Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2015 | 37 | 10 |

Tytuł artykułu

Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach

Warianty tytułu

Języki publikacji



Classical soil science approaches have enabled us to establish basic principles of how the soil system functions and have answered numerous practical agricultural application questions. In recent years, efforts have been refocused on better understanding, managing and benefiting from this system that contains one of the most complex biological communities of the planet. Soil biology is seen as being at the center of scientific research of this century, with novel research objectives and goals being set. In addition, plant nutrition has enabled us to understand nutrient uptake, transport and mobilization mechanisms in plants, and both disciplines have converged on the area of microorganism-mediated plant nutrition. The challenge for these scientific areas is to identify microorganism communities and the roles they play in their habitats, as well as the mechanisms that plants have to make better use of nutrients. Genomics and metagenomics, along with microbiological techniques, are contributing greatly to advances in our understanding of living systems that exist in the soil and their interaction with plants. For its part, molecular plant nutrition has made significant progress in understanding the use of nutrients by plant cells, and has identified molecular mechanisms that can improve nutrient use efficiency. Together, molecular soil microbiology and molecular plant nutrition are projected to be a driving force in agriculture and sustainable food production in the coming years. Herewith, we aim to integrate recent literature on basic and applied research concerning plant and microbe genomics in terms of their potential for developing a novel molecular plant nutrition approach, with special emphasis on nitrogen, potassium and phosphorous as the major macronutrients for crop plants.

Słowa kluczowe








Opis fizyczny

Article: 208 [17 p.], fig.,ref.


  • Colegio de Postgraduados Campus Cordoba, Carretera Cordoba, Veracruz 348, Congregacion Manuel Leon, Mpio. de Amatlan de los Reyes, Veracruz, C. P. 94946, Mexico
  • Colegio de Postgraduados Campus Montecillo, Carretera Mexico-Texcoco km 36.5, Montecillo, Mpio de Texcoco, State of Mexico, C. P. 56230, Mexico
  • Colegio de Postgraduados Campus Montecillo, Carretera Mexico-Texcoco km 36.5, Montecillo, Mpio de Texcoco, State of Mexico, C. P. 56230, Mexico


  • Abou-El-Seoud II, Abdel-Megeed A (2012) Impact of rock materials and biofertilizations on P and K availability for maize (Zea mays) under calcareous soil conditions. Saudi J Biol Sci 19:55–63. doi:10.1016/j.sjbs.2011.09.001
  • Adam G, Duncan H (2001) Development of a sensitive and rapid method for the measurement of total microbial activity using fluorescein diacetate (FDA) in a range of soils. Soil Biol Biochem 33:943–951. doi:10.1016/S0038-0717(00)00244-3
  • AGI (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815. doi:10.1038/35048692
  • Alarcón A, Hernández-Cuevas LV, Ferrera-Cerrato R, Franco-Ramírez A (2012) Diversity and agricultural applications of arbuscular mycorrhizal fungi in Mexico. J Biofertil Biopestici 3:115. doi:10.4172/2155-6202.1000115
  • Alessi DS, Walsh DM, Fein JB (2011) Uncertainties in determining microbial biomass C using the chloroform fumigation–extraction method. Chem Geol 280:58–64. doi:10.1016/j.chemgeo.2010.10.014
  • Amtmann A, Troufflard S, Armengaud P (2008) The effect of potassium nutrition on pest and disease resistance in plants. Physiol Plant 133:682–691. doi:10.1111/j.1399-3054.2008.01075
  • Armengaud P, Breitling R, Amtmann A (2004) The potassiumdependent transcriptome of Arabidopsis reveals a prominent role of jasmonic acid in nutrient signaling. Plant Physiol 136:2556–2576. doi:10.1104/pp.104.046482
