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Assessment of bacterial community composition, methanotrophic and nitrogen-cycling bacteria in three soils with different biochar application rates

  • Soils, Sec 3 • Remediation and Management of Contaminated or Degraded Lands • Research Article
  • Published:
Journal of Soils and Sediments Aims and scope Submit manuscript

Abstract

Purpose

The increased use of biochar as a soil amendment to alleviate the impact of agricultural practices on climate change has been a motivation for many studies to determine the effects of biochar on soil properties, particularly the abundance and activities of soil microbes and related biological processes. This study investigates the impact of different application rates of wood-derived biochar on community structure, nitrogen-cycling and methanotrophic bacteria in three soil types.

Materials and methods

Biochar was added at 0, 2.5, 5 and 10% w/w to black clay loam (BCL, Vertosol), red loam (RL, Dermosol) and brown sandy loam (BSL, Kurosol) soils. Soil chemical analysis and 16S rRNA gene amplicon sequencing using the IIlumina Mi-Seq platform were conducted on initial samples and after 10-month incubation.

Results and discussion

The results indicated that the addition of biochar loading levels to the different soils had a significant impact on NH4 and NO3, total C and N, pH, electrical conductivity (EC) and soil moisture content. These changes were reflected in significant differences in the bacterial diversity between biochar treatments in the BSL and RL soils, while the BCL soil was more resilient to change. Complete ammonia-oxidising (Nitrospira) and nitrite-oxidising bacteria (NOB) were more abundant than standard ammonia-oxidising bacteria (AOB) in all soils. Increased biochar loading raised the abundance of nitrifying bacteria in BCL soil while Nitrospira became more abundant in BSL soil. Biochar addition affected the abundance of certain N2 fixer groups in a soil-dependent manner. Strong positive correlations were observed in Rhizobium (r = 0.99) and Azospirillum abundance (r = 0.70) with increased biochar loading rates in BCL. Greater biochar loading also significantly increased the relative abundance of methanotrophs, especially in BCL soil.

Conclusions

The impact of biochar on community structure and nitrogen-cycling bacteria depended on soil types and biochar rates which correlated to the differences in soil properties. Overall, the abundance of nitrogen-cycling bacterial groups seemed to be most affected by the changes in soil conditions, including aeration, C/N ratio, nutrients and pH in relation to biochar application in different soils. These changes show that short-term biochar loading influences community structure and leads to increases in populations of methanotrophic and nitrifying bacteria.

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References

  • Abujabhah IS, Bound SA, Doyle R, Bowman JP (2016a) Effects of biochar and compost amendments on soil physico-chemical properties and the total community within a temperate agricultural soil. Appl Soil Ecol 98:243–253

    Article  Google Scholar 

  • Abujabhah IS, Doyle R, Bound SA, Bowman JP (2016b) The effect of biochar loading rates on soil fertility, soil biomass, potential nitrification, and soil community metabolic profiles in three different soils. J Soils Sediments 16:2211–2222

    Article  CAS  Google Scholar 

  • Anderson MJ, Willis TJ (2003) Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84:511–525

    Article  Google Scholar 

  • Anderson MJ, Connell SD, Gillanders BM, Diebel CE, Blom WM, Saunders JE, Landers TJ (2005) Relationships between taxonomic resolution and spatial scales of multivariate variation. J Anim Ecol 74:636–646

    Article  Google Scholar 

  • Atkinson CJ, Fitzgerald JD, Hipps NA (2010) Potential mechanisms for achieving agricultural benefits from biochar application to temperate soils: a review. Plant Soil 337:1–18

    Article  CAS  Google Scholar 

  • Ball PN, MacKenzie MD, DeLuca TH, Montana WEH (2010) Wildfire and charcoal enhance nitrification and ammonium-oxidizing bacterial abundance in dry montane forest soils. J Environ Qual 39:1243

    Article  CAS  Google Scholar 

  • Banning NC, Maccarone LD, Fisk LM, Murphy DV (2015) Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil. Scientific Teports 5:11146

    Article  Google Scholar 

  • Beck D (1991) Suitability of charcoal-amended mineral soil as carrier for Rhizobium inoculants. Soil Biol Biochem 23:41–44

    Article  Google Scholar 

  • Berglund LM, DeLuca TH, Zackrisson O (2004) Activated carbon amendments to soil alters nitrification rates in Scots pine forests. Soil Biol Biochem 36:2067–2073

