JIA-2021-0475 土壤理化性质、种植模式和地理位置对中国4个玉米主产区土壤原核生物群落的影响

doi:10.1016/S2095-3119(21)63772-3

Journal of Integrative Agriculture ›› 2022, Vol. 21 ›› Issue (7): 2145-2157.DOI: 10.1016/S2095-3119(21)63772-3

所属专题：农业生态环境-土壤微生物合辑Agro-ecosystem & Environment—Soil microbe

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JIA-2021-0475 土壤理化性质、种植模式和地理位置对中国4个玉米主产区土壤原核生物群落的影响

收稿日期:2021-03-18 接受日期:2021-05-19 出版日期:2022-07-01 发布日期:2021-05-19

The effects of soil properties, cropping systems and geographic location on soil prokaryotic communities in four maize production regions across China

TIAN Xue-liang^{1, 2*}, LIU Jia-jia^3*, LIU Quan-cheng¹, XIA Xin-yao^{1, 3}, PENG Yong⁴, Alejandra I. HUERTA⁵, YAN Jian-bing⁴, LI Hui³, LIU Wen-de¹

¹ State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
² Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, P.R.China
³ School of Biological Science and Technology, University of Jinan, Jinan 250022, P.R.China
⁴ National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P.R.China
⁵ Department of Entomology and Plant Pathology, North Carolina State University, Raleigh 27606, USA

Received:2021-03-18 Accepted:2021-05-19 Online:2022-07-01 Published:2021-05-19
About author:TIAN Xue-liang, E-mail: tianxueliang1978@163.com; LIU Jia-jia, E-mail: jjl1223@126.com; Correspondence LI Hui, Tel: +86-531-82765807, E-mail: bio_lih@ujn.edu.cn; LIU Wen-de, Tel: +86-10-62815921, E-mail: liuwende@caas.cn * These authors contributed equally to this study.
Supported by:
This research was supported by the National Program for Support of Top-notch Young Professionals, China, the Open Research Fund of State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences (SKLQF201508) and the Project of Plant Protection Key Discipline of Henan Province, China.

摘要/Abstract

摘要：

我们利用宏基因组技术研究了玉米种植模式、土壤性质和地理位置对中国4个玉米主产区土壤原核生物群落的影响。在本研究所有土壤样品中，α-变形菌纲、γ-变形菌纲、β-变形菌纲、芽单胞菌纲、酸杆菌纲和放线菌纲是共同优势原核生物类群。非度量多维尺度法分析发现，原核生物群落划分4个组，且与4个玉米种植区相吻合。冗余分析表明，土壤性质(尤其是pH)、地理位置和种植模式共同影响土壤原核生物群落多样性，而地理位置（纬度）、pH和种植模式影响土壤原核生物功能基因。4个玉米生产区土壤原核生物某些代谢途径中的功能基因丰度差异显著，如微生物-微生物相互作用、芳香化合物降解、原核生物固碳途径和微生物在不同环境中代谢等。总之，土壤pH、种植制度和地理位置三者共同影响了我国4个玉米主产区土壤原核生物群落和功能基因。研究结果有助于深入了解大尺度农业生态系统中土壤原核生物群落的组成和基因功能。

Abstract: The diversity of prokaryotic communities in soil is shaped by both biotic and abiotic factors. However, little is known about the major factors shaping soil prokaryotic communities at a large scale in agroecosystems. To this end, we undertook a study to investigate the impact of maize production cropping systems, soil properties and geographic location (latitude and longitude) on soil prokaryotic communities using metagenomic techniques, across four distinct maize production regions in China. Across all study sites, the dominant prokaryotes in soil were Alphaproteobacteria, Gammaproteobacteria, Betaproteobacteria, Gemmatimonadetes, Acidobacteria, and Actinobacteria. Non-metric multidimensional scaling revealed that prokaryotic communities clustered into the respective maize cropping systems in which they resided. Redundancy analysis (RDA) showed that soil properties especially pH, geographic location and cropping system jointly determined the diversity of the prokaryotic communities. The functional genes of soil prokaryotes from these samples were chiefly influenced by latitude, soil pH and cropping system, as revealed by RDA analysis. The abundance of genes in some metabolic pathways, such as genes involved in microbe–microbe interactions, degradation of aromatic compounds, carbon fixation pathways in prokaryotes and microbial metabolism were markedly different across the four maize production regions. Our study indicated that the combination of soil pH, cropping system and geographic location significantly influenced the prokaryotic community and the functional genes of these microbes. This work contributes to a deeper understanding of the composition and function of the soil prokaryotic community across large-scale production systems such as maize.

