Skip to main content
SpringerLink
Log in

Influence of Rosaceous Species and Driving Factors on Differentiation of Rhizospheric Bacteria in a Deciduous Broad-Leaved Forest

  • Published:
Current Microbiology Aims and scope Submit manuscript

Abstract

Understanding plant–microbe interactions could provide the basis for improved phytoremediation, microbial resource utilization, and secondary metabolite production. Rhizosphere bacterial communities are strongly influenced by abiotic factors such as soil nutrient availability and the composition of such communities exhibits differentiation under different host plants. In a deciduous broad-leaved forest in Anhui Province, eastern China, the rhizospheric bacteria of three different tree species of the Rosaceae family (Sorbus alnifolia, Cerasus serrulata, and Photinia beauverdiana) were studied, with the bacteria of the bulk soil as controls. Bacterial community composition was determined using the Illumina platform for high-throughput sequencing of 16S rRNA genes. The results showed that the bacterial community composition varied between rhizospheric and bulk soils, and dominant bacterial phyla as Proteobacteria, Actinobacteria, and Acidobacteria were found in both soils. Information on predicted functional genes and pathways revealed significant differences between rhizospheric and bulk soil bacteria. It provided ample evidence for the different metabolic characteristics of the rhizosphere bacterial communities of the three tree species. Electrical conductivity (22.72%), total phosphorus concentration (21.89%), and urease activity (22%) were the main drivers for changes in the composition of the rhizosphere bacterial communities from the three tree species.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

Data Availability

The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

Code Availability

Part of the mapping code for the current study are available from the corresponding author on reasonable request.

References

  1. Allison SD, Martiny JB (2008) Resistance, resilience, and redundancy in microbial communities. Proc Natl Acad Sci USA 105(Supplement 1):11512–11519. https://doi.org/10.1073/pnas.0801925105

    Article  PubMed  PubMed Central  Google Scholar 

  2. Zhang P, Cui Z, Guo M, Xi R (2020) Characteristics of the soil microbial community in the forestland of Camellia oleifera. PeerJ 8:e9117. https://doi.org/10.7717/peerj.9117

    Article  PubMed  PubMed Central  Google Scholar 

  3. Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J et al (2015) Successional trajectories of rhizosphere bacterial communities over consecutive seasons. mBio 6(4):e00746–e007515. https://doi.org/10.1128/mBio.00746-15

    Article  PubMed  PubMed Central  Google Scholar 

  4. Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17(8):478–486. https://doi.org/10.1016/j.tplants.2012.04.001

    Article  CAS  PubMed  Google Scholar 

  5. Andreote FD, Silva MCPE (2017) Microbial communities associated with plants: learning from nature to apply it in agriculture. Curr Opin Microbiol 37:29–34. https://doi.org/10.1016/j.mib.2017.03.011

    Article  PubMed  Google Scholar 

  6. Zhao S, Liu JJ, Banerjee S, Zhou N, Zhao ZY, Zhang K et al (2018) Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation. Sci Rep 8(1):4550. https://doi.org/10.1038/s41598-018-22788-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M et al (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77(17):5934–5944. https://doi.org/10.1128/AEM.05255-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Ali A, Imran Ghani M, Li Y, Ding H, Meng H, Cheng Z et al (2019) Hiseq base molecular characterization of soil microbial community, diversity structure, and predictive functional profiling in continuous cucumber planted soil affected by diverse cropping systems in an intensive greenhouse region of northern China. Int J Mol Sci 20(11):2619. https://doi.org/10.3390/ijms20112619

    Article  CAS  PubMed Central  Google Scholar 

  9. Truu M, Nõlvak H, Ostonen I, Oopkaup K, Maddison M, Ligi T et al (2020) Soil bacterial and archaeal communities and their potential to perform N-cycling processes in soils of boreal forests growing on well-drained peat. Front Microbiol 11:591358. https://doi.org/10.3389/fmicb.2020.591358

