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Current Genomics

Author(s): Minaxi Sharma, Surya Sudheer, Zeba Usmani*, Rupa Rani and Pratishtha Gupta

DOI: 10.2174/1389202921999200515140420

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Deciphering the Omics of Plant-Microbe Interaction: Perspectives and New Insights

Page: [343 - 362] Pages: 20

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Abstract

Introduction: Plants do not grow in isolation, rather they are hosts to a variety of microbes in their natural environments. While, few thrive in the plants for their own benefit, others may have a direct impact on plants in a symbiotic manner. Unraveling plant-microbe interactions is a critical component in recognizing the positive and negative impacts of microbes on plants. Also, by affecting the environment around plants, microbes may indirectly influence plants. The progress in sequencing technologies in the genomics era and several omics tools has accelerated in biological science. Studying the complex nature of plant-microbe interactions can offer several strategies to increase the productivity of plants in an environmentally friendly manner by providing better insights. This review brings forward the recent works performed in building omics strategies that decipher the interactions between plant-microbiome. At the same time, it further explores other associated mutually beneficial aspects of plant-microbe interactions such as plant growth promotion, nitrogen fixation, stress suppressions in crops and bioremediation; as well as provides better insights on metabolic interactions between microbes and plants through omics approaches. It also aims to explore advances in the study of Arabidopsis as an important avenue to serve as a baseline tool to create models that help in scrutinizing various factors that contribute to the elaborate relationship between plants and microbes. Causal relationships between plants and microbes can be established through systematic gnotobiotic experimental studies to test hypotheses on biologically derived interactions.

Conclusion: This review will cover recent advances in the study of plant-microbe interactions keeping in view the advantages of these interactions in improving nutrient uptake and plant health.

Keywords: Plant-microbe interactions, plant stress response, genomics, transcriptomics, proteomics, metabolomics.

Graphical Abstract

[1]
Olanrewaju, O.S.; Ayangbenro, A.S.; Glick, B.R.; Babalola, O.O. Plant health: feedback effect of root exudates-rhizobiome interactions. Appl. Microbiol. Biotechnol., 2019, 103(3), 1155-1166.
[http://dx.doi.org/10.1007/s00253-018-9556-6] [PMID: 30570692]
[2]
Fürnkranz, M.; Lukesch, B.; Müller, H.; Huss, H.; Grube, M.; Berg, G. Microbial diversity inside pumpkins: microhabitat-specific communities display a high antagonistic potential against phytopathogens. Microb. Ecol., 2012, 63(2), 418-428.
[http://dx.doi.org/10.1007/s00248-011-9942-4] [PMID: 21947430]
[3]
Bragina, A.; Cardinale, M.; Berg, C.; Berg, G. Vertical transmission explains the specific Burkholderia pattern in Sphagnum mosses. Front. Microbiol., 2014, 18, 434-394.
[PMID: 24391630]
[4]
Manias, D.; Verma, A.; Soni, D.K. Isolation and characterization of endophytes: Biochemical and molecular approach; Prospects for Sustainable Agriculture, Woodhead Publishing Series in Food Science, Technology and Nutrition, 2020, pp. 1-14.
[5]
Kumar, V.; Baweja, M.; Singh, P.K.; Shukla, P. Recent developments in system biology and metabolic engineering of plant-microbe interactions. Front. Plant Sci., 2016, 7, 1421.
[http://dx.doi.org/10.3389/fpls.2016.01421] [PMID: 27725824]
[6]
Mishra, A.; Mishra, S.P.; Arshi, A.; Agarwal, A.; Dwivedi, S.K. Plant-microbe interactions for bioremediation and phytoremediation of environmental pollutants and agro-ecosystem development. Bioremediation of Industrial Waste for Environmental Safety; Bharagava,R; Saxena, G., Ed.; Springer: Singapore, 2020.
[http://dx.doi.org/10.1007/978-981-13-3426-9_17]
[7]
Imam, J.; Alam, S.; Mandal, N.P.; Variar, M.; Shukla, P. Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers. Euphytica, 2013, 196, 199-211.
[http://dx.doi.org/10.1007/s10681-013-1024-x]
[8]
Imam, J.; Mahto, D.; Mandal, N.P.; Maiti, D.; Shukla, P.; Variar, M. Molecular analysis of Indian rice germplasm accessions with resistance to blast pathogen pages. J. Crop Improv., 2014, 28, 729-739.
[http://dx.doi.org/10.1080/15427528.2014.921261]
[9]
Imam, J.; Alam, S.; Mandal, N.P.; Maiti, D.; Variar, M.; Shukla, P. Molecular diversity and mating type distribution of the rice blast pathogen Magnaporthe oryzae in North-East and Eastern India. Indian J. Microbiol., 2015, 55, 108-113.
[http://dx.doi.org/10.1007/s12088-014-0504-6]
[10]
Ren, X-M.; Guo, S.J.; Tian, W.; Chen, Y.; Han, H.; Chen, E.; Li, B.L.; Li, Y.Y.; Chen, Z-J. Effects of plant growth-promoting bacteria (PGPB) inoculation on the growth, antioxidant activity, Cu uptake, and bacterial community structure of rape (Brassica napus L.) grown in cu-contaminated agricultural soil. Front. Microbiol., 2019, 10, 1455.
[http://dx.doi.org/10.3389/fmicb.2019.01455] [PMID: 31316489]
[11]
Rani, R.; Kumar, V.; Usmani, Z.; Gupta, P.; Chandra, A. Influence of plant growth promoting rhizobacterial strains Paenibacillus sp. IITISM08, Bacillus sp. PRB77 and Bacillus sp. PRB101 using Helianthus annuus on degradation of endosulfan from contaminated soil. Chemosphere, 2019, 225, 479-489.
[http://dx.doi.org/10.1016/j.chemosphere.2019.03.037] [PMID: 30897471]
[12]
Gupta, P.; Kumar, V.; Usmani, Z.; Rani, R.; Chandra, A.; Gupta, V.K. Implications of plant growth promoting Klebsiella sp. CPSB4 and Enterobacter sp. CPSB49 in luxuriant growth of tomato plants under chromium stress. Chemosphere, 2020, 240, 124944.
[http://dx.doi.org/10.1016/j.chemosphere.2019.124944] [PMID: 31726591]
[13]
Lima-Mendez, G.; Faust, K.; Henry, N.; Decelle, J.; Colin, S.; Carcillo, F.; Chaffron, S.; Ignacio-Espinosa, J.C.; Roux, S.; Vincent, F.; Bittner, L.; Darzi, Y.; Wang, J.; Audic, S.; Berline, L.; Bontempi, G.; Cabello, A.M.; Coppola, L.; Cornejo-Castillo, F.M.; d’Ovidio, F.; De Meester, L.; Ferrera, I.; Garet-Delmas, M.J.; Guidi, L.; Lara, E.; Pesant, S.; Royo-Llonch, M.; Salazar, G.; Sánchez, P.; Sebastian, M.; Souffreau, C.; Dimier, C.; Picheral, M.; Searson, S.; Kandels-Lewis, S.; Gorsky, G.; Not, F.; Ogata, H.; Speich, S.; Stemmann, L.; Weissenbach, J.; Wincker, P.; Acinas, S.G.; Sunagawa, S.; Bork, P.; Sullivan, M.B.; Karsenti, E.; Bowler, C.; de Vargas, C.; Raes, J. Tara Oceans coordinators. Ocean plankton. Determinants of community structure in the global plankton interactome. Science, 2015, 348(6237), 1262073.
[http://dx.doi.org/10.1126/science.1262073] [PMID: 25999517]
[14]
Frantzeskakis, L.; Di Pietro, A.; Rep, M.; Schirawski, J.; Wu, C-H.; Panstruga, R. Rapid evolution in plant-microbe interactions - a molecular genomics perspective. New Phytol., 2020, 225(3), 1134-1142.
[http://dx.doi.org/10.1111/nph.15966] [PMID: 31134629]
[15]
Terauchi, R. KokiFujisaki, K.; Shimizu, M.; Oikawa, K.; Takeda, T.; Takagi, H.; Abe, A.; Okuyama, Y.; Yoshida, K.; Saitoh, H. Using genomics tools to understand plant resistance against pathogens: A case study of Magnaporthe-rice interactions; Applied Plant Biotechnology for Improving Resistance to Biotic Stress, 2020, pp. 181-188.
[16]
Gilbert, J.A.; Jansson, J.K.; Knight, R. The Earth Microbiome project: successes and aspirations. BMC Biol., 2014, 12, 69.
[http://dx.doi.org/10.1186/s12915-014-0069-1] [PMID: 25184604]
[17]
Cordero, J.; de Freitas, J.R.; Germida, J.J. Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada. Can. J. Microbiol., 2020, 66(1), 71-85.
