By Pooja Toshniwal PahariaReviewed by Lexie CornerJun 12 2025A new study in Nature Communications explores how combinations of global change (GC) factors influence soil microbial communities. The results show that multiple GC treatments can affect soil microbes differently than individual factors alone.
These findings support the importance of studying combined environmental stressors, which better reflect real-world conditions where multiple changes occur at once.
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Soil microbes are central to ecosystem processes. They help regulate nutrient cycling, maintain soil health, and support biodiversity. Understanding how microbial communities respond to environmental shifts is key to predicting ecological outcomes.
While earlier studies have focused on single GC factors, little is known about how microbes react to several stressors acting together. Single-factor approaches may overlook the complexity of natural ecosystems.
About the Study
The researchers set up a controlled experiment to examine how individual and combined GC factors influence soil microbial communities.
They applied 10 individual GC treatments and one combination of eight factors to grassland soil samples over six weeks. Each individual treatment had five replicates. The combined treatment had ten.
The treatments included:
- Physical stress: Global warming
- Inorganic chemicals: Drought, nitrogen accumulation, salinity, heavy metals
- Particle contaminants: Microplastics
- Organic toxins: Fungicides, antibiotics, insecticides, herbicides
DNA was extracted from the soil samples and amplified using polymerase chain reaction (PCR). The researchers used shotgun metagenome sequencing to examine the bacterial and viral communities, including their genetic functions. The analysis covered both common and rare microbes. It produced 1,865 viral and 742 bacterial metagenome-assembled genomes (MAGs).
They compared taxonomic profiles built from MAGs with those generated by marker gene tools like mOTUs and SingleM. Microbial genes were mapped to KEGG pathways. Genes not found in existing references were considered novel.
A genetic catalog of 25 million microbial genes was created from these analyses. The catalog included gene predictions from both prokaryotic and eukaryotic microbes. To detect antibiotic resistance, the team mapped genes to the Comprehensive Antibiotic Resistance Database (CARD). Phospholipid fatty acid (PFLA) analysis estimated living bacterial populations. Viral diversity was confirmed using Kraken2.
Key Findings
The eight-factor combination had effects that differed from any single treatment. For instance, single stressors had little effect on how long water droplets penetrated the soil. But when multiple stressors were applied together, water retention increased noticeably. The effect scaled with the number of stressors.
Combined treatments favored the growth of mycobacterial species with known pathogenic traits, such as Mycobacterium tuberculosis, M. manitenii, and M. colombiense. They also selected for certain bacteriophages, including Phychrobacillus, Diplorickettsiaceae, and Alicyclobacillus. These changes may influence soil structure and plant growth.
The gene catalog showed that combined GC factors selected for bacteria that are stationary, metabolically diverse, and often resistant to antibiotics. These bacteria also carried more genes related to nutrient recycling and degradation. This suggests that under high stress, microbes with greater metabolic flexibility may have a survival advantage.
The study also found contrasting effects on microbial diversity. High-abundance species became less diverse under the eight-factor treatment, based on MAGs and mOTUs. However, Kraken2 detected an increase in overall diversity, driven by rare species becoming more visible. These low-abundance microbes may play a role in ecosystem resilience.
Salinity had a particularly strong effect. It favored conditionally rare bacterial families like Sporolactobacillaceae, which are important for monitoring microbial responses. Salinity, drought, and the eight-factor combination also led to a decline in viral diversity. This matters because rare microbes and viruses often carry unique genetic traits that contribute to long-term stability.
The researchers observed differences in microbial strategies. KEGG ortholog (KO) profiles from the eight-factor treatment were distinct from others. For example, genes linked to spore germination were reduced under the combined condition but increased in high-salinity samples.
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Conclusion
This study shows that multiple global change factors can jointly affect soil microbes in ways that differ from individual stressors.
It emphasizes the value of studying combined environmental changes to better understand how ecosystems respond under real-world conditions.
Journal Reference
Rodríguez del Río, Á., Scheu, S. Rillig, M.C. (2025). Soil microbial responses to multiple global change factors as assessed by metagenomics. Nat Commun, 16, 5058, DOI: 10.1038/s41467-025-60390-4, https://www.nature.com/articles/s41467-025-60390-4
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