Key words: metagenome , cropping system , maize , soil prokaryotes

. JIA-2021-0475 土壤理化性质、种植模式和地理位置对中国4个玉米主产区土壤原核生物群落的影响[J]. Journal of Integrative Agriculture, 2022, 21(7): 2145-2157.

TIAN Xue-liang, LIU Jia-jia, LIU Quan-cheng, XIA Xin-yao, PENG Yong, Alejandra I. HUERTA, YAN Jian-bing, LI Hui, LIU Wen-de. The effects of soil properties, cropping systems and geographic location on soil prokaryotic communities in four maize production regions across China [J]. Journal of Integrative Agriculture, 2022, 21(7): 2145-2157.

参考文献

Acosta-Martínez V, Dowd S, Sun Y, Allen V. 2008. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biology and Biochemistry, 40, 2762–2770.
Allen A P, Brown J H, Gillooly J F. 2002. Global biodiversity, biochemical kinetics, and the energetic-equivalence rule. Science, 297, 1545–1548.
Ananda M G, Ananda M R, Reddy V C, Kumar M Y A. 2006. Soil pH, electrical conductivity and organic carbon content of soil as influenced by paddy-groundnut cropping system and different organic sources. Environment and Ecology, 24, 158–160.
Bahram M, Hildebrand F, Forslund S K, Anderson J L, Soudzilovskaia N A, Bodegom P M, Bengtsson-Palme J, Anslan S, Coelho L P, Harend H, Huerta-Cepas J, Medema M H, Maltz M R, Mundra S, Olsson P A, Pent M, Põlme S, Sunagawa S, Ryberg M, Tedersoo L, et al. 2018. Structure and function of the global topsoil microbiome. Nature, 560, 233–237.
Bakker M G, Manter D K, Sheflin A M, Weir T L, Vivanco J M. 2012. Harnessing the rhizosphere microbiome through plant breeding and agricultural management. Plant and Soil, 360, 1–13.
Berendsen R L, Pieterse C M, Bakker P A. 2012. The rhizosphere microbiome and plant health. Trends in Plant Science, 17, 478–486.
Besemer J, Borodovsky M. 2005. GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research, 33, W451–W454.
Bissett A, Richardson A E, Baker G, Wakelin S, Thrall P H. 2010. Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales. Molecular Ecology, 19, 4315–4327.
Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120.
Busby P E, Soman C, Wagner M R, Friesen M L, Kremer J, Bennett A, Morsy M, Eisen J A, Leach J E, Dangl J L. 2017. Research priorities for harnessing plant microbiomes in sustainable agriculture. PLoS Biology, 15, e2001793.
Chai Q, Qin A Z, Gan Y T, Yu A Z. 2014. Higher yield and lower carbon emission by intercropping maize with rape, pea, and wheat in arid irrigation areas. Agronomy for Sustainable Development, 34, 535–543.
Chen Q L, Ding J, Zhu Y G, He J Z, Hu H W. 2020. Soil bacterial taxonomic diversity is critical to maintaining the plant productivity. Environment International, 140, 105766.
Chen Y, Li Z, Fan Y, Wang H, Deng H. 2015. Progress and prospects of climate change impacts on hydrology in the arid region of Northwest China. Environmental Research, 139, 11–19.
Das S, Gwon H S, Khan M I, Van Nostrand J D, Alam M A, Kim P J. 2019. Taxonomic and functional responses of soil microbial communities to slag-based fertilizer amendment in rice cropping systems. Environment International, 127, 531–539.
DeAngelis K M, Brodie E L, DeSantis T Z, Andersen G L, Lindow S E, Firestone M K. 2009. Selective progressive response of soil microbial community to wild oat roots. Multidisciplinary Journal of Microbial Ecology, 3, 168–178.
de Vries F, Wallenstein M. 2017. Below-ground connections underlying above-ground food production: a framework for optimising ecological connections in the rhizosphere. Journal of Ecology, 105, 913–920.
Ding L J, Su J Q, Sun G X, Wu J S, Wei W X. 2018. Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil. Applied Microbiology and Biotechnology, 102, 1969–1982.
