Ecosystem microbiome science

Yong Guan Zhu*, Dong Zhu, Matthias C. Rillig, Yunfeng Yang, Haiyan Chu, Qing-Lin Chen, Josep Penuelas, Hui-Ling Cui, Michael Gillings*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
25 Downloads (Pure)


The microbiome contributes to multiple ecosystem functions and services through its interactions with a complex environment and other organisms. To date, however, most microbiome studies have been carried out on individual hosts or particular environmental compartments. This greatly limits a comprehensive understanding of the processes and functions performed by the microbiome and its dynamics at an ecosystem level. We propose that the theory and tools of ecosystem ecology be used to investigate the connectivity of microorganisms and their interactions with the biotic and abiotic environment within entire ecosystems and to examine their contributions to ecosystem services. Impacts of natural and anthropogenic stressors on ecosystems will likely cause cascading effects on the microbiome and lead to unpredictable outcomes, such as outbreaks of emerging infectious diseases or changes in mutualistic interactions. Despite enormous advances in microbial ecology, we are yet to study microbiomes of ecosystems as a whole. Doing so would establish a new framework for microbiome study: Ecosystem Microbiome Science. The advent and application of molecular and genomic technologies, together with data science and modeling, will accelerate progress in this field.

Original languageEnglish
Pages (from-to)2-10
Number of pages9
Issue number1
Early online date11 Jan 2023
Publication statusPublished - Mar 2023

Bibliographical note

Copyright the Author(s) 2023. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.


  • dynamics
  • ecosystem
  • global change
  • interactions
  • microbiome


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