[http://dx.doi.org/10.1139/cjm-2019-0330] [PMID: 31658427]
[18]
Parray, J.A.; Shameem, N. Sustainable agriculture: Advances in Plant Metabolome and Microbiome; Academic Press, Elsevier: United Kingdom, 2020.
[19]
Bulgarelli, D.; Schlaeppi, K.; Spaepen, S.; Ver Loren van Themaat, E.; Schulze-Lefert, P. Structure and functions of the bacterial microbiota of plants. Annu. Rev. Plant Biol., 2013, 64, 807-838.
[http://dx.doi.org/10.1146/annurev-arplant-050312-120106] [PMID: 23373698]
[20]
Berg, G.; Mahnert, A.; Moissl-Eichinger, C. Beneficial effects of plant-associated microbes on indoor microbiomes and human health? Front. Microbiol., 2014, 5, 15.
[http://dx.doi.org/10.3389/fmicb.2014.00015] [PMID: 24523719]
[21]
Wille, L.; Messmer, M.M.; Studer, B.; Hohmann, P. Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes. Plant Cell Environ., 2019, 42(1), 20-40.
[http://dx.doi.org/10.1111/pce.13214] [PMID: 29645277]
[22]
Schlaeppi, K.; Bulgarelli, D. The plant microbiome at work. Mol. Plant Microbe Interact., 2015, 28(3), 212-217.
[http://dx.doi.org/10.1094/MPMI-10-14-0334-FI] [PMID: 25514681]
[23]
Berg, G.; Rybakova, D.; Grube, M.; Köberl, M. The plant microbiome explored: implications for experimental botany. J. Exp. Bot., 2016, 67(4), 995-1002.
[http://dx.doi.org/10.1093/jxb/erv466] [PMID: 26547794]
[24]
Orozco-Mosqueda, M.D.C.; Rocha-Granados, M.D.C.; Glick, B.R.; Santoyo, G. Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms. Microbiol. Res., 2018, 208, 25-31.
[http://dx.doi.org/10.1016/j.micres.2018.01.005] [PMID: 29551209]
[25]
Compant, S.; Samad, A.; Faist, H.; Sessitsch, A. A review on the plant microbiome: ecology, functions, and emerging trends in microbial application. J. Adv. Res., 2019, 19, 29-37.
[http://dx.doi.org/10.1016/j.jare.2019.03.004] [PMID: 31341667]
[26]
Chang, C.; Nasir, F.; Ma, L.; Tian, C. Molecular communication and nutrient transfer of arbuscular mycorrhizal fungi, symbiotic nitrogen-fixing bacteria, and host plant in tripartite symbiosis. inLegume Nitrogen Fixation in Soils with Low Phosphorus Availability; Springer: Cham, 2017.
[27]
Taiwo, L.B.; Oyedele, A.O.; Ailenokhuoria, B.V.; Okareh, O.T. Plant-microbes relationships in soil ecological system and benefits accruable to food health. Field Crops: Sustainable Management by PGPR. Sustainable Development and Biodiversity; Maheshwari,D; Dheeman, S., Ed.; Springer: Cham, 2019, Vol. 23, .
[http://dx.doi.org/10.1007/978-3-030-30926-8_7]
[28]
Alori, E.T.; Glick, B.R.; Babalola, O.O. Microbial phosphorus solubilization and its potential for use in sustainable agriculture. Front. Microbiol., 2017, 8, 971.
[http://dx.doi.org/10.3389/fmicb.2017.00971] [PMID: 28626450]
[29]
Li, Y.; Zhang, J.; Zhang, J.; Xu, W.; Mou, Z. Characteristics of inorganic phosphate-solubilizing bacteria from the sediments of a eutrophic lake. Int. J. Environ. Res. Public Health, 2019, 16(12), 2141.
[http://dx.doi.org/10.3390/ijerph16122141] [PMID: 31212977]
[30]
Chhabra, S.; Dowling, D.N. Endophyte-promoted nutrient acquisition: phosphorus and iron. Functional Importance of the Plant Microbiome; Doty, S., Ed.; Springer: Cham, 2017.
[http://dx.doi.org/10.1007/978-3-319-65897-1_3]
[31]
Parewa, H.P.; Meena, V.S.; Jain, L.K.; Choudhary, A. Sustainable crop production and soil health management through plant growth-promoting rhizobacteria. Role of Rhizospheric Microbes in Soil; Meena, V., Ed.; Springer: Singapore, 2018.
[http://dx.doi.org/10.1007/978-981-10-8402-7_12]
[32]
Islam, S.; Akanda, A.M.; Prova, A.; Islam, Md. T.; Md. Hossain, M. Isolation and identification of plant growth promoting rhizobacteria from cucumber rhizosphere and their effect on plant growth promotion and disease suppression. Front. Microbiol., 2016.
[http://dx.doi.org/10.3389/fmicb.2015.01360]
[33]
Roth, R.; Paszkowski, U. Plant carbon nourishment of arbuscular mycorrhizal fungi. Curr. Opin. Plant Biol., 2017, 39, 50-56.
[http://dx.doi.org/10.1016/j.pbi.2017.05.008] [PMID: 28601651]
[34]
Finkel, O.M.; Castrillo, G.; Herrera Paredes, S.; Salas González, I.; Dangl, J.L. Understanding and exploiting plant beneficial microbes. Curr. Opin. Plant Biol., 2017, 38, 155-163.
[http://dx.doi.org/10.1016/j.pbi.2017.04.018] [PMID: 28622659]
[35]
Hiruma, K.; Kobae, Y.; Toju, H. Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: evolutionary origins and host-symbiont molecular mechanisms. Curr. Opin. Plant Biol., 2018, 44, 145-154.
[http://dx.doi.org/10.1016/j.pbi.2018.04.009] [PMID: 29738938]
[36]
Berruti, A.; Lumini, E.; Balestrini, R.; Bianciotto, V. Arbuscular mycorrhizal fungi as natural biofertilizers: let’s benefit from past successes. Front. Microbiol., 2016, 6, 1559.
[http://dx.doi.org/10.3389/fmicb.2015.01559] [PMID: 26834714]
[37]
Pathan, S.I.; Ceccherini, M.T.; Sunseri, F.; Lupini, A. Rhizosphere as hotspot for plant-soil-microbe interaction. Carbon and Nitrogen Cycling in Soil; Datta, R.; Meena, R.; Pathan, S; Ceccherini, M., Ed.; Springer, 2020.
[http://dx.doi.org/10.1007/978-981-13-7264-3_2]
[38]
Padda, K.P.; Puri, A.; Chanway, C. Endophytic nitrogen fixation - a possible ‘hidden’ source of nitrogen for lodgepole pine trees growing at unreclaimed gravel mining sites. FEMS Microbiol. Ecol., 2019, 95(11), fiz172.
[http://dx.doi.org/10.1093/femsec/fiz172] [PMID: 31647534]
[39]
Bashandy, S.R.; Abd‐Alla, M.H.; Bagy, M.M.K. Biological Nitrogen Fixation and Biofertilizers as Ideal Potential Solutions for Sustainable Agriculture. In: Integrating Green Chemistry and Sustainable Engineering; Scrivener Publishing LLC, 2019.
[40]
Pankievicz, V.C.S.; Irving, T.B.; Maia, L.G.S.; Ané, J-M. Are we there yet? the long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops. BMC Biol., 2019, 17(1), 99.
[http://dx.doi.org/10.1186/s12915-019-0710-0] [PMID: 31796086]
[41]
Mahmud, K.; Makaju, S.; Ibrahim, R.; Missaoui, A. Current progress in nitrogen fixing plants and microbiome research. Plants (Basel), 2020, 9(1), 97.
[http://dx.doi.org/10.3390/plants9010097] [PMID: 31940996]
[42]
Liu, C.W.; Murray, J.D. The role of flavonoids in nodulation host-range specificity: an update. Plants (Basel), 2016, 5(3), 33.
[http://dx.doi.org/10.3390/plants5030033] [PMID: 27529286]
[43]
Mathesius, U. Flavonoid functions in plants and their interactions with other organisms. Plants (Basel), 2018, 7(2), 30.
[http://dx.doi.org/10.3390/plants7020030] [PMID: 29614017]
[44]
Liu, Y.C.; Qin, X.M.; Xiao, J.X.; Tang, L.; Wei, C.Z.; Wei, J.J.; Zheng, Y. Intercropping influences component and content change of flavonoids in root exudates and nodulation of Faba bean. J. Plant Interact., 2017, 12(1), 187-192.
