1887

Abstract

Several Gram-negative soil bacteria have the ability to differentiate into dormant cysts when faced with harsh environmental conditions. For example, when challenged with nutrient deprivation or desiccation, the plant-growth-promoting bacterium Azospirillum brasilense differentiates from a replicative and motile rod-shaped vegetative cell into a non-motile dormant spherical cyst. Currently, little is known about either the metabolic differences that exist between vegetative and cyst cell types, or about aspects of cyst physiology that allow dormant cells to survive harsh conditions. Here we compared transcriptomic profiles of vegetative and encysted A. brasilense. We observed that approximately one fifth of the A. brasilense transcriptome undergoes changes in expression between replicative vegetative cells and non-replicative cysts. A dramatic alteration in expression of genes involved in cell wall or cell membrane biogenesis was observed, which is congruent with changes in exopolysaccharide and lipid composition that occur between these cell types. Encysted cells also exhibited repressed mRNA abundance of genes involved in amino acid biosynthesis, ribosomal biogenesis and translation. We further observed that cysts create an anaerobic/micro-aerobic environment, as evidenced by repressed expression of oxidative phosphorylation genes coupled with increased expression of nitrate/nitrite reduction and nitrogen fixation genes.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000200
2018-07-30
2019-08-24
Loading full text...

Full text loading...

/deliver/fulltext/mgen/4/8/mgen000200.html?itemId=/content/journal/mgen/10.1099/mgen.0.000200&mimeType=html&fmt=ahah

References

  1. McKenney PT, Driks A, Eichenberger P. The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nat Rev Microbiol 2013;11:33–44 [CrossRef][PubMed]
    [Google Scholar]
  2. Grossman AD. Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis. Annu Rev Genet 1995;29:477–508 [CrossRef][PubMed]
    [Google Scholar]
  3. Higgins D, Dworkin J. Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev 2012;36:131–148 [CrossRef][PubMed]
    [Google Scholar]
  4. Muliukin AL, Suzina NE, Pogorelova Aiu, Antoniuk LP, Duda VI et al. Diverse morphological types of dormant cells and conditions for their formation in Azospirillum brasilense. Microbiology 2009;78:33–41 [CrossRef][PubMed]
    [Google Scholar]
  5. Segura D, Núñez C, Espín G. Azotobacter cysts. eLS 2014
    [Google Scholar]
  6. Gommeaux M, Barakat M, Lesourd M, Thiéry J, Heulin T. A morphological transition in the pleomorphic bacterium Ramlibacter tataouinensis TTB310. Res Microbiol 2005;156:1026–1030 [CrossRef][PubMed]
    [Google Scholar]
  7. Favinger J, Stadtwald R, Gest H. Rhodospirillum centenum, sp. nov., a thermotolerant cyst-forming anoxygenic photosynthetic bacterium. Antonie van Leeuwenhoek 1989;55:291–296 [CrossRef][PubMed]
    [Google Scholar]
  8. Reusch RN, Sadoff HL. Novel lipid components of the Azotobacter vinelandii cyst membrane. Nature 1983;302:268–270 [CrossRef][PubMed]
    [Google Scholar]
  9. Sadasivan L, Neyra CA. Flocculation in Azospirillum brasilense and Azospirillum lipoferum: exopolysaccharides and cyst formation. J Bacteriol 1985;163:716–723[PubMed]
    [Google Scholar]
  10. Okon Y, Itzigsohn R. Poly-β-hydroxybutyrate metabolism in Azospirillum brasilense and the ecological role of PHB in the rhizosphere. FEMS Microbiol Lett 1992;103:131–139 [CrossRef]
    [Google Scholar]
