propagated elephant grass genotypes to diazotrophic bacterial inoculation and in situ confocal microscopy colonization analyses. Symbiosis 2020. [DOI: 10.1007/s13199-020-00730-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Fadiji AE, Babalola OO. Exploring the potentialities of beneficial endophytes for improved plant growth. Saudi J Biol Sci 2020; 27:3622-3633. [PMID: 33304173 PMCID: PMC7714962 DOI: 10.1016/j.sjbs.2020.08.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 11/23/2022] Open
Abstract
Pathogen affects plant growth, host health and productivity. Endophytes, presumed to live inside the plant tissues, might be helpful in sustaining the future of agriculture. Although recent studies have proven that endophytes can be pathogenic, commensal, non-pathogenic, and/or beneficial, this review will focus on the beneficial category only. Beneficial endophytes produce a number of compounds which are useful for protecting plants from environmental conditions, enhancing plant growth and sustainability, while living conveniently inside the hosts. The population of endophytes is majorly controlled by location, and climatic conditions where the host plant grows. Often the most frequently isolated endophytes from the tissues of the plant are fungi, but sometimes greater numbers of bacteria are isolated. Beneficial endophytes stand a chance to replace the synthetic chemicals currently being used for plant growth promotion if carefully explored by researchers and embraced by policymakers. However, the roles of endophytes in plant growth improvement and their behavior in the host plant have not been fully understood. This review presents the current development of research into beneficial endophytes and their effect in improving plant growth.
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Affiliation(s)
- Ayomide Emmanuel Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, Private Mail Bag X2046, North-West University, South Africa
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Romano I, Ventorino V, Pepe O. Effectiveness of Plant Beneficial Microbes: Overview of the Methodological Approaches for the Assessment of Root Colonization and Persistence. FRONTIERS IN PLANT SCIENCE 2020; 11:6. [PMID: 32076431 PMCID: PMC7006617 DOI: 10.3389/fpls.2020.00006] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/06/2020] [Indexed: 05/22/2023]
Abstract
Issues concerning the use of harmful chemical fertilizers and pesticides that have large negative impacts on environmental and human health have generated increasing interest in the use of beneficial microorganisms for the development of sustainable agri-food systems. A successful microbial inoculant has to colonize the root system, establish a positive interaction and persist in the environment in competition with native microorganisms living in the soil through rhizocompetence traits. Currently, several approaches based on culture-dependent, microscopic and molecular methods have been developed to follow bioinoculants in the soil and plant surface over time. Although culture-dependent methods are commonly used to estimate the persistence of bioinoculants, it is difficult to differentiate inoculated organisms from native populations based on morphological characteristics. Therefore, these methods should be used complementary to culture-independent approaches. Microscopy-based techniques (bright-field, electron and fluorescence microscopy) allow to obtain a picture of microbial colonization outside and inside plant tissues also at high resolution, but it is not possible to always distinguish living cells from dead cells by direct observation as well as distinguish bioinoculants from indigenous microbial populations living in soils. In addition, the development of metagenomic techniques, including the use of DNA probes, PCR-based methods, next-generation sequencing, whole-genome sequencing and pangenome methods, provides a complementary approach useful to understand plant-soil-microbe interactions. However, to ensure good results in microbiological analysis, the first fundamental prerequisite is correct soil sampling and sample preparation for the different methodological approaches that will be assayed. Here, we provide an overview of the advantages and limitations of the currently used methods and new methodological approaches that could be developed to assess the presence, plant colonization and soil persistence of bioinoculants in the rhizosphere. We further discuss the possibility of integrating multidisciplinary approaches to examine the variations in microbial communities after inoculation and to track the inoculated microbial strains.
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Affiliation(s)
- Ida Romano
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| | - Valeria Ventorino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- *Correspondence: Valeria Ventorino,
| | - Olimpia Pepe
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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Liu B, Ji M, Zhai H. Anodic potentials, electricity generation and bacterial community as affected by plant roots in sediment microbial fuel cell: Effects of anode locations. CHEMOSPHERE 2018; 209:739-747. [PMID: 29960941 DOI: 10.1016/j.chemosphere.2018.06.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 05/26/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
A planted sediment microbial fuel cell (PSMFC) is a promising new technology for harvesting energy and remediating a contaminated geo-environment. In this study, the effects of roots (of Acorus tatarinowii) on oxygen profiles in sediment, power generation, and anodic bacterial community were investigated in PSMFCs and unplanted SMFCs with different anode locations to roots. The presence of plant did not improve the electricity generation when roots were placed on the surface of an anode because a high amount of oxygen loss from roots increased the redox potential at anode and made aerobic bacteria co-exit and compete with electrochemically active bacteria in substance utilization. It was suggested to place the anode under the roots with a proper distance, where the PSMFCs made use of root-derived organics, avoiding the negative effects of oxygen loss. Oxygen loss could control the diurnal rhythm of power generation in the PSMFCs.
