Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies
Abstract
:1. Introduction
2. Materials and Methods
2.1. Field Site Description
2.2. Soil Sampling and Chemical Properties Analysis
2.3. DNA Extraction and Real-Time PCR
2.4. Illumina MiSeq Sequencing
2.5. Processing of Sequencing Data
2.6. Statistical Analysis
3. Results
3.1. Soil Chemical Properties
3.2. Abundance of the Bacterial 16S rDNA Gene
3.3. Bacterial Community Alpha Diversity
3.4. Bacterial Community Composition
3.5. Bacterial Community Beta Diversity
3.6. Environmental Effects on the Bacterial Community Structure
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Ahn, J.H.; Song, J.; Kim, B.Y.; Kim, M.S.; Joa, J.H.; Weon, H.Y. Characterization of the bacterial and archaeal communities in rice field soils subjected to long-term fertilization practices. J. Microbiol. 2012, 50, 754–765. [Google Scholar] [CrossRef] [PubMed]
- Shang, Q.Y.; Ling, N.; Feng, X.M.; Yang, X.X.; Wu, P.P.; Zou, J.W.; Shen, Q.R.; Guo, S.W. Soil fertility and its significance to crop productivity and sustainability in typical agroecosystem: A summary of long-term fertilizer experiments in China. Plant Soil 2014, 381, 13–23. [Google Scholar] [CrossRef]
- Balasooriya, W.K.; Huygens, D.; Rajapaksha, R.M.C.P.; Boeckx, P. Effect of rice variety and fertilizer type on the active microbial community structure in tropical paddy fields in Sri Lanka. Geoderma 2016, 265, 87–95. [Google Scholar] [CrossRef]
- Chen, C.; Zhang, J.N.; Lu, M.; Qin, C.; Chen, Y.H.; Yang, L.; Huang, Q.W.; Wang, J.C.; Shen, Z.G.; Shen, Q.R. Microbial communities of an arable soil treated for 8 years with organic and inorganic fertilizers. Biol. Fertil. Soils 2016, 52, 455–467. [Google Scholar] [CrossRef]
- Li, C.H.; Yan, K.; Tang, L.S.; Jia, Z.J.; Li, Y. Change in deep soil microbial communities due to long term fertilization. Soil Biol. Biochem. 2014, 75, 264–272. [Google Scholar] [CrossRef]
- Lazcano, C.; Gómez-Brandón, M.; Revilla, P.; Domínguez, J. Short-term effects of organic and inorganic fertilizers on soil microbial community structure and function. Biol. Fertil. Soils 2013, 49, 723–733. [Google Scholar] [CrossRef]
- Wei, M.; Hu, G.Q.; Wang, H.; Bai, E.; Luo, Y.H.; Zhang, A.J.; Zhuge, Y.P. 35 years of manure and chemical fertilizer application alters soil microbial community composition in a Fluvo-aquic soil in Northern China. Eur. J. Soil Biol. 2017, 82, 27–34. [Google Scholar] [CrossRef]
- Nannipieri, P.; Ascher, J.; Ceccherini, M.T.; Landi, L.; Pietramellara, G.; Renella, G. Microbial diversity and soil functions. Eur. J. Soil Sci. 2003, 54, 655–670. [Google Scholar] [CrossRef] [Green Version]
- Brussaard, L.; de Ruiter, P.C.; Brown, G.G. Soil biodiversity for agricultural sustainability. Agric. Ecosyst. Environ. 2007, 121, 233–244. [Google Scholar] [CrossRef]
- Lynn, T.M.; Liu, Q.; Hu, Y.J.; Yuan, H.Z.; Wu, X.H.; Khai, A.A.; Wu, J.H.; Ge, T.D. Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil. Arch. Microbiol. 2017, 199, 711–721. [Google Scholar] [CrossRef]
- Yang, Y.D.; Ren, Y.F.; Wang, X.Q.; Hu, Y.G.; Wang, Z.M.; Zeng, Z.H. Ammonia-oxidizing archaea and bacteria responding differently to fertilizer type and irrigation frequency as revealed by Illumina Miseq sequencing. J. Soils Sediments 2018, 18, 1029–1040. [Google Scholar] [CrossRef]
