Archaeal community succession with fine root growth in poplar plantation

doi:10.13287/j.1001-9332.201903.034

Abstract

Abstract: The archaeal community structure in the rhizosphere soils might change with root growth, which is of great importance for understanding the interaction between roots and microbes. According to root colors, three groups of rhizosphere soils from first-order fine roots of poplar trees (Populus × euramericana) were sampled, including rhizosphere soils surrounding newly born roots (white color, WR), mature roots (yellow color, YR) and aged roots (brown color, BR). Total microbial DNA was extracted from the soils associated with poplar fine roots. The specific primers were used to amplify the 16S rDNA V4-V5 region of soil archaea, and the Illumina MiSeq platform was used for high-throughput sequencing analysis. The results showed that the observed OTU (operational taxonomic unit) abundance of archaeal community in WR and BR rhizosphere soils were similar, while the OTU abundance in YR rhizosphere soil were lower. The WR and BR shared 134 OTUs of archea, the YR and BR shared 87 OTUs, and the WR and BR shared 90 OTUs. The Chao1 index and the ACE index of archaeal community in YR rhizosphere soil were significantly lower than those of WR and BR, while the Simpson index and the Shannon index of BR were significantly lower than WR to YR. Results from the PERMANOVA analysis showed that archaeal community compositions in WR and BR rhizosphere soils were significantly different. Species annotation showed that there were 12 genera of archea in three rhizosphere soils, five genera in WR, 10 genera in YR, and six genera in BR, respectively. The similarity of the archaeal community composition in poplar rhizosphere soils gradually decreased from WR to BR, with large differences among different growth stages of fine roots. The dominant genus was Candidatus_Nitrososphaera, with a relative abundance of more than 70%, indicating this archaea group might be closely related to poplar fine roots development.

Key words: rhizosphere soil, archaeal community, high-throughput sequencing, fine root growth, poplar plantation

ZHU Qi-liang, LIU Hong-kai, CHEN Xu, DONG Yu-feng, WANG Yan-ping. Archaeal community succession with fine root growth in poplar plantation[J]. Chinese Journal of Applied Ecology, 2019, 30(3): 849-856.