[http://dx.doi.org/10.1080/17429145.2017.1308569]
[45]
van Noorden, G.E.; Kerim, T.; Goffard, N.; Wiblin, R.; Pellerone, F.I.; Rolfe, B.G.; Mathesius, U. Overlap of proteome changes in Medicago truncatula in response to auxin and Sinorhizobium meliloti. Plant Physiol., 2007, 144(2), 1115-1131.
[http://dx.doi.org/10.1104/pp.107.099978] [PMID: 17468210]
[46]
Lery, L.M.S.; Hemerly, A.S.; Nogueira, E.M.; von Krüger, W.M.A.; Bisch, P.M. Quantitative proteomic analysis of the interaction between the endophytic plant-growth-promoting bacterium Gluconacetobacter diazotrophicus and sugarcane. Mol. Plant Microbe Interact., 2011, 24(5), 562-576.
[http://dx.doi.org/10.1094/MPMI-08-10-0178] [PMID: 21190439]
[47]
Salavati, A.; Shafeinia, A.; Klubicova, K.; Bushehri, A.A.; Komatsu, S. Proteomic insights into intra- and intercellular plant-bacteria symbiotic association during root nodule formation. Front. Plant Sci., 2013, 4, 28.
[http://dx.doi.org/10.3389/fpls.2013.00028] [PMID: 23443347]
[48]
Zhang, C.; Bousquet, A.; Harris, J.M. Abscisic acid and lateral root organ defective/NUMEROUS INFECTIONS AND POLYPHENOLICS modulate root elongation via reactive oxygen species in Medicago truncatula. Plant Physiol., 2014, 166(2), 644-658.
[http://dx.doi.org/10.1104/pp.114.248542] [PMID: 25192698]
[49]
Kandasamy, S.; Loganathan, K.; Muthuraj, R.; Duraisamy, S.; Seetharaman, S.; Thiruvengadam, R.; Ponnusamy, B.; Ramasamy, S. Understanding the molecular basis of plant growth promotional effect of Pseudomonas fluorescens on rice through protein profiling. Proteome Sci., 2009, 7(47), 47.
[http://dx.doi.org/10.1186/1477-5956-7-47] [PMID: 20034395]
[50]
Chi, F.; Yang, P.; Han, F.; Jing, Y.; Shen, S. Proteomic analysis of rice seedlings infected by Sinorhizobium meliloti 1021. Proteomics, 2010, 10(9), 1861-1874.
[http://dx.doi.org/10.1002/pmic.200900694] [PMID: 20213677]
[51]
Schliemann, W.; Ammer, C.; Strack, D. Metabolite profiling of mycorrhizal roots of Medicago truncatula. Phytochemistry, 2008, 69(1), 112-146.
[http://dx.doi.org/10.1016/j.phytochem.2007.06.032] [PMID: 17706732]
[52]
Pedone-Bonfim, M.V.; Lins, M.A.; Coelho, I.R.; Santana, A.S.; Silva, F.S.; Maia, L.C. Mycorrhizal technology and phosphorus in the production of primary and secondary metabolites in cebil (Anadenanthera colubrina (Vell.) Brenan) seedlings. J. Sci. Food Agric., 2013, 93(6), 1479-1484.
[http://dx.doi.org/10.1002/jsfa.5919] [PMID: 23108717]
[53]
Rispail, N.; Hauck, B.; Bartholomew, B.; Watson, A.A.; Nash, R.J.; Webb, K.J. Secondary metabolite profiling of the model legume Lotus japonicus during its symbiotic interaction with Mesorhizobium loti. Symbiosis, 2010, 50, 119-128.
[http://dx.doi.org/10.1007/s13199-010-0053-7]
[54]
Popovici, J.; Walker, V.; Bertrand, C.; Bellvert, F.; Fernandez, M.P.; Comte, G. Strain specificity in the Myricaceae-Frankia symbiosis is correlated to plant root phenolics. Funct. Plant Biol., 2011, 38(9), 682.
[http://dx.doi.org/10.1071/FP11144]
[55]
Hrynkiewicz, K.; Zloch, M.; Kowalkowski, T.; Baum, C.; Buszewski, B. Efficiency of microbially assisted phytoremediation of heavy-metal contaminated soils. Environ. Rev., 2018, 26(3), 316-332.
[http://dx.doi.org/10.1139/er-2018-0023]
[56]
Mendoza-Hernández, J.C.; Vázquez-Delgado, O.R.; Castillo-Morales, M.; Varela-Caselis, J.L.; Santamaría-Juárez, J.D.; Olivares-Xometl, O.; Arriola Morales, J.; Pérez-Osorio, G. Phytoremediation of mine tailings by Brassica juncea inoculated with plant growth-promoting bacteria. Microbiol. Res., 2019, 228, 126308.
[http://dx.doi.org/10.1016/j.micres.2019.126308] [PMID: 31430656]
[57]
Cheng, Z.; Wei, Y.Y.; Sung, W.W.; Glick, B.R.; McConkey, B.J. Proteomic analysis of the response of the plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stress. Proteome Sci., 2009, 7, 18.
[http://dx.doi.org/10.1186/1477-5956-7-18] [PMID: 19422705]
[58]
Bona, E.; Cattaneo, C.; Cesaro, P.; Marsano, F.; Lingua, G.; Cavaletto, M.; Berta, G. Proteomic analysis of Pteris vittata fronds: two arbuscular mycorrhizal fungi differentially modulate protein expression under arsenic contamination. Proteomics, 2010, 10(21), 3811-3834.
[http://dx.doi.org/10.1002/pmic.200900436] [PMID: 20957753]
[59]
Aloui, A.; Recorbet, G.; Robert, F.; Schoefs, B.; Bertrand, M.; Henry, C.; Gianinazzi-Pearson, V.; Dumas-Gaudot, E.; Aschi-Smiti, S. Arbuscular mycorrhizal symbiosis elicits shoot proteome changes that are modified during cadmium stress alleviation in Medicago truncatula. BMC Plant Biol., 2011, 11, 75.
[http://dx.doi.org/10.1186/1471-2229-11-75] [PMID: 21545723]
[60]
Lingua, G.; Bona, E.; Todeschini, V.; Cattaneo, C.; Marsano, F.; Berta, G.; Cavaletto, M. Effects of heavy metals and arbuscular mycorrhiza on the leaf proteome of a selected poplar clone: a time course analysis. PLoS One, 2012, 7(6), e38662.
[http://dx.doi.org/10.1371/journal.pone.0038662] [PMID: 22761694]
[61]
Farinati, S.; DalCrso, G.; Panigati, M.; Furini, A. Interaction between selected bacterial strains and Arabidopsis halleri modulates shoot proteome and cadmium and zinc accumulation. J. Exp. Bot., 2011, 62(10), 3433-3447.
[http://dx.doi.org/10.1093/jxb/err015] [PMID: 21357773]
[62]
Pozo, M.J.; López-Ráez, J.A.; Azcón-Aguilar, C.; García-Garrido, J.M. Phytohormones as integrators of environmental signals in the regulation of mycorrhizal symbioses. New Phytol., 2015, 205(4), 1431-1436.
[http://dx.doi.org/10.1111/nph.13252] [PMID: 25580981]
[63]
Gomes, D.F.; da Silva Batista, J.S.; Rolla, A.A.; da Silva, L.P.; Bloch, C.; Galli-Terasawa, L.V.; Hungria, M. Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis. BMC Genomics, 2014, 15, 643.
[http://dx.doi.org/10.1186/1471-2164-15-643] [PMID: 25086822]
[64]
Barea, J.M. Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant microbiome interactions. J. Soil Sci. Plant Nutr., 2015, 15(2), 261-282.
[http://dx.doi.org/10.4067/S0718-95162015005000021]]
[65]
Carvalhais, L.C.; Dennis, P.G.; Badri, D.V.; Tyson, G.W.; Vivanco, J.M.; Schenk, P.M. Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS One, 2013, 8(2), e56457.
[http://dx.doi.org/10.1371/journal.pone.0056457] [PMID: 23424661]
[66]
Hirsch, P.R.; Mauchline, T.H. Who’s who in the plant root microbiome? Nat. Biotechnol., 2012, 30(10), 961-962.
[http://dx.doi.org/10.1038/nbt.2387] [PMID: 23051815]
[67]
Barret, M.; Tan, H.; Egan, F.; Morrissey, J.P.; Reen, J.; O’Gara, F. Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere. In: F.J, de Bruijn Molecular Microbial Ecology of the Rhizosphere; Wiley Blackwell: Hoboken, New Jersey, USA, 2013; pp. 57-68.
[http://dx.doi.org/10.1002/9781118297674.ch6]
[68]
Schreiter, S.; Eltlbany, N.; Smalla, K. Microbial communities in the rhizosphere analyzed by cultivation independent DNA-based methods. Principles of Plant-Microbe Interactions; Lugtenberg, B., Ed.; Springer International Publishing Switzerland: Heidelberg, 2015, pp. 289-298.
