Sự hình thành vi sinh vật trong rễ bị ảnh hưởng bởi sự phát triển của cây trồng

ISME Journal - Tập 8 Số 4 - Trang 790-803 - 2014
Jacqueline M. Chaparro1, Dayakar V. Badri1, Jorge M. Vivanco1
1Center for Rhizosphere Biology, Department of Horticulture and Landscape Architecture, Colorado State University , Fort Collins, CO, USA

Tóm tắt

Tóm tắt

Có sự hiểu biết chung về khả năng của các chất tiết từ rễ ảnh hưởng đến cấu trúc của cộng đồng vi sinh vật trong rễ. Tuy nhiên, kiến thức của chúng ta về mối liên hệ giữa sự phát triển của cây, sự tiết rễ và sự tập hợp vi sinh vật còn hạn chế. Ở đây, chúng tôi đã phân tích cấu trúc của cộng đồng vi khuẩn trong rễ liên quan đến Arabidopsis tại bốn thời điểm khác nhau tương ứng với các giai đoạn phát triển khác nhau của cây: cây con, sinh trưởng, ra hoa và ra trái. Tổng thể, không có sự khác biệt đáng kể trong cấu trúc cộng đồng vi khuẩn, nhưng chúng tôi quan sát thấy rằng cộng đồng vi sinh vật ở giai đoạn cây con khác biệt so với các thời điểm phát triển khác. Ở cấp độ chi tiết hơn, các ngành như Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria và một số chi riêng biệt trong các ngành đó theo dõi các mô hình khác nhau liên quan đến sự phát triển của cây và sự tiết rễ. Những kết quả này gợi ý rằng cây có thể chọn một tập hợp con vi sinh vật ở các giai đoạn phát triển khác nhau, có lẽ cho các chức năng cụ thể. Tương ứng, phân tích metatranscriptomics của vi sinh vật trong rễ tiết lộ rằng có 81 bản sao duy nhất được biểu hiện khác biệt (P<0.05) tại các giai đoạn phát triển khác nhau của cây. Chẳng hạn, các gen liên quan đến tổng hợp streptomycin được kích thích đáng kể ở các giai đoạn ra hoa và ra trái, có thể nhằm mục đích kiểm soát bệnh tật. Chúng tôi suy đoán rằng cây tiết ra hỗn hợp các hợp chất và các hóa chất thực vật cụ thể trong các chất tiết từ rễ mà được sản xuất một cách khác nhau ở các giai đoạn phát triển khác nhau nhằm giúp tổ chức sự tập hợp của vi sinh vật trong rễ.

Từ khóa


Tài liệu tham khảo

Abedon, 1996, Corngrass 1 of Maize (Zea mays L.) Delays Development of Adult Plant Resistance to Common Rust (Puccinia sorghi Schw.) and European Corn Borer (Ostrinia nubilalis Hubner), J Hered, 87, 219, 10.1093/oxfordjournals.jhered.a022988

An, 2011, Salicylic acid and its function in plant immunity, J Integr Plant Biol, 53, 412, 10.1111/j.1744-7909.2011.01043.x

Antoun, 1998, Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: effect on radishes (Raphanus sativus L.), Plant Soil, 204, 57, 10.1023/A:1004326910584

Arndt, 2012, METAGENassist: a comprehensive web server for comparative metagenomics, Nucleic Acids Res, 40, W88, 10.1093/nar/gks497

Badri, 2009, An ABC transporter mutation alters root exudation of phytochemicals that provoke an overhaul of natural soil microbiota, Plant Physiol, 151, 2006, 10.1104/pp.109.147462

Badri, 2009, Regulation and function of root exudates, Plant Cell Environ, 32, 666, 10.1111/j.1365-3040.2009.01926.x

Badri, 2013, 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 Chem, 288, 4502, 10.1074/jbc.M112.433300

Badri, 2013, Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior, New Phytol, 198, 264, 10.1111/nph.12124

Bai, 2013, GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves, Appl Microbiol Biotechnol, 97, 7035, 10.1007/s00253-012-4496-z

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

Baker, 2013, Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling, Isme J, 7, 1962, 10.1038/ismej.2013.85

Barns, 1999, Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment, Appl Environ Microbiol, 65, 1731, 10.1128/AEM.65.4.1731-1737.1999