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Affiliation(s)
- Boyue Liu
- School of Environmental Science and Engineering, Tianjin University, Weijin Road 92, Tianjin, 300072, China
| | - Min Ji
- School of Environmental Science and Engineering, Tianjin University, Weijin Road 92, Tianjin, 300072, China
| | - Hongyan Zhai
- School of Environmental Science and Engineering, Tianjin University, Weijin Road 92, Tianjin, 300072, China.
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Kljujev I, Raicevic V, Jovicic-Petrovic J, Vujovic B, Mirkovic M, Rothballer M. Listeria monocytogenes – Danger for health safety vegetable production. Microb Pathog 2018; 120:23-31. [DOI: 10.1016/j.micpath.2018.04.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/12/2018] [Accepted: 04/19/2018] [Indexed: 10/17/2022]
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14
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Towards a better greener future - an alternative strategy using biofertilizers. I: Plant growth promoting bacteria. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Jain P, Pundir RK. Potential Role of Endophytes in Sustainable Agriculture-Recent Developments and Future Prospects. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2017. [DOI: 10.1007/978-3-319-66541-2_7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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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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17
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Glaeser SP, Imani J, Alabid I, Guo H, Kumar N, Kämpfer P, Hardt M, Blom J, Goesmann A, Rothballer M, Hartmann A, Kogel KH. Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. THE ISME JOURNAL 2016; 10:871-84. [PMID: 26495996 PMCID: PMC4796927 DOI: 10.1038/ismej.2015.163] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 07/23/2015] [Accepted: 08/03/2015] [Indexed: 12/23/2022]
Abstract
The Alphaproteobacterium Rhizobium radiobacter F4 (RrF4) was originally characterized as an endofungal bacterium in the beneficial endophytic Sebacinalean fungus Piriformospora indica. Although attempts to cure P. indica from RrF4 repeatedly failed, the bacterium can easily be grown in pure culture. Here, we report on RrF4's genome and the beneficial impact the free-living bacterium has on plants. In contrast to other endofungal bacteria, the genome size of RrF4 is not reduced. Instead, it shows a high degree of similarity to the plant pathogenic R. radiobacter (formerly: Agrobacterium tumefaciens) C58, except vibrant differences in both the tumor-inducing (pTi) and the accessor (pAt) plasmids, which can explain the loss of RrF4's pathogenicity. Similar to its fungal host, RrF4 colonizes plant roots without host preference and forms aggregates of attached cells and dense biofilms at the root surface of maturation zones. RrF4-colonized plants show increased biomass and enhanced resistance against bacterial leaf pathogens. Mutational analysis showed that, similar to P. indica, resistance mediated by RrF4 was dependent on the plant's jasmonate-based induced systemic resistance (ISR) pathway. Consistent with this, RrF4- and P. indica-induced pattern of defense gene expression were similar. In clear contrast to P. indica, but similar to plant growth-promoting rhizobacteria, RrF4 colonized not only the root outer cortex but also spread beyond the endodermis into the stele. On the basis of our findings, RrF4 is an efficient plant growth-promoting bacterium.
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Affiliation(s)
- Stefanie P Glaeser
- Institute of Applied Microbiology, Research Centre for BioSystems, Land Use and Nutrition, Justus-Liebig- University Giessen, Giessen, Germany
| | - Jafargholi Imani
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus-Liebig-University Giessen, Giessen, Germany
| | - Ibrahim Alabid
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus-Liebig-University Giessen, Giessen, Germany
| | - Huijuan Guo
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus-Liebig-University Giessen, Giessen, Germany
| | - Neelendra Kumar
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus-Liebig-University Giessen, Giessen, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Research Centre for BioSystems, Land Use and Nutrition, Justus-Liebig- University Giessen, Giessen, Germany
| | - Martin Hardt
- Biomedical Research Centre Seltersberg-Imaging Unit, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Michael Rothballer
- Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Anton Hartmann
- Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus-Liebig-University Giessen, Giessen, Germany
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Shin W, Islam R, Benson A, Joe MM, Kim K, Gopal S, Samaddar S, Banerjee S, Sa T. Role of Diazotrophic Bacteria in Biological Nitrogen Fixation and Plant Growth Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.7745/kjssf.2016.49.1.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Breidenbach B, Pump J, Dumont MG. Microbial Community Structure in the Rhizosphere of Rice Plants. Front Microbiol 2016; 6:1537. [PMID: 26793175 PMCID: PMC4710755 DOI: 10.3389/fmicb.2015.01537] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/21/2015] [Indexed: 01/26/2023] Open
Abstract
The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth.