  • Badri DV, Weir TL, van der Lelie D, Vivanco JM (2009) Rhizosphere chemical dialogues: plant–microbe interactions. Curr Opin Biotechnol 20:642–650. doi:10.1016/j.copbio.2009.09.014
  • Bakker MG, Schlatter DC, Otto-Hanson L, Kinkel LL (2014) Diffuse symbioses: roles of plant-plant, plant-microbe and microbemicrobe interactions in structuring the soil microbiome. Mol Ecol 23:1571–1583. doi:10.1111/mec.12571
  • Basak BB, Biswas DR (2009) Influence of potassium solubilizing microorganism (Bacillus mucilaginosus) and waste mica on potassium uptake dynamics by sudan grass (Sorghum vulgare Pers.) grown under two Alfisols. Plant Soil 317:235–255. doi:10.1007/s11104-008-9805-z
  • Basak BB, Biswas DR (2010) Co-inoculation of potassium solubilizing and nitrogen fixing bacteria on solubilization of wastemica and their effect on growth promotion and nutrient acquisition by a forage crop. Biol Fertil Soil 46:641–648. doi:10.1007/s00374-010-0456-x
  • Bastida F, Hernández T, Albaladejo J, García C (2013) Phylogenetic and functional changes in the microbial community of long-term restored soils under semiarid climate. Soil Biol Biochem 65:12–21. doi:10.1016/j.soilbio.2013.04.022
  • Becquer A, Trap J, Irshad U, Ali MA, Claude P (2014) From soil to plant, the journey of P through trophic relationships and ectomycorrhizal association. Front Plant Sci 5:548. doi:10 3389/fpls.2014.00548
  • Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KF (2014) Plant genome sequencing—applications for crop improvement. Curr Opin Biotechnol 26:31–37. doi:10.1016/j. copbio.2013.08.019
  • Chai B, Wu Y, Liu P, Liu B, Gao M (2011) Isolation and phosphatesolubilizing ability of a fungus, Penicillium sp. from soil of an alum mine. J Basic Microbiol 51:5–14. doi:10.1002/jobm. 201000192
  • Chang HW, Sung Y, Kim KH, Nam YD, Roh SW, Kim MS, Jeon CO, Bae JW (2008) Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells. Environ Sci Technol 42:6058–6064. doi:10.1021/es8006029
  • Chen XW, Wu FY, Li H, Chan WF, Wu C, Wu SC, Wong MH (2013) Phosphate transporters expression in rice (Oryza sativa L.) associated with arbuscular mycorrhizal fungi (AMF) colonization under different levels of arsenate stress. Environ Exp Bot 87:92–99. doi:10.1016/j.envexpbot.2012.08.002
  • Cleary DFR, Smalla K, Mendonc¸a-Hagler LCS, Gomes NCM (2012) Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing. PLoS One 7:e29380. doi:10.1371/journal.pone.0029380
  • Cordell D, White S (2011) Peak phosphorus: clarifying the key issues of a vigorous debate about long-term phosphorus security. Sustainability 3:2027–2049. doi:10.3390/su3102027
  • Cordell D, Drangert JO, White S (2009) The story of phosphorus: global food security and food for thought. Glob Environ Change 19:292–305. doi:10.1016/j.gloenvcha.2008.10.009
  • Cordell D, Rosemarin A, Schröder JJ, Smit AL (2011) Towards global phosphorus security: a systems framework for phosphorus recovery and reuse options. Chemosphere 84:747–758. doi:10.1016/j.chemosphere.2011.02.032
  • Davinic M, Fultz LM, Acosta-Martinez V, Calderón FJ, Cox SB, Dowd SE, Allen VG, Zak JC, Moore-Kucera J (2012) Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition. Soil Biol Biochem 46:63–72. doi:10.1016/j.soilbio.2011.11.012
  • Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, James GA, Wolcott RD (2008) Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol 8:43. doi:10.1186/1471-2180-8-43
  • Dua M, Singh A, Sethunathan N, Johri AK (2002) Biotechnology and bioremediation: successes and limitations. Appl Microbiol Biotechnol 59:143–152. doi:10.1007/s00253-002-1024-6
  • Dumont MG, Murrell JC (2005) Stable isotope probing-linking microbial identity to function. Nat Rev Microbiol 3:499–504. doi:10.1038/nrmicro1162
  • Edwards RA, Haggerty JM, Cassman N, Busch JC, Aguinaldo K, Chinta S, Vaughn MH, Morey R, Harkins TT, Teiling C, Fredrikson K, Dinsdale EA (2013) Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. BMC Genom 14:600. doi:10.1186/1471-2164-14-600