[http://dx.doi.org/10.1007/978-3-319-08575-3_30]
[69]
Igiehon, N.O.; Babalola, O.O. Below-ground-above-ground Plant-microbial Interactions: focusing on Soybean, Rhizobacteria and Mycorrhizal Fungi. Open Microbiol. J., 2018, 12, 261-279.
[http://dx.doi.org/10.2174/1874285801812010261] [PMID: 30197700]
[70]
Bertani, I.; Abbruscato, P.; Piffanelli, P.; Subramoni, S.; Venturi, V. Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis. Environ. Microbiol. Rep., 2016, 8(3), 388-398.
[http://dx.doi.org/10.1111/1758-2229.12403] [PMID: 27038229]
[71]
Junker, R.R.; Keller, A. Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity. FEMS Microbiol. Ecol., 2015, 91(9), fiv097.
[http://dx.doi.org/10.1093/femsec/fiv097] [PMID: 26253507]
[72]
Romero, F.M.; Marina, M.; Pieckenstain, F.L. The communities of tomato (Solanum lycopersicum L.) leaf endophytic bacteria, analyzed by 16S-ribosomal RNA gene pyrosequencing. FEMS Microbiol. Lett., 2014, 351(2), 187-194.
[http://dx.doi.org/10.1111/1574-6968.12377] [PMID: 24417185]
[73]
Trujillo, M.E.; Riesco, R.; Benito, P.; Carro, L. Endophytic Actinobacteria and the interaction of Micromonospora and nitrogen fixing plants. Front. Microbiol., 2015, 6, 1341.
[http://dx.doi.org/10.3389/fmicb.2015.01341] [PMID: 26648923]
[74]
Fonseca-García, C.; Coleman-Derr, D.; Garrido, E.; Visel, A.; Tringe, S.G.; Partida-Martínez, L.P. The cacti microbiome: interplay between habitat-filtering and host-specificity. Front. Microbiol., 2016, 7, 150.
[http://dx.doi.org/10.3389/fmicb.2016.00150] [PMID: 26904020]
[75]
Rosenberg, E.; Zilber-Rosenberg, I. Microbes drive evolution of animals and plants: the hologenome concept. MBio, 2016, 7(2), e01395.
[http://dx.doi.org/10.1128/mBio.01395-15] [PMID: 27034283]
[76]
Hart, M.L.; Meyer, A.; Johnson, P.J.; Ericsson, A.C. Comparative evaluation of DNA extraction methods from faeces of multiple host species for downstream next-generation sequencing. PLoS One, 2015, 10(11), e0143334.
[http://dx.doi.org/10.1371/journal.pone.0143334] [PMID: 26599606]
[77]
Franzén, O.; Hu, J.; Bao, X.; Itzkowitz, S.H.; Peter, I.; Bashir, A. Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering. Microbiome, 2015, 3, 43.
[http://dx.doi.org/10.1186/s40168-015-0105-6] [PMID: 26434730]
[78]
Felczykowska, A.; Krajewska, A.; Zielińska, S.; Łoś, J.M. Sampling, metadata and DNA extraction - important steps in metagenomic studies. Acta Biochim. Pol., 2015, 62(1), 151-160.
[http://dx.doi.org/10.18388/abp.2014_916] [PMID: 25680373]
[79]
Glassing, A.; Dowd, S.E.; Galandiuk, S.; Davis, B.; Jorden, J.R.; Chiodini, R.J. Changes in 16S RNA Gene microbial community profiling by concentration of prokaryotic DNA. J. Microbiol. Methods, 2015, 119, 239-242.
[http://dx.doi.org/10.1016/j.mimet.2015.11.001] [PMID: 26569458]
[80]
Sunagawa, S.; Mende, D.R.; Zeller, G.; Izquierdo-Carrasco, F.; Berger, S.A.; Kultima, J.R.; Coelho, L.P.; Arumugam, M.; Tap, J.; Nielsen, H.B.; Rasmussen, S.; Brunak, S.; Pedersen, O.; Guarner, F.; de Vos, W.M.; Wang, J.; Li, J.; Doré, J.; Ehrlich, S.D.; Stamatakis, A.; Bork, P. Metagenomic species profiling using universal phylogenetic marker genes. Nat. Methods, 2013, 10(12), 1196-1199.
[http://dx.doi.org/10.1038/nmeth.2693] [PMID: 24141494]
[81]
Shade, A.; McManus, P.S.; Handelsman, J. Unexpected diversity during community succession in the apple flower microbiome. MBio, 2013, 4(2), e00602-e00612.
[http://dx.doi.org/10.1128/mBio.00602-12] [PMID: 23443006]
[82]
Kaul, S.; Sharma, T.; Dhar, M.K. “Omics” tools for better understanding the plant-endophyte interactions. Front. Plant Sci., 2016.
[http://dx.doi.org/10.3389/fpls.2016.00955]
[83]
Kumari, A.; Sumer, S.; Jalan, B.; Lyngdoh, P. Nongbri, Laskar M.A. Impact of Next-Generation Sequencing Technology in Plant-Microbe Interaction Study. Springer International Publishing AG Kalia V.C; Kumar, P., Ed.; Microbial Applications, 2017, Vol. 1, .
[84]
Chaterji, S.; Koo, J.; Li, N.; Meyer, F.; Grama, A.; Bagchi, S. Federation in genomics pipelines: techniques and challenges. Brief. Bioinform., 2019, 20(1), 235-244.
[http://dx.doi.org/10.1093/bib/bbx102] [PMID: 28968781]
[85]
Delmotte, N.; Ahrens, C.H.; Knief, C.; Qeli, E.; Koch, M.; Fischer, H.M.; Vorholt, J.A.; Hennecke, H.; Pessi, G. An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics, 2010, 10(7), 1391-1400.
[http://dx.doi.org/10.1002/pmic.200900710] [PMID: 20104621]
[86]
Ali, A.; Alexandersson, E.; Sandin, M.; Resjo, S.; Lenman, M.; Hedley, P.; Levander, F.; Andreasson, E. Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions. BMC Genomics, 2014, 19, 15-497.
[http://dx.doi.org/10.1186/1471-2164-15-497]
[87]
Mitra, S. Multiple Data Analyses and Statistical Approaches for analyzing data from metagenomic studies and clinical trials, in: evolutionary genomics, 2019, pp. 605-634.
[http://dx.doi.org/10.1007/978-1-4939-9074-0_20]
[88]
Delmotte, N.; Knief, C.; Chaffron, S.; Innerebner, G.; Roschitzki, B.; Schlapbach, R.; von Mering, C.; Vorholt, J.A. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. USA, 2009, 106(38), 16428-16433.
[http://dx.doi.org/10.1073/pnas.0905240106] [PMID: 19805315]
[89]
Sessitsch, A.; Hardoim, P.; Döring, J.; Weilharter, A.; Krause, A.; Woyke, T.; Mitter, B.; Hauberg-Lotte, L.; Friedrich, F.; Rahalkar, M.; Hurek, T.; Sarkar, A.; Bodrossy, L.; van Overbeek, L.; Brar, D.; van Elsas, J.D.; Reinhold-Hurek, B. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol. Plant Microbe Interact., 2012, 25(1), 28-36.
[http://dx.doi.org/10.1094/MPMI-08-11-0204] [PMID: 21970692]
[90]
Knief, C.; Delmotte, N.; Chaffron, S.; Stark, M.; Innerebner, G.; Wassmann, R.; von Mering, C.; Vorholt, J.A. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J., 2012, 6(7), 1378-1390.
[http://dx.doi.org/10.1038/ismej.2011.192] [PMID: 22189496]
[91]
Rascovan, N.; Carbonetto, B.; Perrig, D.; Díaz, M.; Canciani, W.; Abalo, M.; Alloati, J.; González-Anta, G.; Vazquez, M.P. Integrated analysis of root microbiomes of soybean and wheat from agricultural fields. Sci. Rep., 2016, 6(1), 28084.
[http://dx.doi.org/10.1038/srep28084] [PMID: 27312589]
[92]
Thomas, T.; Gilbert, J.; Meyer, F. Metagenomics - a guide from sampling to data analysis. Microb. Inform. Exp., 2012, 2(1), 3.
[http://dx.doi.org/10.1186/2042-5783-2-3] [PMID: 22587947]
[93]
Lucaciu, R.; Pelikan, C.; Gerner, S.M.; Zioutis, C.; Köstlbacher, S.; Marx, H.; Herbold, C.W.; Schmidt, H.; Rattei, T. A bioinformatics guide to plant microbiome analysis. Front. Plant Sci., 2019, 10, 1313.
