Các vi sinh vật đất rễ phân tách theo các kiểu di truyền và kiểu hóa học của cây chủ Populus trichocarpa, nhưng phụ thuộc vào nguồn gốc đất
Tóm tắt
Cây xanh đã phát triển các chiến lược phòng thủ chống lại phytopathogen và đầu tiên bảo vệ thông qua các cơ chế trao đổi chất phối hợp. Các chất chuyển hóa trọng lượng phân tử thấp được sản xuất trong mô thực vật, chẳng hạn như axit salicylic, đại diện cho một cơ chế có khả năng điều chỉnh sự tương tác giữa cây và vi khuẩn trên và dưới mặt đất. Axit salicylic là một phytohormone phổ biến ở mức độ thấp trong hầu hết cây trồng, nhưng là hợp chất phòng thủ tập trung ở
Xuất xứ của đất là bộ lọc chính gây ra sự phân hóa trong các cộng đồng vi khuẩn / cổ vi sinh và nấm, với giống cây ảnh hưởng thứ cấp. Cả độ đều của vi khuẩn / cổ vi sinh và nấm đều thay đổi giữa các nguồn xuất xứ đất và độ đa dạng / đều của vi khuẩn / cổ vi sinh đều tương quan với ít nhất một chất chuyển hóa SA (đa dạng: populin; đều: tổng phenol). Quá trình sản xuất các dẫn xuất axit salicylic riêng lẻ bị ảnh hưởng bởi giống cây chủ dẫn đến sự khác biệt thành phần cho vi khuẩn / cổ vi sinh (tremuloidin) và nấm (axit salicylic) trong một nguồn đất (Clatskanie), trong khi các đất từ Corvallis không thay đổi thành phần vi sinh do các dẫn xuất axit salicylic. Một số loại vi khuẩn chủ đạo (ví dụ,
Kết quả này chỉ ra rằng các cộng đồng vi sinh vật phân tách nhiều nhất giữa các nguồn đất. Tuy nhiên, trong một nguồn đất, các cộng đồng vi khuẩn / cổ vi sinh phản ứng với sản xuất SA của cây trong các microbiome đất rễ dựa trên nhà kính. Các microbiome nấm bị ảnh hưởng bởi các chất chuyển hóa gốc SA, nhưng tổng thể dưới mức này trong ngữ cảnh thực nghiệm này. Những kết quả này cho thấy các chiến lược phòng thủ của cây, chẳng hạn như SA và các chất chuyển hóa thứ cấp của nó, có thể một phần điều chỉnh các mô hình cụ thể về sự xâm lược và tập hợp của các loại vi khuẩn / cổ vi sinh và nấm.
Từ khóa
#Axit Salicylic; Populus trichocarpa; Microbiome đất rễ; Sản xuất chất chuyển hóa; Phân loại vi khuẩn; Phân loại nấm; Sự phân hóa đất.Tài liệu tham khảo
Berendsen RL, Pieterse CMJ, Bakker PAHM. The rhizosphere and plant microbiome health. Trends Plant Sci. 2012;17:478–86.
Badri V, Chaparro JM, Zhang R, Shen Q, Vivanco JM. Application of natural blends of phytochemicals derived from the root exudates of Arabidopsis to the soil reveal that phenolic-related compounds predominantly modulate the soil microbiome. J Biol Chemi. 2013;288:4502–12.
Bonito G, Reynolds H, Robeson MS, Nelson JA, Hodkinson BP, Tuskan G, et al. Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol Ecol. 2014;23:3356–70.
Shakya M, Gottel N, Castro H, Yang ZK, Gunter L, Labbé J, et al. A multifactor analysis of fungal and bacterial community structure in the root microbiome of mature Populus deltoides trees. PLoS One. 2013. https://doi.org/10.1371/journal.pone.0076382.
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, et al. Defining the core Arabidopsis thaliana root microbiome. Nature. 2014;488:86–90.
Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015;349:860–4.
Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun. 2016;7:12151.
Lareen A, Burton F, Schäfer P. Plant root-microbe communication in shaping root microbiome. Plant Mol Biol. 2016;90:575–87.
Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. P Natl Acad Sci USA. 20016;103:626–31.
Kaiser K, Wemheuer B, Korolkow V, Wemheuer F, Heiko N, Schöning I, et al. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests. Sci Rep. 2016. https://doi.org/10.1038/srep33696.
Toljander JF, Santos-Gonzalez JC, Tehler A, Finlay R. Community analysis of arbuscular mycorrhizal fungi and bacteria in the maize mycorrhizophere in a long-term fertilization trial. FEMS Microbiol Ecol. 2008;65:323–38.
Veach AM, Stokes CE, Knoepp J, Jumpponen A, Baird R. Fungal communities and functional guilds shift along an elevational gradient in the southern Appalachian Mountains. Microb Ecol. 2018;76:156–68.