  • Egan AN, Schlueter J, Spooner DM (2012) Applications of nextgeneration sequencing in plant biology. Am J Bot 99:175–185.doi:10.3732/ajb.1200020
  • Ehrlich H (2002) Interactions between microorganisms and minerals under anaerobic conditions. In: Huang PM, Bollag JM, Senesi N (eds) Interactions between soil particles and microorganisms. Wiley, New York, pp 459–494
  • El-Hadad ME, Mustafa MI, Selim ShM, El-Tayeb TS, Mahgoob AE, Abdel Aziz NH (2011) The nematicidal effect of some bacterial biofertilizers on Meloidogyne incognita in sandy soil. Braz J Microbiol 42:105–113. doi:10.1590/S1517-83822011000100014
  • Estrada-Ortiz E, Trejo-Téllez LI, Gómez-Me-rino FC, Núñez-Escobar R, Sandoval-Villa M (2013) The effects of phosphite on strawberry yield and fruit quality. J Soil Sci Plant Nutr 13:612–620. doi:10.4067/S0718-95162013005000049
  • FAO (2006) Plant nutrition for food security. A guide for integrated nutrient management. FAO Fertilizer and Plant Nutrition Bulletin No. 16. Food and Agriculture Organization of the United Nations. Rome, Italy. Accessed 10 June 2015
  • Ferro CJ, Ritz E, Townend JN (2015) Phosphate: are we squandering a scarce commodity+ Nephrol Dial Transplant 30:163–168.doi:10.1093/ndt/gfu295
  • Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S, Knight R, Rohwer F, Jackson RB (2007) Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl Environ Microbiol 73:7059–7066. doi:10.1128/AEM.00358-07
  • Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL, Owens S, Gilbert JA, Wall DH, Caporaso JG (2012a) Crossbiome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109:21390–21395. doi:10.1073/pnas.1215210110
  • Fierer N, Lauber CL, Ramirez KS, Zaneveld J, Bradford MA, Knight R (2012b) Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME J 6:1007–1017. doi:10.1038/ismej.2011.159
  • Franzosa EA, Hsu T, Sirota-Madi A, Shafquat A, Abu-Ali G, Morgan XC, Huttenhower C (2015) Sequencing and beyond: integrating molecular ‘omics’ for microbial community profiling. Nat Rev Microbiol 13:360–372. doi:10.1038/nrmicro3451
  • Fritsch P, Rieseberg LH (1996) The use of random amplified polymorphic DNA (RAPD) in conservation genetics. In: Smith TB, Wayne RK (eds) Molecular genetics approaches in conservation. Oxford University Press, Oxford, pp 54–73
  • García MJ, Lucena C, Romera FJ, Alcántara E, Pérez-Vicente R (2010) Ethylene and nitric oxide involvement in the upregulation of key genes related to iron acquisition and homeostasis in Arabidopsis. J Exp Bot 61:3885–3899. doi:10.1093/jxb/erq203
  • Gierth M, Mäser P (2007) Potassium transporters in plants—involvement in K+ acquisition, redistribution and homeostasis. FEBS Lett 581:2348–2356. doi:10.1016/j.febslet.2007.03.035
  • Gómez-Porras JL, Riaño-Pachón DM, Benito B, Haro R, Sklodowski K, Rodríguez-Navarro A, Dreyer I (2012) Phylogenetic analysis of K+ transporters in bryophytes, lycophytes, and flowering plants indicates a specialization of vascular plants. Front Plant Sci 3:167. doi:10.3389/fpls.2012.00167
  • Green V, Stott D, Diack M (2006) Assay for fluorescein diacetate hydrolytic activity: optimization for soil samples. Soil Biol Biochem 38:693–701. doi:10.1016/j.soilbio.2005.06.020
  • Guazzaroni ME, Morgante V, Mirete S, González-Pastor JE (2013) Novel acid resistance genes from the metagenome of the Tinto River, an extremely acidic environment. Environ Microbiol 15:1088–1102. doi:10.1111/1462-2920.12021
  • Guo B, Jin Y, Wussler C, Blancaflor EB, Motes CM, Versaw WK (2008) Functional analysis of the Arabidopsis PHT4 family of intracellular phosphate transporters. New Phytol 177:889–898. doi:10.1111/j.1469-8137.2007.02331.x
  • Han HS, Supanjani, Lee KD (2006) Effect of co-inoculation with phosphate and potassium solubilizing bacteria on mineral uptake and growth of pepper and cucumber. Plant Soil Environ 52:130–136
  • Hashmi U, Shafqat S, Khan F, Majid M, Hussain H, Kazi AG, John R, Ahmad P (2015) Plant exomics: concepts, applications andmethodologies in crop improvement. Plant Signal Behav 10:e976152. doi:10.4161/15592324.2014.976152