[http://dx.doi.org/10.3389/fpls.2019.01313] [PMID: 31708944]
[94]
Liao, H.L.; Chen, Y.; Vilgalys, R. Metatranscriptomic Study of common and host-specific patterns of gene expression between pines and their symbiotic ectomycorrhizal fungi in the Genus Suillus. PLoS Genet., 2016, 12(10), e1006348.
[http://dx.doi.org/10.1371/journal.pgen.1006348] [PMID: 27736883]
[95]
Thomas, J.; Kim, H.R.; Rahmatallah, Y.; Wiggins, G.; Yang, Q.; Singh, R.; Glazko, G.; Mukherjee, A. rna-seq reveals differentially expressed genes in rice (oryza sativa) roots during interactions with plant-growth promoting bacteria, azospirillum brasilense. plos one 2019, 14(5) e, 0217309.
[http://dx.doi.org/10.1371/journal.pone.0217309] [PMID: 31120967]
[96]
Oliveira, V.H.D.; Ullah, I.; Dunwell, J.M.; Tibbett, M. Mycorrhizal symbiosis induces divergent patterns of transport and partitioning of Cd and Zn in Populus trichocarpa. Environ. Exp. Bot., 2020, 171, 103925.
[http://dx.doi.org/10.1016/j.envexpbot.2019.103925]
[97]
Ithal, N.; Recknor, J.; Nettleton, D.; Hearne, L.; Maier, T.; Baum, T.J.; Mitchum, M.G. Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean. Mol. Plant Microbe Interact., 2007, 20(3), 293-305.
[http://dx.doi.org/10.1094/MPMI-20-3-0293] [PMID: 17378432]
[98]
Brotman, Y.; Lisec, J.; Méret, M.; Chet, I.; Willmitzer, L.; Viterbo, A. Transcript and metabolite analysis of the Trichoderma-induced systemic resistance response to Pseudomonas syringae in Arabidopsis thaliana. Microbiology, 2012, 158(Pt 1), 139-146.
[http://dx.doi.org/10.1099/mic.0.052621-0] [PMID: 21852347]
[99]
Breuillin, F.; Schramm, J.; Hajirezaei, M.; Ahkami, A.; Favre, P.; Druege, U.; Hause, B.; Bucher, M.; Kretzschmar, T.; Bossolini, E.; Kuhlemeier, C.; Martinoia, E.; Franken, P.; Scholz, U.; Reinhardt, D. Phosphate systemically inhibits development of arbuscular mycorrhiza in Petunia hybrida and represses genes involved in mycorrhizal functioning. Plant J., 2010, 64(6), 1002-1017.
[http://dx.doi.org/10.1111/j.1365-313X.2010.04385.x] [PMID: 21143680]
[100]
Medina, J.; Monreal, C.M.; Orellana, L.; Calabi-Floody, M.; González, M.E.; Meier, S.; Borie, F.; Cornejo, P.; Cornejo, P. Influence of saprophytic fungi and inorganic additives on enzyme activities and chemical properties of the biodegradation process of wheat straw for the production of organo-mineral amendments. J. Environ. Manage., 2020, 255, 109922.
[http://dx.doi.org/10.1016/j.jenvman.2019.109922] [PMID: 32063309]
[101]
Scervino, J.M.; Mesa, M.P.; Ivana Della Monica, I.D.; Recchi, M.; Moreno, N.S.; Godeas, A. Soil fungal isolates produce different organic acid patterns involved in phosphate salts solubilisation. Biol. Fertil. Soils, 2010, 46, 755-763.
[http://dx.doi.org/10.1007/s00374-010-0482-8]
[102]
Planchamp, C.; Glauser, G.; Mauch-Mani, B. Root inoculation with Pseudomonas putida KT2440 induces transcriptional and metabolic changes and systemic resistance in maize plants. Front. Plant Sci., 2015, 5(1), 719.
[http://dx.doi.org/10.3389/fpls.2014.00719] [PMID: 25628626]
[103]
Yasmin, S.; Hafeez, F.Y.; Mirza, M.S.; Rasul, M.; Arshad, H.M.I.; Zubair, M.; Iqbal, M. Biocontrol of bacterial leaf blight of rice and profiling of secondary metabolites produced by rhizospheric Pseudomonas aeruginosa BRp3. Front. Microbiol., 2017, 8, 1895.
[http://dx.doi.org/10.3389/fmicb.2017.01895] [PMID: 29018437]
[104]
Verhagen, B.W.M.; Glazebrook, J.; Zhu, T.; Chang, H-S.; van Loon, L.C.; Pieterse, C.M. The transcriptome of rhizobacteria-induced systemic resistance in arabidopsis. Mol. Plant Microbe Interact., 2004, 17(8), 895-908.
[http://dx.doi.org/10.1094/MPMI.2004.17.8.895] [PMID: 15305611]
[105]
Utsumi, Y.; Tanaka, M.; Kurotani, A.; Yoshida, T.; Mochida, K.; Matsui, A.; Ishitani, M.; Sraphet, S.; Whankaew, S.; Asvarak, T.; Narangajavana, J.; Triwitayakorn, K.; Sakurai, T.; Seki, M. Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. J. Plant Res., 2016, 129(4), 711-726.
[http://dx.doi.org/10.1007/s10265-016-0828-x] [PMID: 27138000]
[106]
Sham, A.; Moustafa, K.; Al-Shamisi, S.; Alyan, S.; Iratni, R.; AbuQamar, S. Microarray analysis of Arabidopsis WRKY33 mutants in response to the necrotrophic fungus Botrytis cinerea. PLoS One, 2017, 12(2), e0172343.
[http://dx.doi.org/10.1371/journal.pone.0172343] [PMID: 28207847]
[107]
Xu, L.; Zhu, L.; Tu, L.; Liu, L.; Yuan, D.; Jin, L.; Long, L.; Zhang, X. Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. J. Exp. Bot., 2011, 62(15), 5607-5621.
[http://dx.doi.org/10.1093/jxb/err245] [PMID: 21862479]
[108]
Romero, F.M.; Marina, M.; Pieckenstain, F.L.; Rossi, F.R.; Gonzalez, M.R.; Vignatti, P.; Garriz, A. Gaining insight into plant responses to beneficial and pathogenic microorganisms using metabolomic and transcriptomic approaches. Metabolic Engineering for Bioactive Compounds; Kalia, V; Saini, A., Ed.; Springer: Singapore, 2017.
[http://dx.doi.org/10.1007/978-981-10-5511-9_6]
[109]
Farooq, M.A.; Niazi, A.K.; Akhtar, J. Saifullah; Farooq, M.; Souri, Z.; Karimi, N.; Rengel, Z. Acquiring control: the evolution of ROS-Induced oxidative stress and redox signaling pathways in plant stress responses. Plant Physiol. Biochem., 2019, 141, 353-369.
[http://dx.doi.org/10.1016/j.plaphy.2019.04.039] [PMID: 31207496]
[110]
Schwessinger, B.; Zipfel, C. News from the frontline: recent insights into PAMP-triggered immunity in plants. Curr. Opin. Plant Biol., 2008, 11(4), 389-395.
[http://dx.doi.org/10.1016/j.pbi.2008.06.001] [PMID: 18602859]
[111]
Asai, S.; Rallapalli, G.; Piquerez, S.J.; Caillaud, M.C.; Furzer, O.J.; Ishaque, N.; Wirthmueller, L.; Fabro, G.; Shirasu, K.; Jones, J.D. Expression profiling during arabidopsis/downy mildew interaction reveals a highly-expressed effector that attenuates responses to salicylic acid. PLoS Pathog., 2014, 10(10), e1004443.
[http://dx.doi.org/10.1371/journal.ppat.1004443] [PMID: 25329884]
[112]
Zhuang, X.; McPhee, K.E.; Coram, T.E.; Peever, T.L.; Chilvers, M.I. Rapid transcriptome characterization and parsing of sequences in a non-model host-pathogen interaction; pea-Sclerotinia sclerotiorum. BMC Genomics, 2012, 13(668), 668.
[http://dx.doi.org/10.1186/1471-2164-13-668] [PMID: 23181755]
[113]
Gyetvai, G.; Sønderkær, M.; Göbel, U.; Basekow, R.; Ballvora, A.; Imhoff, M.; Kersten, B.; Nielsen, K.L.; Gebhardt, C. The transcriptome of compatible and incompatible interactions of potato (Solanum tuberosum) with Phytophthora infestans revealed by DeepSAGE analysis. PLoS One, 2012, 7(2), e31526.
