Abstract
Comparative genomics is a powerful technique to identify functional elements accountable for species competence that enables it to thrive in specific environmental niche and for species adaptation to implement particular lifestyles. It also allows insight into genomic island arising from genomic rearrangements. Here, the abundance profile of identified genes, protein families, metabolic pathways, and regulons were computed for endophytes (including nodule-forming plant symbionts), rhizosphere bacteria, and phytopathogens. The lifestyle of endophytes was characterized by significantly overrepresentation of genes encoding for nitrogenase as well as genes involved in the uptake of urea cycle components. The genomes of assigned endophytic bacteria revealed distinct signaling features that differed from those detected among rhizosphere bacteria and phytopathogens. Similar results were also observed for genes encoding proteins involved in transport and secretion systems as well as for transcriptional regulators. Genes involved in chemotaxis receptors are more abundantly represented among phytopathogens than endophytes. Likewise, distinct metabolic functions were enriched for the others plant-associated communities. There was no particular genomic feature that could inhabit common to all genomes in each investigated lifestyle, suggesting that multiple, rather than unique, key features are deployed by the symbionts as strategy to interact with the host plant statically.
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References
Alloisio N, Queiroux C, Fournier P, Pujic P, Normand P, Vallenet D et al (2010) The Frankia alni symbiotic transcriptome. Mol Plant Microb Interac 23:593–607
Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D et al (2008) Genome sequence of the ß-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res 18:1472–1483
Balleza E, Lopez-Bojorquez LN, Martinez-Antonio A, Resendis-Antonio O, Lozada-Chavez I, Balderas-Martinez YI et al (2009) Regulation by transcription factors in bacteria: beyond description. FEMS Microbiol Rev 33:133–151
Barragán MJL, Blázquez B, Zamarro MT, Mancheño JM, García JL, Díaz E et al (2005) BzdR, a repressor that controls the anaerobic catabolism of benzoate in Azoarcus sp. CIB, is the first member of a new subfamily of transcriptional regulators. J Biol Chem 280:10683–10694. doi:10.1074/jbc.M412259200
Blanquart F, Gandon S (2013) Time-shift experiments and patterns of adaptation across time and space. Ecol Lett 16:31–38. doi:10.1111/ele.12007
Bodenhausen N, Horton MW, Bergelson J (2013) Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. Plos One 8:e56329. doi:56310.51371/journal.pone.0056329
Bonfante P, Anca I-A (2009) Plants, mycorrhizal fungi, and bacteria: a network of interactions. Ann Rev Microbiol 63:363–383
Bouchereau A, Aziz A, Larher F, Martin-Tanguy J (1999) Polyamines and environmental challenges: recent development. Plant Sci 140:103–125
Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotechnol 27:30–37. doi:10.1016/j.copbio.2013.09.012
Cavalier-Smith T (2010) Deep phylogeny, ancestral groups and the four ages of life. Phil Trans Royal Soc B: Biologic Sci 365:111–132. doi:10.1098/rstb.2009.0161
Chamam A, Sanguin H, Bellvert F, Meiffren G, Comte G, Wisniewski-Dye F et al (2013) Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum-Oryza sativa association. Phytochemistry 87:65–77
Cheng H-P, Walker GC (1998) Succinoglycan production by Rhizobium meliloti is regulated through the ExoS-ChvI two-component regulatory system. J Bacteriol 180:20–26
