Skip to main content

Advertisement

SpringerLink
Log in

Variation of soil nitrate and bacterial diversity along soil profiles in manure disposal maize field and adjacent woodland

  • Soils, Sec 1 • Soil Organic Matter Dynamics and Nutrient Cycling • Research Article
  • Published:
Journal of Soils and Sediments Aims and scope Submit manuscript

Abstract

Purpose

Intensified livestock system produced large amount of bio-waste, and improper disposal of livestock manure has led to severe environmental consequences. However, knowledge about the time-dependent changes of manure-derived nitrate and soil bacterial diversity along the soil profiles is limited.

Materials and methods

Vertical variation of soil bacterial diversity and composition in a manure-amended maize field and adjacent non-manured woodland was investigated using high-throughput sequencing technique in spring and autumn along a 1-m profile depth. The soil is classified as aquic inceptisol with a bulk density of 1.31 g cm−3, and a sandy loam texture.

Results

The results showed that significant higher amount of nitrate (up to 172.13 mg kg−1) was detected along the soil profile loaded with cattle manure compared with the adjacent non-manured woodland. Soil δ15N-NO3− composition from maize field fall between + 5 and 25‰, while those from woodland fall between − 5 and 15‰. No significant difference in bacterial richness between the two land uses was found, while clear separation of bacterial structure was detected even to the deep soil layers. Canonical correspondence analysis showed that soil organic matter, C/N ratio, nitrate content, pH, and moisture were the major factors influencing the variance of bacterial community composition. Bacterial networks in the maize field harbor more modules than those in the adjacent woodland. Negative standardized effect size measure of mean nearest taxon distance in the soils tended to be more phylogenetically clustered than expected by chance, and was more likely to be clustered along the depth.

Conclusions

These findings suggested that soil bacterial β diversity was strongly affected by multi-nutrient properties in terms of high livestock manure load, and had important implications for assessing the environmental impacts on belowground biodiversity in sandy loam soils.

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
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • 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

    CAS  Google Scholar 

  • Bai ZH, Ma WQ, Ma L, Velthof GL, Wei ZB, Havlik P, Oenema O, Lee MRF, Zhang FS (2018) China’s livestock transition: driving forces, impacts, and consequences. Sci Adv 4:eaar8534

    CAS  Google Scholar 

  • Banerjee S, Walder F, Buchi L, Meyer M, Held AY, Gattinger A, Keller T, Charles R, van der Heijden MGA (2019) Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots. ISME J 13:1722–1736

    Google Scholar 

  • Bardgett RD, van der Putten WH (2014) Belowground biodiversity and ecosystem functioning. Nature 515:505–511

    CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • Chu HY, Sun HB, Tripathi BM, Adams JM, Huang R, Zhang YJ, Shi Y (2016) Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau. Environ Microbiol 18:1523–1533

    CAS  Google Scholar 

  • Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998

    CAS  Google Scholar 

  • Enwall K, Nyberg K, Bertilsson S, Cederlund H, Stenstrom 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

    CAS  Google Scholar 

  • Falkowski PG, Fenchel T, Delong EF (2008) The microbial engines that drive Earth’s biogeochemical cycles. Science 320:1034–1039

    CAS  Google Scholar 

  • Fenech C, Rock L, Nolan K, Tobin J, Morrissey A (2012) The potential for a suite of isotope and chemical markers to differentiate sources of nitrate contamination: a review. Water Res 46:2023–2041

    CAS  Google Scholar 

  • Feng YZ, Chen RR, Hu JL, Zhao F, Wang JH, Chu HY, Zhang JB, Dolfing J, Lin XG (2015) Bacillus asahii comes to the fore in organic manure fertilized alkaline soils. Soil Biol Biochem 81:186–194

    CAS  Google Scholar 

  • Feng MM, Adams JM, Fan KK, Shi Y, Sun RB, Wang DZ, Guo XS, Chu HY (2018) Long-term fertilization influences community assembly processes of soil diazotrophs. Soil Biol Biochem 126:151–158

    CAS  Google Scholar 

  • Fernandez-Gomez B, Richter M, Schuler M, Pinhassi J, Acinas SG, Gonzalez JM, Pedros-Alio C (2013) Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J 7:1026–1037

