Skip to main content
SpringerLink
Log in

Bacterial diversity as affected by application of manure in red soils of subtropical China

  • Original Paper
  • Published:
Biology and Fertility of Soils Aims and scope Submit manuscript

Abstract

A plot experiment was conducted to understand the response of the soil bacterial community to manure application rates and the relationship between the composition of bacterial community and soil chemical properties. The experiment involved gradients of manure combined with chemical fertilizer in red soils from granite, red sandstone and red clay between 2013 and 2015. The soil bacterial community composition was significantly affected by different manure rates. The relative abundances of Burkholderiaceae, Micrococcaceae and Streptomycetaceae were higher at low manure rates (1.75 to 3.5 t·ha−1·yr.−1), whereas the relative abundance of Xanthomonadaceae was higher at high manure rates (7 to 28 t·ha−1·yr.−1). Manure application increased the bacterial abundance but decreased the diversity when its rates were higher than 7, 14 and 14 t·ha−1·yr.−1 in soils from granite, red sandstone and red clay, respectively. Redundancy analysis revealed that soils from different parent materials had different bacterial communities with soil pH and available phosphorus (AP) being determinant factors. The peanut yields exhibited significantly positive correlations with the bacterial diversity in soil, implying the importance of bacterial diversity for soil productivity. Soil AP was correlated with bacterial diversity by parabolic equations and probably AP may be an indicator of declining bacterial diversity at high manure rates. The critical value were 39.71, 65.75 and 90.16 mg·kg−1 in soils from granite, red sandstone and red clay, respectively. This study suggests the importance of maintaining soil bacterial diversity under moderate and balanced applications of manure.

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

  • Abd-El-Malek Y, Hosny I, Shawky BT (1983) Further studies on free-living nitrogen-fixing microorganisms, other than Azotobacter, isolated from Egyptian soils and waters. Zentralblatt Mikrobiol 138:123–134

    CAS  Google Scholar 

  • Acosta-Martínez V, Dowd S, Sun Y, Allen V (2008) Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol Biochem 40:2762–2770

    Article  Google Scholar 

  • Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F, Estrada A, Gaskins HR, Stumpf RM, Yildirim S, Torralba M, Gillis M, Wilson BA, Nelson KE, White BA, Leigh SR (2013) Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. Isme J 7:1344–1353

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anderson CR, Condron LM, Clough TJ, Fiers M, Stewart A, Hill RA, Sherlock RR (2011) Biochar induced soil microbial community change: implications for biogeochemical cycling of carbon, nitrogen and phosphorus. Pedobiologia 54:309–320

    Article  CAS  Google Scholar 

  • Bhattacharyya R, Kundu S, Prakash V, Gupta HS (2008) Sustainability under combined application of mineral and organic fertilizers in a rainfed soybean-wheat system of the Indian Himalayas. Eur J Agron 28:33–46

    Article  CAS  Google Scholar 

  • Bremner JM (1996) Nitrogen–total. In: Bigham JM (Ed) Methods of soil analysis, part 3 chemical methods. The Soil Science Society of American Book Series No 5. Soil Science Society of American, Inc., American Society of Agronomy, Inc., Madison, pp 1085–1121

  • Chen C, Zhang JN, Lu M, Qin C, Chen YH, Yang L, Huang QW, Wang JC, Shen ZG, Shen QR (2016) Microbial communities of an arable soil treated for 8 years with organic and inorganic fertilizers. Biol Fertil Soils 52:1–13

    Article  Google Scholar 

  • Chu HY, Lin XG, Fujii T, Morimoto S, Yagi K, Hu JL, Zhang JB (2007) Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol Biochem 39:2971–2976

    Article  CAS  Google Scholar 

  • Dai XQ, Yuan Y, Wang HM (2016) Changes of anaerobic to aerobic conditions but not of crop type induced bulk soil microbial community variation in the initial conversion of paddy soils to drained soils. Catena 147:578–585

    Article  CAS  Google Scholar 

  • Daudén A, Quílez D (2004) Pig slurry versus mineral fertilization on corn yield and nitrate leaching in a Mediterranean irrigated environment. Eur J Agron 21:7–19

