1
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Harten T, Nimzyk R, Gawlick VEA, Reinhold-Hurek B. Elucidation of Essential Genes and Mutant Fitness during Adaptation toward Nitrogen Fixation Conditions in the Endophyte Azoarcus olearius BH72 Revealed by Tn-Seq. Microbiol Spectr 2022; 10:e0216222. [PMID: 36416558 PMCID: PMC9769520 DOI: 10.1128/spectrum.02162-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/05/2022] [Indexed: 11/24/2022] Open
Abstract
Azoarcus olearius BH72 is a diazotrophic model endophyte that contributes fixed nitrogen to its host plant, Kallar grass, and expresses nitrogenase genes endophytically. Despite extensive studies on biological nitrogen fixation (BNF) of diazotrophic endophytes, little is known about global genetic players involved in survival under respective physiological conditions. Here, we report a global genomic screen for putatively essential genes of A. olearius employing Tn5 transposon mutagenesis with a modified transposon combined with high-throughput sequencing (Tn-Seq). A large Tn5 master library of ~6 × 105 insertion mutants of strain BH72 was obtained. Next-generation sequencing identified 183,437 unique insertion sites into the 4,376,040-bp genome, displaying one insertion every 24 bp on average. Applying stringent criteria, we describe 616 genes as putatively essential for growth on rich medium. COG (Clusters of Orthologous Groups) assignment of the 564 identified protein-coding genes revealed enrichment of genes related to core cellular functions and cell viability. To mimic gradual adaptations toward BNF conditions, the Tn5 mutant library was grown aerobically in synthetic medium or microaerobically on either combined or atmospheric nitrogen. Enrichment and depletion analysis of Tn5 mutants not only demonstrated the role of BNF- and metabolism-related proteins but also revealed that, strikingly, many genes relevant for plant-microbe interactions decrease bacterial competitiveness in pure culture, such type IV pilus- and bacterial envelope-associated genes. IMPORTANCE A constantly growing world population and the daunting challenge of climate change demand new strategies in agricultural crop production. Intensive usage of chemical fertilizers, overloading the world's fields with organic input, threaten terrestrial and marine ecosystems as well as human health. Long overlooked, the beneficial interaction of endophytic bacteria and grasses has attracted ever-growing interest in research in the last decade. Capable of biological nitrogen fixation, diazotrophic endophytes not only provide a valuable source of combined nitrogen but also are known for diverse plant growth-promoting effects, thereby contributing to plant productivity. Elucidation of an essential gene set for a prominent model endophyte such as A. olearius BH72 provides us with powerful insights into its basic lifestyle. Knowledge about genes detrimental or advantageous under defined physiological conditions may point out a way of manipulating key steps in the bacterium's lifestyle and plant interaction toward a more sustainable agriculture.
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Affiliation(s)
- Theresa Harten
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
| | - Rolf Nimzyk
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Nucleic Acid Analysis Facility (NAA), Bremen, Germany
| | - Vivian E. A. Gawlick
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
| | - Barbara Reinhold-Hurek
- University of Bremen, Faculty of Biology and Chemistry, CBIB Center for Biomolecular Interactions, Department of Microbe-Plant Interactions, Bremen, Germany
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2
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Jiang X, Pees T, Reinhold-Hurek B. Deep-learning-based removal of autofluorescence and fluorescence quantification in plant-colonizing bacteria in vivo. THE NEW PHYTOLOGIST 2022; 235:2481-2495. [PMID: 35752974 DOI: 10.1111/nph.18344] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Fluorescence microscopy is common in bacteria-plant interaction studies. However, strong autofluorescence from plant tissues impedes in vivo studies on endophytes tagged with fluorescent proteins. To solve this problem, we developed a deep-learning-based approach to eliminate plant autofluorescence from fluorescence microscopy images, tested for the model endophyte Azoarcus olearius BH72 colonizing Oryza sativa roots. Micrographs from three channels (tdTomato for gene expression, green fluorescent protein (GFP) and AutoFluorescence (AF)) were processed by a neural network based approach, generating images that simulate the background autofluorescence in the tdTomato channel. After subtracting the model-generated signals from each pixel in the genuine channel, the autofluorescence in the tdTomato channel was greatly reduced or even removed. The deep-learning-based approach can be applied for fluorescence detection and quantification, exemplified by a weakly expressed, a cell-density modulated and a nitrogen-fixation gene in A. olearius. A transcriptional nifH::tdTomato fusion demonstrated stronger induction of nif genes inside roots than outside, suggesting extension of the rhizosphere effect for diazotrophs into the endorhizosphere. The pre-trained convolutional neural network model is easily applied to process other images of the same plant tissues with the same settings. This study showed the high potential of deep-learning-based approaches in image processing. With proper training data and strategies, autofluorescence in other tissues or materials can be removed for broad applications.