    CAS  Google Scholar 

  • Guo ZC, Zhang JB, Fan J, Yang XY, Yi YL, Han XR, Wang DZ, Zhu P, Peng XH (2019) Does animal manure application improve soil aggregation? Insights from nine long-term fertilization experiments. Sci Total Environ 660:1029–1037

    CAS  Google Scholar 

  • Hartmann M, Frey B, Mayer J, Mader P, Widmer F (2015) Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 9:1177–1194

    Google Scholar 

  • Herrero M, Thornton PK (2013) Livestock and global change: emerging issues for sustainable food systems. Proc Natl Acad Sci U S A 110:20878–20881

    CAS  Google Scholar 

  • Ho A, Di Lonardo DP, Bodelier PLE (2017) Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiol Ecol 93

  • Horner-Devine MC, Bohannan BJM (2006) Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87:S100–S108

    Google Scholar 

  • Jesus ED, Marsh TL, Tiedje JM, Moreira FMD (2009) Changes in land use alter the structure of bacterial communities in Western Amazon soils. ISME J 3:1222–1222

    CAS  Google Scholar 

  • Jia W, Qin W, Zhang Q, Wang X, Ma Y, Chen Q (2018) Evaluation of crop residues and manure production and their geographical distribution in China. J Clean Prod 188:954–965

    CAS  Google Scholar 

  • Jiao S, Chen WM, Wang JL, Du NN, Li QP, Wei GH (2018) Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems. Microbiome 6

  • 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

    CAS  Google Scholar 

  • Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463–1464

    CAS  Google Scholar 

  • Kennedy AC, Smith KL (1995) Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 170:75–86

    CAS  Google Scholar 

  • Krapac IG, Dey WS, Roy WR, Smyth CA, Storment E, Sargent SL, Steele JD (2002) Impacts of swine manure pits on groundwater quality. Environ Pollut 120:475–492

    CAS  Google Scholar 

  • Lauber CL, Hamady M, Knight R, Fierer N (2009) Pyrosequencing-based assessment of soil ph as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 75:5111–5120

    CAS  Google Scholar 

  • Lee CK, Barbier BA, Bottos EM, McDonald IR, Cary SC (2012) The inter-valley soil comparative survey: the ecology of Dry Valley edaphic microbial communities. ISME J 6:1046–1057

    CAS  Google Scholar 

  • Leip A, Billen G, Garnier J, Grizzetti B, Lassaletta L, Reis S, Simpson D, Sutton MA, de Vries W, Weiss F, Westhoek H (2015) Impacts of European livestock production: nitrogen, sulphur, phosphorus and greenhouse gas emissions, land-use, water eutrophication and biodiversity. Environ Res Lett 10

  • Liao HK, Zheng CL, Li J, Long J (2018) Dynamics of soil microbial recovery from cropland to orchard along a 20-year chronosequence in a degraded karst ecosystem. Sci Total Environ 639:1051–1059

    CAS  Google Scholar 

  • Lin YX, Ye GP, Kuzyakov Y, Liu DY, Fan JB, Ding WX (2019) Long-term manure application increases soil organic matter and aggregation, and alters microbial community structure and keystone taxa. Soil Biol Biochem 134:187–196

    CAS  Google Scholar 

  • Liu T, Wang F, Michalski G, Xia XH, Liu SD (2013) Using N-15, O-17, and O-18 to determine nitrate sources in the Yellow River, China. Environ Sci Technol 47:13412–13421

    CAS  Google Scholar 

  • Lynn TM, Ge TD, Yuan HZ, Wei XM, Wu XH, Xiao KQ, Kumaresan D, Yu SS, Wu JS, Whiteley AS (2017) Soil carbon-fixation rates and associated bacterial diversity and abundance in three natural ecosystems. Microb Ecol 73:645–657

    CAS  Google Scholar 

  • Mayfield MM, Levine JM (2010) Opposing effects of competitive exclusion on the phylogenetic structure of communities. Ecol Lett 13:1085–1093

    Google Scholar 

  • Meng XT, Li YY, Zhang Y, Yao HY (2019a) Green manure application improves rice growth and urea nitrogen use efficiency assessed using 15N labeling. Soil Sci Plant Nutr 65:511–518