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Affiliation(s)
- Björn Breidenbach
- Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Judith Pump
- Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
| | - Marc G Dumont
- Biogeochemistry, Max Planck Institute for Terrestrial Microbiology Marburg, Germany
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Han S, Li D, Trost E, Mayer KF, Vlot AC, Heller W, Schmid M, Hartmann A, Rothballer M. Systemic Responses of Barley to the 3-hydroxy-decanoyl-homoserine Lactone Producing Plant Beneficial Endophyte Acidovorax radicis N35. FRONTIERS IN PLANT SCIENCE 2016; 7:1868. [PMID: 28018401 PMCID: PMC5149536 DOI: 10.3389/fpls.2016.01868] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/25/2016] [Indexed: 05/18/2023]
Abstract
Quorum sensing auto-inducers of the N-acyl homoserine lactone (AHL) type produced by Gram-negative bacteria have different effects on plants including stimulation on root growth and/or priming or acquirement of systemic resistance in plants. In this communication the influence of AHL production of the plant growth promoting endophytic rhizosphere bacterium Acidovorax radicis N35 on barley seedlings was investigated. A. radicis N35 produces 3-hydroxy-C10-homoserine lactone (3-OH-C10-HSL) as the major AHL compound. To study the influence of this QS autoinducer on the interaction with barley, the araI-biosynthesis gene was deleted. The comparison of inoculation effects of the A. radicis N35 wild type and the araI mutant resulted in remarkable differences. While the N35 wild type colonized plant roots effectively in microcolonies, the araI mutant occurred at the root surface as single cells. Furthermore, in a mixed inoculum the wild type was much more prevalent in colonization than the araI mutant documenting that the araI mutation affected root colonization. Nevertheless, a significant plant growth promoting effect could be shown after inoculation of barley with the wild type and the araI mutant in soil after 2 months cultivation. While A. radicis N35 wild type showed only a very weak induction of early defense responses in plant RNA expression analysis, the araI mutant caused increased expression of flavonoid biosynthesis genes. This was corroborated by the accumulation of several flavonoid compounds such as saponarin and lutonarin in leaves of root inoculated barley seedlings. Thus, although the exact role of the flavonoids in this plant response is not clear yet, it can be concluded, that the synthesis of AHLs by A. radicis has implications on the perception by the host plant barley and thereby contributes to the establishment and function of the bacteria-plant interaction.
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Affiliation(s)
- Shengcai Han
- Research Unit Microbe-Plant Interactions, Department Environmental Sciences, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
| | - Dan Li
- Research Unit Microbe-Plant Interactions, Department Environmental Sciences, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
| | - Eva Trost
- Research Unit Plant Genome and Systems Biology, Department Environmental Sciences, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
| | - Klaus F. Mayer
- Research Unit Plant Genome and Systems Biology, Department Environmental Sciences, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
| | - A. Corina Vlot
- Department Environmental Sciences, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
| | - Werner Heller
- Department Environmental Sciences, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
| | - Michael Schmid
- Research Unit Microbe-Plant Interactions, Department Environmental Sciences, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
| | - Anton Hartmann
- Research Unit Microbe-Plant Interactions, Department Environmental Sciences, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
| | - Michael Rothballer
- Research Unit Microbe-Plant Interactions, Department Environmental Sciences, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)Neuherberg, Germany
- *Correspondence: Michael Rothballer
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de Souza R, Ambrosini A, Passaglia LM. Plant growth-promoting bacteria as inoculants in agricultural soils. Genet Mol Biol 2015; 38:401-19. [PMID: 26537605 PMCID: PMC4763327 DOI: 10.1590/s1415-475738420150053] [Citation(s) in RCA: 351] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/22/2015] [Indexed: 12/12/2022] Open
Abstract
Plant-microbe interactions in the rhizosphere are the determinants of plant health, productivity and soil fertility. Plant growth-promoting bacteria (PGPB) are bacteria that can enhance plant growth and protect plants from disease and abiotic stresses through a wide variety of mechanisms; those that establish close associations with plants, such as the endophytes, could be more successful in plant growth promotion. Several important bacterial characteristics, such as biological nitrogen fixation, phosphate solubilization, ACC deaminase activity, and production of siderophores and phytohormones, can be assessed as plant growth promotion (PGP) traits. Bacterial inoculants can contribute to increase agronomic efficiency by reducing production costs and environmental pollution, once the use of chemical fertilizers can be reduced or eliminated if the inoculants are efficient. For bacterial inoculants to obtain success in improving plant growth and productivity, several processes involved can influence the efficiency of inoculation, as for example the exudation by plant roots, the bacterial colonization in the roots, and soil health. This review presents an overview of the importance of soil-plant-microbe interactions to the development of efficient inoculants, once PGPB are extensively studied microorganisms, representing a very diverse group of easily accessible beneficial bacteria.