Combès A, Ndoye I, Bance C, Bruzaud J, Djediat C, Dupont J, et al. (2012) Chemical communication between the endophytic fungus Paraconiothyrium variabile and the phytopathogen Fusarium oxysporum. Plos One 7:e47313. doi:47310.41371/journal.pone.0047313
Compant S, Clement C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42:669–678
Conrath U, Beckers GJM, Flors V, Garcia-Agustin P, Jakab G, Mauch F et al (2006) Priming: getting ready for battle. Mol Plant Microb Interac 19:1062–1071
Döbereiner J, Baldani VLD, Reis VM (2000) The role of biological nitrogen fixation to bioenergy programmes in the tropics. In: Rocha-Miranda E (ed) Transition to global sustainability: the contribution of Brazilian science. Academia Brasileira de Ciências, Rio de Janeiro, Brazil, pp 195–208
Elsen S, Swem LR, Swem DL, Bauer CE (2004) RegB/RegA, a highly conserved redox-responding global two-component regulatory system. Microbiol Mol Biol Rev 68:263–279. doi:10.1128/MMBR.68.2.263-279.2004
Ferando L, Mañay JF, Scavino AF (2012) Molecular and culture-dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (Oryza sativa) varieties. FEMS Microbiol Ecol 80:696–708
Fernandez O, Vandesteene L, Feil R, Baillieul F, Lunn JE, Clement C (2012) Trehalose metabolism is activated upon chilling in grapevine and might participate in Burkholderia phytofirmans induced chilling tolerance. Planta 236:355–369
Frey-Klett P, Garbaye J, Tarkka M (2007) The mycorrhiza helper bacteria revisited. New Phytol 176:22–36. doi:10.1111/j.1469-8137.2007.02191.x
Friesen ML, Porter SS, Stark SC, von Wettberg EJ, Sachs JL, Martinez-Romero E (2011) Microbially mediated plant functional traits. Ann Rev Ecol Evol Syst 42:23–46. doi:10.1146/annurev-ecolsys-102710-145039
Garbaye J (1994) Helper bacteria - a new dimension to the mycorrhizal symbiosis. New Phytol 128:197–210. doi:10.1111/j.1469-8137.1994.tb04003.x
Gerendás J (2007) Significance of polyamines for pectin-methylesterase activity and the ion dynamics in the apoplast. The apoplast of higher plants: compartment of storage, transport and reactions. Springer, The Netherlands, pp 67–83
Gisin J, Müller A, Pfänder Y, Leimkühler S, Narberhaus F, Masepohl B (2010) A Rhodobacter capsulatus member of a universal permease family imports molybdate and other oxyanions. J Bacteriol 192:5943–5952
Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169:30–39
Hardoim PR, Andreote FD, Reinhold-Hurek B, Sessitsch A, van Overbeek LS, van Elsas JD (2011) Rice root-associated bacteria: insights into community structures across 10 cultivars. FEMS Microbiol Ecol 77:154–164
Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev 79:293–320. doi:10.1128/MMBR.00050-14
Haugo AJ, Watnick PI (2002) Vibrio cholerae CytR is a repressor of biofilm development. Mol Microbiol 45:471–483
Herrero N, Sanchez Marquez S, Zabalgogeazcoa I (2009) Mycoviruses are common among different species of endophytic fungi of grasses. Arch Virol 154:327–330. doi:10.1007/s00705-008-0293-5
Hoffman MT, Arnold AE (2010) Diverse bacteria inhabit living hyphae of phylogenetically diverse fungal endophytes. Appl Environ Microbiol 76:4063–4075
Hoffman MT, Gunatilaka MK, Wijeratne K, Gunatilaka L, Arnold AE (2013) Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte. PLoS ONE 8(9):e73132. doi:10.1371/journal.pone.0073132
Iniguez AL, Dong Y, Triplett EW (2004) Nitrogen fixation in wheat provided by Klebsiella pneumoniae 342. Mol Plant Microbe Interac 10:1078–1085
Jones JDG, Dangl JL (2006) The plant immune system. Nature 444:323–329
Karpinets TV, Park BH, Syed MH, Klotz MG, Uberbacher EC (2014) Metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants. Mol Plant Microb Interac 27:664–677