    CAS  Google Scholar 

  • Meng QX, Yang W, Men MQ, Bello A, Xu XH, Xu BS, Deng LT, Jiang X, Sheng SY, Wu XT, Han Y, Zhu HF (2019b) Microbial community succession and response to environmental variables during cow manure and corn straw composting. Front Microbiol 10

  • National Bureau of Statistics of China (2014) China Statistical Yearbook. China Statistics Press, Beijing (In Chinese)

    Google Scholar 

  • Nguyen HQ, Kanwar RS, Hoover NL, Dixon P, Hobbs J, Pederson C, Soupir ML (2013) Long-term effects of poultry manure application on nitrate leaching in tile drain water. Trans ASABE 56:91–101

    CAS  Google Scholar 

  • Peacock AD, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC (2001) Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol Biochem 33:1011–1019

    CAS  Google Scholar 

  • Pelletier N, Tyedmers P (2010) Forecasting potential global environmental costs of livestock production 2000-2050. Proc Natl Acad Sci U S A 107:18371–18374

    CAS  Google Scholar 

  • Pepe-Ranney C, Campbell AN, Koechli CN, Berthrong S, Buckley DH (2016) Unearthing the ecology of soil microorganisms using a high resolution DNA-sip approach to explore cellulose and xylose metabolism in soil. Front Microbiol 7

  • Powell JR, Karunaratne S, Campbell CD, Yao HY, Robinson L, Singh BK (2015) Deterministic processes vary during community assembly for ecologically dissimilar taxa. Nat Commun 6

  • Rebollar EA, Bridges T, Hughey MC, Medina D, Belden LK, Harris RN (2019) Integrating the role of antifungal bacteria into skin symbiotic communities of three Neotropical frog species. ISME J 13:1763–1775

    CAS  Google Scholar 

  • Rodrigues JLM, Pellizari VH, Mueller R, Baek K, Jesus ED, Paula FS, Mirza B, Hamaoui GS, Tsai SM, Feigl B, Tiedje JM, Bohannan BJM, Nusslein K (2013) Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities. Proc Natl Acad Sci U S A 110:988–993

    CAS  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

    Google Scholar 

  • Sigman DM, Casciotti KL, Andreani M, Barford C, Galanter M, Bohlke JK (2001) A bacterial method for the nitrogen isotopic analysis of nitrate in seawater and freshwater. Anal Chem 73:4145–4153

    CAS  Google Scholar 

  • Stegen JC, Lin XJ, Konopka AE, Fredrickson JK (2012) Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J 6:1653–1664

    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

    CAS  Google Scholar 

  • Sun RB, Zhang XX, Guo XS, Wang DZ, Chu HY (2015) 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

    CAS  Google Scholar 

  • Tajima K, Aminov RI, Nagamine T, Ogata K, Nakamura M, Matsui H, Benno Y (1999) Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol Ecol 29:159–169

    CAS  Google Scholar 

  • Thomas F, Hehemann JH, Rebuffet E, Czjzek M, Michel G (2011) Environmental and gut Bacteroidetes: the food connection. Front Microbiol 2

  • Tripathi BM, Kim M, Kim Y, Byun E, Yang JW, Ahn J, Lee YK (2018) Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores. Sci Rep-Uk 8

  • Udikovic-Kolic N, Wichmann F, Broderick NA, Handelsman J (2014) Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. Proc Natl Acad Sci U S A 111:15202–15207

    CAS  Google Scholar 

  • Wang SQ, Zheng WB, Currell M, Yang YH, Zhao H, Lv MY (2017) Relationship between land-use and sources and fate of nitrate in groundwater in a typical recharge area of the North China Plain. Sci Total Environ 609:607–620

    CAS  Google Scholar 

  • Webb CO, Ackerly DD, McPeek MA, Donoghue MJ (2002) Phylogenies and community ecology. Annu Rev Ecol Syst 33:475–505

    Google Scholar 

  • Wei XM, Zhu ZK, Wei L, Wu JS, Ge T (2019) Biogeochemical cycles of key elements in the paddy-rice rhizosphere: microbial mechanisms and coupling processes. Rhizosphere-Neth 10

