1.Kögel-Knabner I, Amelung W, Cao Z, Fiedler S, Frenzel P, Jahn R, Kalbitz K, Kölbl A, Schloter M: Biogeochemistry of paddy soils. Geoderma 2010, 157(1–2):1–14.
2.Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V: Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci USA 2015, 112(8):E911-E920.
3.Sun W, Xiao E, Pu Z, Krumins V, Dong Y, Li B, Hu M: Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace. Sci Total Environ 2018, 612:884–893.
4.Rokunuzzaman M, Ueda Y, Chen L, Tanaka S, Ohnishi K: Effects of land use changes from paddy fields on soil bacterial communities in a hilly and mountainous area. Microbe Environ 2016, 31(2):160–164.
5.Delgado-Baquerizo M, Oliverio AM, Brewer TE, Benavent-González A, Eldridge DJ, Bardgett RD, Maestre FT, Singh BK, Fierer N: A global atlas of the dominant bacteria found in soil. Science 2018, 359(6373):320.
6.Delgado-Baquerizo M, Maestre FT, Reich PB, Jeffries TC, Gaitan JJ, Encinar D, Berdugo M, Campbell CD, Singh BK: Microbial diversity drives multifunctionality in terrestrial ecosystems. Nat Commun 2016, 7:10541.
7.Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, Bengtsson-Palme J, Anslan S, Coelho LP, Harend H et al: Structure and function of the global topsoil microbiome. Nature 2018, 560(7717):233–237.
8.Maestre FT, Delgado-Baquerizo M, Jeffries TC, Eldridge DJ, Ochoa V, Gozalo B, Quero JL, García-Gómez M, Gallardo A, Ulrich W et al: Increasing aridity reduces soil microbial diversity and abundance in global drylands. Proc Natl Acad Sci USA 2015:201516684.
9.Xu J, Zhang Y, Zhang P, Trivedi P, Riera N, Wang Y, Liu X, Fan G, Tang J, Coletta-Filho HD et al: The structure and function of the global citrus rhizosphere microbiome. Nat Commun 2018, 9(1):4894.
10.Fierer N: Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol 2017, 15(10):579–590.
11.Louca S, Parfrey LW, Doebeli M: Decoupling function and taxonomy in the global ocean microbiome. Science 2016, 353(6305):1272.
12.Trivedi P, Delgado-Baquerizo M, Anderson IC, Singh BK: Response of soil properties and microbial communities to agriculture: implications for primary productivity and soil health indicators. Front Plant Sci 2016, 7(990).
13.Gao Q, Yang Y, Feng J, Tian R, Guo X, Ning D, Hale L, Wang M, Cheng J, Wu L et al: The spatial scale dependence of diazotrophic and bacterial community assembly in paddy soil. Global Ecol Biogeogr 2019, 0(0).
14.Jiao S, Yang Y, Xu Y, Zhang J, Lu Y: Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China. The ISME J 2020, 14(1):202–216.
15.Hanson CA, Fuhrman JA, Hornerdevine MC, Martiny JBH: Beyond biogeographic patterns: processes shaping the microbial landscape. Nat Rev Microbiol 2012, 10(7):497–506.
16.Zhou J, Ye D, Shen L, Wen C, Yan Q, Ning D, Qin Y, Kai X, Wu L, He Z: Temperature mediates continental-scale diversity of microbes in forest soils. Nat Commun 2016, 7(12083):12083.
17.Barberán A, Bates ST, Casamayor EO, Fierer N: Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 2012, 6(2):343.
18.Chow CET, Kim DY, Sachdeva R, Caron DA, Fuhrman JA: Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. ISME J 2014, 8(4):816.
19.Ma B, Wang HZ, Dsouza M, Lou J, He Y, Dai ZM, Brookes PC, Xu JM, Gilbert JA: Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China. ISME J 2016, 10(8):1891–1901.
20.Banerjee S, Schlaeppi K, Heijden MGAVD: Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol 2018, 16(9):1.
21.Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F et al: Determinants of community structure in the global plankton interactome. Science 2015, 348(6237).
22.Barberán A, Bates ST, Casamayor EO, Fierer N: Using network analysis to explore co-occurrence patterns in soil microbial communities. ISME J 2012, 6(2):343.
23.Sehgal U, Kaur K, Kumar P: Notice of violation of IEEE publication principles “the anatomy of a large-scale hyper textual web search engine. In: International Conference on Computer and Electrical Engineering: 2009. 491–495.
24.Rong S, Meng D, Wu M, Di… H: Effect of agricultural land use change on community composition of bacteria and ammonia oxidizers. J Soil Sediment, 13(7):1246–1256.