- Wang, J.C.; Song, Y.; Ma, T.F.; Raza, W.; Li, J.; Howland, J.G.; Huang, Q.W.; Shen, Q.R. Impacts of inorganic and organic fertilization treatments on bacterial and fungal communities in a paddy soil. Appl. Soil Ecol. 2017, 112, 42–50. [Google Scholar] [CrossRef]
- Kennedy, A.C.; Smith, K.L. Soil microbial diversity and the sustainability of agricultural soils. Plant Soil 1995, 170, 75–86. [Google Scholar] [CrossRef]
- Saleem, M. Microbiome Community Ecology: Fundamentals and Applications; Springer: Berlin, Germany, 2015. [Google Scholar]
- Lei, Y.P.; Xiao, Y.L.; Li, L.F.; Jiang, C.Q.; Zu, C.L.; Li, T.; Cao, H. Impact of tillage practices on soil bacterial diversity and composition under the tobacco-rice rotation in China. J. Microbiol. 2017, 55, 349–356. [Google Scholar] [CrossRef] [PubMed]
- Gomez, E.; Ferreras, L.; Toresani, S. Soil bacterial functional diversity as influenced by organic amendment application. Bioresour. Technol. 2006, 97, 1484–1489. [Google Scholar] [CrossRef] [PubMed]
- Bonilla, N.; Cazorla, F.M.; Martínez-Alonso, M.; Hermoso, J.M.; González-Fernández, J.J.; Gaju, N.; Landa, B.B.; de Vicente, A. Organic amendments and land management affect bacterial community composition, diversity and biomass in avocado crop soils. Plant Soil 2012, 357, 215–226. [Google Scholar] [CrossRef] [Green Version]
- Yevdokimov, I.; Gattinger, A.; Buegger, F.; Munch, J.C.; Schloter, M. Changes in microbial community structure in soil as a result of different amounts of nitrogen fertilization. Biol. Fertil. Soils 2008, 44, 1103–11106. [Google Scholar] [CrossRef]
- Wu, M.N.; Qin, H.L.; Chen, Z.; Wu, J.S.; Wei, W.X. Effect of long-term fertilization on bacterial composition in rice paddy soil. Biol. Fertil. Soils 2011, 47, 397–405. [Google Scholar] [CrossRef]
- Xun, W.B.; Xu, Z.H.; Li, W.; Ren, Y.; Huang, T.; Ran, W.; Wang, B.R.; Shen, Q.R.; Zhang, R.F. Long-term organic-inorganic fertilization ensures great soil productivity and bacterial diversity after natural-to-agricultural ecosystem conversion. J. Microbiol. 2016, 54, 611–617. [Google Scholar] [CrossRef]
- Mandal, A.; Patra, A.K.; Singh, D.; Swarup, A.; Ebhin, M.R. Effect of long-term application of manure and fertilizer on biological and biochemical activities in soil during crop development stages. Bioresour. Technol. 2007, 98, 3585–3592. [Google Scholar] [CrossRef]
- Treseder, K.K. Nitrogen additions and microbial biomass: A meta-analysis of ecosystem studies. Ecol. Lett. 2008, 11, 1111–1120. [Google Scholar] [CrossRef] [PubMed]
- Shen, J.P.; Zhang, L.M.; Guo, J.F.; Ray, J.L.; He, J.Z. Impact of long-term fertilization practices on the abundance and composition of soil bacterial communities in northeast China. Appl. Soil Ecol. 2010, 46, 119–124. [Google Scholar] [CrossRef]
- Zhong, W.H.; Gu, T.; Wang, W.; Zhang, B.; Lin, X.G.; Huang, Q.R.; Shen, W.S. The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant Soil 2010, 326, 511–522. [Google Scholar] [CrossRef]
- Zhou, J.; Guan, D.W.; Zhou, B.K.; Zhao, B.S.; Ma, M.C.; Qin, J.; Jiang, X.; Chen, S.F.; Cao, F.M.; Shen, D.L.; et al. Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China. Soil Biol. Biochem. 2015, 90, 42–51. [Google Scholar] [CrossRef]
- FAO. Food and Agriculture Organization Statistical Database. 2013. Available online: http://faostat3.fao.org (accessed on 6 June 2018).