  • He Z, Deng Y, Zhou J (2012) Development of functional gene microarrays for microbial community analysis. Curr Opin Biotechnol 23:49–55. doi:10.1016/j.copbio.2011.11.001
  • Hinsinger P (2001) Bioavailability of soil inorganic P in the rhizosphere as affected by root-induced chemical changes: a review. Plant Soil 237:173–181. doi:10.1023/A:1013351617532
  • Huang CY, Roessner U, Eickmeier I, Genc Y, Callahan DL, Shirley N, Langridge P, Bacic A (2008) Metabolite profiling reveals distinct changes in carbon and nitrogen metabolism in phosphate- deficient barley plants (Hordeum vulgare L.). Plant Cell Physiol 49:691–703. doi:10.1093/pcp/pcn044
  • Insam H (2001) Developments in soil microbiology since the mid 1960s. Geoderma 100:389–402. doi:10.1016/S0016-7061(01)00029-5
  • Kahl G (2015) The dictionary of genomics, transcriptomics and proteomics. Wiley-VCH, Weinheim 2742 p
  • Kakavas VK, Plageras P, Vlachos TA, Papaioannou A, Noulas VA (2008) PCR-SSCP: a method for the molecular analysis of genetic diseases. Mol Biotechnol 38:155–163. doi:10.1007/s12033-007-9006-7
  • Kawalia A, Motameny S, Wonczak S, Thiele H, Nieroda L, Jabbari K, Borowski S, Sinha V, Gunia W, Lang U, Achter V, Nürnberg P (2015) Leveraging the power of high performance computing for next generation sequencing data analysis: tricks and twists from a high throughput exome workflow. PLoS One 10:e0126321. doi:10.1371/journal.pone.0126321
  • Kirk JL, Beaudette LA, Hart M, Moutoglis P, Klironomos JN, Lee H, Trevors JT (2004) Methods of studying soil microbial diversity. JMicrobiol Methods 58:169–188. doi:10.1016/j.mimet.2004.04.006
  • Krapp A, David LC, Chardin C, Girin T, Marmagne A, Leprince AS, Chaillou S, Ferrario-Méry S, Meyer C, Daniel-Vedele F (2014) Nitrate transport and signalling in Arabidopsis. J Exp Bot 65:789–798. doi:10.1093/jxb/eru001
  • Kutílek M, Nielsen DR (2015) Soil. The skin of the planet Earth. Springer, Dordrecht, p 239. doi:10.1007/978-94-017-9789-4
  • Lasken RS (2012) Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 10:631–640. doi:10.1038/nrmicro2857
  • Li ESY, Liu WT (2003) DNA microarray technology in microbial ecology studies-principle, applications and current limitations. Microbes Environ 18:175–187. doi:10.1264/jsme2.18.175
  • Li J, Dai X, Liu T, Zhao PX (2012) LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. Nucleic Acids Res 40:D1221–D1229. doi:10.1093/nar/gkr939
  • Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G, Percy RG, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, Liu X, Zhang X, Liu W, Wei H, Wei S, Huang G, Zhang X, Zhu S, Zhang H, Sun F, Wang X, Liang J, Wang J, He Q, Huang L, Wang J, Cui J, Song G, Wang K, Xu X, Yu JZ, Zhu Y, Yu S (2015) Genome sequence of cultivated upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 33:524–530. doi:10.1038/nbt.3208
  • Lindbo DL, Kozlowski DA, Robinson C (2012) Know soil know life. Soil Science Society of America, Madison, p 206. doi:10.2136/2012.knowsoil
  • Liu Y, Shi L, Ye N, Liu R, Jia W, Zhang J (2009) Nitric oxideinduced rapid decrease of abscisic acid concentration is required in breaking seed dormancy in Arabidopsis. New Phytol 183:1030–1042. doi:10.1111/j.1469-8137.2009.02899.x
  • Loman NJ, Constantinidou C, Chan JZM, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ (2012) High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 10:599–606. doi:10.1038/nrmicro2850
  • López-Arredondo DL, Herrera-Estrella L (2012) Engineering phosphorus metabolism in plants to produce a dual fertilization and weed control system. Nat Biotechnol 30:889–893. doi:10.1038/ nbt.2346
  • López-Arredondo DL, Leyva-González MA, González-Morales SI, López-Bucio J, Herrera-Estrella L (2014) Phosphate nutrition: improving low-phosphate tolerance in crops. Annu Rev Plant Biol 65:95–123. doi:10.1146/annurev-arplant-050213-035949