References

[1] DeLong EF. Archaea in coastal marine environments. Proceedings of the National Academy of Sciences of the United States of America, 1992, 89: 5685-5689
[2] Fuhrman JA, McCallum K, Davis AA. Novel major archaebacterial group from marine plankton. Nature, 1992, 356: 148-149
[3] Schleper C, Jurgens G, Jonuscheit M. Genomic studies of uncultivated archaea. Nature Reviews Microbiology, 2005, 3: 479-488
[4] Woese CR, Kandler O, Wheelis ML. Toward a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America, 1990, 87: 4576-4579
[5] Liu T-M (刘天明), Shen Y-L (申玉龙), Liu Q-J (刘庆军), et al. The unique Entner-Doudoroff (ED) glycolysis pathway of glucose in Archaea: A review. Acta Microbiologica Sinica (微生物学报), 2008, 48(8): 1126-1131 (in Chinese)
[6] Valentine DL, Reeburgh WS. New perspectives on anaerobic methane oxidation. Environmental Microbiology, 2010, 2: 477-484
[7] He J-Z (贺纪正), Zhang L-M (张丽梅). Advances in ammonia-oxidizing microorganisms and global nitrogen cycle. Acta Ecologica Sinica (生态学报), 2009, 29(1): 406-415 (in Chinese)
[8] Li S-G (李曙光), Pi Y-D (皮昀丹), Zhang Chuan-lun. The study of archaea: A review and perspectives. Journal of University of Science and Technology of China (中国科学技术大学学报), 2007, 37(8): 830-838 (in Chinese)
[9] Norby RJ, Jackson RB. Root dynamics and global change: Seeking an ecosystem perspective. New Phytolo-gist, 2000, 147: 3-12
[10] Block RMA, Van Rees KCJ, Knight JD. A review of fine root dynamics in Populus plantations. Agroforestry Systems, 2006, 67: 73-84
[11] Hendricks JJ, Aber JD, Nadelhoffer KJ, et al. Nitrogen controls on fine root substrate quality in temperate forest ecosystems. Ecosystems, 2000, 3: 57-69
[12] Hartmann A, Schmid M, Tuinen DV, et al. Plant-driven selection of microbes. Plant and Soil, 2009, 321: 235-257
[13] Jones DL, Hodge A, Kuzyakov Y. Plant and mycorrhizal regulation of rhizodeposition. New Phytologist, 2010, 163: 459-480
[14] Eisenhauer N, Scheu S, Jousset A. Bacterial diversity stabilizes community productivity. PLoS One, 2012, 7(3): e34517
[15] Stéphane U, Marc B, Claude M, et al. Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environmental Microbio-logy Report, 2010, 2: 281-288
[16] Li XZ, Rui JP, Mao YJ, et al. Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar. Soil Biology and Biochemistry, 2014, 68: 392-401
[17] Wang Q-T (汪其同), Gao M-Y (高明宇), Liu M-L (刘梦玲), et al. Illumina Miseq sequencing-based fungal community of rhizosphere soils along root orders of poplar plantation. Chinese Journal of Applied Ecology (应用生态学报), 2017, 28(4): 1177-1183 (in Chinese)
[18] Eissenstat DM, Wells CE, Yanai RD, et al. Building roots in a changing environment: Implications for root longevity. New Phytologist, 2000, 147: 33-42
[19] Mei L (梅莉), Wang Z-Q (王政权), Cheng Y-H (程云环), et al. A review: Factors influencing fine root longevity in forest ecosystems. Acta Phytoecologica Sinica (植物生态学报), 2004, 28(4): 704-710 (in Chinese)
[20] Zhu W-R (朱婉芮), Wang Q-T (汪其同), Liu M-L (刘梦玲), et al. The difference in fine root lifespan between successive rotations of poplar plantation and the dominant causal factors. Acta Ecologica Sinica (生态学报), 2018, 38(1): 226-235 (in Chinese)
[21] Magocˇ T, Salzberg SL. FLASH: Fast length adjustment of short reads to improve genome assemblies. Bioinforma-tics, 2011, 27: 2957-2963
[22] Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 2010, 7: 335-336
[23] Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 2010, 26: 2460, doi: 10.1093/bioinformatics/btq461
[24] Desantis TZ, Hugenholtz P, Larsen N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 2006, 72: 5069-5072
[25] Bokulich NA, Subramanian S, Faith JJ, et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods, 2013, 10: 57-59
[26] Chao A. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 1984, 11: 265-270
[27] Dawid AP. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika, 1993, 80: 193-201
[28] Shannon CE. Mathematical theory of communication. Bell System Technical Journal, 1948, 27: 379-423
[29] Simpson EH. Measurement of diversity. Nature, 1949, 163: 688
[30] Bai Y-F (白永飞), Xu Z-X (许志信). β-diverslty of Stipa communities in Inner Mongolia Platean. Chinese Journal of Applied Ecology (应用生态学报), 2000, 8(3): 408-412 (in Chinese)