    Article  Google Scholar 

  • Demoling F, Figueroa D, Bååth E (2007) Comparison of factors limiting bacterial growth in different soils. Soil Biol Biochem 39:2485–2495

    Article  CAS  Google Scholar 

  • Ding JL, Jiang X, Ma MC, Zhou BK, Guan DW, Zhao BS, Zhou J, Cao FM, Li L, Li J (2016) Effect of 35 years inorganic fertilizer and manure amendment on structure of bacterial and archaeal communities in black soil of northeast China. Appl Soil Ecol 105:187–195

    Article  Google Scholar 

  • Dong WY, Zhang XY, Dai XQ, Fu XL, Yang FT, Liu XY, Sun XM, Wen XF, Schaeffer S (2014) Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China. Appl Soil Ecol 84:140–147

    Article  Google Scholar 

  • Durrer A, Gumiere T, Taketani RG, Costa DPd, Pereira e Silva MdC, Andreote FD (2017) The drivers underlying biogeographical patterns of bacterial communities in soils under sugarcane cultivation. Appl Soil Ecol 110:12–20

  • Edmeades DC (2003) The long-term effects of manures and fertilisers on soil productivity and quality: a review. Nutr Cycl Agroecosyst 66:165–180

    Article  CAS  Google Scholar 

  • Enwall K, Nyberg K, Bertilsson S, Cederlund H, Stenström J, Hallin S (2007) Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil. Soil Biol Biochem 39:106–115

    Article  CAS  Google Scholar 

  • Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103:626–631

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Hamm AC, Tenuta M, Krause DO, Ominski KH, Tkachuk VL, Flaten DN (2016) Bacterial communities of an agricultural soil amended with solid pig and dairy manures, and urea fertilizer. Appl Soil Ecol 103:61–71

    Article  Google Scholar 

  • Hou XQ, Wang XJ, Li R, Jia ZK, Liang LY, Wang JP, Nie JF, Chen X, Wang Z (2012) Effects of different manure application rates on soil properties, nutrient use, and crop yield during dryland maize farming. Soil Res 50:507–514

    Article  Google Scholar 

  • Ju XT, Kou CL, Christie P, Dou ZX, Zhang FS (2007) Changes in the soil environment from excessive application of fertilizers and manures to two contrasting intensive cropping systems on the North China Plain. Environ Pollut 145:497–506

    Article  CAS  PubMed  Google Scholar 

  • Kirby R (2005) Actinomycetes and lignin degradation. Adv Appl Microbiol 58:125–168

    Article  Google Scholar 

  • Koyama A, Wallenstein MD, Simpson RT, Moore JC (2014) Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils. Front Microbiol 5:516. doi:10.3389/fmicb.2014.00516

    Article  PubMed  PubMed Central  Google Scholar 

  • Kuo S (1996) Phosphorus. In: Bigham JM (Ed) Methods of soil analysis, part 3 chemical methods. The Soil Science Society of American Book Series No 5. Soil Science Society of American, Inc., American Society of Agronomy, Inc., Madison, pp 869–919

  • Li R, Khafipour E, Krause DO, Entz MH, de Kievit TR, Dilantha Fernando WG (2012) Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities. PLoS One 7:e51897

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li J, Cooper JM, Lin ZA, Li YT, Yang XD, Zhao BQ (2015) Soil microbial community structure and function are significantly affected by long-term organic and mineral fertilization regimes in the north china plain. Appl Soil Ecol 96:75–87

    Article  Google Scholar 

  • Lu HF, Lashari MS, Liu XY, Ji HS, Li LQ, Zheng JF, Kibue GW, Joseph S, Pan GX (2015) Changes in soil microbial community structure and enzyme activity with amendment of biochar-manure compost and pyroligneous solution in a saline soil from Central China. Eur J Soil Biol 70:67–76

    Article  CAS  Google Scholar 

  • Lupwayi NZ, Benke MB, Hao X, O’Donovan JT, Clayton GW (2014) Relating crop productivity to soil microbial properties in acid soil treated with cattle manure. Agron J 106:612–621

