Microbes in soil function as both a source and a sink of greenhouse gases, performing two dichotomous roles: stabilizing carbon inputs into organic forms and mineralizing soil organic carbon.
Soil stores approximately three times more organic carbon than the Earth's atmosphere, but soil respiration represents the most significant source of carbon dioxide (CO2) from terrestrial ecosystems to the atmosphere—around ten times more than anthropogenic emissions.
However, feedback to climate warming and the underlying microbial mechanisms remain poorly understood, with soil microbial respiration considered a key source of uncertainty in the projection of future climate and carbon cycle feedbacks.
Soil total respiration includes several processes, including heterotrophic respiration from microbial decomposition of litter and soil organic matter (SOM), and autotrophic respiration from plant root growth and root biomass maintenance.
A range of short-term experiments has shown that soil respiration increases exponentially with temperature, suggesting a significant positive feedback effect. More long-term experiments are needed, however, as microbial communities have been shown to shift as part of thermal adaptation.
In one long-term experiment, researchers exposed plots of land to continuous warming for more than seven years. Soil DNA was extracted, and amplicon sequencing (16S and ITS) was performed, with gene abundances quantified using a geochip. This data was then correlated with carbon flux and respiration measurements.
The research revealed that incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly enhances the model’s performance in simulating soil microbial respiration and reduces its parametric uncertainty.
Modeling analyses also showed that heterotrophic respiration and soil carbon loss are notably lower as the microbial population shifts through thermal adaptation.
If these microbially mediated dampening effects can be generalized across various temporal and spatial scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.1
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Climate change impacts on microbes
Microorganisms can alter their metabolism and community structure to adjust their respiratory responses to temperature over long periods. The ecophysiology of microbes is also generally expected to be phylogenetically conserved due to a given species’ evolutionary history.
The ecological traits of microorganisms can be understood as reflecting both phylogenetic constraints and environmental acclimation, but uncertainty remains regarding the extent to which these traits are influenced by phylogeny versus the environment.
Research was conducted to explore the interaction between phylogeny and environment in a long-term climate experiment. Soil plots were exposed to four different climate scenarios over 10 years:
- A control (Cntrl) plot featuring ambient CO2 concentration and temperature
- A plot with temperature raised by +2 °C (eT)
- A plot with CO2 concentration elevated up to 500 ppm (eCO2)
- A plot with combined warming and CO2 enrichment (eTeCO2).
Soil metagenomic analysis was conducted following DNA extraction and was combined with stable isotope probing to evaluate microbial responses to each of the four climate scenarios.
Three growth strategies of bacterial taxa were observed—rapid, intermediate, and slow responders—all of which are phylogenetically conserved.
Members of the classes Bacilli and Sphingobacteria are primarily rapid responders, although these phylogenetic patterns can be somewhat confounded by environmental factors.
Different climate scenarios altered the growth strategies of over 90 % of species. For example, variance in slow responders can be primarily explained by climate, whereas the growth of rapid bacterial responders is more strongly influenced by phylogeny.
The results of the experiment highlight the importance of understanding both the phylogenetic composition of the soil microbiome and climatic constraints. Insight into both factors is essential for predicting the growth strategies of soil microorganisms under global change scenarios.2
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Soil microbes influence food security and agricultural health
Earth’s population is estimated to reach 8 and 9.8 billion people by 2025 and 2050, respectively. New solutions are required to feed this growing population.
This exponential population growth is accompanied by climate change, bringing challenges such as floods, droughts, pests, changes in growing seasons, reduced yields, and loss of biodiversity. These effects are expected to be compounded by anthropogenic inputs, including the continued use of synthetic pesticides and fertilizers.
There is potential to harness the beneficial properties of soil microorganisms to sustainably improve crop production and soil health. Plants and microbial communities share a complex, interdependent relationship, influencing ecological interactions through a wide range of mechanisms.
For example, plants release photosynthates to soil microbes. In return, certain microbial taxa can promote plant growth and protect plants from pathogens by acquiring and transporting nutrients through phytohormone synthesis and metabolite production.
It is also possible to promote plant growth by using specific soil microorganisms or communities as soil inoculants. These inoculants can act as fertilizers or pesticides, or offer protection against stress, improving crop yields while reducing reliance on harmful chemicals.
The development of synthetic microbial communities (SynComs) represents another approach to creating soil microbial inoculants. However, this requires a comprehensive understanding of natural microbial communities, including genome sequences and their metabolic potential.
In one study, researchers used metagenome-assembled genomes (MAGs) from an arid soil community to reconstruct genome-scale metabolic networks (GSMNs). The goal was to identify a minimal community capable of promoting plant growth.
The identified minimal community retained key genes associated with Plant Growth-Promoting Traits (PGPTs), including genes involved in EPS production, potassium solubilization, nitrogen fixation, iron acquisition, GABA production, and plant growth hormones (IAA-related tryptophan metabolism).
The researchers also integrated metabolic modeling from five key crop plants: maize, sorghum, soybean, and sugarcane.
A core set of species was selected for their consistent benefits across different hosts, suggesting their significance regardless of plant type.
Integrating the host into the model allowed researchers to demonstrate that these hosts primarily provided lipids, amino acids, and coenzymes, while the SynCom supplied carbohydrates, amino acids, esters, and aromatic compounds to the hosts, in addition to PGPTs.
