Life and death in the soil microbiome: how ecological processes influence biogeochemistry

Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization

(2022) Craig R. See et al.   GLOBAL CHANGE BIOLOGY

Tracking, targeting, and conserving soil biodiversity

(2021) Carlos A. Guerra et al.   SCIENCE

The mineralosphere—interactive zone of microbial colonization and carbon use in grassland soils

(2021) Runa S. Boeddinghaus et al.   BIOLOGY AND FERTILITY OF SOILS

Biological mechanisms may contribute to soil carbon saturation patterns

(2021) Matthew E. Craig et al.   GLOBAL CHANGE BIOLOGY

Improved model simulation of soil carbon cycling by representing the microbially derived organic carbon pool

(2021) Xianlei Fan et al.   ISME Journal

Trait dimensions in bacteria and archaea compared to vascular plants

(2021) Mark Westoby et al.   ECOLOGY LETTERS

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

(2021) Jake L. Weissman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant- or microbial-derived? A review on the molecular composition of stabilized soil organic matter

(2021) Gerrit Angst et al.   SOIL BIOLOGY & BIOCHEMISTRY

The Functional Significance of Bacterial Predators

(2021) Bruce A. Hungate et al.   mBio

Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

(2021) Man-Young Jung et al.   ISME Journal

Uncertainty quantification of the soil moisture response functions for microbial dormancy and resuscitation

(2021) Gangsheng Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

Rice rhizodeposition promotes the build-up of organic carbon in soil via fungal necromass

(2021) Yu Luo et al.   SOIL BIOLOGY & BIOCHEMISTRY

Visualizing the transfer of organic matter from decaying plant residues to soil mineral surfaces controlled by microorganisms

(2021) Alix Vidal et al.   SOIL BIOLOGY & BIOCHEMISTRY

Particulate organic matter as a functional soil component for persistent soil organic carbon

(2021) Kristina Witzgall et al.   Nature Communications

Integrating Viral Metagenomics into an Ecological Framework

(2021) Pacifica Sommers et al.   Annual Review of Virology

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil

(2021) Evan P. Starr et al.   mSphere

Soil Candidate Phyla Radiation Bacteria Encode Components of Aerobic Metabolism and Co-occur with Nanoarchaea in the Rare Biosphere of Rhizosphere Grassland Communities

(2021) Alexa M. Nicolas et al.   mSystems

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

(2021) Gareth Trubl et al.   Microbiome

Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation

(2021) Carlos Arellano-Caicedo et al.   Communications Biology

Cellular and extracellular C contributions to respiration after wetting dry soil

(2020) Eric W. Slessarev et al.   BIOGEOCHEMISTRY

Phage-specific metabolic reprogramming of virocells

(2020) Cristina Howard-Varona et al.   ISME Journal

Niche differentiation is spatially and temporally regulated in the rhizosphere

(2020) Erin E. Nuccio et al.   ISME Journal

Multiple elements of soil biodiversity drive ecosystem functions across biomes

(2020) Manuel Delgado-Baquerizo et al.   Nature Ecology & Evolution

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil

(2020) Steven J. Blazewicz et al.   ISME Journal

The ecology of heterogeneity: soil bacterial communities and C dynamics

(2020) Naoise Nunan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Microbial extracellular polysaccharide production and aggregate stability controlled by switchgrass (Panicum virgatum) root biomass and soil water potential

(2020) Yonatan Sher et al.   SOIL BIOLOGY & BIOCHEMISTRY

Partitioning sources of CO2 emission after soil wetting using high-resolution observations and minimal models

(2020) Eric W. Slessarev et al.   SOIL BIOLOGY & BIOCHEMISTRY

Persistence of soil organic carbon caused by functional complexity

(2020) Johannes Lehmann et al.   Nature Geoscience

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

(2020) Allison M. Sharrar et al.   mBio

Microbial diversity drives carbon use efficiency in a model soil

(2020) Luiz A. Domeignoz-Horta et al.   Nature Communications

A synthesis of bacterial and archaeal phenotypic trait data

(2020) Joshua S. Madin et al.   Scientific Data

A soil microbial model to analyze decoupled microbial growth and respiration during soil drying and rewetting

