DOCSLIB.ORG

Modulation of Defence and Iron Homeostasis Genes in Rice

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Modulation of Defence and Iron Homeostasis Genes in Rice bioRxiv preprint doi: https://doi.org/10.1101/260380; this version posted February 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte 2 Herbaspirillum seropedicae 3 4 Brusamarello-Santos,1 L.C.C, Alberton,2 D., Valdameri,2 G., Camilios-Neto,1,6 D., Covre,3 R., Lopes,3 5 K., Tadra-Sfeir,1 M.Z., Faoro,1,7 H., Monteiro, R. A.1, Silva,3,8 A.B., Broughton4, W. J., Pedrosa,1 F.O., 6 Wassem,5 R., Souza*,1 E.M. 7 1Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, 8 Brasil 9 2Departamento de Patologia Médica, Setor Ciências da Saúde, Curitiba, PR, Brasil 10 3Setor de Educação Profissional e Tecnológica, Universidade Federal do Paraná, Curitiba, PR, Brasil 11 4Federal Institute of Materials Research and Testing, Division 4 Environment, Berlin, Germany 12 5Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brasil 13 6 Present address: Departamento de Bioquímica e Biotecnologia, Universidade Estadual de Londrina, 14 Londrina, PR, Brasil 15 7 Present address: Instituto Carlos Chagas – Fiocruz, Curitiba, PR, Brasil 16 9 Present address: Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 17 Esch-sur-Alzette, Luxembourg. 18 19 * Corresponding author: 20 Address: Universidade Federal do Paraná/UFPR, Rua Coronel Francisco Heráclito dos 21 Santos, s/n Caixa Postal 19046, 81531-980 – Curitiba, 22 E-mail: [email protected] 23 Telephone and fax : +55413361-1667 24 25 E-mail of authors: 26 Brusamarello-Santos, L.C.C: [email protected] 27 Alberton, D.: [email protected] 28 Valdameri, G.: [email protected] 29 Camilios-Neto, D.: [email protected] 30 Covre, R.: [email protected] 31 Lopes, K.: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/260380; this version posted February 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 32 Tadra-Sfeir,1 M.Z.: [email protected] 33 Faoro, H.: [email protected] 34 Monteiro, R. A.: [email protected] 35 Silva, A.B.: [email protected] 36 Broughton, William J.: [email protected] 37 Pedrosa, F.O.: [email protected] 38 Wassem, R.: [email protected] 39 Date of submission: February 05, 2018 40 Number of tables: 5 41 Number of figures: 6 (Figure 1, 3, 5,6 (colour online-only) , figure 2,4 (black-and-white) 42 Word count: 6421 43 Supplementary data: 3 tables 44 45 Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte 46 Herbaspirillum seropedicae 47 48 Running title: Modulation of defence-related rice genes by H. seropedicae 49 50 Highlights 51 52 RNASeq of H. seropedicae colonised rice roots showed remarkable regulation of defence, metal 53 transport, stress and signalling genes. Fe-uptake genes were highly induced with implications in plant 54 nutrition and immunity. 55 56 Abstract 57 58 Rice is staple food of nearly half the world’s population. Rice yields must therefore increase to feed 59 ever larger populations. By colonising rice and other plants, Herbaspirillum spp. stimulate plant 60 growth and productivity. However the molecular factors involved are largely unknown. To further 61 explore this interaction, the transcription profiles of Nipponbare rice roots inoculated with 62 Herbaspirillum seropedicae were determined by RNA-seq. Mapping the 104 million reads against the 2 bioRxiv preprint doi: https://doi.org/10.1101/260380; this version posted February 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 63 Oryza sativa cv. Nipponbare genome produced 65 million unique mapped reads that represented 64 13,840 transcripts each with at least two-times coverage. About 7.4 % (1,019) genes were 65 differentially regulated and of these 256 changed expression levels more than two times. Several of the 66 modulated genes encoded proteins related to plant defence (e.g. a putative probenazole inducible 67 protein), plant disease resistance as well as enzymes involved in flavonoid and isoprenoid synthesis. 