Rebooting soil microbiomes for soil health and climate resilience

“If we feed the soil, it will feed us” (Hayne 1940). This widely referenced statement by Ralph A. Haynes, highlighting the foundational link between soil health and human health, is of ever-growing importance given the current state of global soils.

It is estimated that ~40% of soils are moderately to severely degraded and approximately half of soil carbon has been lost, directly impacting 3.2 billion people (UNCCD 2022). UNESCO predicts that 90% of the world’s soils could be degraded by 2050. Major drivers for reduction in soil health and soil losses include soil erosion, extractive farming practices that do not return organics and micronutrients to soils, and loss of biodiversity. Besides their importance for agriculture, soils also contain more carbon than the atmosphere and phytobiomass combined. Unfortunately, it is estimated that between 30 and 62 gigatons of carbon has been lost since 1850 from croplands making land use a leading contribution of atmospheric carbon (Sanderman et al. 2017).

This drastic shift in soil health has major implications for world food production and directly affects national food security. Additionally, reduced carbon storage and loss of soil organics which will compound the stresses resulting from poor soil quality, negatively impacts water retention and water infiltration making it more difficult for farmers to achieve high yields during periods of drought and flooding. Similarly, biodiversity losses reduce the abundance of microbes that naturally protect plants from water and heat stress and compete with plant pathogens.

In his now classic paper, Rattan Lal describes this downward spiral of soil degradation and an upward spiral for soil restoration with three basic strategies for restoring soil quality. These include (1) minimizing soil losses, (2) creating a positive soil carbon budget while also enhancing biodiversity, and (3) improving water and elemental cycling. This and other papers make it clear that restoring soil organics alongside soil biodiversity can be key drivers for achieving these other goals by improving soil structure, water retention, and nutrient cycling. As Lal puts it “The importance of soil health on mitigating climate change, improving water quality, enhancing biodiversity, etc. cannot be overemphasized. The environmental consequence of soil health is also determined by the SOC (soil organic carbon) pool, its dynamics and the turnover time, and that of climate change by both SOC and soil inorganic carbon dynamics” (Lal 2016).

The compounding of these factors is both a major liability and opportunity. For example, in a downward spiral, loss of soil organics can reduce plant inputs further increasing losses. Similarly loss of nitrogen-fixing microbes can both reduce the productivity of plants and other microbes, accelerating degradation. However, by restoring soil organics and soil biodiversity we have a chance to turn these negative effects around and increase plant productivity and climate resilience with compounding positive feedback—a win-win-win-win (Lehmann et al. 2020, Qiao et al. 2022).

Here, we focus on the soil microbe-organic axis of soil restoration, especially the development of new technologies that can help improve microbial diversity by identifying missing microbial functions and supporting the growth of resident microbes with these functions. Our hope is that approaches like we describe here can be developed and deployed to help reboot soils as part of national and global soil restoration efforts.

Restoring soil organics

It is estimated that healthy agricultural soils can store up to 5 Pg CO₂-equivalent per year (Bossio et al. 2020). The organic fraction that is associated with minerals in soil has a particular slow turnover time, often in hundreds to several thousands of years, making it one of the most viable pools for managing atmospheric carbon (Georgiou et al. 2022) (Fig. 1). But what defines a healthy soil and why are healthy soils so important? Root-derived carbon is one of the most important, if not the most important, driver of soil organics (Poeplau et al. 2021). While poorly understood, some estimates suggest that rhizosphere processes can account for a large fraction of global primary production on land (Dijkstra et al. 2021).

Figure 1.

Soil organics are key determinants of soil health. Soil organics influence multiple factors, they affect the climate, are consumed (and produced) by plant and soil microbes, thus playing a critical part in agriculture, and influence soil properties, such as water retention.