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Affiliation(s)
- Rocheli de Souza
- Departamento de Genética, Instituto de Biociências, Universidade Federal
do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Adriana Ambrosini
- Departamento de Genética, Instituto de Biociências, Universidade Federal
do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luciane M.P. Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal
do Rio Grande do Sul, Porto Alegre, RS, Brazil
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22
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Zeiller M, Rothballer M, Iwobi AN, Böhnel H, Gessler F, Hartmann A, Schmid M. Systemic colonization of clover (Trifolium repens) by Clostridium botulinum strain 2301. Front Microbiol 2015; 6:1207. [PMID: 26583010 PMCID: PMC4628109 DOI: 10.3389/fmicb.2015.01207] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/16/2015] [Indexed: 12/11/2022] Open
Abstract
In recent years, cases of botulism in cattle and other farm animals and also in farmers increased dramatically. It was proposed, that these cases could be affiliated with the spreading of compost or other organic manures contaminated with Clostridium botulinum spores on farm land. Thus, soils and fodder plants and finally farm animals could be contaminated. Therefore, the colonization behavior and interaction of the botulinum neurotoxin (BoNT D) producing C. botulinum strain 2301 and the non-toxin producing Clostridium sporogenes strain 1739 were investigated on clover (Trifolium repens) in a field experiment as well as in phytochamber experiments applying axenic and additionally soil based systems under controlled conditions. Plants were harvested and divided into root and shoot parts for further DNA isolation and polymerase chain reaction (PCR) assays; subsamples were fixed for fluorescence in situ hybridization analysis in combination with confocal laser scanning microscopy. In addition, we observed significant differences in the growth behavior of clover plants when inoculated with clostridial spores, indicating a plant growth promoting effect. Inoculated plants showed an increased growth index (shoot size, wet and dry weight) and an enlarged root system induced by the systemic colonization of clover by C. botulinum strain 2301. To target C. botulinum and C. sporogenes, 16S rDNA directed primers were used and to specifically detect C. botulinum, BoNT D toxin genes targeted primers, using a multiplex PCR approach, were applied. Our results demonstrate an effective colonization of roots and shoots of clover by C. botulinum strain 2301 and C. sporogenes strain 1739. Detailed analysis of colonization behavior showed that C. botulinum can occur as individual cells, in cell clusters and in microcolonies within the rhizosphere, lateral roots and within the roots tissue of clover.
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Affiliation(s)
- Matthias Zeiller
- Research Unit Microbe-Plant Interactions, Department for Environmental Sciences, German Research Center for Environmental Health - Helmholtz Zentrum München Neuherberg, Germany
| | - Michael Rothballer
- Research Unit Microbe-Plant Interactions, Department for Environmental Sciences, German Research Center for Environmental Health - Helmholtz Zentrum München Neuherberg, Germany
| | - Azuka N Iwobi
- Bavarian Health and Food Safety Authority Oberschleißheim, Germany
| | - Helge Böhnel
- Institute for Applied Biotechnology in the Tropics at the Georg-August University Goettingen Goettingen, Germany
| | - Frank Gessler
- Institute for Applied Biotechnology in the Tropics at the Georg-August University Goettingen Goettingen, Germany ; miprolab GmbH Goettingen, Germany
| | - Anton Hartmann
- Research Unit Microbe-Plant Interactions, Department for Environmental Sciences, German Research Center for Environmental Health - Helmholtz Zentrum München Neuherberg, Germany
| | - Michael Schmid
- Research Unit Microbe-Plant Interactions, Department for Environmental Sciences, German Research Center for Environmental Health - Helmholtz Zentrum München Neuherberg, Germany
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Zgadzaj R, James EK, Kelly S, Kawaharada Y, de Jonge N, Jensen DB, Madsen LH, Radutoiu S. A legume genetic framework controls infection of nodules by symbiotic and endophytic bacteria. PLoS Genet 2015; 11:e1005280. [PMID: 26042417 PMCID: PMC4456278 DOI: 10.1371/journal.pgen.1005280] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 05/14/2015] [Indexed: 11/18/2022] Open
Abstract
Legumes have an intrinsic capacity to accommodate both symbiotic and endophytic bacteria within root nodules. For the symbionts, a complex genetic mechanism that allows mutual recognition and plant infection has emerged from genetic studies under axenic conditions. In contrast, little is known about the mechanisms controlling the endophytic infection. Here we investigate the contribution of both the host and the symbiotic microbe to endophyte infection and development of mixed colonised nodules in Lotus japonicus. We found that infection threads initiated by Mesorhizobium loti, the natural symbiont of Lotus, can selectively guide endophytic bacteria towards nodule primordia, where competent strains multiply and colonise the nodule together with the nitrogen-fixing symbiotic partner. Further co-inoculation studies with the competent coloniser, Rhizobium mesosinicum strain KAW12, show that endophytic nodule infection depends on functional and efficient M. loti-driven Nod factor signalling. KAW12 exopolysaccharide (EPS) enabled endophyte nodule infection whilst compatible M. loti EPS restricted it. Analysis of plant mutants that control different stages of the symbiotic infection showed that both symbiont and endophyte accommodation within nodules is under host genetic control. This demonstrates that when legume plants are exposed to complex communities they selectively regulate access and accommodation of bacteria occupying this specialized environmental niche, the root nodule. Plants have evolved elaborated mechanisms to monitor microbial presence and to control their infection, therefore only particular microbes, so called “endophytes,” are able to colonise the internal tissues with minimal or no host damage. The legume root nodule is a unique environmental niche induced by symbiotic bacteria, but where multiple species, symbiotic and endophytic co-exist. Genetic studies of the binary interaction legume-symbiont led to the discovery of key components evolved in the two partners allowing mutual recognition and nodule infection. In contrast, there is limited knowledge about the endophytic nodule infection, the role of the legume host, or the symbiont in the process of nodule colonisation by endophytes. Here we focus on the early stages of nodule infection in order to identify which molecular signatures and genetic components favour/allow endophyte accommodation, and multiple species co-existence inside nodules. We found that colonisation of Lotus japonicus nodules by endophytic bacteria is a selective process, that endophyte nodule occupancy is host-controlled, and that exopolysaccharides are key bacterial features for chronic infection of nodules. Our strategy based on model legume genetics and co-inoculation can thus be used for identifying mechanisms operating behind host-microbes compatibility in environments where multiple species co-exist.