Baudoin, 2002, Impact of growth stage on the bacterial community structure along maize roots, as determined by metabolic and genetic fingerprinting, Appl Soil Ecol, 19, 135, 10.1016/S0929-1393(01)00185-8

Bednarek, 2012, Chemical warfare or modulators of defence responses - the function of secondary metabolites in plant immunity, Curr Opin Plant Biol, 15, 407, 10.1016/j.pbi.2012.03.002

Behera, 1974, Microbial Growth Rate In Glucose-amended Soil, Soil Sci Soc Am J, 38, 591, 10.2136/sssaj1974.03615995003800040021x

Berendsen, 2012, The rhizosphere microbiome and plant health, Trends Plant Sci, 17, 478, 10.1016/j.tplants.2012.04.001

Bolan, 1991, A critical review on the role of mycorrhizal fungi in the uptake of phosphorus by plants, Plant and Soil, 134, 189, 10.1007/BF00012037

Brimecombe, 2007, The Rhizosphere Biochemistry and Organic Substances at the Soil-Plant Interface, 73

Broeckling, 2008, Root exudates regulate soil fungal community composition and diversity, Appl Environ Microbiol, 74, 738, 10.1128/AEM.02188-07

Bulgarelli, 2012, Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota, Nature, 488, 91, 10.1038/nature11336

Burg, 1979, Avermectins, new family of potent anthelmintic agents: producing organism and fermentation, Antimicrob Agents Chemother, 15, 361, 10.1128/AAC.15.3.361

Burns, 1996, Nitrogen supply, growth and development, Acta Hort, 428, 21, 10.17660/ActaHortic.1996.428.3

Chaparro, 2012, Manipulating the soil microbiome to increase soil health and plant fertility, Biol Fertil Soils, 48, 489, 10.1007/s00374-012-0691-4

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

Chiarini, 2006, Burkholderia cepacia complex species: health hazards and biotechnological potential, Trends Microbiol, 14, 277, 10.1016/j.tim.2006.04.006

Clay, 2009, Glucosinolate metabolites required for an Arabidopsis innate immune response, Science, 323, 95, 10.1126/science.1164627

Cohen, 2005, Brassica napus seed meal soil amendment modifies microbial community structure, nitric oxide production and incidence of Rhizoctonia root rot, Soil Biol and Biochem, 37, 1215, 10.1016/j.soilbio.2004.11.027

Conn, 2008, Endophytic actinobacteria induce defense pathways in Arabidopsis thaliana, Mol Plant Microbe Interact, 21, 208, 10.1094/MPMI-21-2-0208

Coronado, 1995, Alfalfa root flavonoid production is nitrogen regulated, Plant Physiol, 108, 533, 10.1104/pp.108.2.533

Davidson, 1986, Effect of contrasting patterns of nitrate application on the nitrate uptake, N2-fixation, nodulation and growth of white clover, Annals of Botany, 57, 331, 10.1093/oxfordjournals.aob.a087114

De-la-Pena, 2010, Root secretion of defense-related proteins is development-dependent and correlated with flowering time, J Biol Chem, 285, 30654, 10.1074/jbc.M110.119040

De-la-Pena, 2008, Root-microbe communication through protein secretion, J Biol Chem, 283, 25247, 10.1074/jbc.M801967200

de Weert, 2002, Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by pseudomonas fluorescens, Mol Plant Microbe Interact, 15, 1173, 10.1094/MPMI.2002.15.11.1173

Develey-Riviere, 2007, Resistance to pathogens and host developmental stage: a multifaceted relationship within the plant kingdom, New Phytol, 175, 405, 10.1111/j.1469-8137.2007.02130.x

Dugat-Bony, 2012, Detecting unknown sequences with DNA microarrays: explorative probe design strategies, Environ Microbiol, 14, 356, 10.1111/j.1462-2920.2011.02559.x

Eaglesham, 1989, Nitrate inhibition of root-nodule symbiosis in doubly rooted soybean plants, Crop science, 29, 115, 10.2135/cropsci1989.0011183X002900010027x

Eilers, 2010, Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil, Soil Biol and Biochem, 42, 896, 10.1016/j.soilbio.2010.02.003

Elbeltagy, 2001, Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species, Appl Environ Microbiol, 67, 5285, 10.1128/AEM.67.11.5285-5293.2001

