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Soil microbiome interventions for carbon sequestration and climate mitigation

Journal Article · · mSystems
 [1];  [2];  [3];  [4];  [5];  [6];  [4];  [7];  [8];  [9];  [4];  [10];  [11];  [12];  [7]
  1. Iowa State Univ., Ames, IA (United States)
  2. Oath Inc., Mill Valley, CA (United States)
  3. Florida Atlantic Univ., Boca Raton, FL (United States)
  4. Univ. of California, San Diego, CA (United States). Scripps Inst. of Oceanography
  5. Copenhagen Univ. (Denmark)
  6. Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
  7. University of Lausanne (Switzerland)
  8. Indiana Univ., Bloomington, IN (United States)
  9. Univ. of California, Irvine, CA (United States)
  10. California Institute of Technology (CalTech), Pasadena, CA (United States)
  11. King Abdullah University of Science and Technology (KAUST), Thuwal (Saudi Arabia)
  12. Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.
Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
2483407
Journal Information:
mSystems, Journal Name: mSystems Journal Issue: 1 Vol. 10; ISSN 2379-5077
Publisher:
American Society for MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English

References (134)

Contributions of plant breeding to soil carbon storage: Retrospect and prospects journal March 2023
Application of microbial inoculants significantly  enhances crop productivity: A meta‐analysis of studies from 2010 to 2020 journal August 2022
Effects of biostimulant application on soil biological and physicochemical properties: A field study journal June 2023
Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides journal August 2019
Impact of Rhizospheric Microbiome on Rice Cultivation journal May 2024
Inoculation with N2-generating denitrifier strains mitigates N2O emission from agricultural soil fertilized with poultry manure journal April 2014
Interaction of minerals, organic matter, and microorganisms during biogeochemical interface formation as shown by a series of artificial soil experiments journal November 2016
Does arbuscular mycorrhizal fungi inoculation influence soil carbon sequestration? journal January 2024
Influence of plant growth-promoting bacteria on leaf carbon and nitrogen metabolism of two drought-stressed neotropical tree species: a metabolomic approach journal June 2024
Agroecology: the key role of arbuscular mycorrhizas in ecosystem services journal August 2010
Agricultural uses of plant biostimulants journal May 2014
Aboveground biomass and root/shoot ratio regulated drought susceptibility of ecosystem carbon exchange in a meadow steppe journal September 2018
Soil microbial diversity plays an important role in resisting and restoring degraded ecosystems journal January 2024
The trade-in-trade: multifunctionalities, current market and challenges for arbuscular mycorrhizal fungal inoculants journal February 2023
Global evaluation of commercial arbuscular mycorrhizal inoculants under greenhouse and field conditions journal January 2022
Minimal adverse effects of exogenous phage treatment on soil bacterial communities journal March 2024
Long-term restoration with organic amendments is clearer evidenced by soil organic matter composition than by changes in microbial taxonomy and functionality journal June 2024
Electrochemical framework for dynamic tracking of Soil Organic Matter journal April 2024
Seed coating with beneficial microorganisms for precision agriculture journal November 2019
Evaluation of a novel tool for sampling root exudates from soil-grown plants compared to conventional techniques journal March 2013
Organic matter stabilization in soil aggregates: Understanding the biogeochemical mechanisms that determine the fate of carbon inputs in soils journal March 2011
The legacy of microbial inoculants in agroecosystems and potential for tackling climate change challenges journal March 2022
Does fresh farmyard manure introduce surviving microbes into soil or activate soil-borne microbiota? journal September 2021
Effects of three plant growth-promoting bacterial symbiosis with ryegrass for remediation of Cd, Pb, and Zn soil in a mining area journal February 2024
Pioneer plants enhance soil multifunctionality by reshaping underground multitrophic community during natural succession of an abandoned rare earth mine tailing journal July 2024
Inoculation of Rhizoglomus irregulare or Trichoderma atroviride differentially modulates metabolite profiling of wheat root exudates journal January 2019
Effects of extracellular metabolites from a dark septate endophyte at different growth stages on maize growth, root structure and root exudates journal March 2023
Plant biostimulants: Definition, concept, main categories and regulation journal November 2015
Comparing straw, compost, and biochar regarding their suitability as agricultural soil amendments to affect soil structure, nutrient leaching, microbial communities, and the fate of pesticides journal January 2021
Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration journal November 2022
Soil C/N ratios cause opposing effects in forests compared to grasslands on decomposition rates and stabilization factors in southern European ecosystems journal August 2023
Fungal necromass contribution to carbon sequestration in global croplands: A meta-analysis of driving factors and conservation practices journal November 2024