68 Genes related to the synthesis and efflux of phytosiderophores (PS) and transport of PS-iron 69 complexes were also induced by the bacteria. These data suggest that the bacterium represses the rice 70 defence system while concomitantly activating iron uptake. Transcripts of H. seropedicae were also 71 detected amongst which genes involved in nitrogen fixation, cell motility and cell wall synthesis were 72 the most expressed. 73 74 Keywords: Herbaspirillum seropedicae, rice, biotic stresses, flavonoids, nitrogen fixation, pathogenic 75 responses, pathogen-associated molecular patterns (PAMPs) 76 77 Introduction 78 To answer the ever increasing demand for cereals, genetic improvement of rice and the 79 concomitant development of bio-fertilisers are promising, low environmental-impact solutions. After 80 water, the most limiting nutrient in plant development is nitrogen and nitrogenous fertilisers have been 81 heavily used in rice cultivation (Ladha and Reddy, 2003). Heavy use of nitrogen fertilisers causes 82 environmental damage including contamination of ground-water and the release of nitrogen oxides. 83 An alternative to the use of nitrogenous fertilisers is to employ plant-associated micro- 84 organisms that fix nitrogen. Herbaspirillum seropedicae is an endophytic diazotrophic that can 85 colonise many plants and improve their productivity (reviewed by Monteiro et al., 2012; Chubatsu et 86 al., 2012). Inoculation of rice with H. seropedicae increased root and shoot biomass by 38 to 54 % and 87 22 to 50 % respectively (Gyaneshwar et al., 2002) part of which was attributable to biological nitrogen 88 fixation (James, 2000; Gyaneshwar et al., 2002; James et al., 2002; Roncato-Maccari et al., 2003). 89 Pankievicz et al. (2015) showed that the nitrogen fixed by H. seropedicae and Azospirillum brasilense 90 was rapidly incorporated into Setaria viridis. Other factors, including production of phyto-hormones 91 by the bacteria stimulate plant growth and several authors have observed that the increase in biomass 92 of inoculated plants is dependent on the plant genotype (Gyaneshwar et al., 2002; Sasaki et al., 2010). 3 bioRxiv preprint doi: https://doi.org/10.1101/260380; this version posted February 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 93 Transcriptome based studies are powerful tools to detect differentially expressed genes and 94 discover novel molecular processes (Nobuta et al., 2007; Mizuno et al., 2010; Xu et al., 2012, Xu-H et 95 al. 2015; Wakasa et al., 2014; Magbanua et al., 2014; Shankar et al., 2016). Expression analyses 96 (using EST sequencing and RT-qPCR) of rice roots inoculated with H. seropedicae suggested that 97 genes related to auxin and ethylene syntheses as well as defence are modulated by the microorganism 98 in a cultivar dependent manner (Brusamarello-Santos et al., 2011). Here we used RNA-seq to profile 99 the transcriptome of rice inoculated with H. seropedicae. 