Dong N, Tang M M, Zhang W P, Bao X G, Wang Y, Christie P, Li L. 2018. Temporal differentiation of crop growth as one of the drivers of intercropping yield advantage. Scientific Reports, 8, 3110.
Duan P, Qin L, Wang Y, He H. 2016. Spatial pattern characteristics of water footprint for maize production in Northeast China. Journal of the Science of Food and Agriculture, 96, 561–568.
Fierer N, Leff J W, Adams B J, Nielsen U N, Bates S T, Lauber C L, Owens S, Gilbert J A, Wall D H, Caporaso J G. 2012. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proceedings of the National Academy of Sciences of the United States of America, 109, 21390–21395.
Fu L, Niu B, Zhu Z, Wu S, Li W. 2012. CD-HIT: Accelerated for clustering the next-generation sequencing data. Bioinformatics, 28, 3150–3152.
Ge Y, He J Z, Zhu Y G, Zhang J B, Xu Z, Zhang L M, Zheng Y M. 2008. Differences in soil bacterial diversity: Driven by contemporary disturbances or historical contingencies? Multidisciplinary Journal of Microbial Ecology, 2, 254–264.
Green J, Bohannan B J. 2006. Spatial scaling of microbial biodiversity. Trends in Ecology & Evolution, 21, 501–507.
Haichar F Z, Marol C, Berge O, Rangel-Castro J I, Prosser J I, Balesdent J, Heulin T, Achouak W. 2008. Plant host habitat and root exudates shape soil bacterial community structure. Multidisciplinary Journal of Microbial Ecology, 2, 1221–1230.
Hartman K, van der Heijden M G A, Wittwer R A, Banerjee S, Walser J C, Schlaeppi K. 2018. Cropping practices manipulate abundance patterns of root and soil microbiome members paving the way to smart farming. Microbiome, 6, 14.
Hartmann M, Frey B, Mayer J, Mäder P, Widmer F. 2015. Distinct soil microbial diversity under long-term organic and conventional farming. Multidisciplinary Journal of Microbial Ecology, 9, 1177–1194.
Huang R, McGrath S P, Hirsch P R, Clark I M, Storkey J, Wu L, Zhou J, Liang Y. 2019. Plant–microbe networks in soil are weakened by century-long use of inorganic fertilizers. Microbial Biotechnology, 12, 1464–1475.
Jacobsen C S, Hjelmsø M H. 2014. Agricultural soils, pesticides and microbial diversity. Current Opinion in Biotechnology, 27, 15–20.
Jones R T, Robertson M S, Lauber C L, Hamady M, Knight R, Fiere N. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. Multidisciplinary Journal of Microbial Ecology, 3, 442–453.
Kaiser K, Wemheuer B, Korolkow V, Wemheuer F, Nacke H, Schöning I, Schrumpf M, Daniel R. 2016. Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests. Scientific Reports, 6, 33696.
Kennedy A, Smith K. 1995. Soil microbial diversity and the sustainability of agricultural soils. Plant and Soil, 170, 75–86.
Kerou M, Offre P, Valledor L, Abby S S, Melcher M, Nagler M, Weckwerth W, Schleper C. 2016. Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Proceedings of the National Academy of Sciences of the United States of America, 113, E7937–E7946.
Langdon W B. 2015. Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks. BioData Mining, 8, 1.
Lee K C, Morgan X C, Power J F, Dunfield P F, Huttenhower C, Stott M B. 2015. Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22(T). Standards in Genomic Sciences, 10, 101.
Lehtovirta-Morley L E, Ross J, Hink L, Weber E B, Gubry-Rangin C, Thion C, Prosser J I, Nicol G W. 2016. Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiology Ecology, 92, fiw057.
Lehtovirta-Morley L E, Stoecker K, Vilcinskas A, Prosser J I, Nicol G W. 2011. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proceedings of the National Academy of Sciences of the United States of America, 108, 15892–15897.
