2022, Volume 12, Issue 5
Engineering >> 2022, Volume 12, Issue 5 doi: 10.1016/j.eng.2021.09.012
Responses of Soil Bacterial Diversity to Fertilization are Driven by Local Environmental Context Across China
a State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
b Department of Physical, Chemical, and Natural Systems, Pablo de Olavide University, Sevilla 41013, Spain
c State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
d Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
e National Observation Station of the Hailun Agroecology System, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 130102, China
f College of Land and Environment, National Engineering Laboratory for Efficient Utilization of Soil and Fertilizer Resources, Shenyang Agricultural University, Shenyang 110866, China
g Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China
h Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, China
i Institute of Soil and Water Conservation, Northwest A&F University, Chinese Academy of Science & Ministry of Water Resources, Yangling 712100, China
j Fukang Station of Desert Ecology, Key Laboratory of Oasis Ecology and Desert Environment, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
k Key Laboratory of Mountain Environment Evolvement and Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
l Qiyang Agroecosystem of the National Field Experimental Station, Yongzhou 426199, China
m National Engineering Laboratory for Improving the Quality of Arable Land, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
n Jiangxi Institute of Red Soil, Nanchang 331717, China
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Abstract
Soil microbial diversity is extremely vulnerable to fertilization, which is one of the main anthropogenic activities associated with global changes. Yet we know little about how and why soil microbial diversity responds to fertilization across contrasting local ecological contexts. This knowledge is fundamental for predicting changes in soil microbial diversity in response to ongoing global changes. We analyzed soils from ten 20-year field fertilization (organic and/or inorganic) experiments across China and found that the national-scale responses of soil bacterial diversity to fertilization are dependent on ecological context. In acidic soils from regions with high precipitation and soil fertility, inorganic fertilization can result in further acidification, resulting in negative impacts on soil bacterial diversity. In comparison, organic fertilization causes a smaller disturbance to soil bacterial diversity. Despite the overall role of environmental contexts in driving soil microbial diversity, a small group of bacterial taxa were found to respond to fertilization in a consistent way across contrasting regions throughout China. Taxa such as Nitrosospira and Nitrososphaera, which benefit from nitrogen fertilizer addition, as well as Chitinophagaceae, Bacilli, and phototrophic bacteria, which respond positively to organic fertilization, could be used as bioindicators for soil fertility in response to fertilization at the national scale. Overall, our work provides new insights into the importance of local environmental context in determining the responses of soil microbial diversity to fertilization, and identifies regions with acidic soils wherein soil microbial diversity is more vulnerable to fertilization at the national scale.
Keywords
Nutrient addition ; Anthropogenic activity ; Biodiversity ; Soil pH
SupplementaryMaterials
Figures
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References
[ 1 ] Delgado-Baquerizo M, Bardgett RD, Vitousek PM, Maestre FT, Williams MA, Eldridge DJ, et al. Changes in belowground biodiversity during ecosystem development. Proc Natl Acad Sci USA 2019;116(14):6891–6. link1
[ 2 ] Bardgett RD, van der Putten WH. Belowground biodiversity and ecosystem functioning. Nature 2014;515(7528):505–11. link1
[ 3 ] Wall DH, Nielsen UN, Six J. Soil biodiversity and human health. Nature 2015;528(7580):69–76. link1
[ 4 ] Leff JW, Jones SE, Prober SM, Barberán A, Borer ET, Firn JL, et al. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. Proc Natl Acad Sci USA 2015;112(35):10967–72. link1
[ 5 ] Sayer J, Cassman KG. Agricultural innovation to protect the environment. Proc Natl Acad Sci USA 2013;110(21):8345–8. link1
[ 6 ] Seufert V, Ramankutty N, Foley JA. Comparing the yields of organic and conventional agriculture. Nature 2012;485(7397):229–32. link1
[ 7 ] Tilman D, Cassman KG, Matson PA, Naylor R, Polasky S. Agricultural sustainability and intensive production practices. Nature 2002;418 (6898):671–7. link1
[ 8 ] Feng Y, Chen R, Hu J, Zhao F, Wang J, Chu H, et al. Bacillus asahii comes to the fore in organic manure fertilized alkaline soils. Soil Biol Biochem 2015;81:186–94. link1
[ 9 ] Van der Bom F, Nunes I, Raymond NS, Hansen V, Bonnichsen L, Magid J, et al. Long-term fertilisation form, level and duration affect the diversity, structure and functioning of soil microbial communities in the field. Soil Biol Biochem 2018;122:91–103. link1
[10] Sun L, Xun W, Huang T, Zhang G, Gao J, Ran W, et al. Alteration of the soil bacterial community during parent material maturation driven by different fertilization treatments. Soil Biol Biochem 2016;96:207–15. link1
[11] Ye G, Lin Y, Liu D, Chen Z, Luo J, Bolan N, et al. Long-term application of manure over plant residues mitigates acidification, builds soil organic carbon and shifts prokaryotic diversity in acidic Ultisols. Appl Soil Ecol 2019;133:24–33. link1
[12] Feng Y, Guo Z, Zhong L, Zhao F, Zhang J, Lin X. Balanced fertilization decreases environmental filtering on soil bacterial community assemblage in north China. Front Microbiol 2017;8:2376. link1
[13] Sun R, Zhang X, Guo X, Wang D, Chu H. 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. link1
[14] Ramirez KS, Craine JM, Fierer N. Consistent effects of nitrogen amendments on soil microbial communities and processes across biomes. Glob Change Biol 2012;18(6):1918–27. link1
[15] Whitaker RJ, Grogan DW, Taylor JW. Geographic barriers isolate endemic populations of hyperthermophilic archaea. Science 2003;301(5635):976–8. link1
[16] Nelson MB, Martiny AC, Martiny JBH. Global biogeography of microbial nitrogen-cycling traits in soil. Proc Natl Acad Sci USA 2016;113(29):8033–40. link1
[17] Rousk J, Bååth E, Brookes PC, Lauber CL, Lozupone C, Caporaso JG, et al. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J 2010;4(10):1340–51. link1
[18] Chen X, Cui Z, Fan M, Vitousek P, Zhao M, Ma W, et al. Producing more grain with lower environmental costs. Nature 2014;514(7523):486–9. link1
[19] Food and Agriculture Organization of the United Nations. FAOSTAT [Internet]. Rome: Statistics Division of the Food and Agriculture Organization of the United Nations [cited Statistics Division of the Food and Agriculture Organization of the United Nations. Agriculture database. (2017). FAOSTAT http://faostat3.fao.org/faostatgateway/go/to/home/E.