100 101 Materials and Methods 102 Plant material and growth conditions 103 Testas were removed from seeds of rice (Oryza sativa ssp japonica cv. Nipponbare, kindly provided 104 by the Instituto Riograndense do arroz, IRGA – Avenida Missões 342, Porto Alegre, RS, Brazil), then 105 disinfected with 70 % (v/v) ethanol for 5 min followed by 30 min soaking in 8 % sodium hypochlorite 106 (1 mL per seed) containing 0.1 % v/v Triton-X100. After rinsing 20 times with sterile water, the seeds 107 were treated with 0.025 % (v/v) Vitavax-Thiram (Chentura, Avenida Nações Unidas 4777, Alto de 108 Pinheiros, São Paulo, SP, Brazil) fungicide solution and stirred (120 rpm) for 24 h in the dark at 30 ºC. 109 The seeds were then transferred to 0.7 % water-agar and left for two days to germinate after which the 110 seedlings were inoculated with 1 mL of Herbaspirillum seropedicae strain SmR1 (108 cells/seedling) 111 for 30 minutes while control seedlings were treated with 1 mL of N-free NFbHP-malate medium 112 (Klassen et al., 1997) (controls). Seedlings were washed with sterile water and transferred to glass 113 tubes (25 cm long, 2.5 cm diameter) containing propylene beads and 25 mL of modified Hoagland’s 114 solution (Hoagland and Arnon, 1950) without nitrogen (1mM KH2PO4, 1mM K2HPO4, 2mM -1 115 MgSO4.7H2O, 2mM CaCl2.2H2O, 1mL/L micronutrient solution (H3BO3 2.86 g.L , MnCl2.4H2O 1.81 -1 -1 -1 -1 -1 116 g.L , ZnSO4.7H2O 0.22 g.L , CuSO4.5H2O 0.08 g.L , Na2MoO4.2H2O 0.02 g.L ) and 1mL.L Fe- -1 -1 117 EDTA solution (Na2H2EDTA.2H2O 13.4 g.L and FeCl3.6H2O 6 g.L )), pH 6.5-7.0. Plants were 118 cultivated at 24 ºC under 14 h light and 10 h dark for 3 days. H. seropedicae was cultivated in NFbHP 119 malate medium containing 5 mM glutamate as the nitrogen source. Cells were shaken (120 rpm) 120 overnight at 30 °C, then centrifuged, washed once with N-free NFbHP-malate and suspended in the 8 -1 121 same medium to OD600 = 1 (corresponding to 10 cells.mL ). Strain SmR1 (Souza et al., 2000) is a 122 spontaneous streptomycin resistant mutant of strain Z78 (Baldani et al., 1986). Root colonisation was 123 monitored by counting the number of colony forming units (CFU) per gram of fresh root. 4 bioRxiv preprint doi: https://doi.org/10.1101/260380; this version posted February 5, 2018.
Load more

Recommended publications
  • A Case of Infective Endocarditis Due to Herbaspirillum Huttiense in a Pediatric Oncology Patient
    Case Report A case of infective endocarditis due to Herbaspirillum Huttiense in a pediatric oncology patient Ahmet Alptuğ Güngör1, Tugba Bedir Demirdağ2, Bedia Dinç3, Emine Azak4, Arzu Yazal Erdem5, Burçin Kurtipek5, Aslinur Özkaya Parlakay2, Neriman Sarı5 1 Department of Pediatrics, Ankara City Hospital, Ankara, Turkey 2 Pediatric Infectious Diseases Department, Yildirim Beyazit University, Ankara City Hospital, Ankara, Turkey 3 Department of Medical Microbiology, Ankara City Hospital, Ankara, Turkey 4 Department of Pediatric Cardiology, Ankara City Hospital, Ankara, Turkey 5 Department of Pediatric Heamatology and Oncology, Ankara City Hospital, Ankara, Turkey Abstract Infective endocarditis (IE) is an infection of the endocardium and/or heart valves that involves thrombus formation (vegetation). This condition might damage the endocardial tissue and/or valves. An indwelling central venous catheter is a major risk factor for bacteremia at-risked pediatric populations such as premature infants; children with cancer and/or connective tissue disorders. Herbaspirillum huttiense is a Gram-negative opportunistic bacillus that may cause bacteremia and pneumonia rarely in this fragile population. Herein we report the very first case of bacteremia and IE in a pediatric oncology patient caused by H. huttiense. Key words: infective endocarditis; Herbaspirillum huttiense; pediatric; oncology. J Infect Dev Ctries 2020; 14(11):1349-1351. doi:10.3855/jidc.13001 (Received 09 May 2020 – Accepted 02 November 2020) Copyright © 2020 Güngör et al. This is an open-access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Introduction there was no focus of fever; she didn’t have any oral Herbaspirillum huttiense is a Gram-negative mucositis or any inflammation sign on port catheter oxidase-positive non-fermenting bacillus commonly area.