Kiers ET, Rousseau RA, West SA, Denison RF (2003) Host sanctions and the legume-rhizobium mutualism. Nature 425:78–81
Kiers ET, Hutton MG, Denison RF (2007) Human selection and the relaxation of legume defences against ineffective rhizobia. Proc Royal Soc London B: Biologic Sci 274:3119–3126. doi:10.1098/rspb.2007.1187
Kiers ET, Palmer TM, Ives AR, Bruno JF, Bronstein JL (2010) Mutualisms in a changing world: an evolutionary perspective. Ecol Lett 13:1459–1474
Kiers ET, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E et al (2011) Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 333:880–882
Koskella B (2013) Phage-mediated selection on microbiota of a long-lived host. Curr Biol 23:1256–1260
Kusano T, Berberich T, Tateda C, Takahashi Y (2008) Polyamines: essential factors for growth and survival. Planta 228:367–381. doi:10.1007/s00425-008-0772-7
Lackner G, Partida-Martinez LP, Hertweck C (2009) Endofungal bacteria as producers of mycotoxins. Trend Microbiol 17:570–576
Lesk C, Rowhani P, Ramankutty N (2016) Influence of extreme weather disasters on global crop production. Nature 529:84–87. doi:10.1038/nature16467
Letunic I, Bork P (2007) Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127–128
Lu (2006) Pathways and regulation of bacterial arginine metabolism and perspectives for obtaining arginine overproducing strains. Appl Microbiol Biotechnol 70:261–272
Lugtenberg BJJ, Dekkers L, Bloemberg GV (2001) Molecular determinants of rhizosphere colonization by Pseudomonas. Ann Rev Phytopathol 39:461–490
Maheshwari DK (2010) Plant growth and health promoting bacteria. Springer, Netherlands, p 448
Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y et al (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucl Acid Res 40:D115–D122. doi:10.1093/nar/gkr1044
Márquez LM, Redman RS, Rodriguez RJ, Roossinck MJ (2007) A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance. Science 315:513–515
Mitter B, Petric A, Shin MW, Chain PSG, Hauberg-Lotte L, Reinhold-Hurek B, et al (2013) Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Front Plant Sci 4:120 doi:110.3389/fpls.2013.00120
Mitter B, Pfaffenbichler N, Sessitsch A (2016) Plant-microbe partnerships in 2020. Microb Biotechnol. doi:10.1111/1751-7915.12382
Mühling KH, Läuchli A (2001) Influence of chemical form and concentration of nitrogen on apoplastic pH of leaves. J Plant Nut 24:399–411
Naumann M, Schussler A, Bonfante P (2010) The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes. ISME J 4:862–871
Noctor G, Foyer CH (1998) Ascorbate and glutathione: keeping active oxygen under control. Ann Rev Plant Physiol Plant Mol Biol 49:249–279. doi:10.1146/annurev.arplant.49.1.249
Partida-Martinez LP, Hertweck C (2005) Pathogenic fungus harbours endosymbiotic bacteria for toxin production. Nature 437:884–888
Paulson JN, Stine OC, Bravo HC, Pop M (2013) Differential abundance analysis for microbial marker-gene surveys. Nat Methods 10:1200–1202
Pawlowski K, Klosse U, Debruijn FJ (1991) Characterization of a novel Azorhizobium caulinodans ORS571 2-component regulatory system, NtrY/NtrX, involved in nitrogen-fixation and metabolism. Mol Gen Genet 231:124–138
Prell J, White JP, Bourdes A, Bunnewell S, Bongaerts RJ, Poole PS (2009) Legumes regulate Rhizobium bacteroid development and persistence by the supply of branched-chain amino acids. Proc Nat Acad Sci 106:12477–12482
Purugganan MD, Fuller DQ (2009) The nature of selection during plant domestication. Nature 457:12. doi:10.1038/nature07895
Quambusch M, Pirttilä AM, Tejesvi MV, Winkelmann T, Bartsch M (2014) Endophytic bacteria in plant tissue culture: differences between easy- and difficult-to-propagate Prunus avium genotypes. Tree Physiol 34:524–533
