Evolution of the amino acid fingerprint in the unsterilized rhizosphere of a legume in relation to plant maturity

Soil Biology and Biochemistry - Tập 101 - Trang 226-236 - 2016
Hélène Bobille1,2, Anis M. Limami2, Richard J. Robins3, Caroline Cukier2, Gaëtan Le Floch4, Joëlle Fustec1
1UR LEVA, Ecole Supérieure d'Agricultures (ESA), SFR 4207 QUASAV, 55 rue Rabelais, F-49007 Angers Cedex, France
2IRHS, University of Angers, INRA, SFR 4207 QUASAV, 42 rue Georges Morel, F-49071 Beaucouzé Cedex, France
3EBSI Group, CEISAM, CNRS–University of Nantes UMR 6230, F-44322 Nantes, France
4EA 3882 LUBEM, ESIAB Technopôle de Brest-Iroise, F-29280 Plouzané, France

Tài liệu tham khảo

Apostel, 2013, Biochemical pathways of amino acids in soil: assessment by position-specific labeling and 13C-PLFA analysis, Soil Biol. Biochem., 67, 31, 10.1016/j.soilbio.2013.08.005 Aulakh, 2001, Characterization of root exudates at different growth stages of ten rice (Oryza sativa L.) cultivars, Plant Biol., 3, 139, 10.1055/s-2001-12905 Azevedo, 2006, The aspartic acid metabolic pathway, an exciting and essential pathway in plants, Amino Acids, 30, 143, 10.1007/s00726-005-0245-2 Badri, 2009, Regulation and function of root exudates, Plant, Cell & Environ., 32, 666, 10.1111/j.1365-3040.2009.01926.x Bais, 2006, The role of root exudates in rhizosphere interactions with plants and other organisms, Annu. Rev. Plant Biol., 57, 233, 10.1146/annurev.arplant.57.032905.105159 Barber, 1995 Buchan, 2012, Selective sterilisation of undisturbed soil cores by gamma irradiation: effects on free-living nematodes, microbial community and nitrogen dynamics, Soil Biol. Biochem., 47, 10, 10.1016/j.soilbio.2011.12.014 Chaparro, 2013, Root exudation of phytochemicals in Arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions, PLoS ONE, 8, e55731, 10.1371/journal.pone.0055731 Chichester, 2013, Active microorganisms in soil: critical review of estimation criteria and approaches, Soil Biol. Biochem., 67, 192, 10.1016/j.soilbio.2013.08.024 Corre-Hellou, 2005, N2 fixation and N supply in organic pea (Pisum sativum L.) cropping systems as affected by weeds and peaweevil (Sitona lineatus L.), Eur. J. Agron., 22, 449, 10.1016/j.eja.2004.05.005 Dakora, 2002, Root exudates as mediators of mineral acquisition in low-nutrient environments, Plant Soil, 245, 35, 10.1023/A:1020809400075 Darwent, 2003, Biosensor reporting of root exudation from Hordeum vulgare in relation to shoot nitrate concentration, J. Exp. Bot., 54, 325, 10.1093/jxb/erg017 Dashman, 1982, Adsorption and binding of amino acids on homoionic montmorillonite and kaolinite, Soil Biol. Biochem., 14, 447, 10.1016/0038-0717(82)90103-1 de Vries, 2012, Plant-microbial linkages and ecosystem nitrogen retention: lessons for sustainable agriculture, Front. Ecol. Environ., 10, 425, 10.1890/110162 Degens, 1998, Microbial functional diversity can be influenced by the addition of simple organic substrates to soil, Soil Biol. Biochem., 30, 1981, 10.1016/S0038-0717(98)00070-4 Do Amarante, 2006, Growth and stress conditions cause similar changes in xylem amino acids for different legume species, Environ. Exp. Bot., 58, 123, 10.1016/j.envexpbot.2005.07.002 el Zahar Haichar, 2014, Root exudates mediated interactions belowground, Soil Biol. Biochem., 77, 69, 10.1016/j.soilbio.2014.06.017 Farrar, 2003, How roots control the flux of carbon to the rhizosphere, Ecology, 84, 827, 10.1890/0012-9658(2003)084[0827:HRCTFO]2.0.CO;2 Farrell, 2014, Amino acid dynamics across a grassland altitudinal gradient, Soil Biol. Biochem., 76, 179, 10.1016/j.soilbio.2014.05.015 Ferreira, 2005, Are high-lysine cereal crops still a challenge?, Braz. J. Med. Biol. Res., 38, 985, 10.1590/S0100-879X2005000700002 Fischer, 2007, Carbohydrate and amino acid composition of dissolved organic matter leached from soil, Soil Biol. Biochem., 39, 2926, 10.1016/j.soilbio.2007.06.014 Fustec, 