    Article  PubMed  PubMed Central  Google Scholar 

  10. Castro HF, Classen AT, Austin EE, Norby RJ, Schadt CW (2010) Soil microbial community responses to multiple experimental climate change drivers. Appl Environ Microbiol 76(4):999–1007. https://doi.org/10.1128/AEM.02874-09

    Article  CAS  PubMed  Google Scholar 

  11. Dignam BEA, O’Callaghan M, Condron LM, Kowalchuk GA, Van Nostrand JD, Zhou J et al (2018) Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression. PLoS ONE 13(5):e0196581. https://doi.org/10.1371/journal.pone.0196581

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Liang DD, Peng J, Gao G, Hong X, Zhou SB, Chu J et al (2020) Spatial distribution pattern and interspecific correlation analysis of main species of Rosaceae in a deciduous broad-leaved forest in Yaoluoping. Biodiv Sci 28(8):1008–1017

    Article  Google Scholar 

  13. Yuan MM, Guo X, Wu L, Zhang Y, Xiao N, Ning D et al (2021) Climate warming enhances microbial network complexity and stability. Nat Clim Change 11:343–348. https://doi.org/10.1038/s41558-021-00989-9

    Article  Google Scholar 

  14. Fall D, Bakhoum N, Nourou Sall S, Zoubeirou AM, Sylla SN, Diouf D et al (2016) Rhizobial inoculation increases soil microbial functioning and gum Arabic production of 13-year-old Senegalia senegal (L.) Britton, trees in the North Part of Senegal. Front Plant Sci 7:1355. https://doi.org/10.3389/fpls.2016.01355

    Article  PubMed  PubMed Central  Google Scholar 

  15. Han Q, Ma Q, Chen Y, Tian B, Xu L, Bai Y et al (2020) Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. ISME J 14(8):1915–1928. https://doi.org/10.1038/s41396-020-0648-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Bao SD (2000) Soil and agricultural chemistry analysis. Chinese Agriculture Press, Beijing

    Google Scholar 

  17. Akhtar K, Wang W, Ren G, Khan A, Feng Y, Yang G et al (2018) Changes in soil enzymes, soil properties, and maize crop productivity under wheat straw mulching in Guanzhong, China. Soil Tillage Res 182:94–102. https://doi.org/10.1016/j.still.2018.05.007

    Article  Google Scholar 

  18. Li Q, Zhou S, Liu N (2021) Diversity of endophytic bacteria in Cardamine hupingshanensis and potential of culturable selenium-resistant endophytes to enhance seed germination under selenate stress. Curr Microbiol 78(5):2091–2103. https://doi.org/10.1007/s00284-021-02444-6

    Article  CAS  PubMed  Google Scholar 

  19. Zhou Z, Wang C, Luo Y (2020) Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat Commun 11(1):3072. https://doi.org/10.1038/s41467-020-16881-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Rillig MC, Ryo M, Lehmann A, Aguilar-Trigueros CA, Buchert S, Wulf A et al (2019) The role of multiple global change factors in driving soil functions and microbial biodiversity. Science 366(6467):886–890. https://doi.org/10.1126/science.aay2832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G et al (2015) Structure and function of the global ocean microbiome. Science 348(6237):1261359. https://doi.org/10.1126/science.1261359

    Article  CAS  PubMed  Google Scholar 

  22. Karimi B, Terrat S, Dequiedt S, Saby NPA, Horrigue W, Lelièvre M et al (2018) Biogeography of soil bacteria and archaea across France. Sci Adv 4(7):eaat1808. https://doi.org/10.1126/sciadv.aat1808

    Article  PubMed  PubMed Central  Google Scholar 

  23. Griffiths RI, Thomson BC, Plassart P, Gweon HS, Stone D, Creamer RE et al (2016) Mapping and validating predictions of soil bacterial biodiversity using European and national scale datasets. Appl Soil Ecol 97:61–68. https://doi.org/10.1016/j.apsoil.2015.06.018

