Login Register Cart 0
Generic placeholder image

Current Bioinformatics

Editor-in-Chief

ISSN (Print): 1574-8936
ISSN (Online): 2212-392X

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

Bioinformatics Analysis of The Rhizosphere Microbiota of Dangshan Su Pear in Different Soil Types

Author(s): Xiaojing Ma, Sambhaji Balaso Thakar, Huimin Zhang, Zequan Yu, Li Meng and Junyang Yue*

Volume 15, Issue 5, 2020

Page: [503 - 514] Pages: 12

DOI: 10.2174/1574893615666200129104523

Price: $65

Abstract

Background: The rhizosphere microbiota are of vital importance for plant growth and health in terrestrial ecosystems. There have been extensive studies aiming to identify the microbial communities as well as their relationship with host plants in different soil types.

Objective: In the present study, we have employed the high-throughput sequencing technology to investigate the composition and structure of rhizosphere microbiota prosperous at the root of Dangshan Su pear growing in sandy soil and clay soil.

Methods: A high-throughput amplicon sequencing survey of the bacterial 16S rRNA genes and fungal ITS regions from rhizosphere microbiota was firstly performed. Subsequently, several common bacterial and fungal communities were found to be essential to Dangshan Su pear by using a series of bioinformatics and statistics tools. Finally, the soil-preferred microbiota were identified through variance analysis and further characterized in the genus level.

Result: Dangshan Su pears host rich and diverse microbial communities in thin layer of soil adhering to their roots. The composition of dominant microbial phyla is similar across different soil types, but the quantity of each microbial community varies significantly. Specially, the relative abundance of Firmicutes increases from 9.69% to 61.66% as the soil ecosystem changes from clay to sandy, which can be not only conducive to the degradation of complex plant materials, but also responsible for the disinfestation of pathogens.

Conclusion: Our results have a symbolic significance for the potential efforts of rhizosphere microbiota on the soil bioavailability and plant health. Through selecting soil types and altering microbial structures, the improvement of fruit quality of Dangshan Su pear is expected to be achieved.

Keywords: Pyrus bretschneideri, dangshan Su pear, soil microbiota, high-throughput sequencing, 16s rRNA, ITS.