25.Liu C, Ding N, Fu Q, Brookes PC, Xu J, Guo B, Lin Y, Li H, Li N: The influence of soil properties on the size and structure of bacterial and fungal communities along a paddy soil chronosequence. Eur J Soil Biol 2016, 76:9–18.
26.Yuan H-Y, Ding L-J, Wang N, Chen S-C, Deng Y, Li X-M, Zhu Y-G: Geographic distance and amorphous iron affect the abundance and distribution of Geobacteraceae in paddy soils in China. J Soil Sediment 2016, 16(12):2657–2665.
27.Ahn J-H, Lee SA, Kim JM, Kim M-S, Song J, Weon H-Y: Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices. J Microbiol 2016, 54(11):724–731.
28.Chase JM: Drought mediates the importance of stochastic community assembly. Proc Natl Acad Sci USA 2007, 104(44):17430–17434.
29.Li H-Y, Wang H, Wang H-T, Xin P-Y, Xu X-H, Ma Y, Liu W-P, Teng C-Y, Jiang C-L, Lou L-P et al: The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. Microbiome 2018, 6(1):187.
30.Fierer N, Jackson RB: The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 2006, 103(3):626–631.
31.Schmidt TSB, Rodrigues JFM, Mering CV: A family of interaction-adjusted indices of community similarity. ISME J 2016, 11(3).
32.Ding LJ, Su JQ, Xu HJ, Jia ZJ, Zhu YG: Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-C–13-acetate probing coupled with pyrosequencing. ISME J 2015, 9(3):721–734.
33.García-Bayona L, Comstock LE: Bacterial antagonism in host-associated microbial communities. Science 2018, 361(6408):eaat2456.
34.Xia Y, Wang Y, Wang Y, Chin FYL, Zhang T: Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation. Biotechnol Biofuel 2016, 9(1):111.
35.Walker DJF, Dang Y, Holmes DE, Lovley DR: The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer. Microbial Genomics 2016, 2(8).
36.Banerjee S, Schlaeppi K, Heijden MGAVD: Keystone taxa as drivers of microbiome structure and functioning. Nat Rev Microbiol 2018, 16(9):1.
37.Bao SD: Agro-chemical analysis of soil., the third edition edn: China Agricultural Press; 2000.
38.Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI: QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010, 7(5):335–336.
39.Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26(19):2460.
40.Torbjørn R, Tomáš F, Ben N, Christopher Q, Frédéric M: VSEARCH: a versatile open source tool for metagenomics. Peerj 2016, 4(10).
41.Edgar RC: UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 2013, 10(10):996–998.
42.Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J: Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Micr 2017, 67(5):1613.
43.Douglas GM, Maffei VJ, Zaneveld J, Yurgel SN, Brown JR, Taylor CM, Huttenhower C, Langille MGI: PICRUSt2: An improved and extensible approach for metagenome inference. bioRxiv 2019:672295.
44.Emmanuel P, David MM, Jenni H, Neslihan T, Regina L, Jill D, Rachel M, Myrold DD, Ari J, Tringe SG: FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. Nucleic Acids Res 2014(19):19.
45.Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ: Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11(1):119–110.
46.Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M: KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27(1):29–34.
47.Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F, Chaffron S, Ignacio-Espinosa JC, Roux S, Vincent F: Ocean plankton. Determinants of community structure in the global plankton interactome. Science 2015, 348(6237):1262073.
48.Friedman J, Alm EJ: Inferring correlation networks from genomic survey data. PLoS Comput Biol 2012, 8(9):e1002687.
49.Feng L, Zhong J, Yang Y, Scheuermann RH, Zhou J: Application of random matrix theory to biological networks. Phys Lett A 2006, 357(6):420–423.
50.Bastian M, Heymann S, Jacomy M: Gephi: an open source software for exploring and manipulating networks. In: International AAAI Conference On Weblogs and Social Media: 2009.
51.Csardi G: The igraph software package for complex network research. Inter J Complex Syst 2006, 1695.
52.Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens HHH, Wagner H: vegan: community ecology package. R package version 2.3–0. 2015.
53.Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C: Metagenomic biomarker discovery and explanation. Genome Biol 2011, 12(6):R60.
54.Ning D, Deng Y, Tiedje JM, Zhou J: A general framework for quantitatively assessing ecological stochasticity. Proc Natl Acad Sci USA 2019, 116(34):16892–16898.
55.Dini-Andreote F, Stegen JC, van Elsas JD, Salles JF: Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession. Proc Natl Acad Sci USA 2015, 112(11):E1326-E1332.