Bacterial rather than fungal community composition is associated with microbial activities and nutrient-use efficiencies in a paddy soil with short-term organic amendments
- 449 Downloads
Background and aims
Considering the global demands in sustaining agriculture, use of organic amendments is gradually increasing. An improved understanding of the biological process is essential to evaluate the performance of organic amendments on agro-ecosystem.
Soils subjected to different fertilization regimes were collected from a field experiment. Microbial community compositions are assessed with 16S and ITS rRNA gene sequencing and subsequent bioinformatics analysis. Microbial functions are characterized with the geometric mean of the assayed enzyme activities (GMea) and the microbial carbon-use efficiency:nitrogen-use efficiency ratio (CUE:NUE).
Compared with the chemically fertilized soil, the GMea significantly increased in organically amended soils. In contrast, the CUE:NUE was highest in chemically treated soil. These changes of microbial functional indicators were associated with shifts in the bacterial and not the fungal community composition, despite the fact that both the bacterial and fungal community compositions were significantly affected by the fertilization regimes. The abundances of specific soil bacterial taxa, especially the genera Luteimonas and Gemmatimona, were enriched by organic amendments. Soil organic carbon emerged as the major determinant of the bacterial community composition.
Soil microbial activities and nutrient-use efficiencies were dramatically changed along with the alteration of bacterial community composition. Relatively greater abundance of Luteimonas and Gemmatimona taxa in soils might be useful indicators for soil amelioration. Our research could be helpful to provide better strategies for the maintenance of soil fertility.
KeywordsOrganic amendment Bacterial community Fungal community Microbial activity Microbial nutrient-use efficiencies
This work was supported by the National Basic Research Program of China (2015CB150500), the National Key Research and Development Program of China (2017YFD0200206) and the Special Fund for Agro-scientific Research in the Public Interest (20150312205).
- Ai C, Liang GQ, Sun JW, Wang XB, Zhou W (2012) Responses of extracellular enzyme activities and microbial community in both the rhizosphere and bulk soil to long-term fertilization practices in a fluvo-aquic soil. Geoderma 173:330–338. https://doi.org/10.1016/j.geoderma.2011.07.020 CrossRefGoogle Scholar
- Banerjee S, Kirkby CA, Schmutter D, Bissett A, Kirkegaard JA, Richardson AE (2016) Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biol Biochem 97:188–198. https://doi.org/10.1016/j.soilbio.2016.03.017 CrossRefGoogle Scholar
- Blackwood CB, Waldrop MP, Zak DR, Sinsabaugh RL (2007) Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition. Environ Microbiol 9:1306–1316. https://doi.org/10.1111/j.1462-2920.2007.01250.x CrossRefPubMedGoogle Scholar
- Bowles TM, Acosta-Martínez V, Calderón F, Jackson LE (2014) Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively-managed agricultural landscape. Soil Biol Biochem 68:252–262. https://doi.org/10.1016/j.soilbio.2013.10.004 CrossRefGoogle Scholar
- Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena 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. https://doi.org/10.1038/nmeth.f.303 CrossRefPubMedPubMedCentralGoogle Scholar
- Cederlund H, Wessen E, Enwall K, Jones CM, Juhanson J, Pell M, Philippot L, Hallin S (2014) Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla. Appl Soil Ecol 84:62–68. https://doi.org/10.1016/j.apsoil.2014.06.003 CrossRefGoogle Scholar
- Francioli D, Schulz E, Lentendu G, Wubet T, Buscot F, Reitz T (2016) Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front Microbiol 7:1446. https://doi.org/10.3389/fmicb.2016.01446 CrossRefPubMedPubMedCentralGoogle Scholar
- Gardes M, Bruns TD (1993) ITS primers with enhanced specificity for basidiomycetes--application to the identification of mycorrhizae and rusts. Mol Ecol 2:113–118. https://doi.org/10.1111/j.1365-294X.1993.tb00005.x CrossRefPubMedGoogle Scholar