  11. Berleman JE, Bauer CE. Involvement of a Che-like signal transduction cascade in regulating cyst cell development in Rhodospirillum centenum. Mol Microbiol 2005;56:1457–1466 [CrossRef][PubMed]
    [Google Scholar]
  12. He K, Marden JN, Quardokus EM, Bauer CE. Phosphate flow between hybrid histidine kinases CheA3 and CheS3 controls Rhodospirillum centenum cyst formation. PLoS Genet 2013;9:e1004002 [CrossRef][PubMed]
    [Google Scholar]
  13. He K, Bauer CE. Chemosensory signaling systems that control bacterial survival. Trends Microbiol 2014;22:389–398 [CrossRef][PubMed]
    [Google Scholar]
  14. He K, Dragnea V, Bauer CE. Adenylate charge regulates sensor kinase CheS3 to control cyst formation in Rhodospirillum centenum. MBio 2015;6:e00546-15 [CrossRef][PubMed]
    [Google Scholar]
  15. Marden JN, Dong Q, Roychowdhury S, Berleman JE, Bauer CE. Cyclic GMP controls Rhodospirillum centenum cyst development. Mol Microbiol 2011;79:600–615 [CrossRef][PubMed]
    [Google Scholar]
  16. Gomelsky M. cAMP, c-di-GMP, c-di-AMP and now cGMP: bacteria use them all!. Mol Microbiol 2011;79:562–565 [CrossRef][PubMed]
    [Google Scholar]
  17. Roychowdhury S, Dong Q, Bauer CE. DNA-binding properties of a cGMP-binding CRP homologue that controls development of metabolically dormant cysts of Rhodospirillum centenum. Microbiology 2015;161:2256–2264 [CrossRef][PubMed]
    [Google Scholar]
  18. Dong Q, Bauer CE. Transcriptome analysis of cyst formation in Rhodospirillum centenum reveals large global changes in expression during cyst development. BMC Genomics 2015;16:68 [CrossRef][PubMed]
    [Google Scholar]
  19. Dong Q, Fang M, Roychowdhury S, Bauer CE. Mapping the CgrA regulon of Rhodospirillum centenum reveals a hierarchal network controlling Gram-negative cyst development. BMC Genomics 2015;16:1066 [CrossRef][PubMed]
    [Google Scholar]
  20. Bashan Y, de-Bashan LE. How the plant growth-promoting bacterium Azospirillum promotes plant growth – a critical assessment. Adv Agron 2010;108:77–136
    [Google Scholar]
  21. Mehdipour MJ, Emtiazi G, Salehi Z. Enhanced auxin production by Azospirillum pure cultures from plant root exudates. J Agri Sce Tech 2012;14:985–994
    [Google Scholar]
  22. Trujillo-Roldán MA, Valdez-Cruz NA, Gonzalez-Monterrubio CF, Acevedo-Sánchez EV, Martínez-Salinas C et al. Scale-up from shake flasks to pilot-scale production of the plant growth-promoting bacterium Azospirillum brasilense for preparing a liquid inoculant formulation. Appl Microbiol Biotechnol 2013;97:9665–9674 [CrossRef][PubMed]
    [Google Scholar]
  23. Vendan RT, Thangaraju M. Development and standardization of cyst based liquid formulation of Azospirillum bioinoculant. Acta Microbiol Immunol Hung 2007;54:167–177 [CrossRef][PubMed]
    [Google Scholar]
  24. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012;9:357–359 [CrossRef][PubMed]
    [Google Scholar]
  25. Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166–169 [CrossRef][PubMed]
    [Google Scholar]
  26. Robles JA, Qureshi SE, Stephen SJ, Wilson SR, Burden CJ et al. Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing. BMC Genomics 2012;13:484 [CrossRef][PubMed]
    [Google Scholar]
  27. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014;15:550 [CrossRef][PubMed]
    [Google Scholar]
  28. Tal S, Okon Y. Production of the reserve material poly-β-hydroxybutyrate and its function in Azospirillum brasilense Cd. Can J Microbiol 1985;31:608–613 [CrossRef]
    [Google Scholar]