(2020) Albert C. Brangarí et al.   SOIL BIOLOGY & BIOCHEMISTRY

The physical structure of soil: Determinant and consequence of trophic interactions

(2020) Amandine Erktan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Sticky dead microbes: Rapid abiotic retention of microbial necromass in soil

(2020) Kate M. Buckeridge et al.   SOIL BIOLOGY & BIOCHEMISTRY

Assessing microbial residues in soil as a potential carbon sink and moderator of carbon use efficiency

(2020) Kevin Geyer et al.   Biogeochemistry

Global biogeography of fungal and bacterial biomass carbon in topsoil

(2020) Liyuan He et al.   SOIL BIOLOGY & BIOCHEMISTRY

A theory of effective microbial substrate affinity parameters in variably saturated soils and an example application to aerobic soil heterotrophic respiration

(2019) Jinyun Tang et al.   Journal of Geophysical Research-Biogeosciences

Compound‐specific 13 C stable isotope probing confirms synthesis of polyhydroxybutyrate by soil bacteria

(2019) Kyle Mason‐Jones et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Interaction between tannins and fungal necromass stabilizes fungal residues in boreal forest soils

(2019) Bartosz Adamczyk et al.   NEW PHYTOLOGIST

Trophic Regulations of the Soil Microbiome

(2019) Madhav P. Thakur et al.   TRENDS IN MICROBIOLOGY

Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima

(2019) Gang Li et al.   ACS Synthetic Biology

Managing Agroecosystems for Soil Microbial Carbon Use Efficiency: Ecological Unknowns, Potential Outcomes, and a Path Forward

(2019) Cynthia M. Kallenbach et al.   Frontiers in Microbiology

The Evolution and Ecology of Bacterial Warfare

(2019) Elisa T. Granato et al.   CURRENT BIOLOGY

Increased microbial growth, biomass and turnover drive soil organic carbon accumulation at higher plant diversity

(2019) Judith Prommer et al.   GLOBAL CHANGE BIOLOGY

Quantitative assessment of microbial necromass contribution to soil organic matter

(2019) Chao Liang et al.   GLOBAL CHANGE BIOLOGY

Making the Most of Trait-Based Approaches for Microbial Ecology

(2019) Geneviève Lajoie et al.   TRENDS IN MICROBIOLOGY

Probing the active fraction of soil microbiomes using BONCAT-FACS

(2019) Estelle Couradeau et al.   Nature Communications

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

(2019) Gareth Trubl et al.   PeerJ

Bacterial colonization of minerals in grassland soils is selective and highly dynamic

(2019) Selma Vieira et al.   ENVIRONMENTAL MICROBIOLOGY

Mineralogy dictates the initial mechanism of microbial necromass association

(2019) Courtney A. Creamer et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change

(2019) Ashish A. Malik et al.   ISME Journal

The global soil community and its influence on biogeochemistry

(2019) T. W. Crowther et al.   SCIENCE

Mycorrhizal Fungi as Mediators of Soil Organic Matter Dynamics

(2019) Serita D. Frey   Annual Review of Ecology Evolution and Systematics

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands

(2019) Selma Vieira et al.   ISME Journal

Soil microbiomes and climate change

(2019) Janet K. Jansson et al.   NATURE REVIEWS MICROBIOLOGY

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

(2019) Evan P. Starr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial carbon use efficiency predicted from genome-scale metabolic models

(2019) Mustafa Saifuddin et al.   Nature Communications

Predatory Myxococcales are widely distributed in and closely correlated with the bacterial community structure of agricultural land

(2019) Wenhui Wang et al.   APPLIED SOIL ECOLOGY

Equifinality, sloppiness, and emergent structures of mechanistic soil biogeochemical models

(2019) Gianna L. Marschmann et al.   ENVIRONMENTAL MODELLING & SOFTWARE

Functional convergence in the decomposition of fungal necromass in soil and wood

(2019) François Maillard et al.   FEMS MICROBIOLOGY ECOLOGY

Transport, retention, and release of Escherichia coli and Rhodococcus erythropolis through dry natural soils as affected by water repellency

