Skip to main content
SpringerLink
Log in

Effects of xeric shrubs on soil microbial communities in a desert in northern China

  • Regular Article
  • Published:
Plant and Soil Aims and scope Submit manuscript

Abstract

Aims

This study aimed at assessing whether patch type (i.e., under-shrub soil patch and inter-shrub soil patch) has an effect on soil microbes and how different shrub species altered the soil microbes through understanding soil microbial activity, biomass, and community structure.

Methods

We characterized the soil microbes in under-shrub and inter-shrub soil patches in three shrublands (Artemisia ordosica, Salix psammophila, and Caragana microphylla), respectively, in the Mu Us Desert, China, using microbial activity indicators, chloroform fumigation-extraction analysis, and high-throughput 16S rRNA gene sequencing.

Results

Members of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Planctomycetes, Bacteroidetes, Chloroflexi, Firmicutes, and Gemmatimonadetes were dominant. Inter-shrub soil patch differed from under-shrub soil patch in soil bacterial composition, microbial enzyme activity, and biomass, but not in diversity. Soil collected in A. ordosica shrubland exhibited the highest microbial enzyme activity, biomass, and diversity. Shrub species had significant effects on community structure, primarily the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes.

Conclusions

The results indicated that both shrub species and patch type had effects on soil microbial communities. In shrub-dominated desert ecosystems, spatial heterogeneity of soil nutrients and moisture might not be the main factors underlying variations in bacterial diversity. The different compositions of microbial communities in various shrublands provide a foundation for further research into the mechanisms of soil organic carbon accumulation.

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

References

  • Acosta-Martinez V, Dowd SE, Sun Y, Wester D, Allen V (2010) Pyrosequencing analysis for characterization of soil bacterial populations as affected by an integrated livestock-cotton production system. Appl Soil Ecol 45:13–25. doi:10.1016/j.apsoil.2010.01.005

    Article  Google Scholar 

  • Allison SD, Jastrow JD (2006) Activities of extracellular enzymes in physically isolated fractions of restored grassland soils. Soil Biol Biochem 38:3245–3256. doi:10.1016/j.soilbio.2006.04.011

    Article  CAS  Google Scholar 

  • Bachar A, Soares MIM, Gillor O (2012) The effect of resource islands on abundance and diversity of bacteria in arid soils. Microbial Ecol 63:694–700. doi:10.1007/s00248-011-9957-x

    Article  Google Scholar 

  • Bai YF, Wu JG, Xing Q, Pan QM, Huang JH, Yang DL, Han XG (2008) Primary production and rain use efficiency across a precipitation gradient on the Mongolia plateau. Ecology 89:2140–2153. doi:10.1890/07-0992.1

    Article  PubMed  Google Scholar 

  • Ben-David EA, Zaady E, Sher Y, Nejidat A (2011) Assessment of the spatial distribution of soil microbial communities in patchy arid and semi-arid landscapes of the Negev Desert using combined PLFA and DGGE analyses. FEMS Microbiol Ecol 76:492–503. doi:10.1111/j.1574-6941.2011.01075.x

    Article  CAS  PubMed  Google Scholar 

  • Brockett BFT, Prescott CE, Grayston SJ (2012) Soil moisture is the major factor influencing microbial community structure and enzyme activities across seven biogeoclimatic zones in western Canada. Soil Biol Biochem 44:9–20. doi:10.1016/j.soilbio.2011.09.003

    Article  CAS  Google Scholar 

  • Brookes PC, Landman A, Pruden G, Jenkinson DS (1985) Chloroform fumigation and the release of soil nitrogen: a rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biol Biochem 17:837–842. doi:10.1016/0038-0717(85)90144-0

    Article  CAS  Google Scholar 

  • Černohlávková J, Jarkovský J, Nešporová M, Hofman J (2009) Variability of soil microbial properties: effects of sampling, handling and storage. Ecotoxicol Environ Saf 72:2102–2108. doi:10.1016/j.ecoenv.2009.04.023

    Article  PubMed  Google Scholar 

  • Cheng M, Xue ZJ, Xiang Y, Darboux F, An SS (2015) Soil organic carbon sequestration in relation to revegetation on the Loess Plateau, China. Plant Soil 397:31–42. doi:10.1007/s11104-015-2486-5