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Affiliation(s)
- Xun Jiang
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
| | - Tobias Pees
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
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3
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RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process. Microorganisms 2021; 9:microorganisms9091888. [PMID: 34576783 PMCID: PMC8467165 DOI: 10.3390/microorganisms9091888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Azoarcus olearius BH72 is an endophyte capable of biological nitrogen fixation (BNF) and of supplying nitrogen to its host plant. Our previous microarray approach provided insights into the transcriptome of strain BH72 under N2-fixation in comparison to ammonium-grown conditions, which already indicated the induction of genes not related to the BNF process. Due to the known limitations of the technique, we might have missed additional differentially expressed genes (DEGs). Thus, we used directional RNA-Seq to better comprehend the transcriptional landscape under these growth conditions. RNA-Seq detected almost 24% of the annotated genes to be regulated, twice the amount identified by microarray. In addition to confirming entire regulated operons containing known DEGs, the new approach detected the induction of genes involved in carbon metabolism and flagellar and twitching motility. This may support N2-fixation by increasing energy production and by finding suitable microaerobic niches. On the other hand, energy expenditures were reduced by suppressing translation and vitamin biosynthesis. Nonetheless, strain BH72 does not appear to be content with N2-fixation but is primed for alternative economic N-sources, such as nitrate, urea or amino acids; a strong gene induction of machineries for their uptake and assimilation was detected. RNA-Seq has thus provided a better understanding of a lifestyle under limiting nitrogen sources by elucidating hitherto unknown regulated processes.
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Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Plant-Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics 2020; 19:e1800105. [PMID: 31218790 DOI: 10.1002/pmic.201800105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/04/2019] [Indexed: 11/08/2022]
Abstract
Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.
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Affiliation(s)
- Behnam Khatabi
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD, 21853, USA
| | - Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, P. R. China
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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Agtuca BJ, Stopka SA, Tuleski TR, do Amaral FP, Evans S, Liu Y, Xu D, Monteiro RA, Koppenaal DW, Paša-Tolić L, Anderton CR, Vertes A, Stacey G. In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:272-283. [PMID: 31544655 DOI: 10.1094/mpmi-06-19-0174-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix+) or a fix- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix- strain, perhaps reflecting a plant defense response.
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Affiliation(s)
- Beverly J Agtuca
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sylwia A Stopka
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Thalita R Tuleski
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - Fernanda P do Amaral
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Sterling Evans
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Yang Liu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri Columbia
| | - Rose Adele Monteiro
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, CP 19046, 81.531-990 Curitiba, PR, Brazil
| | - David W Koppenaal
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Christopher R Anderton
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99354, U.S.A
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
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6
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Krause A, Julich H, Mankar M, Reinhold-Hurek B. The Regulatory Network Controlling Ethanol-Induced Expression of Alcohol Dehydrogenase in the Endophyte Azoarcus sp. Strain BH72. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:778-785. [PMID: 28657425 DOI: 10.1094/mpmi-01-17-0013-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The habitat of the nitrogen-fixing endophyte Azoarcus sp. strain BH72 is grass roots grown under waterlogged conditions that produce, under these conditions, ethanol. Strain BH72 is well equipped to metabolize ethanol, with eight alcohol dehydrogenases (ADHs), of which ExaA2 and ExaA3 are the most relevant ones. exaA2 and exaA3 cluster and are surrounded by genes encoding two-component regulatory systems (TCSs) termed ExaS-ExaR and ElmS-GacA. Functional genomic analyses revealed that i) expression of the corresponding genes was induced by ethanol, ii) the genes were also expressed in the rhizoplane or even inside of rice roots, iii) both TCSs were indispensable for growth on ethanol, and iv) they were important for competitiveness during rice root colonization. Both TCSs form a hierarchically organized ethanol-responsive signal transduction cascade with ExaS-ExaR as the highest level, essential for effective expression of the ethanol oxidation system based on ExaA2. Transcript and expression levels of exaA3 increased in tcs deletion mutants, suggesting no direct influence of both TCSs on its ethanol-induced expression. In conclusion, this underscores the importance of ethanol for the endophytic lifestyle of Azoarcus sp. strain BH72 and indicates a tight regulation of the ethanol oxidation system during root colonization.
