Variation in soil fungal community structure during successive rotations of Casuarina equisetifolia plantations as determined by high-throughput sequencing analysis


Regeneration failure and productivity decline, which is collectively known as consecutive monoculture problem (CMP), were observed during long-term monoculture Casuarina equisetifolia plantations. In this study, the high-throughput sequencing method was applied to determine whether the rhizospheric microbial community composition would be significantly degenerated by consecutive monoculture in C. equisetifolia plantations. The results showed that the soil fungal community structure exhibited obvious differences among the first rotation plantation (FCP), the second rotation plantation (SCP), and the third rotation plantation (TCP). Both the Shannon and Simpson diversity indices of the soil fungal community in the FCP were significantly higher than in the SCP (P < 0.05). Additionally, the relative abundance of Fusarium, Thelephora, Hortaea and Penicillium were significantly higher in the SCP and TCP soils than in the FCP soils, suggesting that certain fungi gradually became predominant in the continuous monoculture plantation soils. Conversely, the relative abundance of Tolypocladium and Trichoderma were significantly lower in the SCP and TCP soils than in the FCP soils, suggesting that some microbes gradually decreased in the continuous monoculture plantation soils. Overall, the results demonstrated that the long-term pure plantation pattern exacerbated the microecological imbalance in rhizospheric soils of C. equisetifolia and markedly decreased soil microbial community diversity.

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Fig. 1
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Fig. 3



Consecutive monoculture problem


First rotation plantation


Second rotation plantation


Third rotation plantation


Total nitrogen


Alkaline nitrogen


Total phosphorus


Available phosphorus


Total potassium


Operational taxonomic unit


Available potassium


Abundance-based coverage estimator


Principal coordinate analysis


Unweighted pair-group method with arithmetic means


Operational taxonomic units


  1. Bashir K, Ishimaru Y, Nishizawa NK (2012) Molecular mechanisms of zinc uptake and translocation in rice. Plant Soil 361:189–201.

    Article  CAS  Google Scholar 

  2. Bennett AJ, Bending GD, Chandler D, Hilton S, Mills P (2012) Meeting the demand for crop production: the challenge of yield decline in crops grown in short rotations. Biol Rev Camb Philos Soc 87:52–71.

    Article  PubMed  Google Scholar 

  3. Berendsen RL, Pieterse CMJ, Bakker PAHM (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486.

    Article  CAS  Google Scholar 

  4. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Chen J, Arafat Y, Wu LK, Xiao ZG, Li QS, Khan MA, Khan MU, Lin S, Lin WX (2018) Shifts in soil microbial community, soil enzymes and crop yield under peanut/maize intercropping with reduced nitrogen levels. Appl Soil Ecol 124:327–334.

    Article  Google Scholar 

  6. Coyer JA, Hoarau G, Kuo J, Tronholm A, Veldsink J, Olsen JL (2013) Phylogeny and temporal divergence of the seagrass family Zosteraceae using one nuclear and three chloroplast loci. Syst Biodivers 11:271–284.

    Article  Google Scholar 

  7. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996.

    Article  CAS  Google Scholar 

  8. Haichar FZ, Marol C, Berge O, Rangel-Castro JI, Prosser JI, Balesdent J, Heulin T, Achouak W (2008) Plant host habitat and root exudates shape soil bacterial community structure. ISME J 2:1221–1230.

    Article  CAS  Google Scholar 

  9. Haney CH, Ausubel FM (2015) Plant microbiome blueprints. Science 349:788–789.

    Article  CAS  PubMed  Google Scholar 

  10. Harman DG, Blanksby SJ (2006) Trapping of a tert-adamantyl peroxyl radical in the gas phase. Chem Commun 8: 859-861.

    Article  CAS  Google Scholar 

  11. Hata K, Kawakami K, Kachi N (2015) Higher soil water availability after removal of a dominant, nonnative tree (Casuarina equisetifolia Forst.) from a subtropical forest. Pac Sci 9:445–460.

    Article  Google Scholar 

  12. Huang XF, Chaparro JM, Reardon KF, Zhang RF, Shen QR, Vivanco JM (2014) Rhizosphere interactions: root exudates, microbes, and microbial communities. Botany 92:267–275.

    Article  Google Scholar 

  13. Karthikeyan A (2016) Frankia strains for improving growth, biomass and nitrogen fixation in Casuarina equisetifolia seedlings. J Trop For Sci 28:235–242.

    Article  Google Scholar 

  14. Karthikeyan A, Chandrasekaran K, Geetha M, Kalaiselvi R (2013) Growth response of Casuarina equisetifolia Forst. rooted stem cuttings to Frankia in nursery and field conditions. J Biosci 38:741–747.

