Degraded soils and agroecosystems cover roughly 40 percent of Earth's land area and affect half of humanity, including 3.2 billion people touched by drought and desertification. Around 800 million people are food insecure, and between 2 and 3 billion are prone to malnutrition due to deficiencies in protein and micronutrients, according to figures the authors cite from the Food and Agriculture Organization of the United Nations. Land-use intensification has driven compaction and erosion, while chemical imbalances in degraded soils can reduce crop quality, promote bioaccumulation of toxic substances in food chains, and increase human and animal exposure to contaminants.

Declining microbial diversity can compound these harms, accelerating soil organic matter decomposition, reducing soil organic carbon, and altering ecosystem biogeochemistry as warming and drought intensify. Within the One Health framework — which recognizes that the health of people, animals, and ecosystems is interconnected — soil occupies a foundational position. The authors argue that these connections represent a biological reality rather than a purely conceptual association.

Soil health, defined as the capacity of soil to function as a living system that sustains biological productivity, maintains environmental quality, and promotes the health of plants, animals, and humans, underpins soil security and provides the biological basis for implementing One Health. The pathways linking soils to broader health outcomes include climate regulation, soil influences on nutrient density and food quality, the transfer of pollutants and soil-borne pathogens, and microbiome continua that connect soils, plants, animals, and humans. One of the most consequential of these pathways involves carbon.

Soil stores more carbon than the combined amounts found in the atmosphere and plant biomass, making it one of the largest manageable carbon reservoirs on Earth. Microbial diversity and the presence of key functional groups are closely associated with the stability of soil carbon pools, and higher soil organic carbon enhances microbial activity while improving water and nutrient use efficiency through mineral stabilization and humus formation. The authors emphasize that increasing soil carbon stocks requires improved predictive capacity, because carbon accumulation depends on primary productivity, organic matter stabilization, and efficient use of limiting resources — processes strongly mediated by interactions between plants and the soil microbiome.

They call for approaches that link the structure of plant and microbial communities with the processes regulating carbon, water, and nutrient cycling, combining natural and engineered methods with data-driven models. The paper also highlights a quieter crisis: the erosion of micronutrients from the food supply. Of the 29 essential and beneficial elements for plant growth, 18 are obtained from the soil, and microbial communities play a central role in mobilizing them through mineral weathering, chelation, organic acid production, and enzymatic transformations.

Over the past century, concentrations of key mineral nutrients in major food crops — including zinc, calcium, manganese, iron, and copper — have declined markedly, with reported reductions ranging from about 50 percent to nearly 100 percent. The authors attribute this largely to soil nutrient depletion under intensive agriculture and to the cultivation of high-yield varieties that dilute mineral concentrations in edible tissues. Micronutrient levels in vegetables have fallen as well, with iron declining by up to roughly 60 percent and vitamin A by up to about 40 percent in crops such as broccoli, cauliflower, and collard greens.

Because these minerals support antioxidant defense, cellular immunity, bone formation, nerve impulse transmission, and pathogen resistance, their decline feeds directly into what the authors describe as hidden hunger and elevated risk of metabolic disorders. Contamination adds a further layer of stress. Soils are increasingly exposed to heavy metals, per- and polyfluoroalkyl substances (PFAS), and microplastics, all of which alter microbial communities and disrupt nutrient cycling.

PFAS, the so-called forever chemicals, are exceptionally stable and mobile, accumulating in soils and sediments that act as long-term reservoirs; human exposure has been linked to endocrine disruption, immune dysregulation, and developmental effects. Beyond their direct toxicity, PFAS modify microbial community composition and impair the functions that regulate nutrient cycling and soil resilience. Microplastics — defined in the paper as solid polymer-containing particles between 1 and 5 millimeters — modify soil structure, water dynamics, and aggregation, and can act as carriers that alter the adsorption, mobility, and bioavailability of co-occurring heavy metals; the authors cite evidence that microplastics can increase copper availability and accumulation in plant roots.

They also alter soil enzyme activities involved in carbon, nitrogen, and phosphorus cycling, reducing ecosystem multifunctionality. Against this backdrop, the authors see particular promise in microbiomes from harsh, ancient, and extreme environments — deserts, polar regions, saline ecosystems, geothermal habitats, and other long-term stressed systems, including those along Chile's exceptional geoclimatic gradient. Such communities possess exceptional functional diversity and frequently produce novel enzymes, biosurfactants, oxidative catalysts, and bioactive metabolites.