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Affiliation(s)
- Andrea Krause
- Department of Microbe-Plant Interactions, Faculty of Biology/Chemistry, University of Bremen, P.O. Box 330440, 28334 Bremen, Germany
| | - Henrike Julich
- Department of Microbe-Plant Interactions, Faculty of Biology/Chemistry, University of Bremen, P.O. Box 330440, 28334 Bremen, Germany
| | - Manasee Mankar
- Department of Microbe-Plant Interactions, Faculty of Biology/Chemistry, University of Bremen, P.O. Box 330440, 28334 Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology/Chemistry, University of Bremen, P.O. Box 330440, 28334 Bremen, Germany
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7
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Foster ZSL, Sharpton TJ, Grünwald NJ. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data. PLoS Comput Biol 2017; 100:1738-50. [PMID: 28222096 DOI: 10.3732/ajb.1200572] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/07/2017] [Accepted: 02/10/2017] [Indexed: 05/20/2023] Open
Abstract
Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.
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Affiliation(s)
- Zachary S L Foster
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, Oregon, United States of America
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8
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Sarkar A, Marszalkowska M, Schäfer M, Pees T, Klingenberg H, Macht F, Reinhold-Hurek B. Global expression analysis of the response to microaerobiosis reveals an important cue for endophytic establishment of Azoarcus sp. BH72. Environ Microbiol 2016; 19:198-217. [PMID: 27727497 DOI: 10.1111/1462-2920.13569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/26/2016] [Accepted: 10/01/2016] [Indexed: 11/30/2022]
Abstract
The endophyte Azoarcus sp. BH72, fixing nitrogen microaerobically, encounters low O2 tensions in flooded roots. Therefore, its transcriptome upon shift to microaerobiosis was analyzed using oligonucleotide microarrays. A total of 8.7% of the protein-coding genes were significantly modulated. Aerobic conditions induced expression of genes involved in oxidative stress protection, while under microaerobiosis, 233 genes were upregulated, encoding hypothetical proteins, transcriptional regulators, and proteins involved in energy metabolism, among them a cbb3 -type terminal oxidase contributing to but not essential for N2 fixation. A newly established sensitive transcriptional reporter system using tdTomato allowed to visualize even relatively low bacterial gene expression in association with roots. Beyond metabolic changes, low oxygen concentrations seemed to prime transcription for plant colonization: Several genes known to be required for endophytic rice interaction were induced, and novel bacterial colonization factors were identified, such as azo1653. The cargo of the type V autotransporter Azo1653 had similarities to the attachment factor pertactin. Although for short term swarming-dependent colonization, it conferred a competitive disadvantage, it contributed to endophytic long-term establishment inside roots. Proteins sharing such opposing roles in the colonization process appear to occur more generally, as we demonstrated a very similar phenotype for another attachment protein, Azo1684. This suggests distinct cellular strategies for endophyte establishment.