« Previous
Graphical Abstract

[1]
Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 2013; 11(11): 789-99.
[http://dx.doi.org/10.1038/nrmicro3109] [PMID: 24056930]
[2]
Bakker PA, Berendsen RL, Doornbos RF, Wintermans PC, Pieterse CM. The rhizosphere revisited: root microbiomics. Front Plant Sci 2013; 4: 165.
[http://dx.doi.org/10.3389/fpls.2013.00165] [PMID: 23755059]
[3]
Mercado-Blanco J, Abrantes I, Barra Caracciolo A, et al. Belowground microbiota and the health of tree crops. Front Microbiol 2018; 9: 1006.
[http://dx.doi.org/10.3389/fmicb.2018.01006] [PMID: 29922245]
[4]
Uroz S, Oger P, Tisserand E, et al. Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Sci Rep 2016; 6: 27756.
[http://dx.doi.org/10.1038/srep27756] [PMID: 27302652]
[5]
Qiao Q, Wang F, Zhang J, et al. The variation in the rhizosphere microbiome of cotton with soil type, genotype and developmental stage. Sci Rep 2017; 7(1): 3940.
[http://dx.doi.org/10.1038/s41598-017-04213-7] [PMID: 28638057]
[6]
Wang P, Marsh EL, Ainsworth EA, Leakey ADB, Sheflin AM, Schachtman DP. Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3. Sci Rep 2017; 7(1): 15019.
[http://dx.doi.org/10.1038/s41598-017-14936-2] [PMID: 29101364]
[7]
Baetz U, Martinoia E. Root exudates: the hidden part of plant defense. Trends Plant Sci 2014; 19(2): 90-8.
[http://dx.doi.org/10.1016/j.tplants.2013.11.006] [PMID: 24332225]
[8]
Helliwell JR, Sturrock CJ, Mairhofer S, et al. The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface. Sci Rep 2017; 7(1): 14875.
[http://dx.doi.org/10.1038/s41598-017-14904-w] [PMID: 29093533]
[9]
Jacoby R, Peukert M, Succurro A, Koprivova A, Kopriva S. The role of soil microorganisms in plant mineral nutrition-current knowledge and future directions. Front Plant Sci 2017; 8: 1617.
[http://dx.doi.org/10.3389/fpls.2017.01617] [PMID: 28974956]
[10]
Coats VC, Rumpho ME. The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants. Front Microbiol 2014; 5: 368.
[http://dx.doi.org/10.3389/fmicb.2014.00368] [PMID: 25101069]
[11]
Hu L, Robert CAM, Cadot S, et al. Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota. Nat Commun 2018; 9(1): 2738.
[http://dx.doi.org/10.1038/s41467-018-05122-7] [PMID: 30013066]
[12]
Xu YL. Dangshansuli 1st ed 2009.
[13]
Cai YP, Li GQ, Nie JQ, et al. Study of the structure and biosynthetic pathway of lignin in stone cells of pear. Sci Hortic (Amsterdam) 2010; 125: 374-9.
[http://dx.doi.org/10.1016/j.scienta.2010.04.029]
[14]
Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK. FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 2012; 30(5): 460-5.
[http://dx.doi.org/10.1038/nbt.2170] [PMID: 22484455]
[15]
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 2016. 4e2584
[http://dx.doi.org/10.7717/peerj.2584] [PMID: 27781170]
[16]
Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010; 7(5): 335-6.
[http://dx.doi.org/10.1038/nmeth.f.303] [PMID: 20383131]
[17]
DeSantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72(7): 5069-72.
[http://dx.doi.org/10.1128/AEM.03006-05] [PMID: 16820507]
[18]
Abarenkov K, Henrik Nilsson R, Larsson K-H, et al. The UNITE database for molecular identification of fungi--recent updates and future perspectives. New Phytol 2010; 186(2): 281-5.
[http://dx.doi.org/10.1111/j.1469-8137.2009.03160.x] [PMID: 20409185]
[19]
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013; 10(10): 996-8.
[http://dx.doi.org/10.1038/nmeth.2604] [PMID: 23955772]
[20]
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007; 73(16): 5261-7.
[http://dx.doi.org/10.1128/AEM.00062-07] [PMID: 17586664]
[21]
Zhang XF, Zhao L, Xu SJ Jr, Liu YZ, Liu HY, Cheng GD. Soil moisture effect on bacterial and fungal community in Beilu River (Tibetan Plateau) permafrost soils with different vegetation types. J Appl Microbiol 2013; 114(4): 1054-65.