Chau JF, Bagtzoglou AC, Willig MR. The effect of soil texture on richness and diversity of bacterial communities. Environ Forensic. 2011;12:333–41.
Mummey DL, Stahl PD. Analysis of soil whole- and inner-microaggregate bacterial communities. Microb Ecol. 2004;48:41–50.
Hansel CM, Fendorf S, Jardine PM, Francis CA. Changes in bacterial and archaeal community structure and functional diversity along a geochemically variable soil profile. Appl Environ Microb. 2008;74:1620–33.
Garbeva P, Veen JA, Elsas JD. Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annu Rev Phytopathol. 2004;42:243–70.
Bulgarelli D, Rott M, Schlaeppi K. Ver Loren van Themaat E, Ahmadinejad N, Assenza F, et al. revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature. 2012;488:91–5.
Bulgarelli D, Schlaeppi S, Spaepen V, Ver Loren van Themaat E, Schulze-Lefert P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol. 2013;64:807–38.
Keddy PA. Assembly and response rules: two goals for predictive community ecology. J Veg Sci. 1992;3:157–64.
Bello F, Lavorel S, Lavergne S, Albert CH, Boulangeat I, Mazel F, et al. Hierarchical effects of environmental filters on the functional structure of plant communities: a case study in the French Alps. Ecography. 2013;36:393–402.
Chaparro JM, Sheflin AM, Manter DK, Vivanco JM. Manipulating the soil microbiome to increase soil health and plant fertility. Biol Fert Soils. 2012;48:489–99.
Pál M, Kovác V, Szalai G, Soós V, Ma X, Liu H, et al. Salicylic acid and abiotic stress response in rice. J Agron Crop Sci. 2014;200:1–11.
Khan MIR, Fatma M, Per TS, Anjum NA, Khan NA. Salicylic acid-induced abiotic stress tolerance and underlying mechanisms in plants. Front Plant Sci. 2015. https://doi.org/10.3389/fpls.2015.00462.
Rivas-San Vicente M, Plasencia J. Salicylic acid beyond defence: its role in plant growth and development. J Exp Bot. 2011;62:3321–38.
Miura K, Tada Y. Regulation of water, salinity, and cold stress responses by salicylic acid. Front Plant Sci. 2014. https://doi.org/10.3389/fpls.2014.00004.
Malamy J, Carr JP, Klessig DF, Raskin I. Salicylic acid: a likely exogenous signal in the resistance response of Tobacoo to viral infection. Science. 1990;250:1002–4.
Lee H, León J, Raskin I. Biosynthesis and metabolism of salicylic acid. Proc Natl Acad Sci U S A. 1995;92:4076–9.
Kniskern JM, Traw MB, Bergelson J. Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. Mol Plant Microbe In. 2007;20:1512–22.
Doornbos RF, Geraats BPJ, Kuramae EE, Van Loon LC, Bakker PAHM. Effects of jasmonic acid, ethylene, and salicylic acid signaling on the rhizosphere bacterial community of Arabidopsis thaliana. Mol Plant Microbe In. 2011;24:395–407.
Silverman P, Seskar M, Kanter D, Schweizer P, Métraux J, Raskin I. Salicylic acid in rice. Plant Physiol. 1995;108:633–9.
Koch JR, Creelman RA, Eshita SM, Seskar M, Mullet JE, Davis KR. Ozone sensitivity in hybrid poplar correlates with insensitivity to both salicylic acid and jasmonic acid. The role of programmed cell death in lesion formation. Plant Physiol. 2000;123:487–96.
Xue LJ, Guo W, Yuan Y, Anino EO, Nyamdari B, Wilson MC, et al. Constitutively elevated salicylic acid levels alter photosynthesis and oxidative state but not growth in transgenic Populus. Plant Cell. 2013;25:2714–30.
Donaldson JR, Stevens MT, Barnhill HR, Lindroth RL. Age-related shifts in leaf chemistry of clonal aspen (Populus tremuloides). J Chem Ecol. 2006;32:1415–29.
Schweitzer JA, Madritch MD, Bailey JK, LeRoy CJ, Fischer DG, et al. From genes to ecosystems: the genetic basis of condensed tannins and their role in nutrient regulation in a Populus model system. Ecosystems. 2008;11:1005–20.
Schweitzer JA, Bailey JK, Rehill BJ, Martinsen GD, Hart SC, Lindroth RL, et al. Genetically based trait in a dominant tree affects ecosystem processes. Ecol Lett. 2004;7:127–34.
Bailey JK, Deckert R, Schweitzer JA, Rehill BJ, Lindroth RL, Gehring C, et al. Host plant genetics affect hidden ecological players: links among Populus, condensed tannins, and fungal endophyte infection. Can J Botany. 2015;88:356–61.