Fang, 2013, Changes in rice allelopathy and rhizosphere microflora by inhibiting rice phenylalanine ammonia-lyase gene expression, J Chem Ecol, 39, 204, 10.1007/s10886-013-0249-4

Fierer, 2007, Toward an ecological classification of soil bacteria, Ecology, 88, 1354, 10.1890/05-1839

Fierer, 2010, Changes through time: integrating microorganisms into the study of succession, Res Microbiol, 161, 635, 10.1016/j.resmic.2010.06.002

Franche, 2009, Nitrogen-fixing bacteria associated with leguminous and non-leguminous plants, Plant and Soil, 321, 35, 10.1007/s11104-008-9833-8

Gantar, 1991, Colonization of wheat Triticum vulgare L.) by N2-fixing cyanobacteria: I. A survey of soil cyanobacterial isolates forming associations with roots, New Phytologist, 118, 477, 10.1111/j.1469-8137.1991.tb00030.x

Gaworzewska, 1982, Positive Chemotaxis Of Rhizobium-Leguminosarum And Other Bacteria Towards Root Exudates From Legumes And Other Plants, J Gen Microbiol, 128, 1179

Gomez-Alvarez, 2009, Systematic artifacts in metagenomes from complex microbial communities, Isme J, 3, 1314, 10.1038/ismej.2009.72

Gosalbes, 2011, Metatranscriptomic approach to analyze the functional human gut microbiota, PLoS One, 6, e17447, 10.1371/journal.pone.0017447

Gupta Sood, 2003, Chemotactic response of plant-growth-promoting bacteria towards roots of vesicular-arbuscular mycorrhizal tomato plants, FEMS Microbiol Ecol, 45, 219, 10.1016/S0168-6496(03)00155-7

Gutiérrez-Mañero, 2001, The plant-growth-promoting rhizobacteria Bacillus pumilus and Bacillus licheniformis produce high amounts of physiologically active gibberellins, Physiologia Plantarum, 111, 206, 10.1034/j.1399-3054.2001.1110211.x

Hackstadt, 2009, Filtering for increased power for microarray data analysis, BMC Bioinformatics, 10, 11, 10.1186/1471-2105-10-11

Haneline, 1991, Chemotactic behavior of azotobacter vinelandii, Appl Environ Microbiol, 57, 825, 10.1128/aem.57.3.825-829.1991

He, 2007, GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes, Isme J, 1, 67, 10.1038/ismej.2007.2

He, 2011, Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities, Front Environ Sci Engin China, 5, 1, 10.1007/s11783-011-0301-y

Heding, 1964, Radioactive myoinositol: incorporation into streptomycin, Science, 143, 953, 10.1126/science.143.3609.953

Horiuchi, 2005, Soil nematodes mediate positive interactions between legume plants and rhizobium bacteria, Planta, 222, 848, 10.1007/s00425-005-0025-y

Houlden, 2008, Influence of plant developmental stage on microbial community structure and activity in the rhizosphere of three field crops, FEMS Microbiol Ecol, 65, 193, 10.1111/j.1574-6941.2008.00535.x

Inceoglu, 2011, Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing, PLoS One, 6, e23321, 10.1371/journal.pone.0023321

Ivanova, 2001, Aerobic methylobacteria are capable of synthesizing auxins, Mikrobiologiia, 70, 452

Jaeger, 1999, Mapping of sugar and amino acid availability in soil around roots with bacterial sensors of sucrose and tryptophan, Appl Environ Microbiol, 65, 2685, 10.1128/AEM.65.6.2685-2690.1999

Jain, 2002, Plant flavonoids: signals to legume nodulation and soil microorganisms, J Plant Biochem Biot, 11, 1, 10.1007/BF03263127

Junier, 2009, Composition of diazotrophic bacterial assemblages in bean-planted soil compared to unplanted soil, Eur J Soil Biol, 45, 153, 10.1016/j.ejsobi.2008.10.002

Kanehisa, 2004, The KEGG resource for deciphering the genome, Nucleic Acids Res, 32, D277, 10.1093/nar/gkh063

Kanehisa, 2008, KEGG for linking genomes to life and the environment, Nucleic Acids Res, 36, D480, 10.1093/nar/gkm882