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Affiliation(s)
- Abhijit Sarkar
- Faculty of Biology and Chemistry, Department of Microbe-Plant Interactions, University of Bremen, P.O. Box 33 04 40, Bremen, 28334, Germany
| | - Marta Marszalkowska
- Faculty of Biology and Chemistry, Department of Microbe-Plant Interactions, University of Bremen, P.O. Box 33 04 40, Bremen, 28334, Germany
| | - Martin Schäfer
- Faculty of Biology and Chemistry, Department of Microbe-Plant Interactions, University of Bremen, P.O. Box 33 04 40, Bremen, 28334, Germany
| | - Tobias Pees
- Faculty of Biology and Chemistry, Department of Microbe-Plant Interactions, University of Bremen, P.O. Box 33 04 40, Bremen, 28334, Germany
| | - Hannah Klingenberg
- Faculty of Biology and Chemistry, Department of Microbe-Plant Interactions, University of Bremen, P.O. Box 33 04 40, Bremen, 28334, Germany
| | - Franziska Macht
- Faculty of Biology and Chemistry, Department of Microbe-Plant Interactions, University of Bremen, P.O. Box 33 04 40, Bremen, 28334, Germany
| | - Barbara Reinhold-Hurek
- Faculty of Biology and Chemistry, Department of Microbe-Plant Interactions, University of Bremen, P.O. Box 33 04 40, Bremen, 28334, Germany
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Chen X, Miché L, Sachs S, Wang Q, Buschart A, Yang H, Vera Cruz CM, Hurek T, Reinhold-Hurek B. Rice responds to endophytic colonization which is independent of the common symbiotic signaling pathway. THE NEW PHYTOLOGIST 2015; 208:531-43. [PMID: 26009800 DOI: 10.1111/nph.13458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/13/2015] [Indexed: 05/11/2023]
Abstract
As molecular interactions of plants with N2 -fixing endophytes are largely uncharacterized, we investigated whether the common signaling pathway (CSP) shared by root nodule symbioses (RNS) and arbuscular mycorrhizal (AM) symbioses may have been recruited for the endophytic Azoarcus sp.-rice (Oryza sativa) interaction, and combined this investigation with global approaches to characterize rice root responses to endophytic colonization. Putative homologs of genes required for the CSP were analyzed for their putative role in endophytic colonization. Proteomic and suppressive subtractive hybridization (SSH) approaches were also applied, and a comparison of defense-related processes was carried out by setting up a pathosystem for flooded roots with Xanthomonas oryzae pv. oryzae strain PXO99 (Xoo). All tested genes were expressed in rice roots seedlings but not induced upon Azoarcus sp. inoculation, and the oscyclops and oscastor mutants were not impaired in endophytic colonization. Global approaches highlighted changes in rice metabolic activity and Ca(2+) -dependent signaling in roots colonized by endophytes, including some stress proteins. Marker genes for defense responses were induced to a lesser extent by the endophytes than by the pathogen, indicating a more compatible interaction. Our results thus suggest that rice roots respond to endophytic colonization by inducing metabolic shifts and signaling events, for which the CSP is not essential.
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Affiliation(s)
- Xi Chen
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Lucie Miché
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Sabrina Sachs
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Qi Wang
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Anna Buschart
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Haiyuan Yang
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Casiana M Vera Cruz
- The International Rice Research Institute, MCPC Box 3727, 1271, Makati, Philippines
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, PO Box 330440, D-28334, Bremen, Germany
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10
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Hypothetical protein Avin_16040 as the S-layer protein of Azotobacter vinelandii and its involvement in plant root surface attachment. Appl Environ Microbiol 2015; 81:7484-95. [PMID: 26276116 DOI: 10.1128/aem.02081-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/10/2015] [Indexed: 11/20/2022] Open
Abstract
A proteomic analysis of a soil-dwelling, plant growth-promoting Azotobacter vinelandii strain showed the presence of a protein encoded by the hypothetical Avin_16040 gene when the bacterial cells were attached to the Oryza sativa root surface. An Avin_16040 deletion mutant demonstrated reduced cellular adherence to the root surface, surface hydrophobicity, and biofilm formation compared to those of the wild type. By atomic force microscopy (AFM) analysis of the cell surface topography, the deletion mutant displayed a cell surface architectural pattern that was different from that of the wild type. Escherichia coli transformed with the wild-type Avin_16040 gene displayed on its cell surface organized motifs which looked like the S-layer monomers of A. vinelandii. The recombinant E. coli also demonstrated enhanced adhesion to the root surface.