  • Wolinska A, Kuzniar A, Zielenkiewicz U, Izak D, Szafranek-Nakonieczna A, Banach A, Blaszczyk M (2017) Bacteroidetes as a sensitive biological indicator of agricultural soil usage revealed by a culture-independent approach. Appl Soil Ecol 119:128–137

    Google Scholar 

  • Xia LL, Lam SK, Yan XY, Chen DL (2017) How does recycling of livestock manure in agroecosystems affect crop productivity, reactive nitrogen losses, and soil carbon balance? Environ Sci Technol 51:7450–7457

    CAS  Google Scholar 

  • Yang SM, Malhi SS, Song JR, Xiong YC, Yue WY, Lu LL, Wang JG, Guo TW (2006) Crop yield, nitrogen uptake and nitrate-nitrogen accumulation in soil as affected by 23 annual applications of fertilizer and manure in the rainfed region of Northwestern China. Nutr Cycl Agroecosyst 76:81–94

    Google Scholar 

  • Yu CQ, Huang X, Chen H, Godfray HCJ, Wright JS, Hall JW, Gong P, Ni SQ, Qiao SC, Huang GR, Xiao YC, Zhang J, Feng Z, Ju XT, Ciais P, Stenseth NC, Hessen DO, Sun ZL, Yu L, Cai WJ, Fu HH, Huang XM, Zhang C, Liu HB, Taylor J (2019a) Managing nitrogen to restore water quality in China. Nature 567:516–520

    CAS  Google Scholar 

  • Yu YJ, Wu M, Petropoulos E, Zhang JW, Nie J, Liao YL, Li ZP, Lin XG, Feng YZ (2019b) Responses of paddy soil bacterial community assembly to different long-term fertilizations in southeast China. Sci Total Environ 656:625–633

    CAS  Google Scholar 

  • Zheng YM, Cao P, Fu BJ, Hughes JM, He JZ (2013) Ecological drivers of biogeographic patterns of soil archaeal community. PLoS One 8

  • Zheng J, Chen J, Pan G, Wang G, Liu X, Zhang X, Li L, Bian R, Cheng K, Zheng J (2017) A long-term hybrid poplar plantation on cropland reduces soil organic carbon mineralization and shifts microbial community abundance and composition. Appl Soil Ecol 111:94–104

    Google Scholar 

  • Zhou ZM, Yao HY (2020) Effects of composting different types of organic fertilizer on the microbial community structure and antibiotic resistance genes. Microorganisms 8

  • Zhou JY, Gu BJ, Schlesinger WH, Ju XT (2016) Significant accumulation of nitrate in Chinese semi-humid croplands. Sci Rep-Uk 6

Download references

Acknowledgments

We thank Drs. Peng Li and Xuan Guo, Shuai Du, Yu Liang for their assistance in samples collection.

Funding

This work was supported by the Program of Intergovernmental Cooperation in Science and Technology (grant numbers 2017YFE0109800).

Author information

Authors and Affiliations

  1. State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China

    Yujia Cai, Ju-Pei Shen & Li-Mei Zhang

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

    Yujia Cai, Ju-Pei Shen, Li-Mei Zhang & Ji-Zheng He

  3. Centre for Soil and Environmental Research, Lincoln University, Lincoln, Canterbury, 7674, New Zealand

    Hong J. Di

  4. Institute of Plant Nutrition and resources, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China

    Chengjun Zhang

  5. School of Geographical Sciences, Fujian Normal University, Fuzhou, 350117, China

    Ji-Zheng He

Authors
  1. Yujia Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ju-Pei Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hong J. Di
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Li-Mei Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chengjun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ji-Zheng He
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ju-Pei Shen.

Additional information

Responsible editor: Huaiying Yao

Publisher’s note

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

Electronic supplementary material

ESM 1

(DOCX 178 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Cai, Y., Shen, JP., Di, H.J. et al. Variation of soil nitrate and bacterial diversity along soil profiles in manure disposal maize field and adjacent woodland. J Soils Sediments 20, 3557–3568 (2020). https://doi.org/10.1007/s11368-020-02679-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11368-020-02679-z

Keywords

Search

Navigation