(2019) Nasrollah Sepehrnia et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Direct measurement of the in situ decomposition of microbial-derived soil organic matter

(2019) Yuntao Hu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust

(2019) Marc W. Van Goethem et al.   mBio

Ecological and soil hydraulic implications of microbial responses to stress – A modeling analysis

(2018) Albert C. Brangarí et al.   ADVANCES IN WATER RESOURCES

A meta-analysis of temperature sensitivity as a microbial trait

(2018) Charlotte J. Alster et al.   GLOBAL CHANGE BIOLOGY

Tree mycorrhizal type predicts within-site variability in the storage and distribution of soil organic matter

(2018) Matthew E. Craig et al.   GLOBAL CHANGE BIOLOGY

Multiple mechanisms drive phage infection efficiency in nearly identical hosts

(2018) Cristina Howard-Varona et al.   ISME Journal

Greatest soil microbial diversity found in micro-habitats

(2018) Elizabeth M. Bach et al.   SOIL BIOLOGY & BIOCHEMISTRY

The ‘Neglected’ Soil Virome – Potential Role and Impact

(2018) Akbar Adjie Pratama et al.   TRENDS IN MICROBIOLOGY

Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology

(2018) Jennifer L. Wood et al.   Frontiers in Microbiology

Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly

(2018) Kateryna Zhalnina et al.   Nature Microbiology

Host-linked soil viral ecology along a permafrost thaw gradient

(2018) Joanne B. Emerson et al.   Nature Microbiology

Life in Dry Soils: Effects of Drought on Soil Microbial Communities and Processes

(2018) Joshua P. Schimel   Annual Review of Ecology Evolution and Systematics

Improving understanding of soil organic matter dynamics by triangulating theories, measurements, and models

(2018) Joseph C. Blankinship et al.   BIOGEOCHEMISTRY

Microbial community assembly differs across minerals in a rhizosphere microcosm

(2018) Thea Whitman et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

(2018) Roland C. Wilhelm et al.   ISME Journal

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Multiple models and experiments underscore large uncertainty in soil carbon dynamics

(2018) Benjamin N. Sulman et al.   BIOGEOCHEMISTRY

Microbial formation of stable soil carbon is more efficient from belowground than aboveground input

(2018) Noah W. Sokol et al.   Nature Geoscience

The ratio of Gram-positive to Gram-negative bacterial PLFA markers as an indicator of carbon availability in organic soils

(2018) Nicolas Fanin et al.   SOIL BIOLOGY & BIOCHEMISTRY

Assessing fungal contributions to cellulose degradation in soil by using high-throughput stable isotope probing

(2018) Chantal Koechli et al.   SOIL BIOLOGY & BIOCHEMISTRY

Nitrogen-rich microbial products provide new organo-mineral associations for the stabilization of soil organic matter

(2017) Peter M. Kopittke et al.   GLOBAL CHANGE BIOLOGY

Embracing the unknown: disentangling the complexities of the soil microbiome

(2017) Noah Fierer   NATURE REVIEWS MICROBIOLOGY

Bacterial Physiological Adaptations to Contrasting Edaphic Conditions Identified Using Landscape Scale Metagenomics

(2017) Ashish A. Malik et al.   mBio

Microbial community-level regulation explains soil carbon responses to long-term litter manipulations

(2017) Katerina Georgiou et al.   Nature Communications

Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory

(2017) Kurt E. Williamson et al.   Annual Review of Virology

The importance of anabolism in microbial control over soil carbon storage

(2017) Chao Liang et al.   Nature Microbiology

Characteristic Sizes of Life in the Oceans, from Bacteria to Whales

(2016) K.H. Andersen et al.   Annual Review of Marine Science

Microbial carbon use efficiency: accounting for population, community, and ecosystem-scale controls over the fate of metabolized organic matter