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11
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Sarkar A, Reinhold-Hurek B. Transcriptional profiling of nitrogen fixation and the role of NifA in the diazotrophic endophyte Azoarcus sp. strain BH72. PLoS One 2014; 9:e86527. [PMID: 24516534 PMCID: PMC3916325 DOI: 10.1371/journal.pone.0086527] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 12/09/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The model endophyte Azoarcus sp. strain BH72 is known to contribute fixed nitrogen to its host Kallar grass and also expresses nitrogenase genes endophytically in rice seedlings. Availability of nitrogen is a signal regulating the transcription of nitrogenase genes. Therefore, we analysed global transcription in response to differences in the nitrogen source. METHODOLOGY/PRINCIPAL FINDINGS A DNA microarray, comprising 70-mer oligonucleotides representing 3989 open reading frames of the genome of strain BH72, was used for transcriptome studies. Transcription profiles of cells grown microaerobically on N2 versus ammonium were compared. Expression of 7.2% of the genes was significantly up-regulated, and 5.8% down-regulated upon N2 fixation, respectively. A parallel genome-wide prediction of σ(54)-type promoter elements mapped to the upstream region of 38 sequences of which 36 were modulated under the N2 response. In addition to modulation of genes related to N2 fixation, the expressions of gene clusters that might be related to plant-microbe interaction and of several transcription factors were significantly enhanced. While comparing under N2-fixation conditions the transcriptome of wild type with a nifLA(-) insertion mutant, NifA being the essential transcriptional activator for nif genes, 24.5% of the genome was found to be affected in expression. A genome-wide prediction of 29 NifA binding sequences matched to 25 of the target genes whose expression was differential during microarray analysis, some of which were putatively negatively regulated by NifA. For selected genes, differential expression was corroborated by real time RT-PCR studies. CONCLUSION/SIGNIFICANCE Our data suggest that life under conditions of nitrogen fixation is an important part of the lifestyle of strain BH72 in roots, as a wide range of genes far beyond the nif regulon is modulated. Moreover, the NifA regulon in strain BH72 appears to encompass a wider range of cellular functions beyond the regulation of nif genes.
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Affiliation(s)
- Abhijit Sarkar
- University of Bremen, Faculty of Biology, Department of Microbe-Plant Interactions, Bremen, Germany
| | - Barbara Reinhold-Hurek
- University of Bremen, Faculty of Biology, Department of Microbe-Plant Interactions, Bremen, Germany
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12
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Kozyrovska NO. Crosstalk between endophytes and a plant host within information-processing networks. ACTA ACUST UNITED AC 2013. [DOI: 10.7124/bc.00081d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- N. O. Kozyrovska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
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13
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Mitter B, Petric A, Shin MW, Chain PSG, Hauberg-Lotte L, Reinhold-Hurek B, Nowak J, Sessitsch A. Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. FRONTIERS IN PLANT SCIENCE 2013; 4:120. [PMID: 23641251 PMCID: PMC3639386 DOI: 10.3389/fpls.2013.00120] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/16/2013] [Indexed: 05/20/2023]
Abstract
Burkholderia phytofirmans PsJN is a naturally occurring plant-associated bacterial endophyte that effectively colonizes a wide range of plants and stimulates their growth and vitality. Here we analyze whole genomes, of PsJN and of eight other endophytic bacteria. This study illustrates that a wide spectrum of endophytic life styles exists. Although we postulate the existence of typical endophytic traits, no unique gene cluster could be exclusively linked to the endophytic lifestyle. Furthermore, our study revealed a high genetic diversity among bacterial endophytes as reflected in their genotypic and phenotypic features. B. phytofirmans PsJN is in many aspects outstanding among the selected endophytes. It has the biggest genome consisting of two chromosomes and one plasmid, well-equipped with genes for the degradation of complex organic compounds and detoxification, e.g., 24 glutathione-S-transferase (GST) genes. Furthermore, strain PsJN has a high number of cell surface signaling and secretion systems and harbors the 3-OH-PAME quorum-sensing system that coordinates the switch of free-living to the symbiotic lifestyle in the plant-pathogen R. solanacearum. The ability of B. phytofirmans PsJN to successfully colonize such a wide variety of plant species might be based on its large genome harboring a broad range of physiological functions.
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Affiliation(s)
- Birgit Mitter
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbHTulln, Austria
- *Correspondence: Birgit Mitter, Bioresources Unit, Austrian Institute of Technology Gmbh, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria. e-mail:
| | - Alexandra Petric
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbHTulln, Austria
| | - Maria W. Shin
- Department of Energy, Joint Genome InstituteWalnut Creek, CA, USA
| | | | | | | | - Jerzy Nowak
- Department of Agriculture and Life Sciences, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Angela Sessitsch
- Department of Health and Environment, Bioresources Unit, Austrian Institute of Technology GmbHTulln, Austria
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14
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Shidore T, Dinse T, Öhrlein J, Becker A, Reinhold-Hurek B. Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyteAzoarcussp. strain BH72. Environ Microbiol 2012; 14:2775-87. [DOI: 10.1111/j.1462-2920.2012.02777.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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