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Affiliation(s)
- Rafal Zgadzaj
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
- Carbohydrate Recognition and Signalling (CARB) Centre, Aarhus, Denmark
| | - Euan K. James
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Simon Kelly
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
- Carbohydrate Recognition and Signalling (CARB) Centre, Aarhus, Denmark
| | - Yasuyuki Kawaharada
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
- Carbohydrate Recognition and Signalling (CARB) Centre, Aarhus, Denmark
| | - Nadieh de Jonge
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
- Carbohydrate Recognition and Signalling (CARB) Centre, Aarhus, Denmark
| | - Dorthe B. Jensen
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
- Carbohydrate Recognition and Signalling (CARB) Centre, Aarhus, Denmark
| | - Lene H. Madsen
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
- Carbohydrate Recognition and Signalling (CARB) Centre, Aarhus, Denmark
| | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Aarhus University, Aarhus, Denmark
- Carbohydrate Recognition and Signalling (CARB) Centre, Aarhus, Denmark
- * E-mail:
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Farrar K, Bryant D, Cope-Selby N. Understanding and engineering beneficial plant-microbe interactions: plant growth promotion in energy crops. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1193-206. [PMID: 25431199 PMCID: PMC4265282 DOI: 10.1111/pbi.12279] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/22/2014] [Accepted: 10/09/2014] [Indexed: 05/16/2023]
Abstract
Plant production systems globally must be optimized to produce stable high yields from limited land under changing and variable climates. Demands for food, animal feed, and feedstocks for bioenergy and biorefining applications, are increasing with population growth, urbanization and affluence. Low-input, sustainable, alternatives to petrochemical-derived fertilizers and pesticides are required to reduce input costs and maintain or increase yields, with potential biological solutions having an important role to play. In contrast to crops that have been bred for food, many bioenergy crops are largely undomesticated, and so there is an opportunity to harness beneficial plant-microbe relationships which may have been inadvertently lost through intensive crop breeding. Plant-microbe interactions span a wide range of relationships in which one or both of the organisms may have a beneficial, neutral or negative effect on the other partner. A relatively small number of beneficial plant-microbe interactions are well understood and already exploited; however, others remain understudied and represent an untapped reservoir for optimizing plant production. There may be near-term applications for bacterial strains as microbial biopesticides and biofertilizers to increase biomass yield from energy crops grown on land unsuitable for food production. Longer term aims involve the design of synthetic genetic circuits within and between the host and microbes to optimize plant production. A highly exciting prospect is that endosymbionts comprise a unique resource of reduced complexity microbial genomes with adaptive traits of great interest for a wide variety of applications.
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Affiliation(s)
- Kerrie Farrar
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth UniversityAberystwyth, UK
- *Correspondence (Tel +0044 (0)1970 823097; fax 0044 (0)1970 828357; email )
| | - David Bryant
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth UniversityAberystwyth, UK
| | - Naomi Cope-Selby
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth UniversityAberystwyth, UK
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New insights into 1-aminocyclopropane-1-carboxylate (ACC) deaminase phylogeny, evolution and ecological significance. PLoS One 2014; 9:e99168. [PMID: 24905353 PMCID: PMC4048297 DOI: 10.1371/journal.pone.0099168] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 05/09/2014] [Indexed: 01/13/2023] Open
Abstract
The main objective of this work is the study of the phylogeny, evolution and ecological importance of the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, the activity of which represents one of the most important and studied mechanisms used by plant growth–promoting microorganisms. The ACC deaminase gene and its regulatory elements presence in completely sequenced organisms was verified by multiple searches in diverse databases, and based on the data obtained a comprehensive analysis was conducted. Strain habitat, origin and ACC deaminase activity were taken into account when analyzing the results. In order to unveil ACC deaminase origin, evolution and relationships with other closely related pyridoxal phosphate (PLP) dependent enzymes a phylogenetic analysis was also performed. The data obtained show that ACC deaminase is mostly prevalent in some Bacteria, Fungi and members of Stramenopiles. Contrary to previous reports, we show that ACC deaminase genes are predominantly vertically inherited in various bacterial and fungal classes. Still, results suggest a considerable degree of horizontal gene transfer events, including interkingdom transfer events. A model for ACC deaminase origin and evolution is also proposed. This study also confirms the previous reports suggesting that the Lrp-like regulatory protein AcdR is a common mechanism regulating ACC deaminase expression in Proteobacteria, however, we also show that other regulatory mechanisms may be present in some Proteobacteria and other bacterial phyla. In this study we provide a more complete view of the role for ACC deaminase than was previously available. The results show that ACC deaminase may not only be related to plant growth promotion abilities, but may also play multiple roles in microorganism's developmental processes. Hence, exploring the origin and functioning of this enzyme may be the key in a variety of important agricultural and biotechnological applications.