  • Loqué D, von Wirén N (2004) Regulatory levels for the transport of ammonium in plant roots. J Exp Bot 55:1293–1305. doi:10.1093/jxb/erh147
  • Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3:510–516. doi:10.1038/nrmicro1161
  • Louche J, Ali MA, Cloutier-Hurteau B, Sauvage FX, Quiquampoix H, Plassard C (2010) Efficiency of acid phosphatases secreted from the ectomycorrhizal fungus Hebeloma cylindrosporum to hydrolyse organic phosphorus in podzols. FEMS Microbiol Ecol 73:323–335. doi:10.1111/j.1574-6941.2010.00899.x
  • Magi A, Benelli M, Gozzini A, Girolami F, Torricelli F, Brandi ML (2010) Bioinformatics for next generation sequencing data. Genes 1:294–307. doi:10.3390/genes1020294
  • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402. doi:10.1146/annurevanchem-062012-092628
  • Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M, Anderson I, Billis K, Varghese N, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC (2014) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42:D560–D567. doi:10.1093/nar/gkt963
  • Meena VS, Maurya BR, Verma JP (2014) Does a rhizospheric microorganism enhance K+ availability in agricultural soils+ Microbiol Res 169:337–347. doi:10.1016/j.micres.2013.09.003
  • Meena VS, Maurya BR, Verma JP, Aeron A, Kumar A, Kim K, Bajpai VK (2015) Potassium solubilizing rhizobacteria (KSR): isolation, identification, and K-release dynamics from waste mica. Ecol Eng 81:340–347. doi:10.1016/j.ecoleng.2015.04.065
  • Michael TP, VanBuren R (2015) Progress, challenges and the future of crop genomes. Curr Opin Plant Biol 24:71–81. doi:10.1016/j. Pbi.2015.02.002
  • Mills DEK, Entry JA, Gillevet PM, Mathee K (2007) Assessing microbial community diversity using amplicon length heterogeneity polymerase chain reaction. Soil Sci Soc Am J 71:572–578. doi:10.2136/sssaj2006.0147
  • Mirete S, de Figueras CG, González-Pastor JE (2007) Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage. Appl Environ Microbiol 73:6001–6011. doi:10.1128/AEM.00048-07
  • Mission J, Raghotham KG, Jain A, Jouhet J, Block MA, Bligny R, Ortet P, Creff A, Somerville S, Rolland N, Doumas N, Nacry P, Herrera-Estrella L, Nussaume L, Thibuaud MC (2005) A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. Proc Natl Acad Sci USA 102:11934–11939. doi:10. 1073/pnas.0505266102
  • Mohammadi K (2012) Phosphorus Solubilizing Bacteria: occurrence, mechanisms and their role in crop production. Res Environ 2:80–85. doi:10.5923/
  • Morcuende R, Bari R, Gibon Y, Zheng W, Pant BD, Bläsing R, Usadel B, Czechowski T, Udvardi MK, Stitt M, Scheible WR (2007) Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. Plant Cell Environ 30:85–112. doi:10.1111/j.1365-3040.2006.01608.x
  • Moter A, Göbel UB (2000) Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J Microbiol Methods 41:85–112. doi:10.1016/S0167-7012(00)00152-4
  • Murray AE, Lies D, Li G, Nealson K, Zhou J, Tiedje JM (2001) DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc Natl Acad Sci USA 98:9853–9858. doi:10.1073/pnas.171178898
  • Newbury HJ, Ford-Lloyd BV (1993) The use of RAPD for assessing variation in plants. Plant Growth Regul 12:43–51. doi:10.1007/BF00144581
  • Nobandegani MBJ, Saud HM, Yun WM (2015) Phylogenetic relationship of phosphate solubilizing bacteria according to 16S rRNA genes. Biomed Res Int 2015:201379. doi:10.1155/2015/201379
  • Nocker A, Burr M, Camper AK (2007) Genotypic microbial community profiling: a critical technical review. Microb Ecol 54:276–289. doi:10.1007/s00248-006-9199-5
  • Ocio JA, Brookes PC (1990) An evaluation of methods for measuring the microbial biomass in soils following recent additions of wheat straw and the characterization of the biomass that develops. Soil Biol Biochem 22:685–694. doi:10.1016/0038-0717(90)90016-S
  • Ohkama-Ohtsu N, Wasaki J (2010) Recent progress in plant nutrition research: cross-talk between nutrients, plant physiology and soil microorganisms. Plant Cell Physiol 51:1255–1264. doi:10.1093/pcp/pcq095
