skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Soil Microbiomes Under Climate Change and Implications for Carbon Cycling

Journal Article · · Annual Review of Environment and Resources

Communities of soil microorganisms (soil microbiomes) play a major role in biogeochemical cycles and support of plant growth. Here we focus primarily on the roles that the soil microbiome plays in cycling soil organic carbon and the impact of climate change on the soil carbon cycle. We first discuss current challenges in understanding the roles carried out by highly diverse and heterogeneous soil microbiomes and review existing knowledge gaps in understanding how climate change will impact soil carbon cycling by the soil microbiome. Because soil microbiome stability is a key metric to understand as the climate changes, we discuss different aspects of stability, including resistance, resilience, and functional redundancy. We then review recent research pertaining to the impact of major climate perturbations on the soil microbiome and the functions that they carry out. Finally, we review new experimental methodologies and modeling approaches under development that should facilitate our understanding of the complex nature of the soil microbiome to better predict its future responses to climate change.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
Grant/Contract Number:
AC05-76RL01830
OSTI ID:
1706683
Report Number(s):
PNNL-SA-150059
Journal Information:
Annual Review of Environment and Resources, Vol. 45, Issue 1; ISSN 1543-5938
Publisher:
Annual ReviewsCopyright Statement
Country of Publication:
United States
Language:
English

References (194)

Soil and human security in the 21st century journal May 2015
Scientists’ warning to humanity: microorganisms and climate change journal June 2019
Soil Carbon Sequestration Impacts on Global Climate Change and Food Security journal June 2004
Current developments in soil organic matter modeling and the expansion of model applications: a review journal December 2015
Soil microbiomes and climate change journal October 2019
A communal catalogue reveals Earth’s multiscale microbial diversity journal November 2017
Hidden diversity of soil giant viruses journal November 2018
Climate–Carbon Cycle Feedback Analysis: Results from the C 4 MIP Model Intercomparison journal July 2006
Review and synthesis of the effects of elevated atmospheric CO2 on soil processes: No changes in pools, but increased fluxes and accelerated cycles journal January 2019
The importance of anabolism in microbial control over soil carbon storage journal July 2017
Microbe-driven turnover offsets mineral-mediated storage of soil carbon under elevated CO2 journal November 2014
Long-term patterns of mass loss during the decomposition of leaf and fine root litter: an intersite comparison journal May 2009
Long-Term (13 Years) Decomposition Rates of Forest Floor Organic Matter on Paired Coniferous and Deciduous Watersheds with Contrasting Temperature Regimes journal October 2016
Plant diversity increases soil microbial activity and soil carbon storage journal April 2015
Soil carbon saturation: concept, evidence and evaluation journal August 2007
Alive and kicking: Why dormant soil microorganisms matter journal January 2018
Dormancy contributes to the maintenance of microbial diversity journal March 2010
The soil microbiome — from metagenomics to metaphenomics journal June 2018
Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes? journal February 2016
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity journal December 2016
Relationship of soil organic matter dynamics to physical protection and tillage journal February 2000
How relevant is recalcitrance for the stabilization of organic matter in soils? journal February 2008
The Microbial Efficiency-Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter? journal February 2013
Persistence of soil organic matter as an ecosystem property journal October 2011
Effects of Profile Depth and Management on the Composition of Labile and Total Soil Organic Matter journal March 2012
A time for every season: soil aggregate turnover stimulates decomposition and reduces carbon loss in grasslands managed for bioenergy journal June 2015
Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria journal March 2016
Anaerobic microsites have an unaccounted role in soil carbon stabilization journal November 2017
Resistance, resilience, and redundancy in microbial communities journal August 2008
Plant Species Composition Effects on Belowground Properties and the Resistance and Resilience of the Soil Microflora to a Drying Disturbance journal December 2005
Insights into the resistance and resilience of the soil microbial community journal March 2013
Fundamentals of Microbial Community Resistance and Resilience journal January 2012
Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses journal June 2016
Drought Stress and Root-Associated Bacterial Communities journal January 2018
Resistance and Recovery of Methane-Oxidizing Communities Depends on Stress Regime and History; A Microcosm Study journal July 2018
Effects of elevated temperature and elevated CO2 on soil nitrification and ammonia-oxidizing microbial communities in field-grown crop journal July 2019
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients journal December 2011
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe journal August 2015
Severe drought conditions modify the microbial community structure, size and activity in amended and unamended soils journal July 2012
Soil carbon and nitrogen dynamics throughout the summer drought in a California annual grassland journal December 2017
Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting journal July 2010