Kelly, 1995, Genetic variability in nitrogen utilization at four growth stages in soft red winter wheat, J Plant Nutr, 18, 969, 10.1080/01904169509364954

Kent, 2002, BLAT—the BLAST-like alignment tool, Genome Res, 12, 656

Kus, 2002, Age-related resistance in Arabidopsis is a developmentally regulated defense response to Pseudomonas syringae, Plant Cell, 14, 479, 10.1105/tpc.010481

Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, 10, R25, 10.1186/gb-2009-10-3-r25

Lau, 2011, Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits, New Phytologist, 192, 215, 10.1111/j.1469-8137.2011.03790.x

Lee, 2008, Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil, FEMS Microbiol Lett, 285, 263, 10.1111/j.1574-6968.2008.01232.x

Li, 2010, The ARABIDOPSIS accession Pna-10 is a naturally occurring sng1 deletion mutant, Mol Plant, 3, 91, 10.1093/mp/ssp090

Lidstrom, 2002, Plants in the pink: cytokinin production by methylobacterium, J Bacteriol, 184, 1818, 10.1128/JB.184.7.1818.2002

Lin, 2012, Thaxtomin A-deficient endophytic Streptomyces sp. enhances plant disease resistance to pathogenic Streptomyces scabies, Planta, 236, 1849, 10.1007/s00425-012-1741-8

Lundberg, 2012, Defining the core Arabidopsis thaliana root microbiome, Nature, 488, 86, 10.1038/nature11237

Lynch, 1990, The Rhizosphere, p458

Majumdar, 1962, Myo-inositol in the biosynthesis of streptomycin by Streptomyces griseus, Science, 135, 734, 10.1126/science.135.3505.734

Malagoli, 2004, Modeling nitrogen uptake in oilseed rape cv Capitol during a growth cycle using influx kinetics of root nitrate transport systems and field experimental data, Plant Physiol, 134, 388, 10.1104/pp.103.029538

Meier, 2013, Fungal communities influence root exudation rates in pine seedlings, FEMS Microbiol Ecol, 83, 585, 10.1111/1574-6941.12016

Mendes, 2011, Deciphering the rhizosphere microbiome for disease-suppressive bacteria, Science, 332, 1097, 10.1126/science.1203980

Meyer, 2008, The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes, Bmc Bioinformatics, 9, 386, 10.1186/1471-2105-9-386

Micallef, 2009, Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere, Plant Signal Behav, 4, 777, 10.4161/psb.4.8.9229

Micallef, 2009, Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates, J Exp Bot, 60, 1729, 10.1093/jxb/erp053

Millet, 2010, Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns, Plant Cell, 22, 973, 10.1105/tpc.109.069658

Morgan, 2005, Biological costs and benefits to plant-microbe interactions in the rhizosphere, J Exp Bot, 56, 1729, 10.1093/jxb/eri205

Mougel, 2006, Dynamic of the genetic structure of bacterial and fungal communities at different developmental stages of Medicago truncatula Gaertn. cv. Jemalong line J5, New Phytol, 170, 165, 10.1111/j.1469-8137.2006.01650.x

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

Nazoa, 2003, Regulation of the nitrate transporter gene AtNRT2.1 in Arabidopsis thaliana: responses to nitrate, amino acids and developmental stage, Plant Mol Biol, 52, 689, 10.1023/A:1024899808018

Neal, 2012, Benzoxazinoids in root exudates of maize attract pseudomonas putida to the rhizosphere, PLoS One, 7, e35498, 10.1371/journal.pone.0035498

Nicoli, 2012, Resistance of advanced common bean lines to Fusarium root rot, Trop plant pathol, 37, 393, 10.1590/S1982-56762012000600003

Novoa, 1981, Nitrogen and plant production, Plant and Soil, 58, 177, 10.1007/BF02180053

Poretsky, 2009, Analyzing gene expression from marine microbial communities using environmental transcriptomics, J Vis Exp, 24, e1086

Pradella, 2002, Characterisation, genome size and genetic manipulation of the myxobacterium Sorangium cellulosum So ce56, Arch Microbiol, 178, 484, 10.1007/s00203-002-0479-2

Prasanna, 2009, Cyanobacterial diversity in the rhizosphere of rice and its ecological significance, Indian J Microbiol, 49, 89, 10.1007/s12088-009-0009-x