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Cardinale M. Scanning a microhabitat: plant-microbe interactions revealed by confocal laser microscopy. Front Microbiol 2014; 5:94. [PMID: 24639675 PMCID: PMC3945399 DOI: 10.3389/fmicb.2014.00094] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/20/2014] [Indexed: 12/03/2022] Open
Abstract
No plant or cryptogam exists in nature without microorganisms associated with its tissues. Plants as microbial hosts are puzzles of different microhabitats, each of them colonized by specifically adapted microbiomes. The interactions with such microorganisms have drastic effects on the host fitness. Since the last 20 years, the combination of microscopic tools and molecular approaches contributed to new insights into microbe-host interactions. Particularly, confocal laser scanning microscopy (CLSM) facilitated the exploration of microbial habitats and allowed the observation of host-associated microorganisms in situ with an unprecedented accuracy. Here I present an overview of the progresses made in the study of the interactions between microorganisms and plants or plant-like organisms, focusing on the role of CLSM for the understanding of their significance. I critically discuss risks of misinterpretation when procedures of CLSM are not properly optimized. I also review approaches for quantitative and statistical analyses of CLSM images, the combination with other molecular and microscopic methods, and suggest the re-evaluation of natural autofluorescence. In this review, technical aspects were coupled with scientific outcomes, to facilitate the readers in identifying possible CLSM applications in their research or to expand their existing potential. The scope of this review is to highlight the importance of confocal microscopy in the study of plant-microbe interactions and also to be an inspiration for integrating microscopy with molecular techniques in future researches of microbial ecology.
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Affiliation(s)
- Massimiliano Cardinale
- Institute of Plant Sciences, University of GrazGraz, Austria
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, Austria
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Fungal growth promotor endophytes: a pragmatic approach towards sustainable food and agriculture. Symbiosis 2014. [DOI: 10.1007/s13199-014-0273-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Straub D, Yang H, Liu Y, Tsap T, Ludewig U. Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30(T). JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4603-15. [PMID: 24043849 PMCID: PMC3808336 DOI: 10.1093/jxb/ert276] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The bacterial endophyte Herbaspirillum frisingense GSF30(T) is a colonizer of several grasses grown in temperate climates, including the highly nitrogen-efficient perennial energy grass Miscanthus. Inoculation of Miscanthus sinensis seedlings with H. frisingense promoted root and shoot growth but had only a minor impact on nutrient concentrations. The bacterium affected the root architecture and increased fine-root structures. Although H. frisingense has the genetic requirements to fix nitrogen, only minor changes in nitrogen concentrations were observed. Herbaspirillum agglomerates were identified primarily in the root apoplast but also in the shoots. The short-term (3h) and long-term (3 weeks) transcriptomic responses of the plant to bacterial inoculation revealed that H. frisingense induced rapid changes in plant hormone signalling, most prominent in jasmonate signalling. Ethylene signalling pathways were also affected and persisted after 3 weeks in the root. Growth stimulation of the root by the ethylene precursor 1-aminocyclopropane 1-carboxylic acid was dose dependent and was affected by H. frisingense inoculation. Minor changes in the proteome were identified after 3 weeks. This study suggests that H. frisingense improves plant growth by modulating plant hormone signalling pathways and provides a framework to understand the beneficial effects of diazotrophic plant-growth-promoting bacteria, such as H. frisingense, on the biomass grass Miscanthus.
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Affiliation(s)
- Daniel Straub
- Institut für Kulturpflanzenwissenschaften, Ernährungsphysiologie der Kulturpflanzen (340h), Universität Hohenheim, Fruwirthstrasse 20, D-70593 Stuttgart, Germany
| | - Huaiyu Yang
- Institut für Kulturpflanzenwissenschaften, Ernährungsphysiologie der Kulturpflanzen (340h), Universität Hohenheim, Fruwirthstrasse 20, D-70593 Stuttgart, Germany
| | - Yan Liu
- Institut für Kulturpflanzenwissenschaften, Ernährungsphysiologie der Kulturpflanzen (340h), Universität Hohenheim, Fruwirthstrasse 20, D-70593 Stuttgart, Germany
| | - Tatsiana Tsap
- Institut für Kulturpflanzenwissenschaften, Ernährungsphysiologie der Kulturpflanzen (340h), Universität Hohenheim, Fruwirthstrasse 20, D-70593 Stuttgart, Germany
| | - Uwe Ludewig
- Institut für Kulturpflanzenwissenschaften, Ernährungsphysiologie der Kulturpflanzen (340h), Universität Hohenheim, Fruwirthstrasse 20, D-70593 Stuttgart, Germany
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Constitutive expression of fluorescent protein by Aspergillus var. niger and Aspergillus carbonarius to monitor fungal colonization in maize plants. J Microbiol Methods 2013; 94:381-9. [PMID: 23899775 DOI: 10.1016/j.mimet.2013.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 11/21/2022]
Abstract
Aspergillus niger and Aspergillus carbonarius are two species in the Aspergillus section Nigri (black-spored aspergilli) frequently associated with peanut (Arachis hypogea), maize (Zea mays), and other plants as pathogens. These infections are symptomless and as such are major concerns since some black aspergilli produce important mycotoxins, ochratoxins A, and the fumonisins. To facilitate the study of the black aspergilli-maize interactions with maize during the early stages of infections, we developed a method that used the enhanced yellow fluorescent protein (eYFP) and the monomeric red fluorescent protein (mRFP1) to transform A. niger and A. carbonarius, respectively. The results were constitutive expressions of the fluorescent genes that were stable in the cytoplasms of hyphae and conidia under natural environmental conditions. The hyphal in planta distribution in 21-day-old seedlings of maize were similar wild type and transformants of A. niger and A. carbonarius. The in planta studies indicated that both wild type and transformants internally colonized leaf, stem and root tissues of maize seedlings, without any visible disease symptoms. Yellow and red fluorescent strains were capable of invading epidermal cells of maize roots intercellularly within the first 3 days after inoculation, but intracellular hyphal growth was more evident after 7 days of inoculation. We also tested the capacity of fluorescent transformants to produce ochratoxin A and the results with A. carbonarius showed that this transgenic strain produced similar concentrations of this secondary metabolite. This is the first report on the in planta expression of fluorescent proteins that should be useful to study the internal plant colonization patterns of two ochratoxigenic species in the Aspergillus section Nigri.