Post-fire soil functionality and microbial community structure in a Mediterranean shrubland subjected to experimental drought journal December 2016
Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms journal April 2017
Soil microbial community structure explains the resistance of respiration to a dry–rewet cycle, but not soil functioning under static conditions journal December 2015
Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages journal December 2018
Soil Bacterial Community Shifts after Chitin Enrichment: An Integrative Metagenomic Approach journal November 2013
Chronic Physical Disturbance Substantially Alters the Response of Biological Soil Crusts to a Wetting Pulse, as Characterized by Metatranscriptomic Sequencing journal October 2018
Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion journal August 2018
Multiple, Compounding Disturbances in a Forest Ecosystem: Fire Increases Susceptibility of Soil Edaphic Properties, Bacterial Community Structure, and Function to Change with Extreme Precipitation Event journal June 2019
Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world journal October 2017
Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils journal September 2016
Increases in the flux of carbon belowground stimulate nitrogen uptake and sustain the long-term enhancement of forest productivity under elevated CO2: C fluxes belowground and long-term FACE productivity journal February 2011
Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth journal March 2019
Effect of warming and drought on grassland microbial communities journal March 2011
Evolutionary history constrains microbial traits across environmental variation journal June 2019
Toward an Ecological Classification of soil Bacteria journal June 2007
Decline of soil microbial diversity does not influence the resistance and resilience of key soil microbial functional groups following a model disturbance journal September 2007
Comparative Resistance and Resilience of Soil Microbial Communities and Enzyme Activities in Adjacent Native Forest and Agricultural Soils journal March 2009
Resilience of (seed bank) aerobic methanotrophs and methanotrophic activity to desiccation and heat stress journal October 2016
Adaptation of Soil Microorganisms to Trace Element Contamination: A Review of Mechanisms, Methodologies, and Consequences for Risk Assessment and Remediation journal January 2012
Evidence for taxonomic and functional drift of an atrazine-degrading culture in response to high atrazine input journal April 2011
Bacterial and fungal growth in soil heated at different temperatures to simulate a range of fire intensities journal December 2009
Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change journal September 2019
Elevated CO2 and Warming Altered Grassland Microbial Communities in Soil Top-Layers journal August 2018
Contrasting effects of elevated CO2 and warming on nitrogen cycling in a semiarid grassland journal May 2010
Effects of climate warming and elevated CO 2 on autotrophic nitrification and nitrifiers in dryland ecosystems journal January 2016
Two decades of warming increases diversity of a potentially lignolytic bacterial community journal May 2015
Warming Alters Expressions of Microbial Functional Genes Important to Ecosystem Functioning journal May 2016
The Microbiome Stress Project: Toward a Global Meta-Analysis of Environmental Stressors and Their Effects on Microbial Communities journal January 2019
Experimental warming alters the community composition, diversity, and N 2 fixation activity of peat moss ( Sphagnum fallax ) microbiomes journal May 2019
Long-term forest soil warming alters microbial communities in temperate forest soils journal February 2015
Microbial community responses reduce soil carbon loss in Tibetan alpine grasslands under short‐term warming journal August 2019
Microbial mediation of carbon-cycle feedbacks to climate warming journal December 2011
Chronic nitrogen additions suppress decomposition and sequester soil carbon in temperate forests journal July 2014
Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change journal April 2017
Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem journal March 2015
Soil Microbial Responses to Elevated CO2 and O3 in a Nitrogen-Aggrading Agroecosystem journal June 2011
Responses of soil microbial activity to cadmium pollution and elevated CO2 journal March 2014
Common bacterial responses in six ecosystems exposed to 10 years of elevated atmospheric carbon dioxide: Soil bacterial response in six ecosystems journal January 2012
Long-term elevated CO2 shifts composition of soil microbial communities in a Californian annual grassland, reducing growth and N utilization potentials journal February 2019
Long term CO2 enrichment stimulates N-mineralisation and enzyme activities in calcareous grassland journal July 2003
Direct and indirect impacts of climate change on microbial and biocrust communities alter the resistance of the N cycle in a semiarid grassland journal August 2014
Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3 journal November 2017
Sources of increased N uptake in forest trees growing under elevated CO2: results of a large-scale 15N study journal July 2011
Surface soil fungal and bacterial communities in aspen stands are resilient to eleven years of elevated CO2 and O3 journal September 2014
Effect of Elevated CO 2 , O 3 , and UV Radiation on Soils journal January 2014
Soil ecosystem functioning under climate change: plant species and community effects journal March 2010
Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO 2 and warming in an Australian native grassland soil : Climate change effects on microbial communities journal October 2012
Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming journal April 2015
Forest understory plant and soil microbial response to an experimentally induced drought and heat-pulse event: the importance of maintaining the continuum journal April 2016
Soil microbial responses to drought and exotic plants shift carbon metabolism journal March 2019
Increased microbial growth, biomass, and turnover drive soil organic carbon accumulation at higher plant diversity journal August 2019
Cascading effects from plants to soil microorganisms explain how plant species richness and simulated climate change affect soil multifunctionality journal October 2018
Disentangling carbon flow across microbial kingdoms in the rhizosphere of maize journal July 2019
Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2 journal June 2010
Photoautotrophic organisms control microbial abundance, diversity, and physiology in different types of biological soil crusts journal February 2018
Bacteria increase arid-land soil surface temperature through the production of sunscreens journal January 2016
Large Blooms of Bacillales ( Firmicutes ) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity journal March 2018
Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nitrogen-fixing cyanosphere journal April 2019
Dryland photoautotrophic soil surface communities endangered by global change journal February 2018
Increased temperature and altered summer precipitation have differential effects on biological soil crusts in a dryland ecosystem journal May 2012
Are fungal networks key to dryland primary production? journal October 2018
Fungal loop transfer of nitrogen depends on biocrust constituents and nitrogen form journal January 2018
Catch me if you can: dispersal and foraging of Bdellovibrio bacteriovorus 109J along mycelia journal November 2016
Mycelia as a focal point for horizontal gene transfer among soil bacteria journal November 2016
Migration of Paraburkholderia terrae BS001 Along Old Fungal Hyphae in Soil at Various pH Levels journal January 2018
Soil protist communities form a dynamic hub in the soil microbiome journal October 2017
Microbial amendments alter protist communities within the soil microbiome journal August 2019
Quest of Soil Protists in a New Era journal January 2017
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing journal October 2018
Host-linked soil viral ecology along a permafrost thaw gradient journal July 2018
Diversities and potential biogeochemical impacts of mangrove soil viruses journal April 2019
Soil Viruses: A New Hope journal May 2019
Weathering and the global carbon cycle: Geomorphological perspectives journal June 2012
The role of forest trees and their mycorrhizal fungi in carbonate rock weathering and its significance for global carbon cycling: Tree-fungal carbonate rock weathering journal November 2014
Climate-driven changes in chemical weathering and associated phosphorus release since 1850: Implications for the land carbon balance journal May 2014
High sensitivity of the continental-weathering carbon dioxide sink to future climate change journal February 2012
Microbial community composition affects soil organic carbon turnover in mineral soils journal March 2017
Abiotic and Biotic Controls on Soil Organo–Mineral Interactions: Developing Model Structures to Analyze Why Soil Organic Matter Persists journal September 2019
Aggregate stability and associated C and N in a silty loam soil as affected by organic material inputs journal April 2015
Factors affecting soil microbial biomass and functional diversity with the application of organic amendments in three contrasting cropland soils during a field experiment journal September 2018
Fungal–bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality journal December 2016
Links among warming, carbon and microbial dynamics mediated by soil mineral weathering journal July 2018
Soil carbon storage controlled by interactions between geochemistry and climate journal August 2015
Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems journal November 2011
Impact of sequencing depth on the characterization of the microbiome and resistome journal April 2018
Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil journal August 2018
A Primer on Metagenomics journal February 2010
Advances and Challenges in Metatranscriptomic Analysis journal September 2019
Principles of transcriptome analysis and gene expression quantification: an RNA ‐seq tutorial journal April 2013
Addressing the challenge of soil metaproteome complexity by improving metaproteome depth of coverage through two-dimensional liquid chromatography journal October 2018
Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes journal March 2015
Emergent simplicity in microbial community assembly journal August 2018
Two Categories of 13 C/ 12 C Ratios for Higher Plants journal March 1971
Fate of ectomycorrhizal fungal biomass in a soil bioreactor system and its contribution to soil organic matter formation journal September 2015
The source of microbial C has little impact on soil organic matter stabilisation in forest ecosystems journal August 2012
Fate of bacterial biomass derived fatty acids in soil and their contribution to soil organic matter journal January 2009
SOM genesis: microbial biomass as a significant source journal October 2011
Biochar Amendment Stimulates Utilization of Plant-Derived Carbon by Soil Bacteria in an Intercropping System journal June 2019
Quantitative Microbial Ecology through Stable Isotope Probing journal August 2015
Glucose triggers strong taxon‐specific responses in microbial growth and activity: insights from DNA and RNA qSIP journal November 2019
Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA journal July 2018