    [Show full text]
  • Herbaspirillum Seropedicae M.A
    Brazilian Journal of Medical and Biological Research Online Provisional Version ISSN 0100-879X This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Evidence for the endophytic colonization of Phaseolus vulgaris (common bean) roots by the diazotroph Herbaspirillum seropedicae M.A. Schmidt1, E.M. Souza1, V. Baura1, R. Wassem2, M.G. Yates1, F.O. Pedrosa1 and R.A. Monteiro1 1Departamento de Bioquímica e Biologia Molecular, 2Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brasil Abstract Herbaspirillum seropedicae is an endophytic diazotrophic bacterium, which associates with important agricultural plants. In the present study, we have investigated the attachment to and internal colonization of Phaseolus vulgaris roots by the H. seropedicae wild-type strain SMR1 and by a strain of H. seropedicae expressing a red fluorescent protein (DsRed) to track the bacterium in the plant tissues. Two-day-old P. vulgaris roots were incubated at 30°C for 15 min with 6 x 108 CFU/mL H. seropedicae SMR1 or RAM4. Three days after inoculation, 4 x 104 cells of endophytic H. seropedicae SMR1 were recovered per gram of fresh root, and 9 days after inoculation the number of endophytes increased to 4 x 106 CFU/g. The identity of the recovered bacteria was confirmed by amplification and sequencing of the 16SrRNA gene. Furthermore, confocal microscopy of P. vulgaris roots inoculated with H. seropedicae RAM4 showed that the bacterial cells were attached to the root surface 15 min after inoculation; fluorescent bacteria were visible in the internal tissues after 24 h and were found in the central cylinder after 72 h, showing that H.
    [Show full text]
  • Evidence for the Endophytic Colonization of Phaseolus Vulgaris (Common Bean) Roots by the Diazotroph Herbaspirillum Seropedicae
    ISSN 0100-879X Volume 43 (3) 182-267 March 2011 BIOMEDICAL SCIENCES AND www.bjournal.com.br CLINICAL INVESTIGATION Braz J Med Biol Res, March 2011, Volume 44(3) 182-185 doi: 10.1590/S0100-879X2011007500004 Evidence for the endophytic colonization of Phaseolus vulgaris (common bean) roots by the diazotroph Herbaspirillum seropedicae M.A. Schmidt, E.M. Souza, V. Baura, R. Wassem, M.G. Yates, F.O. Pedrosa and R.A. Monteiro The Brazilian Journal of Medical and Biological Research is partially financed by Institutional Sponsors Hotsite of proteomics metabolomics developped by: Campus Ribeirão Preto Faculdade de Medicina de Ribeirão Preto analiticaweb.com.br S C I E N T I F I C All the contents of this journal, except where otherwise noted, is licensed under a Creative Commons Attribution License Brazilian Journal of Medical and Biological Research (2011) 44: 182-185 ISSN 0100-879X Evidence for the endophytic colonization of Phaseolus vulgaris (common bean) roots by the diazotroph Herbaspirillum seropedicae M.A. Schmidt1, E.M. Souza1, V. Baura1, R. Wassem2, M.G. Yates1, F.O. Pedrosa1 and R.A. Monteiro1 1Departamento de Bioquímica e Biologia Molecular, 2Departamento de Genética, Universidade Federal do Paraná, Curitiba, PR, Brasil Abstract Herbaspirillum seropedicae is an endophytic diazotrophic bacterium, which associates with important agricultural plants. In the present study, we have investigated the attachment to and internal colonization of Phaseolus vulgaris roots by the H. seropedicae wild-type strain SMR1 and by a strain of H. seropedicae expressing a red fluorescent protein (DsRed) to track the bacterium in the plant tissues. Two-day-old P.