[20] Lu R. Analytical methods of soil and agricultural chemistry. Beijing: China Agricultural Science and Technology Press; 1999. Chinese. link1
[21] Muyzer G, Teske A, Wirsen CO, Jannasch HW. Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 1995;164(3):165–72. link1
[22] Lane DJ. 16S/23S rRNA sequencing in nucleic acid techniques in bacterial systematics. New York: Wiley; 1991. link1
[23] Magoc T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 2011;27(21):2957–63. link1
[24] Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013;10(10):996–8. link1
[25] Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 2011;17(1):10–2. link1
[26] Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 2007;73(16):5261–7. link1
[27] Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 2010;26(2):266–7. link1
[28] Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009;26 (7):1641–50. link1
[29] Viechtbauer W. Conducting meta-analyses in R with the metafor package. J Stat Softw 2010;36(3):1–48. link1
[30] Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol 2001;26(1):32–46. link1
[31] Evans SE, Wallenstein MD, Fierer N. Climate change alters ecological strategies of soil bacteria. Ecol Lett 2014;17(2):155–64. link1
[32] Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, et al. A global atlas of the dominant bacteria found in soil. Science 2018;359(6373):320–5. link1
[33] Legendre P, Legendre L. Numerical ecology. 3rd ed. Amsterdam: Elsevier; 2002. link1
[34] Veˇtrovsky´ T, Kohout P, Kopecky´ M, Machac A, Man M, Bahnmann BD, et al. A meta-analysis of global fungal distribution reveals climate-driven patterns. Nat Commun 2019;10(1):5142. link1
[35] Neilson JW, Califf K, Cardona C, Copeland A, van Treuren W, Josephson KL, et al. Significant impacts of increasing aridity on the arid soil microbiome. mSystems 2017;2(3):e00195–16. link1
[36] Joner EJ, Eldhuset TD, Lange H, Frostegård Å. Changes in the microbial community in a forest soil amended with aluminium in situ. Plant Soil 2005;275(1-2):295–304. link1
[37] Lammel DR, Barth G, Ovaskainen O, Cruz LM, Zanatta JA, Ryo M, et al. Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures. Microbiome 2018;6(1). link1
[38] Liu W, Wang Q, Wang B, Wang X, Franks AE, Teng Y, et al. Changes in the abundance and structure of bacterial communities under long-term fertilization treatments in a peanut monocropping system. Plant Soil 2015;395(1-2):415–27. link1
[39] Wang Q, Jiang X, Guan D, Wei D, Zhao B, Ma M, et al. Long-term fertilization changes bacterial diversity and bacterial communities in the maize rhizosphere of Chinese Mollisols. Appl Soil Ecol 2018;125:88–96. link1
[40] Lauber CL, Hamady M, Knight R, Fierer N. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl Environ Microbiol 2009;75(15):5111–20. link1
[41] Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 2006;103(3):626–31. link1
[42] Chen R, Zhong L, Jing Z, Guo Z, Li Z, Lin X, et al. Fertilization decreases compositional variation of paddy bacterial community across geographical gradient. Soil Biol Biochem 2017;114:181–8. link1
[43] Conyers M, Liu DL, Kirkegaard J, Orgill S, Oates A, Li G, et al. A review of organic carbon accumulation in soils within the agricultural context of southern New South Wales, Australia. Field Crops Res 2015;184:177–82. link1
[44] Walker TW, Syers JK. The fate of phosphorus during pedogenesis. Geoderma 1976;15(1):1–19. link1
[45] Martin HW, Sparks DL. Kinetics of nonexchangeable potassium release from two coastal plain soils. Soil Sci Soc Am J 1983;47(5):883–7. link1
[46] Fierer N, Bradford MA, Jackson RB. Toward an ecological classification of soil bacteria. Ecology 2007;88(6):1354–64. link1
[47] Wang Z, Zhang Q, Staley C, Gao H, Ishii S, Wei X, et al. Impact of long-term grazing exclusion on soil microbial community composition and nutrient availability. Biol Fertil Soils 2019;55(2):121–34. link1
[48] Wu L, Yang Y, Chen S, Jason Shi Z, Zhao M, Zhu Z, et al. Microbial functional trait of rRNA operon copy numbers increases with organic levels in anaerobic digesters. ISME J 2017;11(12):2874–8. link1
[49] Liang CM, Hung CH, Hsu SC, Yeh IC. Purple nonsulfur bacteria diversity in activated sludge and its potential phosphorus-accumulating ability under different cultivation conditions. Appl Microbiol Biotechnol 2010;86(2):709–19. link1
[50] Wang L, Luo X, Liao H, Chen W, Wei D, Cai P, et al. Ureolytic microbial community is modulated by fertilization regimes and particle-size fractions in a black soil of northeastern China. Soil Biol Biochem 2018;116:171–8. link1
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