专题:土壤生态学

贝叶斯推断在土壤微生物生物地理学中的应用

  • 柳旭 ,
  • 马玉颖 ,
  • 高贵锋 ,
  • 范坤坤 ,
  • 杨腾 ,
  • 褚海燕
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  • 1. 中国科学院南京土壤研究所, 土壤与农业可持续发展国家重点实验室, 南京 210008;
    2. 中国科学院大学, 北京 100049
柳旭,博士研究生,研究方向为土壤微生物空间分布,电子信箱:xliu@issas.ac.cn

收稿日期: 2021-07-19

  修回日期: 2021-11-22

  网络出版日期: 2022-03-25

基金资助

国家自然科学基金项目(31870480)

Application of Bayesian inference in soil microbial biogeography

  • LIU Xu ,
  • MA Yuying ,
  • GAO Guifeng ,
  • FAN Kunkun ,
  • YANG Teng ,
  • CHU Haiyan
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  • 1. State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China;
    2. University of the Chinese Academy of Sciences, Beijing 100049, China

Received date: 2021-07-19

  Revised date: 2021-11-22

  Online published: 2022-03-25

摘要

微生物生物地理学主要研究微生物的分布格局及其驱动机制,经典频率数理统计方法是当前该研究领域中广泛使用的统计方法。近年来,贝叶斯推断作为重要的随机模拟数理统计方法正不断地应用于土壤微生物生物地理学的研究中。介绍了贝叶斯推断与经典频率数理统计的区别;描述了贝叶斯推断在土壤微生物生物地理学研究中的基本分析流程,包括模型构建、模型拟合和模型优化;评价了贝叶斯推断在该研究领域中的自身优势、应用潜力和发展方向;并以岛屿生物地理学理论为研究框架,利用模拟数据,进行了贝叶斯推断流程演示。提出贝叶斯推断未来有望成为研究土壤微生物生物地理学中复杂数据和开展模型模拟的重要工具之一,在土壤微生物生物地理学中具有广阔的应用前景。

本文引用格式

柳旭 , 马玉颖 , 高贵锋 , 范坤坤 , 杨腾 , 褚海燕 . 贝叶斯推断在土壤微生物生物地理学中的应用[J]. 科技导报, 2022 , 40(3) : 112 -120 . DOI: 10.3981/j.issn.1000-7857.2022.03.010

Abstract

Microbial biogeography mainly focuses on the distribution patterns of microorganisms and their driving mechanisms,and currently classical frequency mathematical and statistical methods are widely used in this field.In recent years,Bayesian inference has been continuously applied as an important random simulation mathematical statistics method for soil microbial biogeographical study.In this paper,we briefly introduce the differences between Bayesian inference and classical frequency mathematical statistics,and highlight the basic analytical process of Bayesian inference in soil microbial biogeographical study in terms of model construction,model fitting,and model improvement.We also evaluate the advantages,application potentials and development directions of Bayesian inference in this field and demonstrate the Bayesian inference process using simulated data with island biogeography theory as the research framework.Finally,we give an outlook on the application prospects of Bayesian inference in soil microbial biogeography.We believe that Bayesian inference will become one of the important tools for studying complex data and conducting model simulations in soil microbial biogeography.