    Article  Google Scholar 

  • Ma XY, Liu M, Li ZP (2016) Shifts in microbial biomass and community composition in subtropical paddy soils under a gradient of manure amendment. Biol Fertil Soils 52:775–787

    Article  Google Scholar 

  • Magoč T, Salzberg SL (2011) Flash: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963

    Article  PubMed  PubMed Central  Google Scholar 

  • Maguire RO, Sims JT (2001) Observations on leaching and subsurface transport of phosphorus on the Delmarva Peninsula, USA. Connecting Phosphorus Transfer from Agriculture to Impacts in Surface Waters. International Phosphorus Transfer Workshop, 20

  • Malik S, Beer M, Megharaj M, Naidu R (2008) The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int 34:265–276

    Article  CAS  PubMed  Google Scholar 

  • Marschner P, Kandeler E, Marschner B (2003) Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol Biochem 35:453–461

    Article  CAS  Google Scholar 

  • Mulvaney RL (1996) Nitrogen–inorganic forms. In: Bigham JM (Ed) Methods of soil analysis, part 3 chemical methods. The Soil Science Society of American Book Series No 5. Soil Science Society of American, Inc., American Society of Agronomy, Inc., Madison, pp 1123–1184

  • Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    CAS  PubMed  PubMed Central  Google Scholar 

  • Naguib AI, Foda MS, Shawky BT, Rizkallah LA (1983) Ecological and physiological studies on free-living nitrogen-fixing bacteria, predominating in sandy soils of extension areas in Egypt. Zentralblatt Mikrobiol 138:277–292

    Article  Google Scholar 

  • Nelson DW, Sommers LE (1996) Total carbon, organic carbon, and organic matter. In: Bigham JM (Ed) Methods of soil analysis, part 3 chemical methods. The Soil Science Society of American Book Series No 5. Soil Science Society of American, Inc., American Society of Agronomy, Inc., Madison, pp 961–1010

  • Nicolitch O, Colin Y, Turpault MP, Uroz S (2016) Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees. Soil Biol Biochem 103:429–445

    Article  CAS  Google Scholar 

  • Purkamo L, Bomberg M, Kietäväinen R, Salavirta H, Nyyssönen M, Nuppunen-Puputti M, Ahonen L, Kukkonen I, Itävaara M (2016) Microbial co-occurrence patterns in deep Precambrian bedrock fracture fluids. Biogeosciences 13:3091–3108

    Article  Google Scholar 

  • Reeves DW (1997) The role of soil organic matter in maintaining soil quality in continuous cropping systems. Soil Tillage Res 43:131–167

    Article  Google Scholar 

  • Remus-Emsermann MNP, Lücker S, Müller DB, Potthoff E, Daims H, Vorholt JA (2014) Spatial distribution analyses of natural phyllosphere-colonizing bacteria on Arabidopsis thaliana revealed by fluorescence in situ hybridization. Environ Microbiol 16:2329–2340

    Article  CAS  PubMed  Google Scholar 

  • Schloter M, Dilly O, Munch JC (2003) Indicators for evaluating soil quality. Agric Ecosyst Environ 98:255–262

    Article  Google Scholar 

  • Shen ZZ, Ruan YZ, Chao X, Zhang J, Li R, Shen QR (2015) Rhizosphere microbial community manipulated by 2 years of consecutive biofertilizer application associated with banana Fusarium wilt disease suppression. Biol Fertil Soils 51:553–562

    Article  CAS  Google Scholar 

  • Sun HY, Deng SP, Raun WR (2004) Bacterial community structure and diversity in a century-old manure-treated agroecosystem. Appl Environ Microbiol 70:5868–5874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun RB, Guo XS, Wang DZ, Chu HY (2015a) Effects of long-term application of chemical and organic fertilizers on the abundance of microbial communities involved in the nitrogen cycle. Appl Soil Ecol 95:171–178

    Article  Google Scholar 

  • Sun RB, Zhang XX, Guo XS, Wang DZ, Chu HY (2015b) Bacterial diversity in soils subjected to long-term chemical fertilization can be more stably maintained with the addition of livestock manure than wheat straw. Soil Biol Biochem 88:9–18