Lemetre C, Maniko J, Charlop-Powers Z, Sparrow B, Lowe A J, Brady S F. 2017. Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale. Proceedings of the National Academy of Sciences of the United States of America, 114, 11615–11620.
Li J. 2009. Production, breeding and process of maize in China. In: Bennetzen J L, Hake S C, eds., Handbook of Maize: Its Biology. Springer, New York. pp. 563–576 .
Liu L L, Liu H F, Gao H H, Yang Z Z, Feng X L, Gao J M, Zhao J B. 2019. Genome-based analysis of the type II PKS biosynthesis pathway of xanthones in Streptomyces caelestis and their antifungal activity. RSC Advances, 9, 37376–37383.
Lombard N, Prestat E, van Elsas J D, Simonet P. 2011. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics. FEMS Microbiology Ecology, 78, 31–49.
Lu G H, Hua X M, Cheng J, Zhu Y L, Wang G H, Pang Y J, Yang R W, Zhang L, Shou H, Wang X M, Qi J, Yang Y H. 2018. Impact of Glyphosate on the rhizosphere microbial communities of an EPSPS-transgenic soybean line ZUTS31 by metagenome sequencing. Current Genomics, 19, 36–49.
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung D W, et al. 2015. SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 18.
Ma X L, Zhu Q L, Geng C X, Lu Z G, Long G Q, Tang L. 2017. Contribution of nutrient uptake and utilization on yield advantage in maize and potato intercropping under different nitrogen application rates. Chinese Journal of Applied Ecology, 28, 1265–1273. (in Chinese)
Manuel D B, Angela M O, Tess E B, Alberto B G, David J E, Richard D B, Fernando T M, Brajesh K S, Noah F. 2018. A global atlas of the dominant bacteria found in soil. Science, 359, 320–325.
Maul J E, Cavigelli M A, Vinyard B, Buyer J S. 2019. Cropping system history and crop rotation phase drive the abundance of soil denitrification genes nirK, nirS and nosZ in conventional and organic grain agroecosystems. Agriculture Ecosystems and Environment, 273, 95–106.
McDaniel M D, Tiemann L K, Grandy A S. 2014. Does agricultural crop diversity enhance soil microbial biomass and organic matter dynamics? A meta-analysis. Ecological Applications, 24, 560–570.
Murakami Y, Otsuka S, Senoo K. 2010. Abundance and community structure of sphingomonads in leaf residues and nearby bulk soil. Microbes and Environments, 25, 183–189.
Müller D, Vogel C, Bai Y, Vorholt J. 2016. The plant microbiota: Systems-level insights and perspectives. Annual Review of Genetics, 50, 211–234.
NBSC (National Bureau of Statistics of China). 2017. Announcement of the National Bureau of Statistics on Grain Yield in 2017. National Bureau of Statistics. Beijing. (in Chinese)
Niu B, Paulson J N, Zheng X, Kolte R. 2017. Simplified and representative bacterial community of maize roots. Proceedings of the National Academy of Sciences of the United States of America, 114, E2450–E2459.
Oksanen J, Blanchet F G, Kindt R, Legendre P, Minchin P R, O’Hara R B, Simpson G L, Solymos P, Stevens M H H, Wagner H. 2012. Vegan: Community ecology package. R package version 2.0-4. [2018-05-02]. http://CRAN.R-project.org/package=vegan
Oline D K. 2006. Phylogenetic comparisons of bacterial communities from serpentine and nonserpentine soils. Applied and Environmental Microbiology, 72, 6965–6971.
Parks D H, Tyson G W, Hugenholtz P, Beiko R G. 2013. STAMP: Statistical analysis of taxonomic and functional profiles. Bioinformatics, 30, 3123–3124.
Pennanen T, Liski J, Bååth E, Kitunen V V, Uotila J, Westman C J, Fritze H. 1999. Structure of the microbial communities in coniferous forest soils in relation to site fertility and stand development stage. Microbial Ecology, 38, 168–179.