Rogers, 1996, Mode of action of the Arabidopsis thaliana phytoalexin camalexin and its role in Arabidopsis-pathogen interactions, Mol Plant Microbe In, 9, 748, 10.1094/MPMI-9-0748

Rossato, 2001, Nitrogen storage and remobilization in Brassica napus L. during the growth cycle: nitrogen fluxes within the plant and changes in soluble protein patterns, J Exp Bot, 52, 1655, 10.1093/jexbot/52.361.1655

Rusterucci, 2005, Age-related resistance to Pseudomonas syringae pv. tomato is associated with the transition to flowering in Arabidopsis and is effective against Peronospora parasitica, Physiol Mol Plant P, 66, 222, 10.1016/j.pmpp.2005.08.004

Schloss, 2009, Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities, Appl Environ Microbiol, 75, 7537, 10.1128/AEM.01541-09

Selvakumar, 2012, Bacteria in Agrobiology: Stress Management, 205, 10.1007/978-3-642-23465-1_10

Shade, 2013, A meta-analysis of changes in bacterial and archaeal communities with time, Isme J, 7, 1493, 10.1038/ismej.2013.54

Shaw, 1991, Swimming against the tide: Chemotaxis in Agrobacterium, BioEssays, 13, 25, 10.1002/bies.950130105

Shi, 2011, Effects of selected root exudate components on soil bacterial communities, FEMS Microbiol Ecol, 77, 600, 10.1111/j.1574-6941.2011.01150.x

Stacey, 1995, Signal exchange in the Bradyrhizobium-soybean symbiosis, Soil Biol and Biochem, 27, 473, 10.1016/0038-0717(95)98622-U

Sy, 2001, Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes, J Bacteriol, 183, 214, 10.1128/JB.183.1.214-220.2001

Tokala, 2002, Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum), Appl Environ Microbiol, 68, 2161, 10.1128/AEM.68.5.2161-2171.2002

Turner, 2013, Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants, Isme J, 7, 2248, 10.1038/ismej.2013.119

Urich, 2008, Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome, PLoS One, 3, e2527, 10.1371/journal.pone.0002527

van der Heijden, 2008, The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems, Ecol Lett, 11, 296, 10.1111/j.1461-0248.2007.01139.x

Van Spanning, 2005, Nitrogen Fixation in Agriculture, Forestry, Ecology, and the Environment, 277, 10.1007/1-4020-3544-6_13

Wang, 2007, Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, App Environ Microb, 73, 5261, 10.1128/AEM.00062-07

Ward, 2009, Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils, Appl Environ Microbiol, 75, 2046, 10.1128/AEM.02294-08

Xiong, 2012, Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing, PLoS One, 7, e36009, 10.1371/journal.pone.0036009

Xu, 2009, Bacterial communities in soybean rhizosphere in response to soil type, soybean genotype, and their growth stage, Soil Biol Biochem, 41, 919, 10.1016/j.soilbio.2008.10.027

Yamada, 2011, iPath2.0: interactive pathway explorer, Nucleic Acids Res, 39, W412, 10.1093/nar/gkr313

Yousuf, 2012, Application of targeted metagenomics to explore abundance and diversity of CO(2)-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea, Gene, 506, 18, 10.1016/j.gene.2012.06.083

Zahran, 1999, Rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in an arid climate, Microbiol Mol Biol Rev, 63, 968, 10.1128/MMBR.63.4.968-989.1999

Zaki, 1998, Control of Cotton Seedling Damping-off in the Field by Burkholderia (Pseudomonas) cepacia, Plant Disease, 82, 291, 10.1094/PDIS.1998.82.3.291

Zamioudis, 2012, Modulation of host immunity by beneficial microbes, Mol Plant Microbe Interact, 25, 139, 10.1094/MPMI-06-11-0179

Zhang, 2009, Flavones and flavonols play distinct critical roles during nodulation of Medicago truncatula by Sinorhizobium meliloti, Plant J, 57, 171, 10.1111/j.1365-313X.2008.03676.x

Zhang, 2013, Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau, BMC Microbiol, 13, 72, 10.1186/1471-2180-13-72

Zolla, 2013, Soil microbiomes vary in their ability to confer drought tolerance to Arabidopsis, App Soil Ecol, 68, 1, 10.1016/j.apsoil.2013.03.007