- Kamolmanit B, Vityakon P, Kaewpradit W, Cadisch G, Rasche F (2013) Soil fungal communities and enzyme activities in a sandy, highly weathered tropical soil treated with biochemically contrasting organic inputs. Biol Fertil Soils 49:905–917. https://doi.org/10.1007/s00374-013-0785-7 CrossRefGoogle Scholar
- Lane D (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematicsGoogle Scholar
- Li F, Chen L, Zhang J, Yin J, Huang S (2017) Bacterial community structure after long-term organic and inorganic fertilization reveals important associations between soil nutrients and specific taxa involved in nutrient transformations. Front Microbiol 8:187. https://doi.org/10.3389/fmicb.2017.00187 PubMedPubMedCentralGoogle Scholar
- Mooshammer M, Wanek W, Hammerle I, Fuchslueger L, Hofhansl F, Knoltsch A, Schnecker J, Takriti M, Watzka M, Wild B, Keiblinger KM, Zechmeister-Boltenstern S, Richter A (2014) Adjustment of microbial nitrogen use efficiency to carbon:nitrogen imbalances regulates soil nitrogen cycling. Nat Commun 5:3694. https://doi.org/10.1038/ncomms4694 CrossRefPubMedPubMedCentralGoogle Scholar
- Shanks OC, Kelty CA, Archibeque S, Jenkins M, Newton RJ, McLellan SL, Huse SM, Sogin ML (2011) Community structures of fecal bacteria in cattle from different animal feeding operations. Appl Environ Microbiol 77:2992–3001. https://doi.org/10.1128/AEM.02988-10 CrossRefPubMedPubMedCentralGoogle Scholar
- Smith J, Paul E (1990) The significance of soil microbial biomass estimationsGoogle Scholar
- Sul WJ, Asuming-Brempong S, Wang Q, Tourlousse DM, Penton CR, Deng Y, Rodrigues JLM, Adiku SGK, Jones JW, Zhou JZ, Cole JR, Tiedje JM (2013) Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon. Soil Biol Biochem 65:33–38. https://doi.org/10.1016/j.soilbio.2013.05.007 CrossRefGoogle 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. https://doi.org/10.1016/j.soilbio.2015.05.007 CrossRefGoogle Scholar
- Sun R, Dsouza M, Gilbert JA, Guo X, Wang D, Guo Z, Ni Y, Chu H (2016) Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter. Environ Microbiol 18:5137–5150. https://doi.org/10.1111/1462-2920.13512 CrossRefPubMedGoogle Scholar
- Swift MJ, Heal OW, Anderson JM (1979) Decomposition in terrestrial ecosystems. Q Rev Biol 83:2772–2774Google Scholar
- Tian W, Wang L, Li Y, Zhuang KM, Li G, Zhang JB, Xiao XJ, Xi YG (2015) Responses of microbial activity, abundance, and community in wheat soil after three years of heavy fertilization with manure-based compost and inorganic nitrogen. Agric Ecosyst Environ 213:219–227. https://doi.org/10.1016/j.agee.2015.08.009 CrossRefGoogle Scholar
- Voroney R, Winter J, Beyaert R (1993) Soil microbial biomass C and N. Soil sampling and methods of analysis. 277–286Google Scholar
- Wei WL, Yan Y, Cao J, Christie P, Zhang FS, Fan MS (2016) Effects of combined application of organic amendments and fertilizers on crop yield and soil organic matter: an integrated analysis of long-term experiments. Agric Ecosyst Environ 225:86–92. https://doi.org/10.1016/j.agee.2016.04.004 CrossRefGoogle Scholar
- White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protocols. Academic Press, San DiegoGoogle Scholar
- WRB IWG (2015) World reference base for soil resources 2014, update 2015 International soil classification system for naming soils and creating legends for soil maps. World Soil Resources Reports 106Google Scholar
- Zhang L, Wang X, Yu M, Qiao Y, Zhang X-H (2015) Genomic analysis of Luteimonas abyssi XH031T: insights into its adaption to the subseafloor environment of South Pacific Gyre and ecological role in biogeochemical cycle. BMC Genomics 16. https://doi.org/10.1186/s12864-015-2326-2
- Zhong WH, Bian BY, Gao N, Min J, Shi WM, Lin XG, Shen WS (2016) Nitrogen fertilization induced changes in ammonia oxidation are attributable mostly to bacteria rather than archaea in greenhouse-based high N input vegetable soil. Soil Biol Biochem 93:150–159. https://doi.org/10.1016/j.soilbio.2015.11.003 CrossRefGoogle Scholar