    Article  Google Scholar 

  24. Lan L, Yang F, Zhang L, Yang W, Wu F, Xu Z et al (2019) Non-target effects of naphthalene on the soil microbial biomass and bacterial communities in the subalpine forests of western China. Sci Rep 9(1):9811. https://doi.org/10.1038/s41598-019-46394-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Wagner MR, Lundberg DS, Del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T et al (2016) Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun 7(1):12151. https://doi.org/10.1038/ncomms12151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Nevins CJ, Nakatsu C, Armstrong S (2018) Characterization of microbial community response to cover crop residue decomposition. Soil Biol Biochem 127:39–49. https://doi.org/10.1016/j.soilbio.2018.09.015

    Article  CAS  Google Scholar 

  27. Nardi S, Concheri G, Pizzeghello D, Sturaro A, Rella R, Parvoli G et al (2000) Soil organic matter mobilization by root exudates. Chemosphere 41(5):653–658. https://doi.org/10.1016/s0045-6535(99)00488-9

    Article  CAS  PubMed  Google Scholar 

  28. Yuan CL, Zhang LM, Wang JT, Hu HW, Shen JP, Cao P et al (2019) Distributions and environmental drivers of archaea and bacteria in paddy soils. J Soils Sediments 19:23–37. https://doi.org/10.1007/s11368-018-1997-0

    Article  CAS  Google Scholar 

  29. Zhan Y, Liu W, Bao Y, Zhang J, Petropoulos E, Li Z et al (2018) Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation. Sci Rep 8(1):7981. https://doi.org/10.1038/s41598-018-26375-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Hassani MA, Durán P, Hacquard S (2018) Microbial interactions within the plant holobiont. Microbiome 6:58. https://doi.org/10.1186/s40168-018-0445-0

    Article  PubMed  PubMed Central  Google Scholar 

  31. Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA et al (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31(9):814–821. https://doi.org/10.1038/nbt.2676

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Li X, Rui J, Xiong J, Li J, He Z (2014) Functional potential of soil microbial communities in the maize rhizosphere. PLoS ONE 9(11):e112609. https://doi.org/10.1371/journal.pone.0112609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Ashworth AJ, DeBruyn JM, Allen FL, Radosevich M, Owens PR (2017) Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage. Soil Biol Biochem 114:210–219. https://doi.org/10.1016/j.soilbio.2017.07.019

    Article  CAS  Google Scholar 

  34. Kielak AM, Barreto CC, Kowalchuk GA, van Veen JA, Kuramae EE (2016) The ecology of Acidobacteria: moving beyond genes and genomes. Front Microbiol 7:744. https://doi.org/10.3389/fmicb.2016.00744

    Article  PubMed  PubMed Central  Google Scholar 

  35. Cremer J, Honda T, Tang Y, Wong-Ng J, Vergassola M, Hwa T et al (2019) Chemotaxis as a navigation strategy to boost range expansion. Nature 575:658–663. https://doi.org/10.1038/s41586-019-1733-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Stine ZE, Schug ZT, Salvino JM, Dang CV (2022) Targeting cancer metabolism in the era of precision oncology. Nat Rev Drug Discov 21(2):141–162. https://doi.org/10.1038/s41573-021-00339-6

    Article  CAS  PubMed  Google Scholar 

  37. Sharma SB, Sayyed RZ, Trivedi MH, Gobi TA (2013) Phosphate solubilizing microbes: sustainable approach for managing phosphorus deficiency in agricultural soils. Springerplus 2(1):587. https://doi.org/10.1186/2193-1801-2-587

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Buckley DH, Huangyutitham V, Hsu SF, Nelson TA (2007) Stable isotope probing with 15N2 reveals novel noncultivated diazotrophs in soil. Appl Environ Microbiol 73(10):3196–3204. https://doi.org/10.1128/aem.02610-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Wang W, Wang H, Feng Y, Wang L, Xiao X, Xi Y et al (2016) Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River. Sci Rep 6:35046. https://doi.org/10.1038/srep35046

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Wheatley RM, Ford BL, Li L, Aroney STN, Knights HE, Ledermann R et al (2020) Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis. Proc Natl Acad Sci U S A 117(38):23823–23834. https://doi.org/10.1073/pnas.2009094117