    Article  CAS  Google Scholar 

  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624

    Article  CAS  Google Scholar 

  • Chan K, Van Zwieten L, Meszaros I, Downie A, Joseph S (2008) Using poultry litter biochars as soil amendments. Soil Res 46:437–444

    Article  Google Scholar 

  • Che J, Zhao XQ, Zhou X, Jia ZJ, Shen RF (2015) High pH-enhanced soil nitrification was associated with ammonia-oxidizing bacteria rather than archaea in acidic soils. Appl Soil Ecol 85:21–29

    Article  Google Scholar 

  • Chen J, Li S, Liang C, Xu Q, Li Y, Qin H, Fuhrmann JJ (2017) Response of microbial community structure and function to short-term biochar amendment in an intensively managed bamboo (Phyllostachys praecox) plantation soil: effect of particle size and addition rate. Sci Total Environ 574:24–33

    Article  CAS  Google Scholar 

  • Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A (2015) Complete nitrification by Nitrospira bacteria. Nature 528:504–509

    Article  CAS  Google Scholar 

  • Di H, Cameron K, Shen JP, Winefield C, O’Callaghan M, Bowatte S, He J (2009) Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nat Geosci 2:621–624

    Article  CAS  Google Scholar 

  • Ducey TF, Ippolito JA, Cantrell KB, Novak JM, Lentz RD (2013) Addition of activated switchgrass biochar to an aridic subsoil increases microbial nitrogen cycling gene abundances. Appl Soil Ecol 65:65–72

    Article  Google Scholar 

  • Feng Y, Xu Y, Yu Y, Xie Z, Lin X (2012) Mechanisms of biochar decreasing methane emission from Chinese paddy soils. Soil Biol Biochem 46:80–88

    Article  CAS  Google Scholar 

  • Glaser B, Lehmann J, Zech W (2002) Ameliorating physical and chemical properties of highly weathered soils in the tropics with charcoal—a review. Biol Fertility Soils 35:219–230

    Article  CAS  Google Scholar 

  • Güereña DT, Lehmann J, Thies JE, Enders A, Karanja N, Neufeldt H (2015) Partitioning the contributions of biochar properties to enhanced biological nitrogen fixation in common bean (Phaseolus vulgaris). Biol Fert Soils 51:479–491

    Article  Google Scholar 

  • Gundale MJ, DeLuca TH (2007) Charcoal effects on soil solution chemistry and growth of Koeleria macrantha in the ponderosa pine/Douglas-fir ecosystem. Biol Fert Soils 43:303–311

    Article  CAS  Google Scholar 

  • Hanan EJ, Schimel JP, Dowdy K, D’Antonio CM (2016) Effects of substrate supply, pH, and char on net nitrogen mineralization and nitrification along a wildfire-structured age gradient in chaparral. Soil Biol Biochem 95:87–99

    Article  CAS  Google Scholar 

  • He L, Liu Y, Zhao J, Bi Y, Zhao X, Wang S, Xing G (2016) Comparison of straw-biochar-mediated changes in nitrification and ammonia oxidizers in agricultural oxisols and cambosols. Biol Fert Soils 52:137–149

    Article  CAS  Google Scholar 

  • Jia Z, Conrad R (2009) Bacteria rather than archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11:1658–1671

    Article  CAS  Google Scholar 

  • Keppler F, Boros M, Frankenberg C, Lelieveld J, McLeod A, Pirttilä AM, Röckmann T, Schnitzler J-P (2009) Methane formation in aerobic environments. Environ Chem 6:459

    Article  CAS  Google Scholar 

  • Kolb SE, Fermanich KJ, Dornbush ME (2009) Effect of charcoal quantity on microbial biomass and activity in temperate soils. Soil Science Society of America Journal 1173

  • Kookana R, Sarmah A, Van Zwieten L, Krull E, Singh B (2011) Biochar application to soil: agronomic and environmental benefits and unintended consequences. Adv Agron 112:103

    Article  CAS  Google Scholar 

  • Lane D (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–175

    Google Scholar 

  • Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci 82:6955–6959

    Article  CAS  Google Scholar 

  • Lehmann J, Rillig MC, Thies J, Masiello CA, Hockaday WC, Crowley D (2011) Biochar effects on soil biota—a review. Soil Biol Biochem 43:1812–1836

    Article  CAS  Google Scholar 

  • Liu Y, Yang M, Wu Y, Wang H, Chen Y, Wu W (2011) Reducing CH4 and CO2 emissions from waterlogged paddy soil with biochar. J Soils Sediments 11:930–939