[http://dx.doi.org/10.1111/jam.12106] [PMID: 23241008]
[22]
Zhang X, Xu S, Li C, et al. The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau. Res Microbiol 2014; 165(2): 128-39.
[http://dx.doi.org/10.1016/j.resmic.2014.01.002] [PMID: 24463013]
[23]
Lauber CL, Hamady M, Knight R, Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 2009; 75(15): 5111-20.
[http://dx.doi.org/10.1128/AEM.00335-09] [PMID: 19502440]
[24]
Chu H, Fierer N, Lauber CL, Caporaso JG, Knight R, Grogan P. Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes. Environ Microbiol 2010; 12(11): 2998-3006.
[http://dx.doi.org/10.1111/j.1462-2920.2010.02277.x] [PMID: 20561020]
[25]
de Gannes V, Eudoxie G, Bekele I, Hickey WJ. Relations of microbiome characteristics to edaphic properties of tropical soils from Trinidad. Front Microbiol 2015; 6: 1045.
[http://dx.doi.org/10.3389/fmicb.2015.01045] [PMID: 26483772]
[26]
Qin S, Yeboah S, Xu X, Liu Y, Yu B. Analysis on fungal diversity in rhizosphere soil of continuous cropping potato subjected to different furrow-ridge mulching managements. Front Microbiol 2017; 8: 845.
[http://dx.doi.org/10.3389/fmicb.2017.00845] [PMID: 28539923]
[27]
Trivedi P, Delgado-Baquerizo M, Anderson IC, Singh BK. Response of soil properties and microbial communities to agriculture: implications for primary productivity and soil health indicators. Front Plant Sci 2016; 7: 990.
[http://dx.doi.org/10.3389/fpls.2016.00990] [PMID: 27462326]
[28]
Hou D, Huang Z, Zeng S, et al. Environmental factors shape water microbial community structure and function in shrimp cultural enclosure ecosystems. Front Microbiol 2017; 8: 2359.
[http://dx.doi.org/10.3389/fmicb.2017.02359] [PMID: 29238333]
[29]
Azmi SA, Chatterjee S. Population dynamics of soil bacteria in some areas of Midnapore coastal belt, West Bengal, India. 3 Biotech 2016; 6: 37.
[30]
Faoro H, Alves AC, Souza EM, et al. Influence of soil characteristics on the diversity of bacteria in the Southern Brazilian Atlantic Forest. Appl Environ Microbiol 2010; 76(14): 4744-9.
[http://dx.doi.org/10.1128/AEM.03025-09] [PMID: 20495051]
[31]
Finkel OM, Castrillo G, Herrera Paredes S, Salas González I, Dangl JL. Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol 2017; 38: 155-63.
[http://dx.doi.org/10.1016/j.pbi.2017.04.018] [PMID: 28622659]
[32]
Pérez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Mol Biol 2016; 90(6): 635-44.
[http://dx.doi.org/10.1007/s11103-015-0337-7] [PMID: 26085172]
[33]
Gopal M, Gupta A. Microbiome selection could spur next-generation plant breeding strategies. Front Microbiol 2016; 7: 1971.
[http://dx.doi.org/10.3389/fmicb.2016.01971] [PMID: 28003808]
[34]
Neumann G, Bott S, Ohler MA, et al. Root exudation and root development of lettuce (Lactuca sativa L. cv. Tizian) as affected by different soils. Front Microbiol 2014; 5: 2.
[http://dx.doi.org/10.3389/fmicb.2014.00002] [PMID: 24478764]
[35]
Schreiter S, Ding GC, Heuer H, et al. Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce. Front Microbiol 2014; 5: 144.
[http://dx.doi.org/10.3389/fmicb.2014.00144] [PMID: 24782839]
[36]
Panke-Buisse K, Lee S, Kao-Kniffin J. Cultivated sub-populations of soil microbiomes retain early flowering plant trait. Microb Ecol 2017; 73(2): 394-403.
[http://dx.doi.org/10.1007/s00248-016-0846-1] [PMID: 27655524]
[37]
Kazan K, Lyons R. The link between flowering time and stress tolerance. J Exp Bot 2016; 67(1): 47-60.
[http://dx.doi.org/10.1093/jxb/erv441] [PMID: 26428061]
[38]
Eichorst SA, Kuske CR, Schmidt TM. Influence of plant polymers on the distribution and cultivation of bacteria in the phylum Acidobacteria. Appl Environ Microbiol 2011; 77(2): 586-96.
[http://dx.doi.org/10.1128/AEM.01080-10] [PMID: 21097594]
[39]