    Article  CAS  PubMed  Google Scholar 

  15. Kaur H, Garg N (2017) Recent perspectives on cross talk between cadmium, zinc, and arbuscular mycorrhizal fungi in plants. J Plant Growth Regul 8:1–14.

    CAS  Article  Google Scholar 

  16. Kelderer M, Manici LM, Caputo F, Thalheimer M (2012) Planting in the ‘inter-row’ to overcome replant disease in apple orchards: a study on the effectiveness of the practice based on microbial indicators. Plant Soil 57:381–393.

    Article  CAS  Google Scholar 

  17. Kõljalg U, Nilsson RH, Abarenkov K, Larsson KH (2013) Towards a unified paradigm for sequence-based identification of fungi. Mol Ecol 22:5271–5277.

    Article  CAS  PubMed  Google Scholar 

  18. Leelasuphakul W, Hemmanee P, Chuenchitt S (2008) Growth inhibitory properties of Bacillus subtilis, strains and their metabolites against the green mold pathogen (Penicillium digitatum, Sacc.) of citrus fruit. Postharvest Biol Tec 48:113–121.

    Article  CAS  Google Scholar 

  19. Li N, Zheng YQ, Ding HM, Li HP, Peng HZ, Jiang B, Li HB (2018) Development and validation of SSR markers based on transcriptome sequencing of Casuarina equisetifolia. Trees-Struct Funct 32: 41-49.

    Article  CAS  Google Scholar 

  20. Li XG, Ding CF, Hua K, Zhang TL, Zhang YN, Zhao L, Yang YR, Liu JG, Wang XX (2014a) Soil sickness of peanuts is attributable to modifications in soil microbes induced by peanut root exudates rather than to direct allelopathy. Soil Biol Biochem 78:149–159.

    Article  CAS  Google Scholar 

  21. Li XG, Ding CF, Zhang TL, Wang XX (2014b) Fungal pathogen accumulation at the expense of plant-beneficial fungi as a consequence of consecutive peanut monoculturing. Soil Biol Biochem 72:11–18.

    Article  CAS  Google Scholar 

  22. Liu XZ, Lu YC, Xie YS, Xue Y (2015) The positive interaction between two nonindigenous species, Casuarina (Casuarina equisetifolia) and Acacia (Acacia mangium), in the tropical coastal zone of south China: stand dynamics and soil nutrients. Trop Conserv Sci 8:598–609.

    Article  Google Scholar 

  23. Long F, Xie BB, Liang AJ, Li J (2018) Replant problem in Casuarina equisetifolia L.: isolation and identification of allelochemicals from its roots. Allelopathy J 43:73–82.

    Article  Google Scholar 

  24. Peiffer JA, Spor A, Koren O, Jin Z, Tringe SG, Dangl JL, Buckler ES, Ley RE (2013) Diversity and heritability of the maize rhizosphere microbiome under field conditions. Proc Natl Acad Sci USA 110:6548–6553.

    Article  PubMed  Google Scholar 

  25. Scotti-Campos P, Duro N, Costa MD, Pais IP, Rodrigues AP, Batista-Santos P, Semedo JN, Leitão AE, Lidon FC, Pawlowski K (2016) Antioxidative ability and membrane integrity in salt-induced responses of Casuarina glauca Sieber ex Spreng. in symbiosis with N2-fixing Frankia Thr or supplemented with mineral nitrogen. J Plant Physiol 196–197:60–69.

    Article  CAS  PubMed  Google Scholar 

  26. Shi SJ, Richardson AE, O’Callaghan M, DeAngelis KM, Jones EE, Stewart A, Firestone MK, Condron LM (2011) Effects of selected root exudate components on soil bacterial communities. FEMS Microbiol Ecol 77:600–610.

    Article  CAS  PubMed  Google Scholar 

  27. Sun J, Zhang Q, Zhou J, Wei QP (2014) Pyrosequencing technology reveals the impact of different manure doses on the bacterial community in apple rhizosphere soil. Appl Soil Ecol 78:28–36.

    Article  Google Scholar 

  28. Tanja M, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963.

    Article  CAS  Google Scholar 

  29. Thomas JC, Berger F, Jacquier M, Bernillon D, Baud-Grasset F, Truffaut N, Normand P, Vogel T M, Simonet P (1996) Isolation and characterization of a novel gamma-hexachlorocyclohexane-degrading bacterium. J Bacteriol 178: 6049-6055.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Van Wees SC, Van der Ent S, Pieterse CM (2008) Plant immune responses triggered by beneficial microbes. Curr Opin Plant Biol 11:443–448.