    Article  CAS  Google Scholar 

  • Thomas GW (1996) Soil pH and soil acidity. In: Bigham JM (Eds) Methods of soil analysis, part 3, chemical methods. The Soil Science Society of American Book Series No 5. Soil Science Society of American, Inc., American Society of Agronomy, Inc., Madison, pp 475–490

  • Uwah DF, Eyo VE (2014) Effects of number and rate of goat manure application on soil properties, growth and yield of sweet maize (Zea mays L. saccharata Strut). Sustain Agric Res. doi:10.5539/sar.v3n4p75

  • Verstraete W, Mertens B (2004) The key role of soil microbes. In: Doelman P, Eijsackers HJP (eds) Vital soil: function, value, and properties, vol 29. Elsevier, Amsterdam, pp 127–157

    Chapter  Google Scholar 

  • Xu N, Tan GC, Wang HY, Gai XP (2016) Effect of biochar additions to soil on nitrogen leaching, microbial biomass and bacterial community structure. Eur J Soil Biol 74:1–8

    Article  Google Scholar 

  • Yang YR, Li XG, Zhou ZG, Zhang TL, Wang XX (2016) Differential responses of soil nematode community to pig manure application levels in Ferric Acrisols. Sci Rep-UK 6, 35334. doi:10.1038/srep35334

    Article  CAS  Google Scholar 

  • Yarwood S, Wick A, Williams M, Daniels WL (2015) Parent material and vegetation influence soil microbial community structure following 30-years of rock weathering and pedogenesis. Microb Ecol 69:383–394

    Article  PubMed  Google Scholar 

  • Yevdokimov I, Gattinger A, Buegger F, Munch JC, Schloter M (2008) Changes in microbial community structure in soil as a result of different amounts of nitrogen fertilization. Biol Fertil Soils 44:1103–1106

    Article  CAS  Google Scholar 

  • Zhalnina K, Dias R, de Quadros PD, Davis-Richardson A, Camargo FAO, Clark IM, McGrath SP, Hirsch PR, Triplett EW (2015) Soil pH determines microbial diversity and composition in the park grass experiment. Microb Ecol 69:395–406

    Article  CAS  PubMed  Google Scholar 

  • Zhao J, Ni T, Li J, Lu Q, Fang ZY, Huang QW, Zhang RF, Li R, Shen B, Shen QR (2016) Effects of organic-inorganic compound fertilizer with reduced chemical fertilizer application on crop yields, soil biological activity and bacterial community structure in a rice-wheat cropping system. Appl Soil Ecol 99:1–12

    Article  Google Scholar 

Download references

Acknowledgements

Research in this work was funded by the Special Fund for Agro-scientific Research in the Public Interest (201203050-3), the Knowledge Innovation Program of the Chinese Academy of Sciences (ISSASIP1632) and the GanPo 555 Talents Program of Jiangxi Province, China. We are very grateful to the help of two anonymous reviewers. We also thank Prof. Wietse de Boer from the Netherlands Institute of Ecology (NIOO-KNAW) for his constructive comments and language help.

Author information

Author notes

  1. Yiru Yang and Xiaogang Li contributed equally to this work

Authors and Affiliations

  1. Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China

    Yiru Yang, Xiaogang Li, Jinguang Liu, Zhigao Zhou, Taolin Zhang & Xingxiang Wang

  2. University of the Chinese Academy of Sciences, Beijing, 100049, China

    Yiru Yang & Jinguang Liu

  3. Ecological Experimental Station of Red Soil, Chinese Academy of Sciences, Yingtan, 335211, China

    Xingxiang Wang

Authors
  1. Yiru Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiaogang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jinguang Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Zhigao Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Taolin Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xingxiang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xingxiang Wang.

Electronic supplementary material

Fig. S1

(DOCX 226 kb)

Fig. S2

(DOCX 109 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yang, Y., Li, X., Liu, J. et al. Bacterial diversity as affected by application of manure in red soils of subtropical China. Biol Fertil Soils 53, 639–649 (2017). https://doi.org/10.1007/s00374-017-1209-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00374-017-1209-x

Keywords

Search

Navigation