    Article  CAS  Google Scholar 

  • McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P (2011) An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6:610–618

    Article  Google Scholar 

  • Nunes-Alves C (2016) Microbial ecology: do it yourself nitrification. Nat Rev Microbiol 14:61–61

    Article  CAS  Google Scholar 

  • O’Neill B, Grossman J, Tsai MT, Gomes JE, Lehmann J, Peterson J, Neves E, Thies JE (2009) Bacterial community composition in Brazilian Anthrosols and adjacent soils characterized using culturing and molecular identification. Microb Ecol 58:23–35

    Article  Google Scholar 

  • Prommer J, Wanek W, Hofhansl F, Trojan D, Offre P, Urich T, Schleper C, Sassmann S, Kitzler B, Soja G (2014) Biochar decelerates soil organic nitrogen cycling but stimulates soil nitrification in a temperate arable field trial. PLoS One 9:e86388

    Article  Google Scholar 

  • Rondon M, Ramirez J, Lehmann J (2005) Greenhouse gas emissions decrease with charcoal additions to tropical soils, Proceedings of the 3rd USDA Symposium on Greenhouse Gases and Carbon Sequestration. Baltimore pp 208

  • Rondon MA, Lehmann J, Ramírez J, Hurtado M (2007) Biological nitrogen fixation by common beans (Phaseolus vulgaris L.) increases with bio-char additions. Biol Fert Soils 43:699–708

    Article  Google Scholar 

  • Sorrenti G, Buriani G, Gaggìa F, Baffoni L, Spinelli F, Di Gioia D, Toselli M (2017) Soil CO 2 emission partitioning, bacterial community profile and gene expression of Nitrosomonas spp. and Nitrobacter spp. of a sandy soil amended with biochar and compost. Appl Soil Ecol 112:79–89

    Article  Google Scholar 

  • Steinbeiss S, Gleixner G, Antonietti M (2009) Effect of biochar amendment on soil carbon balance and soil microbial activity. Soil Biol Biochem 41:1301–1310

    Article  CAS  Google Scholar 

  • Uzoma K, Inoue M, Andry H, Fujimaki H, Zahoor A, Nishihara E (2011) Effect of cow manure biochar on maize productivity under sandy soil condition. Soil Use Manage 27:205–212

    Article  Google Scholar 

  • van Kessel MA, Speth DR, Albertsen M, Nielsen PH, den Camp HJO, Kartal B, Jetten MS, Lücker S (2015) Complete nitrification by a single microorganism. Nature 528:555–559

    Article  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  CAS  Google Scholar 

  • Xu N, Tan G, Wang H, Gai X (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 

  • Yao Q, Liu J, Yu Z, Li Y, Jin J, Liu X, Wang G (2017) Changes of bacterial community compositions after three years of biochar application in a black soil of northeast China. Appl Soil Ecol 113:11–21

    Article  Google Scholar 

  • Yu L, Tang J, Zhang R, Wu Q, Gong M (2013) Effects of biochar application on soil methane emission at different soil moisture levels. Biol Fert Soils 49:119–128

    Article  Google Scholar 

  • Zhang A, Cui L, Pan G, Li L, Hussain Q, Zhang X, Zheng J, Crowley D (2010) Effect of biochar amendment on yield and methane and nitrous oxide emissions from a rice paddy from Tai Lake plain, China. Agric Ecosyst Environ 139:469–475

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We gratefully thank Mr. Stephen Paterson for technical assistance, and also we would like to express our appreciation to all colleagues who provided help during the sample collection. This research did not receive any specific grant from funding agencies in the public, commercial or not-for-profit sectors.

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Authors and Affiliations

  1. Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 98, Hobart, TAS, 7001, Australia

    Ibrahim S. Abujabhah, Richard B. Doyle, Sally A. Bound & John P. Bowman

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  1. Ibrahim S. Abujabhah
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  2. Richard B. Doyle
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  3. Sally A. Bound
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  4. John P. Bowman
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Correspondence to Ibrahim S. Abujabhah.

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Responsible editor: Hong Jie Di

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Abujabhah, I.S., Doyle, R.B., Bound, S.A. et al. Assessment of bacterial community composition, methanotrophic and nitrogen-cycling bacteria in three soils with different biochar application rates. J Soils Sediments 18, 148–158 (2018). https://doi.org/10.1007/s11368-017-1733-1

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