    [Show full text]
  • Herbaspirillum Massiliense Sp. Nov
    Standards in Genomic Sciences (2012) 7:200-209 DOI:10.4056/sigs.3086474 Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov. Jean-Christophe Lagier1, Gregory Gimenez1, Catherine Robert1, Didier Raoult1 and Pierre- Edouard Fournier1* 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université *Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Herbaspirillum massiliense, genome Herbaspirillum massiliense strain JC206T sp. nov. is the type strain of H. massiliense sp. nov., a new species within the genus Herbaspirillum. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. H. massiliense is an aerobic rod. Here we describe the features of this organism, together with the complete genome se- quence and annotation. The 4,186,486 bp long genome (one chromosome but no plasmid) contains 3,847 protein-coding and 54 RNA genes, including 3 rRNA genes. Introduction Herbaspirillum massiliense strain JC206T (= CSUR seropedicae (Baldini et al. 1986) [5], and H. soli P159 = DSMZ 25712) is the type strain of H. (Carro et al. 2011) [8]. Members of the genus massiliense sp. nov. This bacterium was isolated Herbaspirillum have mainly been isolated from the from the stool of a healthy Senegalese patient. It is environment, in particular from soil, and from a Gram-negative, aerobic, flagellated, indole- plants for which they play the role of growth pro- negative bacillus. moters, but have also occasionally been isolated The current approach to classification of prokary- from humans, either as proven pathogens, causing otes, generally referred to as polyphasic taxono- bacteremia in leukemic patients [15,16], as poten- my, relies on a combination of phenotypic and tial pathogens in aortic aneurysms [17], or in res- genotypic characteristics [1].
    [Show full text]
  • Assessment of Native Cadmium-Resistant Bacteria in Cacao (Theobroma Cacao L.) - Cultivated Soils 2 3 Henry A
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.06.455168; this version posted August 6, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Assessment of native cadmium-resistant bacteria in cacao (Theobroma cacao L.) - cultivated soils 2 3 Henry A. Cordoba-Novoa1 §, Jeimmy Cáceres-Zambrano2, §, Esperanza Torres-Rojas2* 4 5 1Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, Canada. 2Faculty of 6 Agricultural Sciences, Universidad Nacional de Colombia, Bogotá D.C., Colombia. §These authors 7 contributed equally. 8 9 *Correspondence: 10 [email protected] 11 +57 3165000 ext. 19072 12 13 Abstract 14 Traces of cadmium (Cd) have been reported in some chocolate products due to soils with Cd and the high 15 ability of cacao plants to extract, transport, and accumulate it in their tissues. An agronomic strategy to 16 minimize the uptake of Cd by plants is the use of cadmium-resistant bacteria (Cd-RB). However, knowledge 17 about Cd-RB associated with cacao soils is scarce. This study was aimed to isolate and characterize Cd-RB 18 associated with cacao-cultivated soils in Colombia that may be used in the bioremediation of Cd-polluted 19 soils. Diversity of culturable Cd-RB, qualitative functional analysis related to nitrogen, phosphorous, carbon, 20 and Cd were performed. Thirty different Cd-RB morphotypes were isolated from soils with medium (NC, Y1, 21 Y2) and high (Y3) Cd concentrations using culture media with 6 mg Kg-1 Cd.