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Ren F, Dong W, Yan DH (2019) Organs, cultivars, soil, and fruit properties affect structure of endophytic mycobiota of pinggu peach trees. Microorganisms 7(9):322. https://doi.org/10.3390/microorganisms7090322

    Article  CAS  PubMed Central  Google Scholar 

  42. Tian W, Xiang X, Wang H (2021) Differential impacts of water table and temperature on bacterial communities in pore water from a subalpine peatland, central China. Front Microbiol 12:649981. https://doi.org/10.3389/fmicb.2021.649981

    Article  PubMed  PubMed Central  Google Scholar 

  43. Shen C, Xiong J, Zhang H, Feng Y, Lin X, Li X et al (2013) Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biol Biochem 57:204–211. https://doi.org/10.1016/j.soilbio.2012.07.013

    Article  CAS  Google Scholar 

  44. Wang L, Pang X, Li N, Qi K, Huang J, Yin C et al (2020) Effects of vegetation type, fine and coarse roots on soil microbial communities and enzyme activities in eastern Tibetan plateau. CATENA 194:104694. https://doi.org/10.1016/j.catena.2020.104694

    Article  CAS  Google Scholar 

  45. Jiao S, Du N, Zai X, Gao X, Chen W, Wei G et al (2019) Temporal dynamics of soil bacterial communities and multifunctionality are more sensitive to introduced plants than to microbial additions in a multicontaminated soil. Land Degrad Dev 30(7):852–865. https://doi.org/10.1002/ldr.3272

    Article  Google Scholar 

  46. Kim JM, Roh AS, Choi SC, Kim EJ, Choi MT, Ahn BK et al (2016) Soil pH and electrical conductivity are key edaphic factors shaping bacterial communities of greenhouse soils in Korea. J Microbiol 54(12):838–845. https://doi.org/10.1007/s12275-016-6526-5

    Article  CAS  PubMed  Google Scholar 

  47. Shi Y, Li Y, Xiang X, Sun R, Yang T, He D et al (2018) Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain. Microbiome 6(1):27. https://doi.org/10.1186/s40168-018-0409-4

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors gratefully acknowledge the Yaoluoping National Nature Reserve Management Committee for assisting in the sample collection. We thank International Science Editing (http://www.internationalscienceediting.com) for editing this manuscript.

Funding

This work was financially supported by the special fiscal fund for repairing and purchasing in national public institutions (831440): Anhui Yaoluoping National Nature Reserve large-scale fixed sample plot and animal fixed sample line repair.

Author information

Authors and Affiliations

  1. School of Ecology and Environment, Anhui Normal University, 189# South Jiuhua Road, Yijiang District, Wuhu, 241002, China

    Yukun Wang, Yuran He, Mao Ding & Shoubiao Zhou

  2. Anhui Provincial Engineering Laboratory of Water and Soil Pollution Control and Remediation, Anhui Normal University, Wuhu, 241002, China

    Shoubiao Zhou

  3. Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection of the People’s Republic of China, Nanjing, 210042, China

    Zhi Wang

Authors
  1. Yukun Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuran He
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mao Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhi Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shoubiao Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

SZ developed the idea of the study and participated in its design; YW contributed to the acquisition of data and drafted the manuscript; YH and MD provided critical review and substantially revised the manuscript; ZW contributed to the acquisition of funds.

Corresponding author

Correspondence to Shoubiao Zhou.

Ethics declarations

Conflict of interest

All authors read and approved the final manuscript. The authors declare that they have no conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 3647 kb)

Supplementary file2 (XLSX 40 kb)

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, Y., He, Y., Ding, M. et al. Influence of Rosaceous Species and Driving Factors on Differentiation of Rhizospheric Bacteria in a Deciduous Broad-Leaved Forest. Curr Microbiol 79, 368 (2022). https://doi.org/10.1007/s00284-022-03049-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00284-022-03049-3

Search

Navigation