- He, J.Z.; Shen, J.P.; Zhang, L.M.; Zhu, Y.G.; Zheng, Y.M.; Xu, M.G.; Di, H.J. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environ. Microbiol. 2007, 9, 2364–2374. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- FAO. FAO-Unesco Soil Map of the World; UNESCO: Paris, France, 1974; Volume VIII. [Google Scholar]
- Bao, S.D. Soil Agro-Chemistrical Analysis, 3rd ed.; China Agricultural Press: Beijing, China, 2000. [Google Scholar]
- Suzuki, M.T.; Taylor, L.T.; DeLong, E.F. Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl. Environ. Microbiol. 2000, 66, 4605–4614. [Google Scholar] [CrossRef] [PubMed]
- Walter, J.; Tannock, G.W.; Tilsalatimisjarvi, A.; Rodtong, S.; Loach, D.M.; Munro, K.; Alatossava, T. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Appl. Environ. Microbiol. 2000, 66, 297–303. [Google Scholar] [CrossRef] [PubMed]
- McBain, A.J.; Bartolo, R.G.; Catrenich, C.E.; Charbonneau, D.; Ledder, R.G.; Rickard, A.H.; Symmons, S.A.; Gilbert, P. Microbial characterization of biofilms in domestic drains and the establishment of stable biofilm microcosms. Appl. Environ. Microbiol. 2003, 69, 177–185. [Google Scholar] [CrossRef] [PubMed]
- Caporaso, G.; Kuczynski, J.; Stombaugh, J.; Bittinger, K.; Bushman, F.D.; Costello, E.K.; Fierer, N.; Pea, A.G.; Goodrich, J.K.; Gordon, J.I.; et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7, 335–336. [Google Scholar] [CrossRef] [Green Version]
- Edgar, R.C. UPARSE: Highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 2013, 10, 996–998. [Google Scholar] [CrossRef]
- Edgar, R.C.; Haas, B.J.; Clemente, J.C.; Quince, C.; Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27, 2194–2200. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Wang, Q.; Garrity, G.M.; Tiedje, J.M.; Cole, J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73, 5261–5267. [Google Scholar] [CrossRef] [PubMed]
- Amato, K.R.; Yeoman, C.J.; Kent, A.; Righini, N.; Carbonero, F.; Estrada, A.; Gaskins, H.R.; Stumpf, R.M.; Yildirim, S.; Torralba, M.; et al. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J. 2013, 7, 1344–1353. [Google Scholar] [CrossRef] [PubMed]
- Schloss, P.D.; Gevers, D.; Westcott, S.L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 2011, 6, e27310. [Google Scholar] [CrossRef] [PubMed]
- Paliy, O.; Shankar, V. Application of multivariate statistical techniques in microbial ecology. Mol. Ecol. 2016, 25, 1032–1057. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Team, R.C. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2014; Available online: http://cran.r-project.org (accessed on 10 June 2018).
- Rousk, J.; Bååth, E.; Brookes, P.C.; Lauber, C.L.; Lozupone, C.; Caporaso, J.G.; Knight, R.; Fierer, N. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 2010, 4, 1340–1351. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, J.J.; Sui, Y.Y.; Yu, Z.H.; Shi, Y.; Chu, H.Y.; Jin, J.; Liu, X.B.; Wang, G.H. High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China. Soil Biol. Biochem. 2014, 70, 113–122. [Google Scholar] [CrossRef]
- Zhu, Y.G.; Johnson, T.A.; Su, J.Q.; Qiao, M.; Guo, G.X.; Stedtfeld, R.D.; Hashsham, A.S.; Tiedje, J.M. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc. Natl. Acad. Sci. USA 2013, 110, 3435–3440. [Google Scholar] [CrossRef] [Green Version]
- Green, J.L.; Holmes, A.J.; Westoby, M.; Oliver, I.; Briscoe, D.; Dangerfield, M.; Gillings, M.; Beattie, A.J. Spatial scaling of microbial eukaryote diversity. Nature 2004, 432, 747–750. [Google Scholar] [CrossRef]