Selected microorganisms and synthetic microbial communities (SynComs) can catalyze the transformation, defluorination, and partial degradation of specific PFAS compounds under defined conditions, and microbial biofilms known as the plastisphere initiate weathering of microplastics, with polymers such as PET generally more susceptible to enzymatic attack than highly crystalline polyolefins like polyethylene and polypropylene. While these biological processes rarely achieve complete mineralization, the authors argue they can reduce contaminant toxicity and persistence as part of integrated remediation strategies combined with adsorption, phytoremediation, or electrochemical treatment. The ecological logic underpinning microbiome engineering rests on how biodiversity is generated and maintained.

Ecosystems with greater functional diversity are generally more resistant to invasions, pollution, and climate extremes, benefiting from complementarity effects, in which organisms with different traits exploit resources more efficiently, and selection effects, in which highly productive or stress-tolerant species disproportionately shape ecosystem processes. Horizontal gene transfer is especially active in biofilms and under strong environmental selection, allowing unrelated microorganisms to acquire genes for stress tolerance, specialized metabolism, pollutant degradation, and nutrient acquisition. Bacterial strains sharing nearly identical 16S rRNA gene sequences may differ substantially in functional capabilities because of differences in accessory genes, which is why the authors argue that taxonomy alone cannot predict ecosystem function.

This leads to the concept of the extended genotype, in which microbial genomes contribute directly to the phenotype, fitness, and adaptive capacity of their hosts, meaning plants, animals, humans, and their microbiomes should be viewed as integrated biological units. The authors are candid about the obstacles. Microbial inoculants that perform well in greenhouses often fail in the field, where environmental heterogeneity and competition from well-adapted indigenous microbiota limit establishment and persistence.

Many ecosystem functions emerge from dynamic interactions among bacteria, archaea, fungi, viruses, and protists rather than from individual species, making rational design of stable SynComs difficult. Scalable manufacturing, formulation, shelf-life maintenance, and suitable carrier materials — including biochar-based matrices — remain unsolved engineering problems, and standardized methods for evaluating efficacy, persistence, and ecological safety are still lacking. Regulatory frameworks, such as the European Union's Fertilising Products Regulation (EU) 2019/1009, were developed primarily for single-strain inoculants and provide limited guidance for synthetic communities or engineered consortia.

Long development timelines and uncertain regulatory pathways also discourage private investment, particularly among small biotechnology companies, and the authors stress that public acceptance depends on transparent communication about safety and environmental benefits. The greatest challenge, the paper concludes, may no longer be technological but conceptual: identifying which ecological functions should be manipulated and selecting methodologies capable of resolving them. Plants recruit microbiomes primarily according to functional traits rather than taxonomic identity, so functional analyses must complement taxonomic profiling.

The authors advocate integrating high-resolution mass spectrometry, multi-omics approaches, synthetic transparent microscale soil models that allow visualization of microbial colonization and chemical gradients, and machine learning applied to multi-omics datasets to guide the rational design of synthetic consortia. They also point to comparative analyses of wheat cultivars showing that approximately 95 percent of differentially abundant functional genes were depleted in modern varieties following the Green Revolution, suggesting that microbiome recruitment capacity should be incorporated into future crop breeding. As an opinion paper, the work sets out research priorities rather than presenting new experimental results, but its central message is clear: soils and their microbial diversity are foundational to One Health, and harnessing the functional biodiversity of extreme and ancient ecosystems offers an actionable path toward climate-resilient agroecosystems in the Anthropocene.

Subject of Research: Microbiome engineering as a research priority for soil health and One Health in the Anthropocene

Article Title: Soil health and One Health implications in the anthropocene: a perspective on microbiome engineering

Article References: Timmusk, S., Ribeli, E., Behers, L., Muñoz, C., Schoebitz, M., Ubhayasekera, K., Karlsson, E., Suazo-Hernandez, J., de los Angeles Sepulveda, M., Tsiukalo, L., Espoz, J. P. F., Jara, R. E. G., Ortiz, J., Zagal, E., & Bergquist, J. (2026). Soil health and One Health implications in the anthropocene: a perspective on microbiome engineering. Plant and Soil. https://doi.org/10.1007/s11104-026-09120-3

Image Credits: AI Generated

DOI: 10.1007/s11104-026-09120-3

Keywords: soil health, One Health, microbiome engineering, synthetic microbial communities, PFAS, microplastics, carbon sequestration, hidden hunger, horizontal gene transfer, extremophiles, climate-resilient agriculture, Chile geoclimatic gradient