Active microorganisms in soil: Critical review of estimation criteria and approaches journal December 2013
Rhizosphere priming effect: A meta-analysis journal August 2017
Sticky dead microbes: Rapid abiotic retention of microbial necromass in soil journal October 2020
Direct cell extraction from fresh and stored soil samples: Impact on microbial viability and community compositions journal April 2021
Microbial necromass as the source of soil organic carbon in global ecosystems journal November 2021
The Inherent Conflicts in Developing Soil Microbial Inoculants journal February 2019
Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction journal December 2013
Horizon scanning the application of probiotics for wildlife journal March 2024
The rhizosphere microbiome and plant health journal August 2012
Chemodiversity of Dissolved Organic Matter and Its Molecular Changes Driven by Rhizosphere Activities in Fe Ore Tailings Undergoing Eco-Engineered Pedogenesis journal September 2021
E-SCAN: Electrochemical Scanning of Carbonates, an In Situ Approach for Screening and Quantifying Inorganic Carbon in Soil journal October 2023
On Upscaling of Soil Microbial Processes and Biogeochemical Fluxes From Aggregates to Landscapes journal May 2018
Mineral control of soil organic carbon storage and turnover journal September 1997
Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships journal May 2016
Persistence of soil organic matter as an ecosystem property journal October 2011
Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls journal November 2016
Formation of soil organic matter via biochemical and physical pathways of litter mass loss journal September 2015
Soil inoculation steers restoration of terrestrial ecosystems journal July 2016
Embracing the unknown: disentangling the complexities of the soil microbiome journal August 2017
Going back to the roots: the microbial ecology of the rhizosphere journal September 2013
Microbiome-based interventions to modulate gut ecology and the immune system journal November 2022
Cable bacteria reduce methane emissions from rice-vegetated soils journal April 2020
Fast-decaying plant litter enhances soil carbon in temperate forests but not through microbial physiological traits journal March 2022
Niche availability and competitive loss by facilitation control proliferation of bacterial strains intended for soil microbiome interventions journal March 2024
Meta-analysis reveals the effects of microbial inoculants on the biomass and diversity of soil microbial communities journal June 2024
Persistence of soil organic carbon caused by functional complexity journal July 2020
Different climate sensitivity of particulate and mineral-associated soil organic matter journal April 2021
Formation of necromass-derived soil organic carbon determined by microbial death pathways journal January 2023
Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly journal March 2018
Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon journal June 2022
Harnessing the microbiome to prevent global biodiversity loss journal July 2022
Defending Earth’s terrestrial microbiome journal October 2022
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity journal November 2022
Soil microbiome indicators can predict crop growth response to large-scale inoculation with arbuscular mycorrhizal fungi journal November 2023
Soil microbiomes and climate change journal October 2019
Life and death in the soil microbiome: how ecological processes influence biogeochemistry journal February 2022
Microbial oxidation of atmospheric trace gases journal April 2022
Trichoderma: a multipurpose, plant-beneficial microorganism for eco-sustainable agriculture journal November 2022
Microbiota-mediated colonization resistance: mechanisms and regulation journal December 2022
The interplay between microbial communities and soil properties journal October 2023
Microbial carbon use efficiency promotes global soil carbon storage journal May 2023
Unlocking bacterial potential to reduce farmland N2O emissions journal May 2024
RNA demethylation increases the yield and biomass of rice and potato plants in field trials journal July 2021
Soil microbiome engineering for sustainability in a changing environment journal October 2023
Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis journal November 2018
Glomalin contributed more to carbon, nutrients in deeper soils, and differently associated with climates and soil properties in vertical profiles journal October 2017
Global Sequestration Potential of Increased Organic Carbon in Cropland Soils journal November 2017
Environmental connectivity controls diversity in soil microbial communities journal April 2021
Soil structure and microbiome functions in agroecosystems journal November 2022
“Reactive Mineral Sink” drives soil organic matter dynamics and stabilization journal November 2023
Increased plant productivity and decreased microbial respiratory C loss by plant growth-promoting rhizobacteria under elevated CO2 journal March 2015
Mitigation of soil N2O emission by inoculation with a mixed culture of indigenous Bradyrhizobium diazoefficiens journal September 2016
Copper control of bacterial nitrous oxide emission and its impact on vitamin B12-dependent metabolism journal November 2013