There are several conceptional frameworks for stabilization of organics in soils including the Microbial Efficiency-Matrix Stabilization framework (Cotrufo et al. 2013) where organics are stabilized through entombment and interaction with mineral surfaces. It has been shown that most agricultural soils are currently undersaturated in soil organics (Georgiou et al. 2022) further supporting the large potential for soils as a natural and high-capacity atmospheric carbon sink. Influencing microbial functions in the rhizosphere would thus directly impact entombment and could boost organic soil carbon.

Restoring microbial functional diversity

We refer to microbial functional diversity as a direct measure of in vivo activity of microbes, in contrast to widely used diversity measurements by tracking phylogenetic markers (i.e. 16S rRNA by amplicon sequencing) or genetic potential (i.e. metagenomics by shotgun sequencing) (Fierer et al. 2021).

Microbial functional diversity can in theory be modulated by adding probiotics (i.e. biologicals), adding prebiotics, or by altering plant exudation directly (Fig. 1). Major efforts have been made to use biologicals to help improve soil functions. However, there are many challenges to this approach. Typically microbes are not adapted to compete with the resident microflora and environmental conditions. We can speculate that this may partially explain why conservation strategies that are focused on first building soil organics which in turn increases soil microbial biodiversity generally work across diverse ecosystems. While there are many key microbial functions related to plant and soil health, key ones include: Nitrogen fixation and phosphorous mobilization, priming for drought tolerance and EPS production, pathogen exclusion or induction of plant defenses, and growth promotion.

New technologies for prescriptive microbial and organic management

Over the last years several methods have become available to determine microbial functional diversity in soils and to predict strategies to alter this diversity. Exometabolomics is an approach for measuring composition and biological transformations of small molecule metabolites (Zhalnina et al. 2018). Relevant applications include characterization of root exudates coupled with analysis of microbial consumption to provide insights into plant selection of rhizosphere microbial community assembly and dynamics (Zhalnina et al. 2018). AI tools like the webofmicrobes.org use exometabolomic data to predict metabolites that can be added to alter soil microbial community composition (in addition to other applications) (Northen et al. 2026). Another approach is Microbial Interaction and Niche Determination (MIND) that allows for rapid analysis of what microbes occupy what niches in vivo and provides a framework to design intervention strategies to boost microbial functional diversity, e.g. by addition of prebiotics (Moyne et al. 2026).

Exometabolomics and MIND generate hypotheses that are readily testable in the lab, if needed, by using synthetic microbial communities (synComs) (Coker et al. 2022). Furthermore, both exometabolomics as well as MIND generate AI-ready data sets that can be interoperable, linking multi-omic measurements with soil physicochemical, climatic, ecological, and soil management context with the goal to improve prediction of soil functions across ecosystems and crop types (Fig. 2). The webofmicrobes.org is one example of using AI for predicting metabolites that can be added to soils to boost the growth of target organisms (Northen et al. 2026). However, it will be critical to go beyond taxonomy based predictions to actual functions. One promising opportunity is the integration of MIND with the exometabolomics to improve predictions of metabolites that can selectively boost the growth of microbes expressing the target functions (Fig. 2).

Figure 2.

Concept of rebooting soil metabolism with targeted soil amendments.

Conclusion

We argue here that measurements and evaluations of soil functional diversity in vivo will provide us with a direct readout of soil health and a roadmap for designing interventions to improve soil health. If effective, these interventions could aid in haltering soil degradation or, ideally, help soil health restoration—i.e. turning the downward spiral upward again. These targeted soil alterations could potentially remediate soil loss, reboot soil organic and micronutrient content, and positively impact water and carbon management.

Authors contribution

Both K. Zengler and T. Northen contributed equally to conceptualization, investigation, writing, and editing of this manuscript, as well as in directing and reviewing the work generated by the Gen AI Tool to ensure accuracy of the figure output.

Conflicts of interest

K. Zengler and T. Northen are co-founders of the Prosper Soils Institute, a nonprofit organization to build resilient agriculture.

Funding

None declared.

Data availability

No data were generated or analyzed for this Editorial.