[31] Huang Y-M (黄玉梅), Zhang J (张健), Yang W-Q (杨万勤). Ecological distribution patterns of soil microbes under artificial Eucalyptus grandis stand. Chinese Journal of Applied Ecology (应用生态学报), 2006, 17(12): 2327-2331 (in Chinese)
[32] Nicol GW, Tscherko D, Embley TM, et al. Primary succession of soil Crenarchaeota across a receding glacier foreland. Environmental Microbiology, 2005, 7: 337-347
[33] Nicol GW, Glover LA, Prosser JI. Spatial analysis of archaeal community structure in grassland soil. Applied and Environmental Microbiology, 2003, 69: 7420-7429
[34] Francis CA, Roberts KJ, Beman JM, et al. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102: 14683-14688
[35] Leininger S, Urich T, Schloter M, et al. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature, 2006, 442: 806-809
[36] Liu J-J (刘晶静), Wu W-X (吴伟祥), Ding Y (丁颖), et al. Ammonia-oxidizing archaea and their important roles in nitrogen biogeochemical cycling: A review. Chinese Journal of Applied Ecology (应用生态学报), 2010, 21(8): 2154-2160 (in Chinese)
[37] Boer WD, Gunnewiek PJAK, Veenhuis M, et al. Nitrification at low pH by aggregated chemolithotrophic bacteria. Applied and Environmental Microbiology, 1991, 57: 3600-3604
[38] He J-Z (贺纪正), Shen J-P (沈菊培), Zhang L-M (张丽梅). Advance in the research of soil non-thermophiilic Crenarchaeota. Acta Eclogica Sinica (生态学报), 2009, 29(9): 5047-5055 (in Chinese)
[39] Hajek P, Hertel D, Leuschner C. Root order- and root age-dependent response of two poplar species to belowground competition. Plant and Soil, 2014, 377: 337-355
[40] Bagniewska-Zadworna A, Stelmasik A, Minicka J. From birth to death: Populus trichocarpa fibrous roots functional anatomy. Biologia Plantarum, 2014, 58: 551-560
[41] Kuzyakov Y. Priming effects: Interactions between living and dead organic matter. Soil Biology and Biochemistry, 2010, 42: 1363-1371
[42] Craine JM, Morrow C, Fierer N. Microbial nitrogen limi-tation increases decomposition. Ecology, 2007, 88: 2105-2113
[43] Fontaine S, Henault C, Aamor A, et al. Fungi mediate long term sequestration of carbon and nitrogen in soil through their priming effect. Soil Biology and Biochemi-stry, 2011, 43: 86-96
[44] Nannipieri P, Ascher J, Ceccherini MT, et al. Microbial diversity and soil functions. European Journal of Soil Science, 2010, 54: 655-670
[45] Sun Y (孙悦), Xu X-L (徐兴良), Yakov KUZYAKOV. Mechanisms of rhizosphere priming effects and their ecological significance. Chinese Journal of Plant Ecology (植物生态学报), 2014, 38(1): 62-75 (in Chinese)
[46] Eissenstat DM, Yanai RD. The ecology of root lifespan. Advances in Ecological Research, 1997, 27: 1-60
[47] Zhu W-R (朱婉芮). Difference of Poplar Fine Roots Longevity Between Successive Rotation Plantations and Its Regulation Mechanism. Master Thesis. Tai’an, Shandong: Shandong Agricultural University, 2016 (in Chinese)
[48] Hense BA, Kuttler C, Mueller J, et al. Opinion: Does efficiency sensing unify diffusion and quorum sensing? Nature Reviews Microbiology, 2007, 5: 230-239
[49] Von Bodman SB, Bauer WD, Coplin DL. Quorum sen-sing in plant-pathogenic bacteria. Annual Review of Phytopathology, 2003, 41: 455-482
[50] Guo X-P (郭晓鹏), Zhang G-S (张桂山), Liu X-L (刘晓黎), et al. Detection of the quorum sensing signal in methanogenic archaea. Acta Microbiologica Sinica (微生物学报), 2011, 51(9): 1200-1204 (in Chinese)
[51] Tateda K, Ishii Y, Horikawa M, et al. The Pseudomonas aeruginosa autoinducer N-3-oxododecanoyl homoserine lactone accelerates apoptosis in macrophages and neutrophils. Infection and Immunity, 2003, 71: 5785-5793
[52] Mathesius U, Mulders S, Gao M, et al. Extensive and specific responses of a eukaryote to bacterial quorum-sensing signals. Proceedings of the National Academy of Sciences of the United States of America, 2003, 100: 1444-1449
[53] Díaz-Tielas C, Graña E, Sotelo T, et al. The natural compound trans-chalcone induces programmed cell death in Arabidopsis thaliana roots. Plant, Cell and Envi-ronment, 2012, 35: 1500-1517
[54] Francis CA, Roberts KJ, Beman JM, et al. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102: 14683-14688