  • Okubo A, Sugiyama S (2009) Comparison of molecular fingerprinting methods for analysis of soil microbial community structure. Ecol Res 24:1399–1405. doi:10.1007/s11284-009-0602-9
  • Ouziad F, Wilde P, Schmelzer E, Hildebrandt U, Bothe H (2006) Analysis of expression of aquaporins and Na+/H+ transporters in tomato colonized by arbuscular mycorrhizal fungi and affected by salt stress. Environ Exp Bot 57:177–186. doi:10.1016/j. envexpbot.2005.05.011
  • Oyarburo NS, Machinandiarena MF, Feldman ML, Daleo GR, Andreu AB, Olivieri FP (2015) Potassium phosphite increases tolerance to UV-B in potato. Plant Physiol Biochem 88:1–8.doi:10.1016/j.plaphy.2015.01.003
  • Pérez-Tienda J, Testillano PS, Balestrini R, Fiorilli V, Azcón-Aguilar C, Ferrol N (2011) GintAMT2, a new member of the ammonium transporter family in the arbuscular mycorrhizal fungus Glomus intraradices. Fungal Genet Biol 48:1044–1055. doi:10.1016/j.fgb.2011.08.003
  • Pérez-Tienda J, Corrêa A, Azcón-Aguilar C, Ferrol N (2014) Transcriptional regulation of host transporters and GS/GOGAT pathway in arbuscular mycorrhizal rice roots. Plant Physiol Biochem 75:1–8. doi:10.1016/j.plaphy.2013.11.029
  • Pich A, Manteuffel R, Hillmer S, Scholz G, Schmidt W (2001) Fe homeostasis in plant cells: does nicotianamine play multiple roles in the regulation of cytoplasmic Fe concentration+ Planta 213:967–976. doi:10.1007/s004250100573
  • Plassard C, Dell B (2010) Phosphorus nutrition of mycorrhizal trees. Tree Physiol 30:1129–1139. doi:10.1093/treephys/tpq063
  • Poirier Y, Bucher M (2002) Phosphate transport and homeostasis in Arabidopsis. In: Somerville CR, Meyerowitz EM (eds) The Arabidopsis book. The American Society of Plant Biologists, Rockville, pp 1–35. doi:10.1199/tab.0024
  • Prescott CE, Grayston SJ (2013) Tree species influence on microbial communities in litter and soil: current knowledge and research needs. For Ecol Manag 309:19–27. doi:10.1016/j.foreco.2013. 02.034
  • Rajendhran J, Gunasekaran P (2008) Strategies for accessing soil metagenome for desired applications. Biotechnol Adv 26:576–590. doi:10.1016/j.biotechadv.2008.08.002
  • Rajesh T, Rajendhran J, Gunasekaran P (2012) Genomic technologies in environmental bioremediation. In: Satyanarayana T, Johri BN, Prakash A (eds) Microorganisms in environmental management: microbes and environment. Springer, Heidelberg, p 819. doi:10. 1007/978-94-007-2229-3_31
  • Rastogi G, Sani RK (2011) Molecular techniques to assess microbial community structure, function, and dynamics in the environment. In: Ahmad I, Ahmad F, Pichtel J (eds) Microbes and microbial technology: 29. Agricultural and environmental applications. Springer, New York, pp 29–57. doi:10.1007/978-1-4419-7931-5_2.Springer2011
  • Reddy PP (2014) Potential role of PGPR in agriculture. In: Reddy PP(ed) Plant growth promoting Rhizobacteria for horticultural crop protection. Springer, India, pp 17–34. doi:10.1007/978-81-322-1973-6_2
  • Renella G, Ogunseitan O, Giagnoni L, Arenella M (2014) Environmental proteomics: a long march in the pedosphere. Soil Biol Biochem 69:34–37. doi:10.1016/j.soilbio.2013.10.035
  • Rincon-Florez VA, Carvalhais LC, Schenk PM (2013) Cultureindependent molecular tools for soil and rhizosphere microbiology. Diversity 5:581–612. doi:10.3390/d5030581
  • Russo SE, Legge R, Weber KA, Brodie EL, Goldfarb KC, Benson AK, Tan S (2012) Bacterial community structure of contrasting soils underlying Bornean rain forests: inferences from microarray and next-generation sequencing methods. Soil Biol Biochem 55:48–59. doi:10.1016/j.soilbio.2012.05.021
  • Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA (2012) GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 22:557–567. doi:10.1101/gr.131383.111
  • Santi C, Bogusz D, Franche C (2013) Biological nitrogen fixation in non-legume plants. Ann Bot 111:743–767. doi:10.1093/aob/mct048
  • Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe S, Ono A, Kawashima K, Fujishiro T, Katoh M, Kohara M, Kishida Y, Minami C, Nakayama S, Nakazaki N, Shimizu Y, Shinpo S, Takahashi C, Wada T, Yamada M, Ohmido N, Hayashi M, Fukui F, Baba T, Nakamichi T, Mori H, Tabata S (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227–239. doi:10.1093/dnares/dsn008
  • Schadt EE, Turner S, Kasarskis A (2010) A window into thirdgeneration sequencing. Hum Mol Genet 19:R227–R240. doi:10.1093/hmg/ddq416 Acta Physiol Plant (2015) 37:208 Page 15 of 17 208
  • Schatz MC, Witkowski J, McCombie WR (2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biol 13:243. doi:10.1186/gb-2012-13-4-243
  • Schoebitz M, Ceballos C, Ciampi L (2013) Effect of immobilized phosphate solubilizing bacteria on wheat growth and phosphate uptake. J Soil Sci Plant Nutr 13:1–10. doi:10.4067/S0718-95162013005000001
  • Servín-Garcidueñas LE, Rogel MA, Ormeño-Orrillo E, Delgado-Salinas A, Martínez-Romero J, Sánchez F, Martínez-Romero E (2012) Genome sequence of Rhizobium sp. strain CCGE510, a symbiont isolated from nodules of the endangered wild bean Phaseolus albescens. J Bacteriol 194:6310–6311. doi:10.1128/JB.01536-12
  • Sessitsch A, Weilharter A, Gerzabeck MH, Kirchmann H, Kandeler E (2001) Microbial population structure in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67:4215–4224. doi:10.1128/AEM.67.9.4215-4224.2001
  • Sharma T, Dreyer I, Riedelsberger J (2013) The role of K+ channels in uptake and redistribution of potassium in the model plant Arabidopsis thaliana. Front Plant Sci 4:224. doi:10.3389/fpls. 2013.00224
  • Sheng XF (2005) Growth promotion and increased potassium uptake of cotton and rape by a potassium releasing strain of Bacillus edaphicus. Soil Biol Biochem 37:1918–1922. doi:10.1016/j. soilbio.2005.02.026
  • Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Nextgeneration sequencing technologies for environmental DNA research. Mol Ecol 21:1794–1805. doi:10.1111/j.1365-294X.2012.05538.x
  • Singh B, Satyanarayana T (2011) Microbial phytases in phosphorus acquisition and plant growth promotion. Physiol Mol Biol Plants 17:93–103. doi:10.1007/s12298-011-0062-x
  • Smith CJ, Osborn AM (2009) Advantages and limitations of quantitative PCR (qPCR)-based approaches in microbial ecology. FEMS Microbiol Ecol 67:6–20. doi:10.1111/j.1574-6941. 2008.00629.x
  • Smith VH, Schindler DW (2009) Eutrophication science: where do we go from here+ Trends Ecol Evol 24:201–207. doi:10.1016/j. tree.2008.11.009
  • Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194:4151–4160. doi:10.1128/JB.00345-12
  • Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, Stocks K, Allen EE, Ellisman M, Grethe J, Wooley J (2011) Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res 39:D546–D551. doi:10.1093/nar/gkq1102
  • Takei K, Sakakibara H, Taniguchi M, Suguyama T (2001) Nitrogendependent accumulation of cytokinins in root and the translocation to leaf: implication of cytokinin species that induces gene expression of maize response regulator. Plant Cell Physiol 42:85–93. doi:10.1093/pcp/pce009
  • Thamdrup B (2012) New pathways and processes in the global nitrogen cycle. Annu Rev Ecol Evol Syst 43:407–428. doi:10.1146/annurev-ecolsys-102710-145048
  • Van Nostrand JD, He Z, Zhou J (2011) New developments and applications of microarrays for microbial community analysis in natural and impacted ecosystems. In: Moo-Young M (ed) Comprehensive biotechnology. Elsevier, Amsterdam, pp 37–45
  • Vance CP (2001) Symbiotic nitrogen fixation and phosphorus acquisition. Plant nutrition in a world of declining renewable resources. Plant Physiol 127:390–397. doi:10.1104/pp.010331
  • Vance CP, Uhde-Stone C, Allan DL (2003) Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. New Phytol 157:423–447. doi:10.1046/j.1469-8137.2003.00695.x
  • Vassileva M, Serrano M, Bravo V, Jurado E, Nikolaeva I, Martos V, Vassilev N (2010) Multifunctional properties of phosphatesolubilizing microorganisms grown on agro-industrial wastes in fermentation and soil conditions. Appl Microbiol Biotechnol 85:1287–1299. doi:10.1007/s00253-009-2366-0