  29. Kadouri D, Jurkevitch E, Okon Y. Involvement of the reserve material poly-β-hydroxybutyrate in Azospirillum brasilense stress endurance and root colonization. Appl Environ Microbiol 2003;69:3244–3250 [CrossRef][PubMed]
    [Google Scholar]
  30. Heikal A, Nakatani Y, Dunn E, Weimar MR, Day CL et al. Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation. Mol Microbiol 2014;91:950–964 [CrossRef]
    [Google Scholar]
  31. Kerscher SJ, Okun JG, Brandt U. A single external enzyme confers alternative NADH:unbiquinone oxidoreductase activity in Yarrowia lipolytica. J Cell Sci 1999;112:2347–2354
    [Google Scholar]
  32. Pitcher RS, Brittain T, Watmough NJ. Cytochrome cbb3 oxidase and bacterial microaerobic metabolism. Biochem Soc Trans 2002;30:653–658[PubMed]
    [Google Scholar]
  33. Zimmer W, Stephan MP, Bothe H. Denitrification by Azospirillum brasilense Sp 7. Arch Microbiol 1984;138:206–211 [CrossRef]
    [Google Scholar]
  34. Bothe H, Klein B, Stephan MP, Döbereiner J. Transformations of inorganic nitrogen by Azospirillum spp. Arch Microbiol 1981;130:96–100 [CrossRef]
    [Google Scholar]
  35. Danneberg G, Zimmer W, Bothe H. Energy transduction efficiencies in nitrogenous oxide respirations of Azospirillum brasilense Sp7. Arch Microbiol 1989;151:445–453 [CrossRef]
    [Google Scholar]
  36. Hernandez JA, Curatti L, Aznar CP, Perova Z, Britt RD et al. Metal trafficking for nitrogen fixation: NifQ donates molybdenum to NifEN/NifH for the biosynthesis of the nitrogenase FeMo-cofactor. Proc Natl Acad Sci USA 2008;105:11679–11684 [CrossRef][PubMed]
    [Google Scholar]
  37. Itzigsohn R, Yarden O, Okon Y. Polyhydroxyalkanoate analysis in Azospirillum brasilense. Can J Microbiol 1995;41:73–76 [CrossRef]
    [Google Scholar]
  38. Sadasivan L, Neyra CA. Cyst production and brown pigment formation in aging cultures of Azospirillum brasilense ATCC 29145. J Bacteriol 1987;169:1670–1677 [CrossRef][PubMed]
    [Google Scholar]
  39. Reusch RN, Sadoff HL. Lipid metabolism during encystment of Azotobacter vinelandii. J Bact 1981;145:889–895
    [Google Scholar]
  40. Miyanaga A, Funa N, Awakawa T, Horinouchi S. Direct transfer of starter substrates from type I fatty acid synthase to type III polyketide synthases in phenolic lipid synthesis. Proc Natl Acad Sci USA 2008;105:871–876 [CrossRef][PubMed]
    [Google Scholar]
  41. Valverde A, Castro-Sowinski S, Lerner A, Fibach S, Matan O et al. Exopolysaccharide production and cell aggregation in Azospirillum brasilense. In Dakora FD, Chimphango SBM, Valentine AJ, Elmerich C, Newton WE et al. (editors) Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture Dordrecht: 2008; pp.319–320
    [Google Scholar]
  42. Wu L, Cui Y, Hong Y, Chen S. A CheR/CheB fusion protein is involved in cyst cell development and chemotaxis in Azospirillum brasilense Sp7. Microbiol Res 2011;166:606–617 [CrossRef][PubMed]
    [Google Scholar]
  43. Konnova SA, Brykova OS, Sachkova OA, Egorenkova IV, Ignatov VV. Protective role of the polysaccharide-containing capsular components of Azospirillum brasilense. Microbiology 2001;70:436–440 [CrossRef]
    [Google Scholar]
  44. Lindemann A, Pessi G, Schaefer AL, Mattmann ME, Christensen QH et al. Isovaleryl-homoserine lactone, an unusual branched-chain quorum-sensing signal from the soybean symbiont Bradyrhizobium japonicum. Proc Natl Acad Sci USA 2011;108:16765–16770 [CrossRef][PubMed]
    [Google Scholar]
  45. Riou N, Le Rudulier D. Osmoregulation in Azospirillum brasilense: glycine betaine transport enhances growth and nitrogen fixation under salt stress. J Gen Microbiol 1990;136:1455–1461 [CrossRef][PubMed]
