Ideas and perspectives: Using meta-omics to unravel biogeochemical changes from cell to planetary scales
Abstract
Increased human impacts on Earth systems are radically altering biogeochemical cycles. While long-term environmental observatories and Earth System Models (ESMs) provide valuable insights into the mechanisms of nutrient dynamics, their performance is limited at the fine spatial scales controlled by the functional diversity of plant and microbial communities. This gap in our understanding concerning the roles of microbial diversity and plant-microbial interactions in decomposition and nutrient dynamics extends across many global ecosystems. Recent advances in meta-omics technologies, including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, offer a wide array of tools for assessing metabolic to genetic to evolutionary drivers of ecosystem functioning. Here, we explore the integration of meta-omics with traditional ecological approaches to examine responses to global environmental changes. We present case studies from diverse environments – soils, aquatic systems, clouds, and paleoarchives – demonstrating how meta-omics can unravel the roles of microbial diversity, metabolic pathways, and trait distributions critical to understanding greenhouse gas fluxes, nutrient cycling, and biogeochemistry. Although meta-omics is still beset with challenges including data heterogeneity arising from wide-ranging methods, omics-derived traits, kinetic parameters, and machine learning tools can be used to enhance ESM predictive capability. For example, emerging applications of meta-omics to ancient environmental DNA are extending our capacity to link historical patterns with future projections, offering a long-term perspective on ecosystem dynamics. This review highlights the potential of integrating omics with experimental manipulations alongside existing monitoring and modelling efforts to refine predictions of ecosystem responses to natural and anthropogenic-driven environmental changes. Because omics approaches cross a range of scientific domains, they could be used to foster collaboration and even integration within existing models, thus laying the foundation for informed conservation and ecosystem management strategies from local to global scales.
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BibTeX
@article{abs2026ideas,
title = {{Ideas and perspectives: Using meta-omics to unravel biogeochemical changes from cell to planetary scales}},
author = {Elsa Abs and Christoph Keuschnig and Pierre Amato and Chris Bowler and Eric Capo and Alexander B Chase and Luciana Chavez Rodriguez and Abraham N Dabengwa and Thomas Dussarrat and Thomas Guzman and Linnea K Hernandez and Jenni Hultman and Kirsten Küsel and Zhen Li and Anna Mankowski and William J Riley and Scott R Saleska and Lisa Wingate},
journal = {Biogeosciences},
year = {2026},
month = jul,
doi = {10.5194/bg-23-5205-2026},
url = {https://hal.science/hal-05762928v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Ideas and perspectives: Using meta-omics to unravel biogeochemical changes from cell to planetary scales
AU - Elsa Abs
AU - Christoph Keuschnig
AU - Pierre Amato
AU - Chris Bowler
AU - Eric Capo
AU - Alexander B Chase
AU - Luciana Chavez Rodriguez
AU - Abraham N Dabengwa
AU - Thomas Dussarrat
AU - Thomas Guzman
AU - Linnea K Hernandez
AU - Jenni Hultman
AU - Kirsten Küsel
AU - Zhen Li
AU - Anna Mankowski
AU - William J Riley
AU - Scott R Saleska
AU - Lisa Wingate
PY - 2026
DA - 2026/07/30
JO - Biogeosciences
DO - 10.5194/bg-23-5205-2026
UR - https://hal.science/hal-05762928v1
AB - Increased human impacts on Earth systems are radically altering biogeochemical cycles. While long-term environmental observatories and Earth System Models (ESMs) provide valuable insights into the mechanisms of nutrient dynamics, their performance is limited at the fine spatial scales controlled by the functional diversity of plant and microbial communities. This gap in our understanding concerning the roles of microbial diversity and plant-microbial interactions in decomposition and nutrient dynamics extends across many global ecosystems. Recent advances in meta-omics technologies, including metagenomics, metatranscriptomics, metaproteomics, and metabolomics, offer a wide array of tools for assessing metabolic to genetic to evolutionary drivers of ecosystem functioning. Here, we explore the integration of meta-omics with traditional ecological approaches to examine responses to global environmental changes. We present case studies from diverse environments – soils, aquatic systems, clouds, and paleoarchives – demonstrating how meta-omics can unravel the roles of microbial diversity, metabolic pathways, and trait distributions critical to understanding greenhouse gas fluxes, nutrient cycling, and biogeochemistry. Although meta-omics is still beset with challenges including data heterogeneity arising from wide-ranging methods, omics-derived traits, kinetic parameters, and machine learning tools can be used to enhance ESM predictive capability. For example, emerging applications of meta-omics to ancient environmental DNA are extending our capacity to link historical patterns with future projections, offering a long-term perspective on ecosystem dynamics. This review highlights the potential of integrating omics with experimental manipulations alongside existing monitoring and modelling efforts to refine predictions of ecosystem responses to natural and anthropogenic-driven environmental changes. Because omics approaches cross a range of scientific domains, they could be used to foster collaboration and even integration within existing models, thus laying the foundation for informed conservation and ecosystem management strategies from local to global scales.
SN - 1726-4170
SN - 1726-4189
ER -