This multi-species, community-wide GSMNs analysis provided valuable insight into the metabolic complementarity between bacterial species and host crop plants, advancing the development of a widely applicable microbial soil inoculant.3
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The soil microbiome, climate change, and livestock
Soil microbes also influence livestock through a range of direct and indirect mechanisms. One study examined the interaction between soil microbes, climate change, and livestock practices.
In addition to rising temperatures, the use of antibiotics in livestock is also increasing. Approximately 11 million kg of antibiotics were sold in the United States in 2017 alone, specifically for livestock use. Once administered, up to 90 % of these antibiotics are excreted onto soils as unmetabolized, biologically active compounds.
Samples of prairie soil were collected and treated with either a high dose, low dose, or no dose of a common livestock antibiotic (Monensin). The soil was then heated at three different temperatures before being left to incubate.
Researchers monitored acidity, microbial community composition and function, carbon and nitrogen cycling, soil respiration, and interactions among microbes for each specific treatment.
A 16S/ITS metabarcoding approach was used to assess community composition, revealing that rising heat and antibiotic additions led to the collapse of bacterial populations. This allowed fungi to dominate, resulting in fewer total microbes and reduced overall microbial diversity. Antibiotics alone were found to increase bioavailable carbon and reduce microbial efficiency.4
The role of genetic engineering and CRISPR in soil science
New avenues in soil science are emerging thanks to advances in genetic engineering, high-throughput sequencing, and culture-independent 'omics.
New methods of manipulating the soil microbiome are being developed, offering the potential to mitigate the adverse effects of climate change. Advances in genetic engineering tools and synthetic biology are also being used to explore and enhance native microbial functions, develop biological sensors, introduce new traits, and combine multiple beneficial traits into a single organism.5
One recent example of soil bacteria engineering involved researchers using a combinatorial synthetic biology–based approach to generate a collection of plant-associated bacteria capable of efficient phytate hydrolysis.
Microbes that can release soluble phosphate from naturally occurring sources in the soil may offer a way to reduce the need for synthetic fertilizers. The researchers analyzed the full range of available microbial genomes and environmental metagenomes, identifying more than 2,000 phytate genes across three enzyme classes.
A total of 82 genes were selected, with sequence optimization performed to ensure optimal expression in proteobacteria. These genes were synthesized, cloned into high-expression inducible cassettes, and sequence-verified.
The researchers then used conjugation to transfer all 82 sequences into the genomes of three root-associated proteobacteria (Pseudomonas simiae, Pseudomonas putida, and Ralstonia sp.).
Experiments confirmed that these engineered strains enhanced plant growth under phosphorus-limited conditions. This work represents an initial step in developing phosphate-mining bacteria suitable for future use in crop systems and a step toward reducing dependence on synthetic fertilizers.6
A recent microbiome-wide application of genetic engineering featured in situ microbial community editing via CRISPR-Cas technologies and conjugation.
Researchers successfully developed a computational program capable of modifying microbial consortia using strain-specific CRISPR guide RNAs. They demonstrated the ability to isolate a specific strain from a community and selectively eliminate a target strain.
Strain purification was achieved using guide RNAs (gRNAs) designed to target and kill all microbes in the community except the desired strain. Strain elimination was achieved by using gRNAs to remove only the unwanted microbe while sparing all others.
This technique (ssCRISPR) is expected to be applicable to a wide range of microbiota engineering applications, including isolating beneficial microbes from the environment and addressing the issue of antibiotic-resistant microbes.7
However, questions remain regarding the ecological impacts of engineered microbes and microbial consortia. It is important that engineered microbes and communities first be tested in fabricated ecosystems to provide relevant community contexts.
Image Credit: Norgen Biotek Corp.
Norgen's soil-related kits for soil science research
The extraction of nucleic acids from soil is expected to become an integral part of developing a systems-level understanding of the soil microbiome.
The combination of PCR, NGS, metabolomics, genetic engineering, and other techniques will be key to addressing the challenges of climate change and a growing human population.
References and further reading
- Guo, X., et al. (2020). Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-18706-z.
- Ruan, Y., et al. (2023). Elevated temperature and CO2 strongly affect the growth strategies of soil bacteria. Nature Communications, (online) 14(1), p.391. https://doi.org/10.1038/s41467-023-36086-y.
- Gonçalves, O. S., Creevey, C. J., and Santana, M. F. (2023). Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction. Environmental Microbiome, 18(1), 81. https://doi.org/10.1186/s40793-023-00536-3.
- Lucas, J.M. et al. (2021). Antibiotics and temperature interact to disrupt soil communities and nutrient cycling. Soil Biology and Biochemistry, 163, p. 108437. https://doi.org/10.1016/j.soilbio.2021.108437.
- Jansson, J.K., McClure, R. and Egbert, R.G. (2023). Soil microbiome engineering for sustainability in a changing environment. Nature Biotechnology, (online) pp.1–13. https://doi.org/10.1038/s41587-023-01932-3.
- Shulse, C.N., et al. (2019). Engineered Root Bacteria Release Plant-Available Phosphate from Phytate. Applied and Environmental Microbiology, (online) 85(18), pp.e01210-19. https://doi.org/10.1128/AEM.01210-19.
- Rottinghaus, A.G., Vo, S. and Tae Seok Moon (2022). Computational design of CRISPR guide RNAs to enable strain-specific control of microbial consortia. Proceedings of the National Academy of Sciences of the United States of America, 120(1). https://doi.org/10.1073/pnas.2213154120.
Acknowledgments
Produced from materials originally authored by Norgen Biotek Corporation.
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