    [Show full text]
  • Microbial Hitchhikers on Intercontinental Dust: Catching a Lift in Chad
    The ISME Journal (2013) 7, 850–867 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Microbial hitchhikers on intercontinental dust: catching a lift in Chad Jocelyne Favet1, Ales Lapanje2, Adriana Giongo3, Suzanne Kennedy4, Yin-Yin Aung1, Arlette Cattaneo1, Austin G Davis-Richardson3, Christopher T Brown3, Renate Kort5, Hans-Ju¨ rgen Brumsack6, Bernhard Schnetger6, Adrian Chappell7, Jaap Kroijenga8, Andreas Beck9,10, Karin Schwibbert11, Ahmed H Mohamed12, Timothy Kirchner12, Patricia Dorr de Quadros3, Eric W Triplett3, William J Broughton1,11 and Anna A Gorbushina1,11,13 1Universite´ de Gene`ve, Sciences III, Gene`ve 4, Switzerland; 2Institute of Physical Biology, Ljubljana, Slovenia; 3Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA; 4MO BIO Laboratories Inc., Carlsbad, CA, USA; 5Elektronenmikroskopie, Carl von Ossietzky Universita¨t, Oldenburg, Germany; 6Microbiogeochemie, ICBM, Carl von Ossietzky Universita¨t, Oldenburg, Germany; 7CSIRO Land and Water, Black Mountain Laboratories, Black Mountain, ACT, Australia; 8Konvintsdyk 1, Friesland, The Netherlands; 9Botanische Staatssammlung Mu¨nchen, Department of Lichenology and Bryology, Mu¨nchen, Germany; 10GeoBio-Center, Ludwig-Maximilians Universita¨t Mu¨nchen, Mu¨nchen, Germany; 11Bundesanstalt fu¨r Materialforschung, und -pru¨fung, Abteilung Material und Umwelt, Berlin, Germany; 12Geomatics SFRC IFAS, University of Florida, Gainesville, FL, USA and 13Freie Universita¨t Berlin, Fachbereich Biologie, Chemie und Pharmazie & Geowissenschaften, Berlin, Germany Ancient mariners knew that dust whipped up from deserts by strong winds travelled long distances, including over oceans. Satellite remote sensing revealed major dust sources across the Sahara. Indeed, the Bode´le´ Depression in the Republic of Chad has been called the dustiest place on earth.
    [Show full text]
  • The Herbaspirillum Seropedicae Smr1 Fnr Orthologs Controls The
    OPEN The Herbaspirillum seropedicae SmR1 SUBJECT AREAS: Fnr orthologs controls the cytochrome BACTERIAL GENETICS TRANSCRIPTION FACTORS composition of the electron transport BACTERIAL TRANSCRIPTION TRANSCRIPTOMICS chain Marcelo B. Batista1, Michelle Z. T. Sfeir1, Helisson Faoro1, Roseli Wassem2, Maria B. R. Steffens1, Received Fa´bio O. Pedrosa1, Emanuel M. Souza1, Ray Dixon3 & Rose A. Monteiro1 10 June 2013 Accepted 1Department of Biochemistry and Molecular Biology, UFPR, Curitiba-PR – Brazil, 2Department of Genetics, UFPR, Curitiba-PR - Brazil, 12 August 2013 3Department of Molecular Microbiology, John Innes Centre, Colney Lane, NR4 7UH, Norwich - UK. Published 2 September 2013 The transcriptional regulatory protein Fnr, acts as an intracellular redox sensor regulating a wide range of genes in response to changes in oxygen levels. Genome sequencing of Herbaspirillum seropedicae SmR1 revealed the presence of three fnr-like genes. In this study we have constructed single, double and triple fnr Correspondence and deletion mutant strains of H. seropedicae. Transcriptional profiling in combination with expression data requests for materials from reporter fusions, together with spectroscopic analysis, demonstrates that the Fnr1 and Fnr3 proteins not only regulate expression of the cbb3-type respiratory oxidase, but also control the cytochrome content should be addressed to and other component complexes required for the cytochrome c-based electron transport pathway. R.A.M. (roseadele@ Accordingly, in the absence of the three Fnr paralogs, growth is restricted at low oxygen tensions and ufpr.br) nitrogenase activity is impaired. Our results suggest that the H. seropedicae Fnr proteins are major players in regulating the composition of the electron transport chain in response to prevailing oxygen concentrations.
    [Show full text]
  • Herbaspirillum Seropedicae Reveals a Potential New Emerging Bacterium Adapted to Human Hosts Helisson Faoro1,2,3* , Willian K
    Faoro et al. BMC Genomics (2019) 20:630 https://doi.org/10.1186/s12864-019-5982-9 RESEARCH ARTICLE Open Access Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts Helisson Faoro1,2,3* , Willian K. Oliveira2,3, Vinicius A. Weiss1,2, Michelle Z. Tadra-Sfeir1, Rodrigo L. Cardoso1, Eduardo Balsanelli1, Liziane C. C. Brusamarello-Santos1, Doumit Camilios-Neto1,5, Leonardo M. Cruz1, Roberto T. Raittz2, Ana C. Q. Marques4, John LiPuma6, Cyntia M. T. Fadel-Picheth4, Emanuel M. Souza1 and Fabio O. Pedrosa1* Abstract Background: Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of H. seropedicae have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of H. seropedicae, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin. Results: Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus Herbaspirillum. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (nif) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes.