2010, Nitrogen rhizodeposition of legumes. A review, Agron. Sustain. Dev., 30, 57, 10.1051/agro/2009003 Galloway, 2003, The nitrogen cascade, BioScience, 53, 341, 10.1641/0006-3568(2003)053[0341:TNC]2.0.CO;2 Garg, 2007, Symbiotic nitrogen fixation in legume nodules: process and signaling. A review, Agron. Sustain. Dev., 27, 59, 10.1051/agro:2006030 Gaufichon, 2013, Arabidopsis thaliana ASN2 encoding asparagine synthetase is involved in the control of nitrogen assimilation and export during vegetative growth, Plant, Cell & Environ., 36, 328, 10.1111/j.1365-3040.2012.02576.x Grayston, 1997, Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability, Appl. Soil Ecol., 5, 29, 10.1016/S0929-1393(96)00126-6 Grayston, 1998, Selective influence of plant species on microbial diversity in the rhizosphere, Soil Biol. Biochem., 30, 369, 10.1016/S0038-0717(97)00124-7 Hamlen, 1972, Influence of age and stage of development on the neutral carbohydrate components in root exudates from alfalfa plants grown in a gnotobiotic environment, Can. J. Plant Sci., 52, 633, 10.4141/cjps72-097 Hartmann, 2009, Plant-driven selection of microbes, Plant Soil, 321, 235, 10.1007/s11104-008-9814-y Helal, 1984, 175 Henry, 2005, How does nitrogen availability alter rhizodeposition in Lolium multiflorum Lam. during vegetative growth?, Plant Soil, 269, 181, 10.1007/s11104-004-0490-2 Hinsinger, 2005, Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes, New Phytol., 168, 293, 10.1111/j.1469-8137.2005.01512.x Hütsch, 2002, Plant rhizodeposition—an important source for carbon turnover in soils, J. Plant Nutr. Soil Sci., 165, 397, 10.1002/1522-2624(200208)165:4<397::AID-JPLN397>3.0.CO;2-C Ireland, 1997, Amino acid and ureide biosynthesis, Plant Metab., 478 Ivarson, 1970, Amino-acid composition of rhizosphere as affected by soil temperature, fertility and growth stage, Can. J. Soil Sci., 50, 183, 10.4141/cjss70-026 Jensen, 1996, Barley uptake of N deposited in the rhizosphere of associated field pea, Soil Biol. Biochem., 28, 159, 10.1016/0038-0717(95)00134-4 Jones, 1998, Organic acids in the rhizosphere–a critical review, Plant Soil, 205, 25, 10.1023/A:1004356007312 Jones, 1994, Role of root derived organic acids in the mobilization of nutrients from the rhizosphere, Plant Soil, 166, 247, 10.1007/BF00008338 Jones, 1999, Biodegradation kinetics and sorption reactions of three differently charged amino acids in soil and their effects on plant organic nitrogen availability, Soil Biol. Biochem., 31, 1331, 10.1016/S0038-0717(99)00056-5 Jones, 2006, Experimental evaluation of methods to quantify dissolved organic nitrogen (DON) and dissolved organic carbon (DOC) in soil, Soil Biol. Biochem., 38, 991, 10.1016/j.soilbio.2005.08.012 Jones, 2002, Simple method to enable the high resolution determination of total free amino acids in soil solutions and soil extracts, Soil Biol. Biochem., 34, 1893, 10.1016/S0038-0717(02)00203-1 Jones, 2004, Plant and mycorrhizal regulation of rhizodeposition, New Phytol., 163, 459, 10.1111/j.1469-8137.2004.01130.x Jones, 2005, Dissolved organic nitrogen uptake by plants—an important N uptake pathway?, Soil Biol. Biochem., 37, 413, 10.1016/j.soilbio.2004.08.008 Jones, 2009, Carbon flow in the rhizosphere: carbon trading at the soil–root interface, Plant Soil, 321, 5, 10.1007/s11104-009-9925-0 Kataoka, 1996, Derivatization reactions for the determination of amines by gas chromatography and their applications in environmental analysis, J. Chromatogr. A, 733, 19, 10.1016/0021-9673(95)00726-1 Kelley, 1996, 407 Khan, 2002, Quantifying below-ground nitrogen of legumes, Plant Soil, 245, 327, 10.1023/A:1020407006212 Kielland, 1995, Landscape patterns of free amino acids in arctic tundra soils, Biogeochemistry, 31, 85, 10.1007/BF00000940 Kuijken, 2015, The importance of a sterile rhizosphere when phenotyping for root exudation, Plant Soil, 387, 131, 