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Straub D, Rothballer M, Hartmann A, Ludewig U. The genome of the endophytic bacterium H. frisingense GSF30(T) identifies diverse strategies in the Herbaspirillum genus to interact with plants. Front Microbiol 2013; 4:168. [PMID: 23825472 PMCID: PMC3695564 DOI: 10.3389/fmicb.2013.00168] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/03/2013] [Indexed: 01/14/2023] Open
Abstract
The diazotrophic, bacterial endophyte Herbaspirillum frisingense GSF30T has been identified in biomass grasses grown in temperate climate, including the highly nitrogen-efficient grass Miscanthus. Its genome was annotated and compared with related Herbaspirillum species from diverse habitats, including H. seropedicae, and further well-characterized endophytes. The analysis revealed that Herbaspirillum frisingense lacks a type III secretion system that is present in some related Herbaspirillum grass endophytes. Together with the lack of components of the type II secretion system, the genomic inventory indicates distinct interaction scenarios of endophytic Herbaspirillum strains with plants. Differences in respiration, carbon, nitrogen and cell wall metabolism among Herbaspirillum isolates partially correlate with their different habitats. Herbaspirillum frisingense is closely related to strains isolated from the rhizosphere of phragmites and from well water, but these lack nitrogen fixation and metabolism genes. Within grass endophytes, the high diversity in their genomic inventory suggests that even individual plant species provide distinct, highly diverse metabolic niches for successful endophyte-plant associations.
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Affiliation(s)
- Daniel Straub
- Institut für Kulturpflanzenwissenschaften, Ernährungsphysiologie der Kulturpflanzen (340h), Universität Hohenheim Stuttgart, Germany
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Schmidt MA, Balsanelli E, Faoro H, Cruz LM, Wassem R, de Baura VA, Weiss V, Yates MG, Madeira HMF, Pereira-Ferrari L, Fungaro MHP, de Paula FM, Pereira LFP, Vieira LGE, Olivares FL, Pedrosa FO, de Souza EM, Monteiro RA. The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between Herbaspirillum rubrisubalbicans and Poaceae. BMC Microbiol 2012; 12:98. [PMID: 22672506 PMCID: PMC3487950 DOI: 10.1186/1471-2180-12-98] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/24/2012] [Indexed: 11/17/2022] Open
Abstract
Background Herbaspirillum rubrisubalbicans was first identified as a bacterial plant pathogen, causing the mottled stripe disease in sugarcane. H. rubrisubalbicans can also associate with various plants of economic interest in a non pathogenic manner. Results A 21 kb DNA region of the H. rubrisubalbicans genome contains a cluster of 26 hrp/hrc genes encoding for the type three secretion system (T3SS) proteins. To investigate the contribution of T3SS to the plant-bacterial interaction process we generated mutant strains of H. rubrisubalbicans M1 carrying a Tn5 insertion in both the hrcN and hrpE genes. H. rubrisulbalbicans hrpE and hrcN mutant strains of the T3SS system failed to cause the mottled stripe disease in the sugarcane susceptible variety B-4362. These mutant strains also did not produce lesions on Vigna unguiculata leaves. Oryza sativa and Zea mays colonization experiments showed that mutations in hrpE and hrcN genes reduced the capacity of H. rubrisulbalbicans to colonize these plants, suggesting that hrpE and hrcN genes are involved in the endophytic colonization. Conclusions Our results indicate that the T3SS of H. rubrisubalbicans is necessary for the development of the mottled stripe disease and endophytic colonization of rice.