    [Show full text]
  • Case Report Herbaspirillum Infection in Humans: a Case Report and Review of Literature
    Hindawi Case Reports in Infectious Diseases Volume 2020, Article ID 9545243, 6 pages https://doi.org/10.1155/2020/9545243 Case Report Herbaspirillum Infection in Humans: A Case Report and Review of Literature Rashmi Dhital , Anish Paudel, Nidrit Bohra, and Ann K. Shin Reading Hospital and Medical Center, Tower Health System, West Reading, PA, USA Correspondence should be addressed to Rashmi Dhital; [email protected] Received 5 December 2019; Revised 2 February 2020; Accepted 4 February 2020; Published 20 February 2020 Academic Editor: Raul Colodner Copyright © 2020 Rashmi Dhital et al. &is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Introduction. Herbaspirillum seropedicae are Gram-negative oxidase-positive nonfermenting rods of Betaproteobacteria class, commonly found in rhizosphere. More recently, some Herbaspirillium species have transitioned from environment to human hosts, mostly as opportunistic (pathogenic) bacteria. We present a 58-year-old female with non-small-cell lung cancer (NSCLC) who presented with pneumonia and was found to have Herbaspirillum seropedicae bacteremia. Case History. A 58-year-old woman with NSCLC on Pralsetinib presented with fevers and rigors for 2 days. Coarse breath sounds were auscultated on the right upper lung field. Labs revealed leukopenia and mild neutropenia. CTchest revealed right upper lobe pneumonia. She was admitted for sepsis secondary to pneumonia and placed on broad spectrum antibiotics with intravenous piperacillin-tazobactam and vancomycin. &e patient continued to have fever 2 days after admission (max: 102.8°F). Preliminary blood cultures grew Gram- ° negative rods.
    [Show full text]
  • Infection Or Environment?
    Article 364 CASES IN CLINICAL MICROBIOLOGY 1 Clock Hour Case Eighteen: Infection or Environment? Anamarija Morovic, Ashley Bowman, Connie Meeks, and Joel Mortensen Background EDITOR’S NOTE: BEFORE reading the Case Cystic fibrosis is an autosomal recessive disease, Follow-up and Discussion below, study the Case resulting from mutations in the cystic fibrosis trans- Description on page 60 of this issue, and formu- late your own answers to the questions posed. membrane conductance regulator. Disease involves multiple systems, and is characterized by production of sticky, dehydrated mucus that lines epithelial cells Case Follow-up and Discussion of the respiratory tract, predisposing the patient to in- The patient returned to the Clinic after completion fections by a variety of opportunistic pathogens. The of antibiotic therapy, reporting significant improve- most commonly isolated pathogen is Pseudomonas ment of symptoms. Values of his pulmonary function aeruginosa (80%). Other more infrequent species in- tests returned to baseline (FEV1-102%). clude Burkholderia cepacia, Achromobacter xy- Because the patient had not previously had B. losoxidans and Stenotrophomonas maltophilia. The cepacia, the specimen was sent for final identifica- incidence of Herbaspirillum colonization/infection tion to the Cystic Fibrosis Foundation Burkholderia in patients with cystic fibrosis is uncertain. Spilker, cepacia Research Laboratory and Repository in Ann et al., report incidence of less than 3%, which is sim- Arbor, MI. Sequencing of 16s rRNA was performed ilar to the incidence of Burkholderia cepacia. This and the organism was identified as a Gram-negative study included 28 cystic fibrosis patients infected bacillus with the highest identity to Herbaspirillum with Herbaspirillum, who ranged in age from 20 species.