参考文献

[1] Fierer N. Embracing the unknown:Disentangling the complexities of the soil microbiome[J]. Nature Reviews Microbiology, 2017, 15(10):579-590.
[2] Tedersoo L, Bahram M, Polme S, et al. Fungal biogeography. Global diversity and geography of soil fungi[J]. Science, 2014, 346(6213):1256688.
[3] Fierer N, Jackson R B. The diversity and biogeography of soil bacterial communities[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(3):626-631.
[4] 褚海燕,王艳芬,时玉,等.土壤微生物生物地理学研究现状与发展态势[J].中国科学院院刊, 2017, 32(6):45-52.
[5] Chu H, Gao G, Ma Y, et al. Soil microbial biogeography in a changing world:Recent advances and future perspectives[J]. Msystems, 2020, 5(2):e00803-19.
[6] Wasserstein R L, Lazar N A. The ASA's statement on pvalues:Context, process, and purpose[J]. American Statistician, 2016, 70(2):129-131.
[7] Wasserstein R L, Schirm A L, Lazar N A. Moving to a world beyond "P<0.05"[J]. American Statistician, 2019, 73:1-19.
[8] Benjamin D J, Berger J O, Johannesson M, et al. Redefine statistical significance[J]. Nature Human Behaviour, 2018, 2(1):6-10.
[9] Amrhein V, Greenland S, McShane B. Retire statistical significance[J]. Nature, 2019, 567(7748):305-307.
[10] Jain A K, Duin R P W, Mao J C. Statistical pattern recognition:A review[J]. Ieee Transactions on Pattern Analysis and Machine Intelligence, 2000, 22(1):4-37.
[11] 谢俊.贝叶斯统计方法与传统统计方法的比较分析与展望[J].中国商界, 2009(4):115-117.
[12] Gelman A. Bayesian statistics then and now[J]. Statistical Science, 2010, 25(2):162-165.
[13] Csillery K, Blum M G, Gaggiotti O E, et al. Approximate bayesian computation (ABC) in practice[J]. Trends in Ecology and Evolution, 2010, 25(7):410-418.
[14] Jackman S. Estimation and inference via bayesian simulation:An introduction to markov chain monte carlo[J]. American Journal of Political Science, 2000, 44(2):375-404.
[15] Cornell S J, Suprunenko Y F, Finkelshtein D, et al. A unified framework for analysis of individual-based models in ecology and beyond[J]. Nature Communications, 2019, 10:14.
[16] 曹鹏,贺纪正.微生物生态学理论框架[J].生态学报, 2015, 35(22):6-16.
[17] Ma Kowski, Ben-Shachar M S, Lüdecke D. BayestestR:Describing effects and their uncertainty, existence and significance within the bayesian framework[J]. The Journal of Open Source Software, 2019, 4(40):1541.
[18] Hadfield J D. MCMC methods for multi-response generalized linear mixed models:The MCMCglmm R Package[J]. Journal of Statistical Software, 2010, 33(2):1-22.
[19] Makowski D. Indices of effect existence in the bayesian framework[J]. Frontiers in Psychology, 2018, 10:2067.
[20] Vellend M. Conceptual synthesis in community ecology[J]. Quarterly Review of Biology, 2010, 85(2):183-206.
[21] Pedregosa F, Varoquaux G, Gramfort A, et al. Scikitlearn:Machine learning in python[J]. Journal of Machine Learning Research, 2011, 12:2825-2830.
[22] Edgar R C. Search and clustering orders of magnitude faster than BLAST[J]. Bioinformatics, 2010, 26(19):2460-2461.
[23] Kaye J P, Majumdar A, Gries C, et al. Hierarchical bayesian scaling of soil properties across urban, agricultural, and desert ecosystems[J]. Ecological Applications, 2008, 18(1):132-145.
[24] Majumdar A, Kaye J, Gries C, et al. Hierarchical spatial modeling and prediction of multiple soil nutrients and carbon concentrations[J]. Communications in Statistics B Simulation and Computation, 2008, 37(1/2):434-453.
[25] Tikhonov G, Opedal O H, Abrego N, et al. Joint species distribution modelling with the r-package Hmsc[J]. Methods in Ecology and Evolution, 2020, 11(3):442-447.
[26] Jabot F, Chave J. Inferring the parameters of the neutral theory of biodiversity using phylogenetic information and implications for tropical forests[J]. Ecology Letters, 2010, 12(3):239-248.
[27] Ribeiro J W, Siqueira Jr T, Brejao G L, et al. Effects of agriculture and topography on tropical amphibian species and communities[J]. Ecological Applications, 2018, 28(6):1554-1564.
[28] Bush A, Sollmann R, Wilting A, et al. Connecting Earth observation to high-throughput biodiversity data[J]. Nature Ecology and Evolution, 2017, 1(7):9.
[29] Li S P, Wang P, Chen Y, et al. Island biogeography of soil bacteria and fungi:Similar patterns, but different mechanisms[J]. The ISME Journal, 2020, 14(7):1886-1896.
[30] MacArthur R H, Wilson E O. The theory of island biogeography[M]. Princeton:Princeton University Press, 2001.
[31] Whittaker R J, Maria Fernandez-Palacios J, Matthews T J, et al. Island biogeography:Taking the long view of nature's laboratories[J]. Science, 2017, 357(6354):885.
[32] Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes?[J]. Ecography, 2019, 42(11):1877-1886.
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