10.1007/s11104-014-2283-6 Kuzyakov, 2002, Review: factors affecting rhizosphere priming effects, J. Plant Nutr. Soil Sci., 165, 382, 10.1002/1522-2624(200208)165:4<382::AID-JPLN382>3.0.CO;2-# Lesuffleur, 2007, Root amino acid exudation: measurement of high efflux rates of glycine and serine from six different plant species, Plant Soil, 294, 235, 10.1007/s11104-007-9249-x Lipson, 1999, Variation in competitive abilities of plants and microbes for specific amino acids, Biol. Fertil. Soils, 29, 257, 10.1007/s003740050550 Lynch, 1990, Substrate flow in the rhizosphere, Plant Soil, 129, 1, 10.1007/BF00011685 Mahieu, 2007, Comparison of two 15N labelling methods for assessing nitrogen rhizodeposition of pea, Plant Soil, 295, 193, 10.1007/s11104-007-9275-8 McDougall, 1970, Sites of exudation of 14C-labelled compounds from wheat roots, New Phytol., 69, 999, 10.1111/j.1469-8137.1970.tb02479.x McNamara, 2003, Effects of acute gamma irradiation on chemical, physical and biological properties of soils, Appl. Soil Ecol., 24, 117, 10.1016/S0929-1393(03)00073-8 Meharg, 1994, A critical review of labelling techniques used to quantify rhizosphere carbon-flow, Plant Soil, 166, 55, 10.1007/BF02185481 Meharg, 1991, A novel method of quantifying root exudation in the presence of soil microflora, Plant Soil, 133, 111, 10.1007/BF00011905 Merbach, 1999, Release of carbon and nitrogen compounds by plant roots and their possible ecological importance, J. Plant Nutr. Soil Sci., 162, 373, 10.1002/(SICI)1522-2624(199908)162:4<373::AID-JPLN373>3.0.CO;2-# Mimmo, 2011, Time and substrate dependent exudation of carboxylates by Lupinus albus L. and Brassica napus L, Plant Physiol. Biochem., 49, 1272, 10.1016/j.plaphy.2011.08.012 Moe, 2013, Amino acids in the rhizosphere: from plants to microbes, Am. J. Bot., 100, 1692, 10.3732/ajb.1300033 Murashige, 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiol. Plant, 15, 473, 10.1111/j.1399-3054.1962.tb08052.x Murray, 1996, Impact of insect root herbivory on the growth and nitrogen and carbon contents of white clover (Trifolium repens) seedlings, Can. J. Bot., 74, 1591, 10.1139/b96-192 Nadkarni, 2002, Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set, Microbiology, 148, 257, 10.1099/00221287-148-1-257 Neumann, 2009, Strategies and methods for studying the rhizosphere-the plant science toolbox, Plant Soil, 321, 431, 10.1007/s11104-009-9953-9 Nguyen, 2003, Rhizodeposition of organic C by plants: mechanisms and controls, Agronomie, 23, 375, 10.1051/agro:2003011 Nyfeler, 2011, Grass–legume mixtures can yield more nitrogen than legume pure stands due to mutual stimulation of nitrogen uptake from symbiotic and non-symbiotic sources, Agric. Ecosyst. Environ., 140, 155, 10.1016/j.agee.2010.11.022 Oberson, 2013, Nitrogen fixation and transfer in grass-clover leys under organic and conventional cropping systems, Plant Soil, 371, 237, 10.1007/s11104-013-1666-4 Oburger, 2013, Evaluation of a novel tool for sampling root exudates from soil-grown plants compared to conventional techniques, Environ. Exp. Bot., 87, 235, 10.1016/j.envexpbot.2012.11.007 Owen, 2001, Competition for amino acids between wheat roots and rhizosphere microorganisms and the role of amino acids in plant N acquisition, Soil Biol. Biochem., 33, 651, 10.1016/S0038-0717(00)00209-1 Paterson, 2003, Importance of rhizodeposition in the coupling of plant and microbial productivity, Eur. J. Soil Sci., 54, 741, 10.1046/j.1351-0754.2003.0557.x Paterson, 2005, Defoliation alters the relative contributions of recent and non-recent assimilate to root exudation from Festuca rubra, Plant, Cell & Environ., 28, 1525, 10.1111/j.1365-3040.2005.01389.x Paynel, 2003, N transfer from white clover to perennial ryegrass, via exudation of nitrogenous compounds, Agronomie, 23, 503, 10.1051/agro:2003022 Paynel, 2001, Root exudates: a pathway for short-term N transfer from clover and ryegrass, Plant