    Article  CAS  Google Scholar 

  • Clark JS, Campbell JH, Grizzle H, Acosta-Martìnez V, Zak JC (2009) Soil microbial community response to drought and precipitation variability in the Chihuahuan Desert. Microbial Ecol 57:248–260. doi:10.1007/s00248-008-9475-7

    Article  Google Scholar 

  • Diedhiou-Sall S, Dossa EL, Diedhiou I, Badiane AN, Assigbetsé KB, Samba SAN, Khoumag M, Sèneh M, Dick RP (2013) Microbiology and macrofaunal activity in soil beneath shrub canopies during residue decomposition in agroecosystems of the Sahel. Soil Sci Soc Am J 77:501–511. doi:10.2136/sssaj2012.0284

    Article  CAS  Google Scholar 

  • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. doi:10.1093/bioinformatics/btq461

    Article  CAS  PubMed  Google Scholar 

  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194–2200. doi:10.1093/bioinformatics/btr381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eilers KG, Lauber CL, Knight R, Fierer N (2010) Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol Biochem 42:896–903. doi:10.1016/j.soilbio.2010.02.003

    Article  CAS  Google Scholar 

  • Eisenhauer N, Beßler H, Engels C, Gleixner G, Habekost M, Milcu A, Partsch S, Sabais ACW, Scherber C, Steinbeiss S, Weigelt A, Weisser WW, Scheu S (2010) Plant diversity effects on soil microorganisms support the singular hypothesis. Ecology 91:485–496. doi:10.1890/08-2338.1

    Article  CAS  PubMed  Google Scholar 

  • Evenari M, Shanan L, Tadmor N (1982) The Negev: the challenge of a desert. Harvard University Press, Cambridge

    Book  Google Scholar 

  • Ewing SA, Southard RJ, Macalady JL, Hartshorn AS, Johnson MJ (2007) Soil microbial fingerprints, carbon, and nitrogen in a Mojave Desert creosote-bush ecosystem. Soil Sci Soc Am J 71:469–475. doi:10.2136/sssaj2005.0283

    Article  CAS  Google Scholar 

  • Fierer N, Bradford MA, Jackson RB (2007) Toward an ecological classification of soil bacteria. Ecology 88:1354–1364. doi:10.1890/05-1839

    Article  PubMed  Google Scholar 

  • Fließbach A, Sarig S, Steinberger Y (1994) Effects of water pulses and climatic conditions on microbial biomass kinetics and microbial activity in a Yermosol of the central Negev. Arid Land Res Manag 8:353–362. doi:10.1080/15324989409381409

    Google Scholar 

  • Geisseler D, Horwath WR, Scow KM (2011) Soil moisture and plant residue addition interact in their effect on extracellular enzyme activity. Pedobiologia 54:71–78. doi:10.1016/j.pedobi.2010.10.001

    Article  Google Scholar 

  • Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800–1809. doi:10.1128/AEM.69.3.1800-1809.2003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goberna M, Pascual JA, Garcia C, Sánchez J (2007) Do plant clumps constitute microbial hotspots in semiarid Mediterranean patchy landscapes? Soil Biol Biochem 39:1047–1054. doi:10.1016/j.soilbio.2006.11.015

    Article  CAS  Google Scholar 

  • Guan SY, Zhang DS, Zhang ZM (1991) Methods of soil enzyme activities analysis. Agriculture Press, Beijing, pp 368–386

    Google Scholar 

  • Herzberger AJ, Meiners SJ, Towey JB, Butts PA, Armstrong DL (2015) Plant–microbe interactions change along a tallgrass prairie restoration chronosequence. Restor Ecol 23:220–227. doi:10.1111/rec.12165

    Article  Google Scholar 

  • Hortal S, Bastida F, Armas C, Lozano YM, Moreno JL, Garcia C, Pugnaire FI (2013) Soil microbial community under a nurse-plant species changes in composition, biomass and activity as the nurse grows. Soil Biol Biochem 64:139–146. doi:10.1016/j.soilbio.2013.04.018