  • Versaw WK, Harrison MJ (2002) A chloroplast phosphate transporter, PHT2; 1, influences allocation of phosphate within the plant and phosphate-starvation responses. Plant Cell 14:1751–1766.doi:10.1105/tpc.002220
  • Véry AA, Nieves-Cordones M, Daly M, Khan I, Fizames C, Sentenac H (2014) Molecular biology of K+ transport across the plant cell membrane: what do we learn from comparison between plant species+ J Plant Physiol 171:748–769. doi:10.1016/j.jplph.2014.01.011
  • von Wirén N (2011) Grand challenges in plant nutrition. Front Plant Sci 2:4. doi:10.3389/fpls.2011.00004
  • von Wittgenstein NJJB, Le CH, Hawkins BJ, Ehlting J (2014) Evolutionary classification of ammonium, nitrate, and peptide transporters in land plants. BMC Evol Biol 14:11. doi:10.1186/1471-2148-14-11
  • Wang R, Okamoto M, Xing X, Crawford NM (2003) Microarray analysis of the nitrate response in Arabidopsis roots and shoots reveals over 1000 rapidly responding genes and new linkages to glucose, trehalose-6-phosphate, iron, and sulfate metabolism. Plant Physiol 132:556–567. doi:10.1104/pp.103.021253
  • Wang M, Shen Q, Xu G, Guo S (2014a) New insight into the strategy for nitrogen metabolism in plant cells. Int Rev Cell Mol Biol 310:1–37. doi:10.1016/B978-0-12-800180-6.00001-3
  • Wang G, Zhang C, Battle S, Lu H (2014b) The phosphate transporter PHT4;1 is a salicylic acid regulator likely controlled by the circadian clock protein CCA1. Front Plant Sci 5:701. doi:10.3389/fpls.2014.00701
  • Wasaki J, Shinano T, Onishi K, Yonetani R, Yazaki J, Fuji F, Shimbo K, Ishikawa M, Shimatani Z, Nagata Y, Hashimoto A, Ohta T, Sato Y, Miyamoto C, Honda S, Kojima K, Sasaki T, Kishimoto N, Kikuchi S, Osaki M (2006) Transcriptomic analysis indicates putative metabolic changes caused by manipulation of phosphorus availability in rice leaves. J Exp Bot 57:2049–2059. doi:10. 1093/jxb/erj158
  • Wu Y, He Y, Yin H, Chen W, Wang Z, Xu L, Zhang A (2012a) Isolation of phosphate-solubilizing fungus and its application in solubilization of rock phosphates. Pak J Biol Sci 15:1144–1151. doi:10.3923/pjbs.2012.1144.1151
  • Wu Z, Guo L, Qin S, Li C (2012b) Encapsulation of R. planticola Rs-2 from alginate-starch-bentonite and its controlled release and swelling behavior under simulated soil conditions. J Ind Microbiol Biotechnol 39:317–327. doi:10.1007/s10295-011-1028-2
  • Xiong H, Shen H, Zhang L, Zhang Y, Guo X, Wang P, Duan P, Ji C, Zhong L, Zhang F, Zuo Y (2013) Comparative proteomic analysis for assessment of the ecological significance of maize and peanut intercropping. J Proteomics 78:447–460. doi:10.1016/j.jprot.2012.10.013
  • Xu G, Fan X, Miller AJ (2012) Plant nitrogen assimilation and use efficiency. Annu Rev Plant Biol 63:153–182. doi:10.1146/annurev-arplant-042811-105532
  • Yadav UP, Ayre BG, Bush DR (2015) Transgenic approaches to altering carbon and nitrogen partitioning in whole plants: assessing the potential to improve crop yields and nutritional quality. Front Plant Sci 6:275. doi:10.3389/fpls.2015.00275
  • Zaidi A, Khan MS, Ahemad M, Oves M (2009) Plant growth promotion by phosphate solubilizing bacteria. Acta Microbiol Immunol Hung 56:263–284. doi:10.1556/AMicr.56.2009.3.6
  • Zhang QC, Wang GH, Yao HY (2007) Phospholipid fatty acid patterns of microbial communities in paddy soil under different fertilizer treatments. J Environ Sci 19:55–59. doi:10.1016/ S1001-0742(07)60009-6
  • Zhou J, Xia B, Treves DS, Wu LY, Marsh TL, O’Neill RV, Palumbo AV, Tiedje JM (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68:326–334. doi:10.1128/AEM.68.1.326-334.2002
  • Zörb C, Senbayram M, Peiter E (2014) Potassium in agriculture—status and perspectives. J Plant Physiol 171:656–669. doi:10.1016/j.jplph.2013.08.008

Typ dokumentu



Identyfikator YADDA

JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.