[http://dx.doi.org/10.1371/journal.pone.0031526] [PMID: 22328937]
[114]
Liao, W.; Ji, L.; Wang, J.; Chen, Z.; Ye, M.; Ma, H.; An, X. Identification of glutathione S-transferase genes responding to pathogen infestation in Populus tomentosa. Funct. Integr. Genomics, 2014, 14(3), 517-529.
[http://dx.doi.org/10.1007/s10142-014-0379-y] [PMID: 24870810]
[115]
Xin, M.; Wang, X.; Peng, H.; Yao, Y.; Xie, C.; Han, Y.; Ni, Z.; Sun, Q. Transcriptome comparison of susceptible and resistant wheat in response to powdery mildew infection. Genomics Proteomics Bioinformatics, 2012, 10(2), 94-106.
[http://dx.doi.org/10.1016/j.gpb.2012.05.002] [PMID: 22768983]
[116]
De Cremer, K.; Mathys, J.; Vos, C.; Froenicke, L.; Michelmore, R.W.; Cammue, B.P.; De Coninck, B. RNAseq-based transcriptome analysis of Lactuca sativa infected by the fungal necrotroph Botrytis cinerea. Plant Cell Environ., 2013, 36(11), 1992-2007.
[PMID: 23534608]
[117]
Passos, M.A.; de Cruz, V.O.; Emediato, F.L.; de Teixeira, C.C.; Azevedo, V.C.; Brasileiro, A.C.; Amorim, E.P.; Ferreira, C.F.; Martins, N.F.; Togawa, R.C.; Júnior, G.J.; da Silva, O.B., Jr; Miller, R.N. Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development. BMC Genomics, 2013, 14, 78.
[http://dx.doi.org/10.1186/1471-2164-14-78] [PMID: 23379821]
[118]
Nejat, N.; Cahill, D.M.; Vadamalai, G.; Ziemann, M.; Rookes, J.; Naderali, N.; Ziemann, M.; Rookes, J.; Naderali, N. Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection. Mol. Genet. Genomics, 2015, 290(5), 1899-1910.
[http://dx.doi.org/10.1007/s00438-015-1046-2] [PMID: 25893418]
[119]
Jaiswal, S.; Jadhav, P.V.; Jasrotia, R.S.; Kale, P.B.; Kad, S.K.; Moharil, M.P.; Dudhare, M.S.; Kheni, J.; Deshmukh, A.G.; Mane, S.S.; Nandanwar, R.S.; Penna, S.; Manjaya, J.G.; Iquebal, M.A.; Tomar, R.S.; Kawar, P.G.; Rai, A.; Kumar, D. Transcriptomic signature reveals mechanism of flower bud distortion in witches’-broom disease of soybean (Glycine max). BMC Plant Biol., 2019, 19(1), 26.
[http://dx.doi.org/10.1186/s12870-018-1601-1] [PMID: 30646861]
[120]
Feng, H.; Li, H.; Zhang, M.; Song, Y.; Yuan, G.; Han, Q.; Huang, L. Responses of Fuji (Malus domestica) and Shandingzi (Malus baccata) apples to Marssonina coronaria infection revealed by comparative transcriptome analysis. Physiol. Mol. Plant Pathol., 2019, 106, 87-95.
[http://dx.doi.org/10.1016/j.pmpp.2018.12.007]
[121]
Zhao, T.; Liu, W.; Zhao, Z.; Yang, H.; Bao, Y.; Zhang, D.; Wang, Z.; Jiang, J.; Xu, Y.; Zhang, H.; Li, J.; Chen, Q.; Xu, X. Transcriptome profiling reveals the response process of tomato carrying Cf-19 and Cladosporium fulvum interaction. BMC Plant Biol., 2019, 19(1), 572.
[http://dx.doi.org/10.1186/s12870-019-2150-y] [PMID: 31856725]
[122]
Neu, E.; Domes, H.S.; Menz, I.; Kaufmann, H.; Linde, M.; Debener, T. Interaction of roses with a biotrophic and a hemibiotrophic leaf pathogen leads to differences in defense transcriptome activation. Plant Mol. Biol., 2019, 99(4-5), 299-316.
[http://dx.doi.org/10.1007/s11103-018-00818-2] [PMID: 30706286]
[123]
Bhat, N.N.; Bilal Padder, B.A.; Barthelson, R.A.; Andrabi, K.I. Compendium of Colletotrichum graminicola responsive infection-induced transcriptomic shifts in the maize. Plant Gene, 2019, 17100166
[http://dx.doi.org/10.1016/j.plgene.2018.11.001]
[124]
Parker, J.; Koh, J.; Yoo, M.J.; Zhu, N.; Feole, M.; Yi, S.; Chen, S. Quantitative proteomics of tomato defense against Pseudomonas syringae infection. Proteomics, 2013, 13(12-13), 1934-1946.
[http://dx.doi.org/10.1002/pmic.201200402] [PMID: 23533086]
[125]
Bernardo, L.; Prinsi, B.; Negri, A.S.; Cattivelli, L.; Espen, L.; Valè, G. Proteomic characterization of the Rph15 barley resistance gene-mediated defence responses to leaf rust. BMC Genomics, 2012, 13, 642.
[http://dx.doi.org/10.1186/1471-2164-13-642] [PMID: 23167439]
[126]
Margaria, P.; Abbà, S.; Palmano, S. Novel aspects of grapevine response to phytoplasma infection investigated by a proteomic and phospho-proteomic approach with data integration into functional networks. BMC Genomics, 2013, 14, 38.
[http://dx.doi.org/10.1186/1471-2164-14-38] [PMID: 23327683]
[127]
Kundu, S.; Chakraborty, D.; Kundu, A.; Pal, A. Proteomics approach combined with biochemical attributes to elucidate compatible and incompatible plant-virus interactions between Vigna mungo and Mungbean Yellow Mosaic India Virus. Proteome Sci., 2013, 11(15), 15.
[http://dx.doi.org/10.1186/1477-5956-11-15] [PMID: 23587433]
[128]
Petriccione, M.; Di Cecco, I.; Arena, S.; Scaloni, A.; Scortichini, M. Proteomic changes in Actinidia chinensis shoot during systemic infection with a pandemic Pseudomonas syringae pv. actinidiae strain. J. Proteomics, 2013, 78, 461-476.
[http://dx.doi.org/10.1016/j.jprot.2012.10.014] [PMID: 23099348]
[129]
Holtappels, M.; Noben, J.P.; Van Dijck, P.; Valcke, R. Fire blight host-pathogen interaction: proteome profiles of Erwinia amylovora infecting apple rootstocks. Sci. Rep., 2018, 8(1), 11689.
[http://dx.doi.org/10.1038/s41598-018-30064-x] [PMID: 30076380]
[130]
Meng, Q.; Gupta, R.; Min, C.W.; Kwon, S.W.; Wang, Y.; Je, B.I.; Kim, Y.J.; Jeon, J.S.; Agrawal, G.K.; Rakwal, R.; Kim, S.T. Proteomics of rice-Magnaporthe oryzae interaction: what have we learned so far? Front. Plant Sci., 2019, 10, 1383.
[http://dx.doi.org/10.3389/fpls.2019.01383] [PMID: 31737011]
[131]
Li, Y.; Feng, Y.; Lü, Q.; Yan, D.; Liu, Z.; Zhang, X. Comparative proteomic analysis of plant-pathogen interactions in resistant and susceptible poplar ecotypes infected with Botryosphaeria dothidea. Phytopathology, 2019, 109(12), 2009-2021.
[http://dx.doi.org/10.1094/PHYTO-12-18-0452-R] [PMID: 31369364]
[132]
Dos Santos, E.C.; Pirovani, C.P.; Correa, S.C.; Micheli, F.; Gramacho, K.P. The pathogen Moniliophthora perniciosa promotes differential proteomic modulation of cacao genotypes with contrasting resistance to witches´ broom disease. BMC Plant Biol., 2020, 20(1), 1.
[http://dx.doi.org/10.1186/s12870-019-2170-7] [PMID: 31898482]
[133]
Hu, X.; Puri, K.D.; Gurung, S.; Klosterman, S.J.; Wallis, C.M.; Britton, M.; Johnson, B.D.; Phinney, B.; Salemi, M.; Short, D.P.G.; Subbarao, K.V. Proteome and metabolome analyses reveal differential responses in tomato-Verticillium dahliae-interactions. J. Proteomics, 2019, 207, 15-103449.
[134]
Jashni, K.M.; Burgt, A.; Battaglia, E.; Mehrabi, R.; Collemare, J.; Pierre, J.G.M. de Wit. Transcriptome and proteome analyses of proteases in biotroph fungal pathogen Cladosporium fulvum. J. Plant Pathol., 2019, 102, 377-386.