    Article  CAS  Google Scholar 

  • Hortal S, Bastida F, Moreno JL, Armas C, García C, Pugnaire FI (2015) Benefactor and allelopathic shrub species have different effects on the soil microbial community along an environmental severity gradient. Soil Biol Biochem 88:48–57. doi:10.1016/j.soilbio.2015.05.009

    Article  CAS  Google Scholar 

  • Hu R, Wang XP, Zhang YF, Shi W, Jin YX, Chen N (2016) Insight into the influence of sand-stabilizing shrubs on soil enzyme activity in a temperate desert. Catena 137:526–535. doi:10.1016/j.catena.2015.10.022

    Article  CAS  Google Scholar 

  • Huang L, Zhang ZS (2015) Stable isotopic analysis on water utilization of two xerophytic shrubs in a revegetated desert area: Tengger Desert, China. Water 7:1030–1045. doi:10.3390/w7031030

    Article  Google Scholar 

  • Jia X, Zha TS, Wu B, Zhang YQ, Gong JN, Qing SG, Chen GP, Qian D, Kellomäki S, Peltola H (2014) Biophysical controls on net ecosystem CO2 exchange over a semiarid shrubland in northwest China. Biogeosciences 11:4679–4693. doi:10.5194/bg-11-4679-2014

    Article  CAS  Google Scholar 

  • Jiang YM, Chen CR, Xu ZH, Liu YQ (2012) Effects of single and mixed species forest ecosystems on diversity and function of soil microbial community in subtropical China. J Soil Sediment 12:228–240. doi:10.1007/s11368-011-0442-4

    Article  Google Scholar 

  • Kardol P, Wardle DA (2010) How understanding aboveground–belowground linkages can assist restoration ecology. Trends Ecol Evol 25:670–679. doi:10.1016/j.tree.2010.09.001

    Article  PubMed  Google Scholar 

  • Kersters K, De Vos P, Gillis M, Swings J, Vandamme P, Stackebrandt E (2006) Introduction to the Proteobacteria. In: Dwarkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) The prokaryotes, vol 5. Springer, New York, pp 3–37

    Chapter  Google Scholar 

  • Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microb 79:5112–5120. doi:10.1128/AEM.01043-13

  • Ladygina N, Hedlund K (2010) Plant species influence microbial diversity and carbon allocation in the rhizosphere. Soil Biol Biochem 42:162–168. doi:10.1016/j.soilbio.2009.10.009

    Article  CAS  Google Scholar 

  • Lai ZR, Zhang YQ, Liu JB, Wu B, Qin SG, Fa KY (2016) Fine-root distribution, production, decomposition, and effect on soil organic carbon of three revegetation shrub species in northwest China. Forest Ecol Manag 359:381–388. doi:10.1016/j.foreco.2015.04.025

    Article  Google Scholar 

  • Lamb EG, Kennedy N, Siciliano SD (2011) Effects of plant species richness and evenness on soil microbial community diversity and function. Plant Soil 338:483–495. doi:10.1007/s11104-010-0560-6

    Article  CAS  Google Scholar 

  • Lange M, Habekost M, Eisenhauer N, Roscher C, Bessler H, Engels C, Oelmann Y, Scheu S, Wilcke W, Schulze E-D, Gleixner G (2014) Biotic and abiotic properties mediating plant diversity effects on soil microbial communities in an experimental grassland. PLoS One 9(5):e96182. doi:10.1371/journal.pone.0096182

    Article  PubMed  PubMed Central  Google Scholar 

  • Legay N, Baxendale C, Grigulis K, Krainer U, Kastl E, Schloter M, Bardgett RD, Arnoldi C, Bahn M, Dumont M, Poly F, Pommier T, Clément JC, Lavorel S (2014) Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities. Ann Bot-London 114:1011–1021. doi:10.1093/aob/mcu169

    Article  CAS  Google Scholar 

  • Li JJ, Zhou XM, Yan JX, Li HJ, He JZ (2015) Effects of regenerating vegetation on soil enzyme activity and microbial structure in reclaimed soils on a surface coal mine site. Appl Soil Ecol 87:56–62. doi:10.1016/j.apsoil.2014.11.010