Rasche F, Velvis H, Zachow C, Berg G, van Elsas JD, Sessitsch A (2006) Impact of transgenic potatoes expressing anti-bacterial agents on bacterial endophytes is comparable with the effects of plant genotype, soil type and pathogen infection. J Appl Ecol 43:555–566
Reinhold-Hurek B, Hurek T (2011) Living inside plants: bacterial endophytes. Curr Opin Plant Biol 14:435–443
Rodriguez RJ, Henson J, van Volkenburgh E, Hoy M, Wright L, Beckwith F et al (2008) Stress tolerance in plants via habitat-adapted symbiosis. ISME J 2:404–416
Saikkonen K, Gundel PE, Helander M (2013) Chemical ecology mediated by fungal endophytes in grasses. J Chem Ecol 39:962–968. doi:10.1007/s10886-013-0310-3
Schnepf E, Crickmore N, van Rie J, Lereclus D, Baum J, Feitelson J et al (1998) Bacillus thuringiensis and its pesticidal crystal proteins. Microbiol Mol Biol Rev 62:775–806
Schulz B, Boyle C (2005) The endophytic continuum. Mycoloic Res 109:661–686
Sessitsch A, Hardoim PR, Döring J, Weilharter A, Krause A, Woyke T et al (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant Microbe Interac 25:28–36
Shade A, McManus PS, Handelsman J (2013) Unexpected diversity during community succession in the apple flower microbiome. mBio 4:e00602–00612 doi:00610.01128/mBio.00602-00612
Steffen W, Broadgate W, Deutsch L, Gaffney O, Ludwig C (2015) The trajectory of the Anthropocene: the great acceleration. Anthrop Rev 2:81–98. doi:10.1177/2053019614564785
Taghavi S, van der Lelie D, Hoffman A, Zhang YB, Walla MD, Vangronsveld J, et al (2010) Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp 638. Plos Genetics 6:e1000943 doi:1000910.1001371/journal.pgen.1000943
Tian CF, Zhou YJ, Zhang YM, Li QQ, Zhang YZ, Li DF et al (2012) Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations. Proc Nat Acad Sci USA 109:8629–8634. doi:10.1073/pnas.1120436109
Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R et al (2013) Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Nat Acad Sci USA 110:20117–20122. doi:10.1073/pnas.1313452110
Udvardi M, Poole PS (2013) Transport and metabolism in legume-Rhizobia symbioses. Ann Rev Plant Biol 64:781–805
Unterseher M, Gazis R, Chaverri P, Guarniz CFG, Tenorio DHZ (2013) Endophytic fungi from peruvian highland and lowland habitats form distinctive and host plant-specific assemblages. Biodivers Conser 22:999–1016
van Overbeek LS, Franke AC, Nijhuis EHM, Groeneveld RMW, da Rocha UN, Lotz LAP (2011) Bacterial communities associated with Chenopodium album and Stellaria media seeds from arable soils. Microbiol Ecol 62:257–264
Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, et al (2015) Microbial species delineation using whole genome sequences. Nucl Acid Res 657
Wright KM, Chapman S, McGeachy K, Humphris S, Campbell E, Toth IK et al (2013) The endophytic lifestyle of Escherichia coli O157:H7: quantification and internal localization in roots. Phytopathology 103:333–340
Zamioudis C, Pieterse CMJ (2012) Modulation of host immunity by beneficial microbes. Mol Plant Microb Interac 25:139–150. doi:10.1094/MPMI-06-11-0179
Zhu J, Oger PM, Schrammeijer B, Hooykaas PJJ, Farrand SK, Winans SC (2000) The bases of crown gall tumorigenesis. J Bacteriol 182:3885–3895
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Hardoim, P.R., Hardoim, C.C.P. (2017). Genomic Features of Mutualistic Plant Bacteria. In: Maheshwari, D. (eds) Endophytes: Biology and Biotechnology. Sustainable Development and Biodiversity, vol 15. Springer, Cham. https://doi.org/10.1007/978-3-319-66541-2_5
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