[http://dx.doi.org/10.1007/s42161-019-00433-0]
[135]
Scandiani, M.M.; Luque, A.G.; Razori, M.V.; Ciancio Casalini, L.; Aoki, T.; O’Donnell, K.; Cervigni, G.D.; Spampinato, C.P. Metabolic profiles of soybean roots during early stages of Fusarium tucumaniae infection. J. Exp. Bot., 2015, 66(1), 391-402.
[http://dx.doi.org/10.1093/jxb/eru432] [PMID: 25336687]
[136]
Aliferis, K.A.; Faubert, D.; Jabaji, S. A metabolic profiling strategy for the dissection of plant defense against fungal pathogens. PLoS One, 2014, 9(11), e111930.
[http://dx.doi.org/10.1371/journal.pone.0111930] [PMID: 25369450]
[137]
Hong, Y.S.; Martinez, A.; Liger-Belair, G.; Jeandet, P.; Nuzillard, J.M.; Cilindre, C. Metabolomics reveals simultaneous influences of plant defence system and fungal growth in Botrytis cinerea-infected Vitis vinifera cv. Chardonnay berries. J. Exp. Bot., 2012, 63(16), 5773-5785.
[http://dx.doi.org/10.1093/jxb/ers228] [PMID: 22945941]
[138]
Allwood, J.W.; Clarke, A.; Goodacre, R.; Mur, L.A. Dual metabolomics: a novel approach to understanding plant-pathogen interactions. Phytochemistry, 2010, 71(5-6), 590-597.
[http://dx.doi.org/10.1016/j.phytochem.2010.01.006] [PMID: 20138320]
[139]
Yogendra, K.N.; Ajjamada, C.K.; Sarmiento, F.; Rodriguez, E.B.; Mosquera, T. Metabolomics deciphers quantitative resistance mechanisms in diploid potato clones against late blight. Funct. Plant Biol., 2014, 42(3), 284-298.
[http://dx.doi.org/10.1071/FP14177]
[140]
Waskiewicz, A.; Irzykowska, L.; Drzewiecka, K.; Bocianowski, J.; Dobosz, B.; Weber, Z.; Karolewski, Z.; Krzyminiewski, R.; Golinski, P. Plant-pathogen interactions during infection process of Asparagus with Fusarium spp. Cent. Eur. J. Biol., 2013, 8(11), 1065-1076.
[141]
Pasquet, J.C.; Chaouch, S.; Macadré, C.; Balzergue, S.; Huguet, S.; Martin-Magniette, M.L.; Bellvert, F.; Deguercy, X.; Thareau, V.; Heintz, D.; Saindrenan, P.; Dufresne, M. Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum. BMC Genomics, 2014, 15, 629.
[http://dx.doi.org/10.1186/1471-2164-15-629] [PMID: 25063396]
[142]
Negrel, L.; Halter, D.; Wiedemann-Merdinoglu, S.; Rustenholz, C.; Merdinoglu, D.; Hugueney, P.; Baltenweck, R. Identification of lipid markers of Plasmopara viticola infection in grapevine using a non-targeted metabolomic approach. Front. Plant Sci., 2018, 9, 360.
[http://dx.doi.org/10.3389/fpls.2018.00360] [PMID: 29619037]
[143]
Su, X.; Lu, G.; Guo, H.; Zhang, K.; Li, X.; Cheng, H. The dynamic transcriptome and metabolomics profiling in Verticillium dahliae inoculated Arabidopsis thaliana. Sci. Rep., 2018, 8(1), 15404.
[http://dx.doi.org/10.1038/s41598-018-33743-x] [PMID: 30337674]
[144]
de Falco, B.; Manzo, D.; Incerti, G.; Garonna, A.P.; Ercolano, M.; Lanzotti, V. Metabolomics approach based on NMR spectroscopy and multivariate data analysis to explore the interaction between the leafminer Tuta absoluta and tomato (Solanum lycopersicum). Phytochem. Anal., 2019, 30(5), 556-563.
[http://dx.doi.org/10.1002/pca.2850] [PMID: 31286582]
[145]
Azizi, P.; Osman, M.; Hanafi, M.M.; Sahebi, M.; Yusop, M.R.; Taheri, S. Adaptation of the metabolomics profile of rice after Pyricularia oryzae infection. Plant Physiol. Biochem., 2019, 144, 466-479.
[http://dx.doi.org/10.1016/j.plaphy.2019.10.014] [PMID: 31655345]
[146]
Zhu, L.; Zhou, Y.; Li, X.; Zhao, J.; Guo, N.; Xing, H. Metabolomics analysis of soybean hypocotyls in response to Phytophthora sojae infection. Front. Plant Sci., 2018, 9, 1530.
[http://dx.doi.org/10.3389/fpls.2018.01530] [PMID: 30405667]
[147]
Kawahara, Y.; Oono, Y.; Kanamori, H.; Matsumoto, T.; Itoh, T.; Minami, E. Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction. PLoS One, 2012, 7(11), e49423.
[http://dx.doi.org/10.1371/journal.pone.0049423] [PMID: 23139845]
[148]
Aragona, M.; Minio, A.; Ferrarini, A.; Valente, M.T.; Bagnaresi, P.; Orrù, L.; Tononi, P.; Zamperin, G.; Infantino, A.; Valè, G.; Cattivelli, L.; Delledonne, M. De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici. BMC Genomics, 2014, 15, 313.
[http://dx.doi.org/10.1186/1471-2164-15-313] [PMID: 24767544]
[149]
Hane, J.K.; Anderson, J.P.; Williams, A.H.; Sperschneider, J.; Singh, K.B. Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8. PLoS Genet., 2014, 10(5), e1004281.
[http://dx.doi.org/10.1371/journal.pgen.1004281] [PMID: 24810276]
[150]
Coutinho, B.G.; Licastro, D.; Mendonça-Previato, L.; Cámara, M.; Venturi, V. Plant-influenced gene expression in the rice endophyte Burkholderia kururiensis M130. Mol. Plant Microbe Interact., 2015, 28(1), 10-21.
[http://dx.doi.org/10.1094/MPMI-07-14-0225-R] [PMID: 25494355]
[151]
Roux, B.; Rodde, N.; Jardinaud, M-F.; Timmers, T.; Sauviac, L.; Cottret, L.; Carrère, S.; Sallet, E.; Courcelle, E.; Moreau, S.; Debellé, F.; Capela, D.; de Carvalho-Niebel, F.; Gouzy, J.; Bruand, C.; Gamas, P. An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing. Plant J., 2014, 77(6), 817-837.
[http://dx.doi.org/10.1111/tpj.12442] [PMID: 24483147]
[152]
Pankievicz, V.C.S.; Camilios-Neto, D.; Bonato, P.; Balsanelli, E.; Tadra-Sfeir, M.Z.; Faoro, H.; Chubatsu, L.S.; Donatti, L.; Wajnberg, G.; Passetti, F.; Monteiro, R.A.; Pedrosa, F.O.; Souza, E.M. RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots. Plant Mol. Biol., 2016, 90(6), 589-603.
[http://dx.doi.org/10.1007/s11103-016-0430-6] [PMID: 26801330]
[153]
Paungfoo-Lonhienne, C.; Lonhienne, T.G.A.; Yeoh, Y.K.; Donose, B.C.; Webb, R.I.; Parsons, J.; Liao, W.; Sagulenko, E.; Lakshmanan, P.; Hugenholtz, P.; Schmidt, S.; Ragan, M.A. Crosstalk between sugarcane and a plant-growth promoting Burkholderia species. Sci. Rep., 2016, 6, 37389.
[http://dx.doi.org/10.1038/srep37389] [PMID: 27869215]
[154]
Nobori, T.; Velásquez, A.C.; Wu, J.; Kvitko, B.H.; Kremer, J.M.; Wang, Y.; He, S.Y.; Tsuda, K. Transcriptome landscape of a bacterial pathogen under plant immunity. Proc. Natl. Acad. Sci. USA, 2018, 115(13), E3055-E3064.
[http://dx.doi.org/10.1073/pnas.1800529115] [PMID: 29531038]
[155]
Saberi, F.; Kamali, M.; Najafi, A. Yazdanparast. A.; Moghaddam, M.M. Natural antisense RNAs as mRNA regulatory elements in bacteria: a review on function and applications. Cell. Mol. Biol. Lett., 2016, 21, 6.
[PMID: 28536609 ]
[156]
Hör, J.; Gorski, S.A.; Vogel, J. Bacterial RNA biology on a genome scale. Mol. Cell, 2018, 70(5), 785-799.
[http://dx.doi.org/10.1016/j.molcel.2017.12.023] [PMID: 29358079]
[157]
Chaparro, J.M.; Badri, D.V.; Vivanco, J.M. Rhizosphere microbiome assemblage is affected by plant development. ISME J., 2014, 8(4), 790-803.