Soil biodiversity and soil community composition determine ecosystem multifunctionality journal March 2014
Soil carbon debt of 12,000 years of human land use journal August 2017
Moisture-driven divergence in mineral-associated soil carbon persistence journal February 2023
The role of glomalin in mitigation of multiple soil degradation problems journal December 2020
Root exudation of organic acids as affected by plant growth-promoting rhizobacteria Bacillus subtilis RR4 in rice journal April 2020
Biophysical processes supporting the diversity of microbial life in soil journal August 2017
Bacterial–fungal interactions: ecology, mechanisms and challenges journal February 2018
Quantitative assessment of microbial necromass contribution to soil organic matter journal August 2019
Conceptualizing soil organic matter into particulate and mineral‐associated forms to address global change in the 21st century journal November 2019
Clarifying the evidence for microbial‐ and plant‐derived soil organic matter, and the path toward a more quantitative understanding journal September 2022
A stoichiometric approach to estimate sources of mineral‐associated soil organic matter journal December 2023
Ruminating on soil carbon: Applying current understanding to inform grazing management journal March 2024
The effects of arbuscular mycorrhizal fungal species and taxonomic groups on stressed and unstressed plants: a global meta‐analysis journal April 2022
Home‐based microbial solution to boost crop growth in low‐fertility soil journal May 2023
Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral‐associated organic matter journal February 2024
Transient invaders can induce shifts between alternative stable states of microbial communities journal February 2020
Climate change effects on plant-soil feedbacks and consequences for biodiversity and functioning of terrestrial ecosystems journal November 2019
Plant rhizodeposition: A key factor for soil organic matter formation in stable fractions journal April 2021
Soil warming increases the number of growing bacterial taxa but not their growth rates journal February 2024
Soil Carbon Sequestration Impacts on Global Climate Change and Food Security journal June 2004
Bacteria-Phage Antagonistic Coevolution in Soil journal March 2011
Arbuscular Mycorrhizal Fungi Increase Organic Carbon Decomposition Under Elevated CO2 journal August 2012
Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world journal October 2017
Grassland soil carbon sequestration: Current understanding, challenges, and solutions journal August 2022
Shifting microbial communities can enhance tree tolerance to changing climates journal May 2023
Microbiome diversity protects against pathogens by nutrient blocking journal December 2023
3775-year-old wood burial supports “wood vaulting” as a durable carbon removal method journal September 2024
Soil Aggregate Microbial Communities: Towards Understanding Microbiome Interactions at Biologically Relevant Scales journal May 2019
Use of Plant Growth-Promoting Bacteria for Biocontrol of Plant Diseases: Principles, Mechanisms of Action, and Future Prospects journal September 2005
Microbial Community Resilience across Ecosystems and Multiple Disturbances journal May 2021
Microbes and Climate Change: a Research Prospectus for the Future journal June 2022
Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry journal September 2023
From microbiome composition to functional engineering, one step at a time journal December 2023
Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation journal April 2022
Soil Microbiomes Under Climate Change and Implications for Carbon Cycling journal October 2020
DENSE: DiElectric Novel Soil Evaluation System to Electrochemically Profile Soil Matrices journal June 2022
Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture journal December 2019
Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation journal September 2018
Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere journal September 2023
Microbiome Modulation—Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants journal April 2021
Entomopathogen-based biopesticides: insights into unraveling their potential in insect pest management journal July 2023
Polyphenol-Mediated Gut Microbiota Modulation: Toward Prebiotics and Further journal June 2021
Improving Crop Yield and Nutrient Use Efficiency via Biofertilization—A Global Meta-analysis journal January 2018
The Recent Use of Plant-Growth-Promoting Bacteria to Promote the Growth of Agricultural Food Crops journal May 2023
Arbuscular Mycorrhizal Fungi and Associated Microbiota as Plant Biostimulants: Research Strategies for the Selection of the Best Performing Inocula journal January 2020
Facing Climate Change: Application of Microbial Biostimulants to Mitigate Stress in Horticultural Crops journal June 2020
Effects of Commercial Arbuscular Mycorrhizal Inoculants on Plant Productivity and Intra-Radical Colonization in Native Grassland: Unintentional De-Coupling of a Symbiosis? journal August 2022
Soil Carbon Sequestration in the Context of Climate Change Mitigation: A Review journal July 2023
Optimal Sampling and Assay for Estimating Soil Organic Carbon journal January 2021

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