- Fierer, N.; Jackson, R.B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA 2006, 103, 626–631. [Google Scholar] [CrossRef] [Green Version]
- Fierer, N.; Bradford, M.A.; Jackson, R.B. Toward an ecological classification of soil bacteria. Ecology 2007, 88, 1354–1364. [Google Scholar] [CrossRef] [PubMed]
- Eilers, K.G.; Lauber, C.L.; Knight, R.; Fierer, N. Shifts in bacterial community structure associated with inputs of low molecular weight carbon compounds to soil. Soil Biol. Biochem. 2010, 42, 896–903. [Google Scholar] [CrossRef]
- Jones, R.T.; Robeson, M.S.; Lauber, C.L.; Hamady, M.; Knight, R.; Fierer, N. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analysis. ISME J. 2009, 3, 442–453. [Google Scholar] [CrossRef] [PubMed]
- Ramirez, K.S.; Lauber, C.L.; Knight, R.; Bradford, M.A.; Fierer, N. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology 2010, 91, 3463–3470. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Tian, J.; Lou, Y.L.; Gao, Y.; Fang, H.J.; Liu, S.T.; Xu, M.G.; Blagodatskaya, E.; Kuzyakov, Y. Response of soil organic matter fractions and composition of microbial community to long-term organic and mineral fertilization. Biol. Fertil. Soils 2017, 53, 523–532. [Google Scholar] [CrossRef]
- Sun, R.B.; Zhang, X.X.; Guo, X.S.; Wang, D.Z.; Chu, H.Y. 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. 2015, 88, 9–18. [Google Scholar] [CrossRef]
- Chen, D.M.; Xing, W.; Lan, Z.C.; Saleem, M.; Wu, Y.; Hu, S.J.; Bai, Y.F. Direct and indirect effects of nitrogen enrichment on soil organisms and carbon and nitrogen mineralization in a semi-arid grassland. Funct. Ecol. 2018. [Google Scholar] [CrossRef]
Treatment | pH (H2O) | NH4+-N (mg kg−1) | NO3−-N (mg kg−1) | TN (g kg−1) | SOC (g kg−1) | C/N Ratio |
---|---|---|---|---|---|---|
CK | 6.78 ± 0.02a | 1.99 ± 0.18a | 2.14 ± 0.07c | 2.15 ± 0.04d | 13.23 ± 0.49c | 6.15 ± 0.14a |
CF | 6.73 ± 0.01ab | 1.55 ± 0.04b | 4.45 ± 0.23b | 2.33 ± 0.06c | 14.33 ± 0.22c | 6.17 ± 0.20a |
CFM1 | 6.70 ± 0.01b | 1.64 ± 0.07b | 6.20 ± 0.28a | 3.21 ± 0.06b | 20.04 ± 0.25b | 6.26 ± 0.16a |
CFM2 | 6.69 ± 0.01b | 1.54 ± 0.08b | 6.33 ± 0.40a | 3.51 ± 0.02a | 22.40 ± 0.36a | 6.39 ± 0.12a |
Item | pH | NH4+-N | NO3−-N | TN | SOC | C/N Ratio |
---|---|---|---|---|---|---|
Abundance | −0.705 * | −0.740 ** | 0.855 ** | 0.581 * | 0.579 * | 0.229 |
ACE index | 0.077 | 0.271 | −0.162 | −0.274 | −0.278 | −0.192 |
Chao1 index | 0.076 | 0.308 | −0.191 | −0.282 | −0.285 | −0.199 |
Shannon index | 0.249 | 0.400 | −0.395 | −0.299 | −0.283 | −0.088 |
inverse Simpson index | 0.196 | 0.335 | −0.301 | −0.122 | −0.100 | −0.008 |
© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Yang, Y.; Wang, P.; Zeng, Z. Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies. Agronomy 2019, 9, 14. https://doi.org/10.3390/agronomy9010014
Yang Y, Wang P, Zeng Z. Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies. Agronomy. 2019; 9(1):14. https://doi.org/10.3390/agronomy9010014
Chicago/Turabian StyleYang, Yadong, Peixin Wang, and Zhaohai Zeng. 2019. "Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies" Agronomy 9, no. 1: 14. https://doi.org/10.3390/agronomy9010014
APA StyleYang, Y., Wang, P., & Zeng, Z. (2019). Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies. Agronomy, 9(1), 14. https://doi.org/10.3390/agronomy9010014