    Article  Google Scholar 

  • Liu JB, Zhang YQ, Wu B, Qin SG, Lai ZR (2014) Changes in soil organic carbon and its density fractions after shrub-planting for desertification control. Pol J Ecol 62:205–216. doi:10.3161/104.062.0202

    Article  CAS  Google Scholar 

  • Liu JB, Zhang YQ, Wu B, Qin SG, Jia X, Fa KY, Feng W, Lai ZR (2015) Effect of vegetation rehabilitation on soil carbon and its fractions in Mu Us Desert, northwest China. Int J Phytoremediation 17:529–537. doi:10.1080/15226514.2014.922923

    Article  CAS  PubMed  Google Scholar 

  • Lozano YM, Hortal S, Armas C, Pugnaire FI (2014) Interactions among soil, plants, and microorganisms drive secondary succession in a dry environment. Soil Biol Biochem 78:298–306. doi:10.1016/j.soilbio.2014.08.007

    Article  CAS  Google Scholar 

  • Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. doi:10.1093/bioinformatics/btr507

    Article  PubMed  PubMed Central  Google Scholar 

  • Merilä P, Malmivaara-Lämsä M, Spetz P, Stark S, Vierikko K, Derome J, Fritze H (2010) Soil organic matter quality as a link between microbial community structure and vegetation composition along a successional gradient in a boreal forest. Appl Soil Ecol 46:259–267. doi:10.1016/j.apsoil.2010.08.003

    Article  Google Scholar 

  • Nemergut DR, Cleveland CC, Wieder WR, Washenberger CL, Townsend AR (2010) Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest. Soil Biol Biochem 42:2153–2160. doi:10.1016/j.soilbio.2010.08.011

    Article  CAS  Google Scholar 

  • Prober SM, Leff JW, Bates ST et al (2015) Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide. Ecol Lett 18:85–95. doi:10.1111/ele.12381

    Article  PubMed  Google Scholar 

  • R Development Core Team (2011) R: A language and environment for statistical computing. R 21 Foundation for statistical computing, Vienna, Austria.

  • Scheibe A, Steffens C, Seven J, Jacob A, Hertel D, Leuschner C, Gleixner G (2015) Effects of tree identity dominate over tree diversity on the soil microbial community structure. Soil Biol Biochem 81:219–227. doi:10.1016/j.soilbio.2014.11.020

    Article  CAS  Google Scholar 

  • Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60. doi:10.1186/gb-2011-12-6-r60

    Article  PubMed  PubMed Central  Google Scholar 

  • Shen JP, Zhang LM, Guo JF, Ray JL, He JZ (2010) Impact of long-term fertilization practices on the abundance and composition of soil bacterial communities in northeast China. Appl Soil Ecol 46:119–124. doi:10.1016/j.apsoil.2010.06.015

    Article  Google Scholar 

  • Šnajdr J, Dobiášová P, Urbanová M, Petránková M, Cajthaml T, Frouz J, Baldrian P (2013) Dominant trees affect microbial community composition and activity in post-mining afforested soils. Soil Biol Biochem 56:105–115. doi:10.1016/j.soilbio.2012.05.004

    Article  Google Scholar 

  • Uroz S, Buée M, Murat C, Frey-Klett P, Martin F (2010) Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil. Environ Microbiol Rep 2:281–288. doi:10.1111/j.1758-2229.2009.00117.x

    Article  CAS  PubMed  Google Scholar 

  • Vance ED, Brookes PC, Jenkinson DS (1987) An extraction method for measuring soil microbial biomass C. Soil Biol Biochem 19:703–707. doi:10.1016/0038-0717(87)90052-6

    Article  CAS  Google Scholar 

  • Vokou D, Chalkos D, Karamanlidou G, Yiangou M (2002) Activation of soil respiration and shift of the microbial population balance in soil as a response to Lavandula stoechas essential oil. J Chem Ecol 28:755–768. doi:10.1023/A:1015236709767