Pankratov TA, Ivanova AO, Dedysh SN, Liesack W. Bacterial populations and environmental factors controlling cellulose degradation in an acidic Sphagnum peat. Environ Microbiol 2011; 13(7): 1800-14.
[http://dx.doi.org/10.1111/j.1462-2920.2011.02491.x] [PMID: 21564458]
[40]
Barka EA, Vatsa P, Sanchez L, et al. Taxonomy, physiology, and natural products of Actinobacteria. Microbiol Mol Biol Rev 2015; 80(1): 1-43.
[http://dx.doi.org/10.1128/MMBR.00019-15] [PMID: 26609051]
[41]
Kersters K, De Vos P, Gillis M, et al. Introduction to the Proteobacteria 2006; 5: 3-37.
[http://dx.doi.org/10.1007/0-387-30745-1_1]
[42]
Ma A, Zhuang X, Wu J, et al. Ascomycota members dominate fungal communities during straw residue decomposition in arable soil. PLoS One 2013; 8(6) e66146
[http://dx.doi.org/10.1371/journal.pone.0066146] [PMID: 23840414]
[43]
Wallenstein MD. Managing and manipulating the rhizosphere microbiome for plant health: a systems approach. Rhizosphere 2017; 3: 230-2.
[http://dx.doi.org/10.1016/j.rhisph.2017.04.004]
[44]
Yousuf B, Keshri J, Mishra A, Jha B. Application of targeted metagenomics to explore abundance and diversity of CO2-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea. Gene 2012; 506(1): 18-24.
[http://dx.doi.org/10.1016/j.gene.2012.06.083] [PMID: 22766402]
[45]
Zhang S, Liu X, Jiang Q, Shen G, Ding W. Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity. AMB Express 2017; 7(1): 178.
[http://dx.doi.org/10.1186/s13568-017-0475-1] [PMID: 28921475]
[46]
Sharmin F, Wakelin S, Huygens F, Hargreaves M. Firmicutes dominate the bacterial taxa within sugar-cane processing plants. Sci Rep 2013; 3: 3107.
[http://dx.doi.org/10.1038/srep03107] [PMID: 24177592]
[47]
Tolonen AC, Cerisy T, El-Sayyed H, Boutard M, Salanoubat M, Church GM. Fungal lysis by a soil bacterium fermenting cellulose. Environ Microbiol 2015; 17(8): 2618-27.
[http://dx.doi.org/10.1111/1462-2920.12495] [PMID: 24798076]
[48]
Kasap M, Chen JS. Clostridium pasteurianum W5 synthesizes two NifH-related polypeptides under nitrogen-fixing conditions. Microbiology 2005; 151(Pt 7): 2353-62.
[http://dx.doi.org/10.1099/mic.0.27931-0] [PMID: 16000725]
[49]
Kawasaki S, Watamura Y, Ono M, Watanabe T, Takeda K, Niimura Y. Adaptive responses to oxygen stress in obligatory anaerobes Clostridium acetobutylicum and Clostridium aminovalericum. Appl Environ Microbiol 2005; 71(12): 8442-50.
[http://dx.doi.org/10.1128/AEM.71.12.8442-8450.2005] [PMID: 16332833]
[50]
Schwarz WH. The cellulosome and cellulose degradation by anaerobic bacteria. Appl Microbiol Biotechnol 2001; 56(5-6): 634-49.
[http://dx.doi.org/10.1007/s002530100710] [PMID: 11601609]
[51]
Cereijo AE, Asencion Diez MD, Ballicora MA, Iglesias AA. Regulatory properties of the ADP-glucose pyrophosphorylase from the clostridial Firmicutes member Ruminococcus albus. J Bacteriol 2018; 200(17): 1.
[http://dx.doi.org/10.1128/JB.00172-18] [PMID: 29941423]
[52]
Biddle A, Stewart L, Blanchard J, et al. Untangling the genetic basis of fibrolytic specialization by Lachnospiraceae and Ruminococcaceae in diverse gut communities. Diversity (Basel) 2013; 5: 627-40.
[http://dx.doi.org/10.3390/d5030627]
[53]
Ueki A, Kaku N, Ueki K. Role of anaerobic bacteria in biological soil disinfestation for elimination of soil-borne plant pathogens in agriculture. Appl Microbiol Biotechnol 2018; 102(15): 6309-18.
[http://dx.doi.org/10.1007/s00253-018-9119-x] [PMID: 29858952]
[54]
Huang X, Liu L, Zhao J, et al. The families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae are the dominant bacterial groups during reductive soil disinfestation with incorporated plant residues. Appl Soil Ecol 2019; 135: 65-72.
[http://dx.doi.org/10.1016/j.apsoil.2018.11.011]

Rights & Permissions Print Cite
Article Metrics
22
© 2024 Bentham Science Publishers | Privacy Policy