    [Google Scholar]
  46. Bandi C, Bazzicalupo M, Ceccherin MT, Fancelli S, Gallori E et al. Phylogeny of the genus Azospirillum on 16S rDNA sequence. FEMS Microbiol Lttrs 1995;129:195–200
    [Google Scholar]
  47. Berleman JE, Hasselbring BM, Bauer CE. Hypercyst mutants in Rhodospirillum centenum identify regulatory loci involved in cyst cell differentiation. J Bacteriol 2004;186:5834–5841 [CrossRef][PubMed]
    [Google Scholar]
  48. Lu YK, Marden J, Han M, Swingley WD, Mastrian SD et al. Metabolic flexibility revealed in the genome of the cyst-forming α-1 proteobacterium Rhodospirillum centenum. BMC Genomics 2010;11:325 [CrossRef][PubMed]
    [Google Scholar]
  49. Wang D, Xu A, Elmerich C, Ma LZ. Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions. Isme J 2017;11:1602–1613 [CrossRef][PubMed]
    [Google Scholar]
  50. Haywood GW, Anderson AJ, Chu L, Dawes EA. The role of NADH- and NADPH-linked acetoacetyl-CoA reductases in the poly-3-hydroxybutyrate synthesizing organism Alcaligenes eutrophus. FEMS Microbiol Lett 1988;52:259–264 [CrossRef]
    [Google Scholar]
  51. Senior PJ, Dawes EA. The regulation of poly-β-hydroxybutyrate metabolism in Azotobacter beijerinckii. Biochem J 1973;134:225–238 [CrossRef]
    [Google Scholar]
  52. Ueckert J, Doebereiner J, Fendrik I, Niemann E-G. Nitrate reductase activity of Azospirillum brasilense SP7 and SP245 V and C forms in continuous culture. In Polsinelli M, Materassi R, Vincenzini M. (editors) Nitrogen Fixation: Proceedings of the Fifth International Symposium on Nitrogen Fixation with Non-Legumes, Florence, Italy, 10-14 September 1990 Dordrecht: 1991; pp.249–253
    [Google Scholar]
  53. Nur I, Steinitz YL, Okon Y, Henis Y. Carotenoid composition and function in nitrogen-fixing bacteria of the genus Azospirillum. Microbiology 1981;122:27–32 [CrossRef]
    [Google Scholar]
  54. Berg RH, Tyler ME, Novick NJ, Vasil V, Vasil IK. Biology of Azospirillum–sugarcane association: enhancement of nitrogenase activity. AEM 1980;39:642–649
    [Google Scholar]
  55. Chowdhury-Paul S, Pando-Robles V, Jiménez-Jacinto V, Segura D, Espín G et al. Proteomic analysis revealed proteins induced upon Azotobacter vinelandii encystment. J Proteomics 2018;181:47–59 [CrossRef][PubMed]
    [Google Scholar]
  56. Malinich EA, Bauer CE. The plant growth promoting bacterium Azospirillum brasilense is vertically transmitted in Phaseolus vulgaris (common bean). Symbiosis 2018;3: (in press). doi: [CrossRef]
    [Google Scholar]
  57. Assmus B, Huzler P, Kirchhof G, Amann R, Lawrence JR et al. In situ localization of Azospirillum brasilense in the rhizosphere of wheat with fluorescently labeled, rRNA-targeted oligonucleotide probes and scanning confocal laser microscopy. AEM 1999;61:1013–1019
    [Google Scholar]
  58. Bashan Y, Levanony H, Whitmoyer RE. Root surface colonization of non-cereal crop plants by pleomorphic Azospirillum brasilense Cd. J Gen Microbiol 1991;137:187–196 [CrossRef]
    [Google Scholar]
  59. Dobbelaere S, Croonenborghs A, Thys A, Ptacek D, Vanderleyden J et al. Okon Y Responses of agronomically important crops to inoculation with Azospirillum. Aust J Plant Physiol 2001;28:871–879
    [Google Scholar]
  60. Okon Y, Labandera-Gonzalez CA. Agronomic applications of Azospirillum: an evaluation of 20 years worldwide field inoculation. Soil Bio Biochem 1994;26:1591–1601 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000200
Loading
/content/journal/mgen/10.1099/mgen.0.000200
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error