    Article  CAS  PubMed  Google Scholar 

  • Wagg C, Bender SF, Widmer F, van der Heijden MGA (2014) Soil biodiversity and soil community composition determine ecosystem multifunctionality. Proc Natl Acad Sci U S A 111:5266–5270. doi:10.1073/pnas.1320054111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Walkley A, Black IA (1934) An examination of the Degtjareff method for determining soil organic matter, and a proposed modification of the chromic acid titration method. Soil Sci 37:29–38

    Article  CAS  Google Scholar 

  • Wang B, Xue S, Liu GB, Zhang GH, Li G, Ren ZP (2012) Changes in soil nutrient and enzyme activities under different vegetations in the Loess Plateau area, northwest China. Catena 92:186–195. doi:10.1016/j.catena.2011.12.004

    Article  CAS  Google Scholar 

  • Xu XF, Thornton PE, Post WM (2013) A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems. Glob Ecol Biogeogr 22:737–749. doi:10.1111/geb.12029

    Article  Google Scholar 

  • Yang ZP, Zhang Q, Wang YL, Zhang JJ, Chen MC (2011) Spatial and temporal variability of soil properties under Caragana microphylla shrubs in the northwestern Shanxi Loess Plateau, China. J Arid Environ 75:538–544. doi:10.1016/j.jaridenv.2011.01.007

    Article  Google Scholar 

  • Yang XL, Deng SQ, De Philippis R, Chen LZ, Hu CZ, Zhang WH (2012) Chemical composition of volatile oil from Artemisia ordosica and its allelopathic effects on desert soil microalgae, Palmellococcus miniatus. Plant Physiol Biochem 51:153–158. doi:10.1016/j.plaphy.2011.10.019

    Article  CAS  PubMed  Google Scholar 

  • Zak DR, Holmes WE, White DC, Peacock AD, Tilman D (2003) Plant diversity, soil microbial communities, and ecosystem function: are there any links? Ecology 84:2042–2050. doi:10.1890/02-0433

    Article  Google Scholar 

  • Zeller B, Liu JX, Buchmann N, Richter A (2008) Tree girdling increases soil N mineralization in two spruce stands. Soil Biol Biochem 40:1155–1166. doi:10.1016/j.soilbio.2007.12.009

    Article  CAS  Google Scholar 

  • Zhu BB, Li ZB, Li P, Liu GB, Xue S (2010) Soil erodibility, microbial biomass, and physical–chemical property changes during long-term natural vegetation restoration: a case study in the Loess Plateau, China. Ecol Res 25:531–541. doi:10.1007/s11284-009-0683-5

    Article  Google Scholar 

Download references

Acknowledgments

This study was supported by the National Key Research and Development Program of China (no. 2016YFC0500905), National Natural Science Foundation of China (no. 31470711), and the Fundamental Research Funds for the Central Universities (no. 2015ZCQ-SB-02). We would like to thank the staff of the Yanchi Research Station. Special thanks to Weiwei She, Jun Liu and Li Wang for their help with sampling and measurements in the field and laboratory.

Author information

Authors and Affiliations

  1. Yanchi Research Station, School of Soil and Water Conservation, Beijing Forestry University, Beijing, 100083, China

    Yanfei Sun, Yuqing Zhang, Wei Feng, Shugao Qin, Zhen Liu, Yuxuan Bai, Ru Yan & Keyu Fa

  2. Engineering Research Center of Forestry Ecological Engineering of the Ministry of Education, Beijing Forestry University, Beijing, 100083, China

    Yuqing Zhang, Wei Feng & Shugao Qin

  3. School of Soil and Water Conservation, Beijing Forestry University, No. 35, Qinghua Eastroad, Haidian District, Beijing, 100083, People’s Republic of China

    Yuqing Zhang

Authors
  1. Yanfei Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuqing Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wei Feng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shugao Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhen Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yuxuan Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ru Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Keyu Fa
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuqing Zhang.

Additional information

Responsible Editor: Liz Shaw.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sun, Y., Zhang, Y., Feng, W. et al. Effects of xeric shrubs on soil microbial communities in a desert in northern China. Plant Soil 414, 281–294 (2017). https://doi.org/10.1007/s11104-016-3111-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11104-016-3111-y

Keywords

Search

Navigation