    Article  CAS  PubMed  Google Scholar 

  31. Veluthakkal R, Dasgupta MG (2012) Isolation and characterization of pathogen defence-related class I chitinase from the actinorhizal tree Casuarina equisetifolia. For Pathol 42:467–480.

    Article  Google Scholar 

  32. Vijayabhama M, Jaisankar R, Raj SV, Baranidharan K (2018) Spatial–temporal variation of casuarina spread in Cauvery delta and north eastern zone of Tamil Nadu, India: a spatial autoregressive model. J Appl Stat 45:1–7.

    Article  Google Scholar 

  33. Wardle DA, Bardgett RD, Klironomos JN, Setälä H, van der Putten WH, Wall DH (2004) Ecological linkages between aboveground and belowground biota. Science 304:1629–1633.

    Article  CAS  Google Scholar 

  34. Wu LK, Chen J, Wu HM, Qin XJ, Wang JY, Wu HM, Khan MU, Lin S, Xiao ZG, Luo XM (2016a) Insights into the regulation of rhizosphere bacterial communities by application of bio-organic fertilizer in Pseudostellaria heterophylla monoculture regime. Front Microbiol 7:1788.

    Article  PubMed  PubMed Central  Google Scholar 

  35. Wu LK, Chen J, Wu HM, Wang JY, Wu YH, Lin S, Khan MU, Zhang ZY, Lin WX (2016b) Effects of consecutive monoculture of Pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing. Sci Rep UK 6:26601.

    Article  CAS  Google Scholar 

  36. Xiong W, Zhao Q, Xue C, Xun W, Zhao J, Wu H, Li R, Shen Q (2016) Comparison of fungal community in black pepper-vanilla and vanilla monoculture systems associated with vanilla Fusarium wilt disease. Front Microbiol 7:117.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Zhang Y, Zhong CL, Han Q, Jiang QB, Chen Y, Chen Z, Pinyopusarerk K, Bush D (2016) Reproductive biology and breeding system in Casuarina equisetifolia (Casuarinaceae)—implication for genetic improvement. Aust J Bot 64:120–128.

    Article  Google Scholar 

  38. Zhao J, Wan SZ, Zhang CL, Liu ZF, Zhou LX, Fu SL (2013) Contributions of understory and/or overstory vegetations to soil microbial PLFA and nematode diversities in Eucalyptus monocultures. PLoS ONE 9:e85513.

    Article  CAS  Google Scholar 

  39. Zhao J, Mei Z, Zhang X, Xue C, Zhang CZ, Ma TF, Zhang SS (2017) Suppression of Fusarium wilt of cucumber by ammonia gas fumigation via reduction of Fusarium population in the field. Sci Rep-UK 7:43103.

    Article  CAS  Google Scholar 

  40. Zhong CL, Mansour S, Nambiar-Veetil M, Franche C (2013) Casuarina glauca: a model tree for basic research in actinorhizal symbiosis. J Biosci 38:815–823.

    Article  PubMed  Google Scholar 

  41. Zhou X, Yu G, Wu F (2012) Soil phenolics in a continuously mono-cropped cucumber (Cucumis sativus L.) system and their effects on cucumber seedling growth and soil microbial communities. Eur J Soil Sci 63:332–340.

    Article  CAS  Google Scholar 

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We thank LetPub ( for providing linguistic assistance during the preparation of this manuscript. This work was supported by the Chinese National Natural Science Foundation (Grant No. 31500443), Natural Science Foundation of Fujian Province, China (Grant No. 2018J01617), the Scientific Research Foundation of Fujian Agriculture and Forestry University (Grant No. XJQ201718), and the Fujian-Taiwan Joint Innovative Centre for Germplasm Resources and Cultivation of Crops (Grant No. 2015-75. FJ 2011 Program, China).

Author information




WZY and LWX conceived and directed the project. WZY, ZLT and LWX designed all experiments. LY, LJJ, WJY, CJ, LSY and BY did all of experiments. ZLT and LJJ performed the integrated data analysis. ZLT and WZY wrote the manuscript with the assistance and approval of all authors.

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Correspondence to Wu Zeyan.

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This study has been approved by the Hui’an National Forest Farm Management Committee, which takes care of the planning and protection of Hui’an National Forest Farm. The study did not involve any endangered or protected species. All of the data in this study can be published and shared.

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Liuting, Z., Jianjuan, L., Yang, L. et al. Variation in soil fungal community structure during successive rotations of Casuarina equisetifolia plantations as determined by high-throughput sequencing analysis. Plant Growth Regul 87, 445–453 (2019).

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  • Casuarina equisetifolia
  • High-throughput sequencing
  • Successive rotation
  • Microbial community composition