Soil, 229, 235, 10.1023/A:1004877214831 Phillips, 2004, Microbial products trigger amino acid exudation from plant roots, Plant Physiol., 136, 2887, 10.1104/pp.104.044222 Powlson, 2011, Soil management in relation to sustainable agriculture and ecosystem services, Food Policy, 36, S72, 10.1016/j.foodpol.2010.11.025 Qualls, 2003, Factors controlling concentration, export, and decomposition of dissolved organic nutrients in the Everglades of Florida, Biogeochemistry, 62, 197, 10.1023/A:1021150503664 Ramos-González, 2005, Analysis of Pseudomonas putida KT2440 gene expression in the maize rhizosphere: in vitro expression technology capture and identification of root-activated promoters, J. Bacteriol., 187, 4033, 10.1128/JB.187.12.4033-4041.2005 Ravanel, 1998, The specific features of methionine biosynthesis and metabolism in plants, Proc. Natl. Acad. Sci., 95, 7805, 10.1073/pnas.95.13.7805 Sauheitl, 2010, Amino acid fingerprint of a grassland soil reflects changes in plant species richness, Plant Soil, 334, 353, 10.1007/s11104-010-0387-1 Schenck zu Schweinsberg-Mickan, 2012, Rhizodeposition: its contribution to microbial growth and carbon and nitrogen turnover within the rhizosphere, J. Plant Nutr. Soil Sci., 175, 750, 10.1002/jpln.201100300 Schneegurt, 2003, Direct extraction of DNA from soils for studies in microbial ecology, Curr. Issues Mol. Biol., 5, 1 Schreiter, 2015, Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce. The plant microbiome and its importance for plant and human health, Front. Microbiol., 5, 144 Shepherd, 1994, Patterns of short-term amino acid accumulation and loss in the root-zone of liquid-cultured forage rape (Brassica napus L.), Plant Soil, 158, 99, 10.1007/BF00007922 Söderberg, 1998, Bacterial activity along a young barley root measured by the thymidine and leucine incorporation techniques, Soil Biol. Biochem., 30, 1259, 10.1016/S0038-0717(98)00058-3 Sposito, 2008 Stevenson, 1982, Organic forms of soil nitrogen, 67 Tanaka, 2003, Properties and metabolic diversity of microbial communities in soils treated with steam sterilization compared with methyl bromide and chloropicrin fumigations, Soil Sci. Plant Nutr., 49, 603, 10.1080/00380768.2003.10410050 Todorovic, 2001, Root and microbial involvement in the kinetics of 14C-partitioning to rhizosphere respiration after a pulse labelling of maize assimilates, Plant Soil, 228, 179, 10.1023/A:1004830011382 Vranova, 2013, Methods of collection of plant root exudates in relation to plant metabolism and purpose: a review, J. Plant Nutr. Soil Sci., 176, 175, 10.1002/jpln.201000360 Vranová, 2014, Dominant amino acids, organic acids and sugars in water-soluble root exudates of C4 plants: a mini-review, Acta Univ. Agric. Silvic. Mendelianae Brunensis, 58, 441, 10.11118/actaun201058050441 Walker, 2003, Metabolic profiling of root exudates of Arabidopsis thaliana, J. Agric. Food Chem., 51, 2548, 10.1021/jf021166h Wang, 1993, Adsorption and desorption of aliphatic amines, amino acids and acetate by clay minerals and marine sediments, Mar. Chem., 44, 1, 10.1016/0304-4203(93)90002-6 White, 1990, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, PCR Protoc. a guide methods Appl., 18, 315 Wichern, 2007, Rhizodeposition of C and N in peas and oats after 13C–15N double labelling under field conditions, Soil Biol. Biochem., 39, 2527, 10.1016/j.soilbio.2007.04.022 Wichern, 2008, Nitrogen rhizodeposition in agricultural crops: methods, estimates and future prospects, Soil Biol. Biochem., 40, 30, 10.1016/j.soilbio.2007.08.010 Yu, 2002, Contribution of amino compounds to dissolved organic nitrogen in forest soils, Biogeochemistry, 61, 173, 10.1023/A:1020221528515 Zancarini, 2012, Soil nitrogen availability and plant genotype modify the nutrition strategies of Medicago truncatula and the associated rhizosphere microbial communities, PLoS ONE, 7, e47096, 10.1371/journal.pone.0047096