    [Show full text]
  • Herbaspirillum Hiltneri Sp. Nov., Isolated from Surface-Sterilized Wheat Roots
    International Journal of Systematic and Evolutionary Microbiology (2006), 56, 1341–1348 DOI 10.1099/ijs.0.64031-0 Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots Michael Rothballer,1 Michael Schmid,1 Ilona Klein,13 Andreas Gattinger,2 Sabine Grundmann2 and Anton Hartmann1 Correspondence 1,2Department of Rhizosphere Biology1, Institute of Soil Ecology1,2, GSF – National Research Anton Hartmann Centre for Environment and Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, [email protected] Germany The genus Herbaspirillum of the Betaproteobacteria mainly comprises diazotrophic bacteria with a potential for endophytic and systemic colonization of a variety of plants. The plant-associated bacterial isolates N3T, N5 and N9 were derived from surface-sterilized wheat roots. After phylogenetic analysis of 16S rRNA gene sequence data the isolates could be allocated to the genus Herbaspirillum, and 99?9 % similarity to the sequence of Herbaspirillum lusitanum P6-12T was found. A set of 16S rRNA gene-targeted oligonucleotide probes was developed for the identification of the three novel isolates and H. lusitanum (Hhilu446), and for the specific detection of several other Herbaspirillum species described recently. For higher phylogenetic resolution, the 23S rRNA gene sequences of all members of the genus was sequenced and used to construct a phylogenetic tree. Isolates N3T, N5 and N9 formed a group that was distinct from all other Herbaspirillum species. In addition, isolate N3T and H. lusitanum P6-12T exhibited a DNA–DNA hybridization value of only 25 %. The value for DNA–DNA hybridization between N3T and other members of the genus Herbaspirillum was between 14 and 32 %; DNA–DNA hybridization between strain N3T and isolates N5 and N9 produced values above 95 %.
    [Show full text]
  • Herbaspirillum Seropedicae Z78 Glycopolymers
    Annals of Microbiology (2019) 69:1113–1121 https://doi.org/10.1007/s13213-019-01490-7 ORIGINAL ARTICLE Phage antibodies for the immunochemical characterization of Herbaspirillum seropedicae Z78 glycopolymers Natalya S. Velichko1 & Yulia P. Fedonenko1 Received: 13 March 2019 /Accepted: 29 May 2019 /Published online: 15 JJJ uly 2019 # Università degli studi di Milano 2019 Abstract Purpose Microbial carbohydrate antigens are targets of the immune systems of hosts. In this context, it is of interest to obtain data that will permit judgment of the degree of heterogeneity, chemical makeup, and localization of the antigenic determinants of the Herbaspirillum surface glycopolymers. Methods A sheep single-chain antibody-fragment phage library (Griffin.1, UK) was used to obtain miniantibodies to the exopolysaccharides (EPS-I and EPS-II), capsular polysaccharides (CPS-I and CPS-II) and lipopolysaccharide (LPS) of Herbaspirillum seropedicae Z78. To infer about the presence or absence of common antigenic determinants in the cell-surface polysaccharides of H. seropedicae Z78, we ran a comparative immunoassay using rabbit polyclonal and phage recombinant antibodies to the surface glycopolymers of H. seropedicae Z78. Results We isolated and purified the exopolysaccharides (EPS-I and EPS-II), capsular polysaccharides (CPS-I and CPS-II), and lipopolysaccharide (LPS) of Herbaspirillum seropedicae Z78. Using rabbit polyclonal antibodies, we found that these cell- surface polysaccharides were of a complex nature. EPS-I, EPS-II, CPS-I, CPS-II, and LPS contained common antigenic deter- minants. CPS-I, CPS-II, and LPS also contained individual antigenic determinants composed of rhamnose, N-acetyl-D-glucos- amine, and N-acetyl-D-galactosamine—sugars responsible for cross-reactions with miniantibodies.
    [Show full text]