Pu L, Zhang S, Yang J, Chang L, Bai S. 2019. Spatio-temporal dynamics of maize potential yield and yield gaps in Northeast China from 1990 to 2015. International Journal of Environmental Research and Public Health, 16, E1211.
Reith F, Brugger J, Zammit C M, Gregg A L, Goldfarb K C, Andersen G L, DeSantis T Z, Piceno Y M, Brodie E L, Lu Z, He Z, Zhou J, Wakelin S A. 2012. Influence of geogenic factors on microbial communities in metallogenic Australian soils. Multidisciplinary Journal of Microbial Ecology, 6, 2107–2118.
Rohde K. 1992. Latitudinal gradients in species diversity: The search for the primary cause. Oikos, 65, 514–527.
Shayan Z, Mohammad Gholi Mezerji N, Shayan L, Naseri P. 2015. Prediction of depression in cancer patients with different classification criteria, linear discriminant analysis versus logistic regression. Journal of Global Health, 8, 41–46.
Shi Y, Manuel D B, Li Y T, Yang Y F, Zhu Y G, Josep P, Chu H Y. 2020. Abundance of kinless hubs within soil microbial networks are associated with high functional potential in agricultural ecosystems. Journal of Global Health, 142, 105869.
Sofi J A, Bhat A G, Kirmai N A, Wani J A, Lone A H, Ganie M A, Dar G I. 2016. Soil quality index as affected by different cropping systems in northwestern Himalayas. Environmental Monitoring and Assessment, 188, 161.
Sun Z, Liu J, Zhuo S, Chen Y, Zhang Y, Shen H, Yun X, Shen G, Liu W, Zeng E Y, Tao S. 2017. Occurrence and geographic distribution of polycyclic aromatic hydrocarbons in agricultural soils in eastern China. Environmental Science and Pollution Research International, 24, 12168–12175.
Umair M, Shen Y, Qi Y, Zhang Y, Ahmad A, Pei H, Liu M. 2017. Evaluation of the CropSyst model during wheat–maize rotations on the North China plain for identifying soil evaporation losses. Frontiers in Plant Science, 8, 1667.
Vílchez S, Manzanera M, Ramos J L. 2000. Control of expression of divergent Pseudomonas putida put promoters for proline catabolism. Applied and Environmental Microbiology, 66, 5221–5225.
Wang C, Wang G, Wu P, Rafique R, Zi H, Li X, Luo Y, James E K. 2016. Effects of ant mounds on the plant and soil microbial community in an alpine meadow of Qinghai-Tibet Plateau. Land Degradation & Development, 28, 1538–1548.
Wang H, Zeng Y, Guo C, Bao Y, Lu G, Reinfelder J R, Dang Z. 2018. Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem. Science of the Total Environment, 616–617, 107–116.
Wang X, Van Nostrand J D, Deng Y, Lü X, Wang C, Zhou J, Han X. 2015. Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiology Ecology, 91, fiv133.
Wang X M, Jin Q M, Shi J, Wang Z Y, Li X. 2006. The status of maize diseases and the possible effect of variety resistance on disease occurrence in the future. Acta Phytopathologica Sinica, 36, 1–11. (in Chinese)
Xu R K, Coventry D R. 2003. Soil pH changes associated with lupin and wheat plant materials. Plant and Soil, 250, 113–119.
Zhang Y, Shen H, He X, Thomas B W, Lupwayi N Z, Hao X, Thomas M C, Shi X. 2017. Fertilization shapes bacterial community structure by alteration of soil pH. Frontiers in Microbiology, 18, 1325.
Zhao Y, Cheng C, Jiang T, Xu H, Chen Y, Ma Z, Qian G, Liu F. 2019. Control of wheat Fusarium head blight by heat-stable antifungal factor (HSAF) from Lysobacter enzymogenes. Plant Disease, 103, 1286–1292.
Zuñiga C, Zaramela L, Zengler K. 2017. Elucidation of complexity and prediction of interactions in microbial communities. Microbial Biotechnology, 10, 1500–1522.

JIA-2021-0475 土壤理化性质、种植模式和地理位置对中国4个玉米主产区土壤原核生物群落的影响

The effects of soil properties, cropping systems and geographic location on soil prokaryotic communities in four maize production regions across China

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