[http://dx.doi.org/10.1038/ismej.2013.196] [PMID: 24196324]
[158]
Chapelle, E.; Mendes, R.; Bakker, P.A.H.; Raaijmakers, J.M. Fungal invasion of the rhizosphere microbiome. ISME J., 2016, 10(1), 265-268.
[http://dx.doi.org/10.1038/ismej.2015.82] [PMID: 26023875]
[159]
Yergeau, E.; Sanschagrin, S.; Maynard, C.; St-Arnaud, M.; Greer, C.W. Microbial expression profiles in the rhizosphere of willows depend on soil contamination. ISME J., 2014, 8(2), 344-358.
[http://dx.doi.org/10.1038/ismej.2013.163] [PMID: 24067257]
[160]
Robison, F.M.; Turner, M.F.; Jahn, C.E.; Schwartz, H.F.; Prenni, J.E.; Brick, M.A.; Heuberger, A.L. Common bean varieties demonstrate differential physiological and metabolic responses to the pathogenic fungus Sclerotinia sclerotiorum. Plant Cell Environ., 2018, 41(9), 2141-2154.
[PMID: 29476531]
[161]
Nordzieke, D.E.; Fernandes, T.R.; El Ghalid, M.; Turrà, D.; Di Pietro, A. NADPH oxidase regulates chemotropic growth of the fungal pathogen Fusarium oxysporum towards the host plant. New Phytol., 2019, 224(4), 1600-1612.
[http://dx.doi.org/10.1111/nph.16085] [PMID: 31364172]
[162]
Delaunois, B.; Jeandet, P.; Clément, C.; Baillieul, F.; Dorey, S.; Cordelier, S. Uncovering plant-pathogen crosstalk through apoplastic proteomic studies. Front. Plant Sci., 2014, 5, 249.
[http://dx.doi.org/10.3389/fpls.2014.00249] [PMID: 24917874]
[163]
Ashwin, N.M.R.; Barnabas, L.; Ramesh Sundar, A.; Malathi, P.; Viswanathan, R.; Masi, A.; Agrawal, G.K.; Rakwal, R. Advances in proteomic technologies and their scope of application in understanding plant-pathogen interactions. J. Plant Biochem. Biotechnol., 2017, 26, 371-386.
[http://dx.doi.org/10.1007/s13562-017-0402-1]
[164]
Wright, M.H. Chemical proteomics of host-microbe interactions. Proteomics, 2018, 18(18), e1700333.
[http://dx.doi.org/10.1002/pmic.201700333] [PMID: 29745013]
[165]
Li, X.; Bai, T.; Li, Y.; Ruan, X.; Li, H. Proteomic analysis of Fusarium oxysporum sp. cubense tropical race 4-inoculated response to Fusarium wilts in the banana root cells. Proteome Sci., 2013, 11(1), 41.
[http://dx.doi.org/10.1186/1477-5956-11-41] [PMID: 24070062]
[166]
Lambais, M.R.; Barrera, S.E.; Santos, E.C.; Crowley, D.E.; Jumpponen, A. Phyllosphere metaproteomes of trees from the Brazilian Atlantic forest show high levels of functional redundancy. Microb. Ecol., 2017, 73(1), 123-134.
[http://dx.doi.org/10.1007/s00248-016-0878-6] [PMID: 27853840]
[167]
Kierul, K.; Voigt, B.; Albrecht, D.; Chen, X.H.; Carvalhais, L.C.; Borriss, R. Influence of root exudates on the extracellular proteome of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Microbiology, 2015, 161(Pt 1), 131-147.
[http://dx.doi.org/10.1099/mic.0.083576-0] [PMID: 25355936]
[168]
Bao, Z.; Okubo, T.; Kubota, K.; Kasahara, Y.; Tsurumaru, H.; Anda, M.; Ikeda, S.; Minamisawa, K. Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants. Appl. Environ. Microbiol., 2014, 80(16), 5043-5052.
[http://dx.doi.org/10.1128/AEM.00969-14] [PMID: 24928870]
[169]
Zhalnina, K.; Louie, K.B.; Hao, Z.; Mansoori, N.; da Rocha, U.N.; Shi, S.; Cho, H.; Karaoz, U.; Loqué, D.; Bowen, B.P.; Firestone, M.K.; Northen, T.R.; Brodie, E.L. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat. Microbiol., 2018, 3(4), 470-480.
[http://dx.doi.org/10.1038/s41564-018-0129-3] [PMID: 29556109]
[170]
de Bruijn, F. phytohormone regulation of medicago truncatularhizobia interactions. a review. the model legume medicago truncatula, 2019.
[http://dx.doi.org/10.1002/9781119409144.ch92]
[171]
Brechenmacher, L.; Weidmann, S.; van Tuinen, D.; Chatagnier, O.; Gianinazzi, S.; Franken, P.; Gianinazzi-Pearson, V. Expression profiling of up-regulated plant and fungal genes in early and late stages of Medicago truncatula-Glomus mosseae interactions. Mycorrhiza, 2004, 14(4), 253-262.
[http://dx.doi.org/10.1007/s00572-003-0263-4] [PMID: 13680319]
[172]
Moy, P.; Qutob, D.; Chapman, B.P.; Atkinson, I.; Gijzen, M. Patterns of gene expression upon infection of soybean plants by Phytophthora sojae. Mol. Plant Microbe Interact., 2004, 17(10), 1051-1062.
[http://dx.doi.org/10.1094/MPMI.2004.17.10.1051] [PMID: 15497398]
[173]
Mosquera, G.; Giraldo, M.C.; Khang, C.H.; Coughlan, S.; Valent, B. Interaction transcriptome analysis identifies Magnaporthe oryzae BAS1-4 as Biotrophy-associated secreted proteins in rice blast disease. Plant Cell, 2009, 21(4), 1273-1290.
[http://dx.doi.org/10.1105/tpc.107.055228] [PMID: 19357089]
[174]
Torto-Alalibo, T.; Collmer, C.W.; Gwinn-Giglio, M. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: the plant-associated microbe gene ontology (pamgo) consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions. BMC Microbiol., 2009, 9(Suppl. 1), S1.
[http://dx.doi.org/10.1186/1471-2180-9-S1-S1] [PMID: 19278549]
[175]
Zhang, J.; Wang, P.; Tian, H.; Tao, Z.; Guo, T. Transcriptome analysis of ice plant growth-promoting endophytic Bacterium Halomonas sp. Strain MC1 to identify the genes involved in salt tolerance. Microorganisms, 2020, 8(1), 88.
[http://dx.doi.org/10.3390/microorganisms8010088] [PMID: 31936448]
[176]
Orozco-Mosqueda, M.D.C.; Duan, J.; DiBernardo, M.; Zetter, E.; Campos-García, J.; Glick, B.R.; Santoyo, G. The production of ACC deaminase and trehalose by the plant growth promoting bacterium Pseudomonas sp. UW4 synergistically protect tomato plants against salt stress. Front. Microbiol., 2019, 10, 1392.
[http://dx.doi.org/10.3389/fmicb.2019.01392] [PMID: 31275294]
[177]
Niu, S.-Q.; Li, H-R.; Pare, P.W.; Aziz, M.; Wang, S.-M.; Shi, H.; Li, J.; Han, Q.-Q.; Guo, S.-Q.; Li, J. Induced growth promotion and higher salt tolerance in the halophyte grass Puccinelliatenuiflora by beneficial rhizobacteria. Plant Soil, 2016, 407, 217-230.
[http://dx.doi.org/10.1007/s11104-015-2767-z]
[178]
Larsen, P.E.; Sreedasyam, A.; Trivedi, G.; Podila, G.K.; Cseke, L.J.; Collart, F.R.; Collart, F.R. Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome. BMC Syst. Biol., 2011, 5, 70.
[http://dx.doi.org/10.1186/1752-0509-5-70] [PMID: 21569493]
[179]
Dal’Molin, C.G.O.; Quek, L.E.; Palfreyman, R.W.; Brumbley, S.M.; Nielsen, L.K. C4GEM, a genome-scale metabolic model to study C4 plant metabolism. Plant Physiol., 2010, 154(4), 1871-1885.
[http://dx.doi.org/10.1104/pp.110.166488] [PMID: 20974891]
[180]
Atamna-Ismaeel, N.; Finkel, O.; Glaser, F.; von Mering, C.; Vorholt, J.A.; Koblížek, M.; Belkin, S.; Béjà, O. Bacterial anoxygenic photosynthesis on plant leaf surfaces. Environ. Microbiol. Rep., 2012, 4(2), 209-216.
[http://dx.doi.org/10.1111/j.1758-2229.2011.00323.x] [PMID: 23757275]