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Affiliation(s)
- Maria Augusta Schmidt
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
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Mao Y, Yannarell AC, Mackie RI. Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops. PLoS One 2011; 6:e24750. [PMID: 21935454 PMCID: PMC3173469 DOI: 10.1371/journal.pone.0024750] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 08/16/2011] [Indexed: 11/18/2022] Open
Abstract
Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.
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Affiliation(s)
- Yuejian Mao
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Anthony C. Yannarell
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Roderick I. Mackie
- Energy Biosciences Institute, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Animal Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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Reinhold-Hurek B, Hurek T. Living inside plants: bacterial endophytes. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:435-43. [PMID: 21536480 DOI: 10.1016/j.pbi.2011.04.004] [Citation(s) in RCA: 365] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 04/08/2011] [Accepted: 04/11/2011] [Indexed: 05/03/2023]
Abstract
As current research activities have focused on symbiotic or parasitic plant-microbe interactions, other types of associations between plants and microorganisms are often overlooked. Endophytic bacteria colonize inner host tissues, sometimes in high numbers, without damaging the host or eliciting strong defense responses. Unlike endosymbionts they are not residing in living plant cells or surrounded by a membrane compartment. The molecular basis of endophytic interactions is still not well understood. Several traits involved in the establishment of endophytes have been elucidated. Culture-independent methods for community analysis and functional genomic as well as comparative genomic analyses will provide a better understanding of community dynamics, signaling, and functions in endophyte-plant associations.
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Affiliation(s)
- Barbara Reinhold-Hurek
- University Bremen, Department of Molecular Plant Microbiology, Center for Biomolecular Interactions Bremen, 28334 Bremen, Germany.
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Li Z, Chang S, Lin L, Li Y, An Q. A colorimetric assay of 1-aminocyclopropane-1-carboxylate (ACC) based on ninhydrin reaction for rapid screening of bacteria containing ACC deaminase. Lett Appl Microbiol 2011; 53:178-85. [DOI: 10.1111/j.1472-765x.2011.03088.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Paungfoo-Lonhienne C, Rentsch D, Robatzek S, Webb RI, Sagulenko E, Näsholm T, Schmidt S, Lonhienne TGA. Turning the table: plants consume microbes as a source of nutrients. PLoS One 2010; 5:e11915. [PMID: 20689833 PMCID: PMC2912860 DOI: 10.1371/journal.pone.0011915] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 07/07/2010] [Indexed: 11/21/2022] Open
Abstract
Interactions between plants and microbes in soil, the final frontier of ecology, determine the availability of nutrients to plants and thereby primary production of terrestrial ecosystems. Nutrient cycling in soils is considered a battle between autotrophs and heterotrophs in which the latter usually outcompete the former, although recent studies have questioned the unconditional reign of microbes on nutrient cycles and the plants' dependence on microbes for breakdown of organic matter. Here we present evidence indicative of a more active role of plants in nutrient cycling than currently considered. Using fluorescent-labeled non-pathogenic and non-symbiotic strains of a bacterium and a fungus (Escherichia coli and Saccharomyces cerevisiae, respectively), we demonstrate that microbes enter root cells and are subsequently digested to release nitrogen that is used in shoots. Extensive modifications of root cell walls, as substantiated by cell wall outgrowth and induction of genes encoding cell wall synthesizing, loosening and degrading enzymes, may facilitate the uptake of microbes into root cells. Our study provides further evidence that the autotrophy of plants has a heterotrophic constituent which could explain the presence of root-inhabiting microbes of unknown ecological function. Our discovery has implications for soil ecology and applications including future sustainable agriculture with efficient nutrient cycles.
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Fekete A, Kuttler C, Rothballer M, Hense BA, Fischer D, Buddrus-Schiemann K, Lucio M, Müller J, Schmitt-Kopplin P, Hartmann A. Dynamic regulation ofN-acyl-homoserine lactone production and degradation inPseudomonas putidaIsoF. FEMS Microbiol Ecol 2010; 72:22-34. [DOI: 10.1111/j.1574-6941.2009.00828.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Abstract
This review describes the chemistry of the bacterial biofilms including the chemistry of their constituents and signalling compounds that mediate or inhibit the formation of biofilms. Systems are described with special emphasis, in which quorum sensing molecules (autoinducers) trigger the formation of biofilms. In the first instance, N-acyl-L-homoserine lactones (AHLs) are the focus of this review, whereas the inter-species signal known as furanosyl borate diester and peptide autoinducers used by Gram-positive bacteria are not discussed in detail. Since the first discovery of an AHL autoinducer from Vibrio fischeri a large and further increasing number of different AHL structures from Gram-negative bacteria have been identified. This review gives a summary of all known AHL autoinducers and producing bacterial species. A few systems are discussed, where biofilm formation is suppressed by enzymatic degradation of AHL molecules or interference of secondary metabolites from other species with the quorum sensing systems of communicating bacteria. Finally, the multi-channel quorum sensing system, the intracellular downstream processing of the signal, and the resulting response of whole populations including biofilm formation are discussed for the Vibrio genus that has been extensively investigated.
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Affiliation(s)
- Jeroen S Dickschat
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, Braunschweig, Germany.
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