: A Method for Quantifying Putative Biotic Associations of Microbes at the Community Level

Overview

Journal Imeta

Specialty Biology

Date 2024 Jun 13

PMID 38868428

Authors

Xu Liu

Yu Shi

Teng Yang

Gui-Feng Gao

Haiyan Chu

Affiliations

Soon will be listed here.

Abstract

A workflow has been compiled as "qcmi" R package-the uantifying ommunity-level icrobial nteractions-to identify and quantify the putative biotic associations of microbes at the community level from ecological networks.

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References

Wen T, Xie P, Yang S, Niu G, Liu X, Ding Z . ggClusterNet: An R package for microbiome network analysis and modularity-based multiple network layouts. Imeta. 2024; 1(3):e32. PMC: 10989811. DOI: 10.1002/imt2.32. View

Yang X, Gomez-Aparicio L, Lortie C, Verdu M, Cavieres L, Huang Z . Net plant interactions are highly variable and weakly dependent on climate at the global scale. Ecol Lett. 2022; 25(6):1580-1593. DOI: 10.1111/ele.14010. View

Stegen J, Lin X, Konopka A, Fredrickson J . Stochastic and deterministic assembly processes in subsurface microbial communities. ISME J. 2012; 6(9):1653-64. PMC: 3498916. DOI: 10.1038/ismej.2012.22. View

Fierer N . Embracing the unknown: disentangling the complexities of the soil microbiome. Nat Rev Microbiol. 2017; 15(10):579-590. DOI: 10.1038/nrmicro.2017.87. View

Kurtz Z, Muller C, Miraldi E, Littman D, Blaser M, Bonneau R . Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015; 11(5):e1004226. PMC: 4423992. DOI: 10.1371/journal.pcbi.1004226. View

Dehling D, Barreto E, Graham C . The contribution of mutualistic interactions to functional and phylogenetic diversity. Trends Ecol Evol. 2022; 37(9):768-776. DOI: 10.1016/j.tree.2022.05.006. View

Deng Y, Jiang Y, Yang Y, He Z, Luo F, Zhou J . Molecular ecological network analyses. BMC Bioinformatics. 2012; 13:113. PMC: 3428680. DOI: 10.1186/1471-2105-13-113. View

Chase J, Myers J . Disentangling the importance of ecological niches from stochastic processes across scales. Philos Trans R Soc Lond B Biol Sci. 2011; 366(1576):2351-63. PMC: 3130433. DOI: 10.1098/rstb.2011.0063. View

Swain A, Fussell L, Fagan W . Higher-order effects, continuous species interactions, and trait evolution shape microbial spatial dynamics. Proc Natl Acad Sci U S A. 2021; 119(1). PMC: 8740587. DOI: 10.1073/pnas.2020956119. View

10.

Crowther T, van den Hoogen J, Wan J, Mayes M, Keiser A, Mo L . The global soil community and its influence on biogeochemistry. Science. 2019; 365(6455). DOI: 10.1126/science.aav0550. View

11.

Romdhane S, Spor A, Aubert J, Bru D, Breuil M, Hallin S . Unraveling negative biotic interactions determining soil microbial community assembly and functioning. ISME J. 2021; 16(1):296-306. PMC: 8692615. DOI: 10.1038/s41396-021-01076-9. View

12.

Liu C, Zhu L, Wang J, Ju J, Ma Q, Qiao B . In-situ water quality investigation of the lakes on the Tibetan Plateau. Sci Bull (Beijing). 2023; 66(17):1727-1730. DOI: 10.1016/j.scib.2021.04.024. View

13.

Xiao N, Zhou A, Kempher M, Zhou B, Shi Z, Yuan M . Disentangling direct from indirect relationships in association networks. Proc Natl Acad Sci U S A. 2022; 119(2). PMC: 8764688. DOI: 10.1073/pnas.2109995119. View

14.

Goberna M, Montesinos-Navarro A, Valiente-Banuet A, Colin Y, Gomez-Fernandez A, Donat S . Incorporating phylogenetic metrics to microbial co-occurrence networks based on amplicon sequences to discern community assembly processes. Mol Ecol Resour. 2019; 19(6):1552-1564. DOI: 10.1111/1755-0998.13079. View

15.

Ho A, Angel R, Veraart A, Daebeler A, Jia Z, Kim S . Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System. Front Microbiol. 2016; 7:1285. PMC: 4993757. DOI: 10.3389/fmicb.2016.01285. View

16.

Jiao S, Chu H, Zhang B, Wei X, Chen W, Wei G . Linking soil fungi to bacterial community assembly in arid ecosystems. Imeta. 2024; 1(1):e2. PMC: 10989902. DOI: 10.1002/imt2.2. View

17.

Delgado-Baquerizo M, Reich P, Trivedi C, Eldridge D, Abades S, Alfaro F . Multiple elements of soil biodiversity drive ecosystem functions across biomes. Nat Ecol Evol. 2020; 4(2):210-220. DOI: 10.1038/s41559-019-1084-y. View

18.

Guseva K, Darcy S, Simon E, Alteio L, Montesinos-Navarro A, Kaiser C . From diversity to complexity: Microbial networks in soils. Soil Biol Biochem. 2022; 169:108604. PMC: 9125165. DOI: 10.1016/j.soilbio.2022.108604. View

19.

Li M, Wei Z, Wang J, Jousset A, Friman V, Xu Y . Facilitation promotes invasions in plant-associated microbial communities. Ecol Lett. 2018; 22(1):149-158. DOI: 10.1111/ele.13177. View

20.

Liu C, Cui Y, Li X, Yao M . microeco: an R package for data mining in microbial community ecology. FEMS Microbiol Ecol. 2020; 97(2). DOI: 10.1093/femsec/fiaa255. View