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. 2023 Jan 11;2(1):2-10.
doi: 10.1002/mlf2.12054. eCollection 2023 Mar.

Ecosystem Microbiome Science

Yong-Guan Zhu  1   2 , Dong Zhu  2 , Matthias C Rillig  3   4 , Yunfeng Yang  5 , Haiyan Chu  6 , Qing-Lin Chen  7 , Josep Penuelas  8   9 , Hui-Ling Cui  2 , Michael Gillings  10
Affiliations

Ecosystem Microbiome Science

Yong-Guan Zhu et al. mLife. .

Abstract

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.

Keywords: dynamics; ecosystem; global change; interactions; microbiome.

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Figures

Figure 1
Figure 1
The concept of ecosystem microbiomes and a technique map to briefly show how to study microbial genomes and functions in whole ecosystems. In general, omics methods could provide taxonomic and metabolic information at the community level. The recently developed functional Raman spectroscopy‐based single‐cell technology as a next‐generation physiology method could provide information on microbiome function at the single‐cell level.
Figure 2
Figure 2
The connectivity of the ecosystem microbiome. Trophic regulation including bottom‐up and top‐down control of the ecosystem microbiome is the key ecological process that links to the flow of materials and energy in the ecosystem.
Figure 3
Figure 3
Microbial cycling between humans and ecosystems. It is generally accepted that microbes are important for human health, and novel functions of the microbiome in human health and well‐being are being increasingly recognized. Therefore, there is a need to better understand the potential connections between ecosystem and human health in an ecosystem context.
See this image and copyright information in PMC

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