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon journal July 2018
13 C pulse-chase labeling comparative assessment of the active methanogenic archaeal community composition in the transgenic and nontransgenic parental rice rhizospheres journal December 2013
Seasonal switchgrass ecotype contributions to soil organic carbon, deep soil microbial community composition and rhizodeposit uptake during an extreme drought journal September 2017
Drought decreases incorporation of recent plant photosynthate into soil food webs regardless of their trophic complexity journal August 2019
Identification of organic solutes accumulated by purple and green sulphur bacteria during osmotic stress using natural abundance 13C nuclear magnetic resonance spectroscopy journal December 1993
Modeling soil metabolic processes using isotopologue pairs of position-specific 13C-labeled glucose and pyruvate journal September 2011
Soil microorganisms can overcome respiration inhibition by coupling intra- and extracellular metabolism: 13C metabolic tracing reveals the mechanisms journal February 2017
Networking our science to characterize the state, vulnerabilities, and management opportunities of soil organic matter journal September 2017
Integrating plant-soil interactions into global carbon cycle models journal September 2009
Global soil carbon projections are improved by modelling microbial processes journal July 2013
Causes of variation in soil carbon predictions from CMIP5 Earth system models and comparison with observations journal January 2012
Managing uncertainty in soil carbon feedbacks to climate change journal July 2016
Temperature and soil organic matter decomposition rates - synthesis of current knowledge and a way forward journal August 2011
Unifying soil organic matter formation and persistence frameworks: the MEMS model journal January 2019
Soil carbon and nitrogen mineralization: Theory and models across scales journal July 2009
Estimating heterotrophic respiration at large scales: challenges, approaches, and next steps journal June 2016
Combined Metabarcoding and Co-occurrence Network Analysis to Profile the Bacterial, Fungal and Fusarium Communities and Their Interactions in Maize Stalks journal February 2019
Diversity and Co-occurrence Patterns of Soil Bacterial and Fungal Communities in Seven Intercropping Systems journal July 2018
Soil bacterial networks are less stable under drought than fungal networks journal August 2018
Toward a Better Understanding of Species Interactions through Network Biology journal June 2019
From hairballs to hypotheses–biological insights from microbial networks journal July 2018
Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil journal February 2017
Species-specific transcriptomic network inference of interspecies interactions journal May 2018
Microbial interactions and community assembly at microscales journal June 2016
The influence of aggregate size fraction and horizon position on microbial community composition journal June 2018
Local biotic interactions drive species-specific divergence in soil bacterial communities journal July 2019
Biogeography of soil bacteria and archaea across France journal July 2018
Selection imposed by local environmental conditions drives differences in microbial community composition across geographically distinct groundwater aquifers journal October 2019
Local and Regional Scale Heterogeneity Drive Bacterial Community Diversity and Composition in a Polar Desert journal August 2018
Spatial scale drives patterns in soil bacterial diversity: Spatial scale drives soil diversity journal March 2016
Detecting macroecological patterns in bacterial communities across independent studies of global soils journal November 2017
Biophysical processes supporting the diversity of microbial life in soil journal August 2017
Spatial and temporal variability of the soil microbiological properties in two soils with a different pedogenesis cropped to winter rape (Brassica napus L.) journal April 2019
Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27‐year chronosequence journal July 2017
Stewards of a changing planet: commentaries from ISME13 Plenary Lecturers journal August 2010
Central Role of the Cell in Microbial Ecology journal November 2009
Finding generality in ecology: a model for globally distributed experiments journal December 2013
Bacterial Extracellular Polymeric Substances Amplify Water Content Variability at the Pore Scale journal September 2018
SoilChip-XPS integrated technique to study formation of soil biogeochemical interfaces journal October 2017
Pore-Scale Monitoring of the Effect of Microarchitecture on Fungal Growth in a Two-Dimensional Soil-Like Micromodel journal July 2018
Cell-to-cell bacterial interactions promoted by drier conditions on soil surfaces journal September 2018
EcoFABs: advancing microbiome science through standardized fabricated ecosystems journal June 2019
Transparent Soil for Imaging the Rhizosphere journal September 2012
Interactive priming of soil N transformations from combining biochar and urea inputs: A 15N isotope tracer study journal April 2019
Long-term carbon and nitrogen dynamics at SPRUCE revealed through stable isotopes in peat profiles journal January 2017
Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model journal June 2016
The microbial ecology of permafrost journal May 2014
Permafrost Meta-Omics and Climate Change journal June 2016
Protozoa and plant growth: the microbial loop in soil revisited journal June 2004
Modeling Soil Processes: Review, Key Challenges, and New Perspectives journal January 2016
Agent Based Modeling and Adaptation to Climate Change journal April 2005
Metabolic Network Modeling for Computer-Aided Design of Microbial Interactions book January 2018