Schweitzer JA, Bailey JK, Bangert RK, Hart SC, Whitham TG. The role of plant genetics in determining above- and below-ground microbial communities. In: Bailey MJ, Lilley AK, Timms-Wilson TM, Spencer-Phillips PTN, editors. Microbial ecology of aerial plant surfaces. Wallingford: CABI Publishing; 2007. p. 107–19.
Schweitzer JA, Bailey JK, Fischer DG, LeRoy CL, Lonsdorf EV, et al. Plant-soil-microorganism interactions: heritable relationship between plant genotype and associated soil microorganisms. Ecology. 2008;89:773–81.
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & gray). Science. 2006;15:1596–15604.
Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, et al. Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microb. 2011;77:5934–44.
Marschner P, Crowley D, Yang CH. Development of specific rhizospheres bacterial communities in relation to plant species, nutrition and soil type. Plant Soil. 2004;261:199–208.
Colin Y, Nicolitch O, Van Nostrand JD, Zhou JZ, Turpault MP, Uroz S. Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence. Sci Rep. 2017. https://doi.org/10.1038/s41598-017-07639-1.
Sigurdssson BD, Thorgeirsson H, Linder S. Growth and dry-matter partitioning of young Populus trichocarpa in response to carbon dioxide concentration and mineral nutrient availability. Tree Physiol. 2001;21:941–50.
Kettler TA, Doran JW, Gilbert TL. Simplified method for soil particle-size determination to accompany soil-quality analyses. Soil Sci Soc Am J. 2001;65:849–52.
Eo J, Park KC, Kim MH. Plant-specific effects of sunn hemp (Crotalaria juncea) and sudex (Sorghum bicolor x Sorghum biocolor var. sudanense) on the abundance and composition of soil microbial community. Agric Ecosyst Environ. 2015;213:86–93.
Loake G, Grant M. Salicylic acid in plant defence – the players and protagonists. Curr Opin Plant Biol. 2007;10:466–72.
Zhalnina K, Louie KB, Hao Z, Mansoori N, Nunes da Rocha U, Shi S, et al. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol. 2018. https://doi.org/10.1038/s41564-018-0129-3.
Mason CJ, Rubert-Nason KF, Lindroth RL, Raffa KF. Aspen defense chemicals influence midgut bacterial community composition of gypsy moth. J Chem Ecol. 2015;41:75–84.
Medina MJH, Gagnon H, Piché Y, Ocampo JA, Garrido JMG, Vierheilig H. Root colonization by arbuscular mycorrhizal fungi is affected by the salicylic acid content of the plant. Plant Sci. 2003;164:993–8.
Blilou I, Ocampo JA, Garrido JMG. Resistance of pea roots to endomycorrhizal fungus or rhizobium correlated with enhanced levels of endogenous salicylic acid. J Exp Bot. 1999;50:1663–8.
Ansari A, Razmjoo J, Karimmojeni H. Mycorrhizal colonization and seed treatment with salicylic acid to improve physiological traits and tolerance of flaxseed (Linum usitatissimum L.) plants grown under drought stress. Acta Physiol Plant. 2016;38:34.
Pfabel C, Eckhardt KU, Baum C, Struck C, Frey P, Weih M. Impact of ectomycorrhizal colonization and rust infection on the secondary metabolism of poplar (Populus trichocarpa x deltoides). Tree Physiol. 2012;32:1357–64.
Payyavula RS, Tschaplinski TJ, Jawdy SS, Sykes RW, Tuskan GA, Kalluri UC. Metabolic profiling reveals altered sugar and secondary metabolites in response to UGPase overexpression in Populus. BMC Plant Biol. 2014. https://doi.org/10.1186/s12870-014-0265-8.
Cregger MA, Veach AM, Yang ZK, Crouch MJ, Vilgalys R, Tuksan GA, et al. The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome. Microbiome. 2018. https://doi.org/10.1186/s40168-018-0413-8.
Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL. Practical innovations for high-throughput amplicon sequencing. Nat Methods. 2013;10:999–1002.
Martin M. Cutadapt removes adapter sequences from high throughput sequencing reads. EMBnet J. 2011;17:10.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–200.
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb. 2007;73:5261–7.
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.
Altschul SF, Gish W, Miller W, Myers EW, Lipman D. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Abarenkov K, Nilsson HR, Larsson KH, Alexander IJ, Eberhardt U, Erland S, et al. The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytol. 2010;186:281–5.
Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional and this is not optional. Front Microbiol. 2017;8:2224.
Venables WN, Riley BD. Modern applied statistics with S. New York: Springer Science & Business Media; 2013.
Wehrens R. Chemometrics with R: multivariate data analysis in the natural sciences and life sciences. Heidelberg: Springer; 2011.
Oksanen J, Blanchet JG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. Vegan: community ecology package. Ordination methods, diversity analysis and other function for community and vegetation ecologists: R package; 2018.