(2016) Kevin M. Geyer et al.   BIOGEOCHEMISTRY

Ectomycorrhizal fungi slow soil carbon cycling

(2016) Colin Averill et al.   ECOLOGY LETTERS

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model

(2016) Ali Ebrahimi et al.   GLOBAL CHANGE BIOLOGY

Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere

(2016) Yan Yan et al.   ISME Journal

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure

(2016) Benjamin Bolduc et al.   ISME Journal

Evolutionary tradeoffs in cellular composition across diverse bacteria

(2016) Christopher P Kempes et al.   ISME Journal

Dilution reveals how viral lysis and grazing shape microbial communities

(2016) Jacob A. Cram et al.   LIMNOLOGY AND OCEANOGRAPHY

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

(2016) Simon Roux et al.   NATURE

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

Synergistic effects of diffusion and microbial physiology reproduce the Birch effect in a micro-scale model

(2016) Sarah Evans et al.   SOIL BIOLOGY & BIOCHEMISTRY

The decomposition of ectomycorrhizal fungal necromass

(2016) Christopher W. Fernandez et al.   SOIL BIOLOGY & BIOCHEMISTRY

Direct evidence for microbial-derived soil organic matter formation and its ecophysiological controls

(2016) Cynthia M. Kallenbach et al.   Nature Communications

Managing uncertainty in soil carbon feedbacks to climate change

(2016) Mark A. Bradford et al.   Nature Climate Change

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

(2016) Paul Carini et al.   Nature Microbiology

Quantitative Microbial Ecology through Stable Isotope Probing

(2015) Bruce A. Hungate et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbe–mineral interactions: The impact of surface attachment on mineral weathering and element selectivity by microorganisms

(2015) Engy Ahmed et al.   CHEMICAL GEOLOGY

A general mathematical framework for representing soil organic matter dynamics

(2015) Carlos A. Sierra et al.   ECOLOGICAL MONOGRAPHS

Resilience vs. historical contingency in microbial responses to environmental change

(2015) Christine V. Hawkes et al.   ECOLOGY LETTERS

Rhizosphere processes are quantitatively important components of terrestrial carbon and nutrient cycles

(2015) Adrien C. Finzi et al.   GLOBAL CHANGE BIOLOGY

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors

(2015) Firoz Shah et al.   NEW PHYTOLOGIST

Revisiting the ‘Gadgil effect’: do interguild fungal interactions control carbon cycling in forest soils?

(2015) Christopher W. Fernandez et al.   NEW PHYTOLOGIST

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe

(2015) Jonathan W. Leff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Microbial physiology and necromass regulate agricultural soil carbon accumulation

(2015) C.M. Kallenbach et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial contribution to SOM quantity and quality in density fractions of temperate arable soils

(2015) Marie Ludwig et al.   SOIL BIOLOGY & BIOCHEMISTRY

Environmental stress response limits microbial necromass contributions to soil organic carbon

(2015) Thomas W. Crowther et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial hotspots and hot moments in soil: Concept & review

(2015) Yakov Kuzyakov et al.   SOIL BIOLOGY & BIOCHEMISTRY

Social dynamics within decomposer communities lead to nitrogen retention and organic matter build-up in soils

(2015) Christina Kaiser et al.   Nature Communications

Sensitivity of decomposition rates of soil organic matter with respect to simultaneous changes in temperature and moisture

(2015) Carlos A. Sierra et al.   Journal of Advances in Modeling Earth Systems

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Bacterial impact on the wetting properties of soil minerals

(2014) Jan Achtenhagen et al.   BIOGEOCHEMISTRY

Microbial community dynamics alleviate stoichiometric constraints during litter decay

(2014) Christina Kaiser et al.   ECOLOGY LETTERS

Microbial dormancy improves development and experimental validation of ecosystem model

(2014) Gangsheng Wang et al.   ISME Journal

High prevalence of biofilm synergy among bacterial soil isolates in cocultures indicates bacterial interspecific cooperation

(2014) Dawei Ren et al.   ISME Journal

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage

(2014) Colin Averill et al.   NATURE

The elemental composition of virus particles: implications for marine biogeochemical cycles

(2014) Luis F. Jover et al.   NATURE REVIEWS MICROBIOLOGY

Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation

(2014) Christina Kaiser et al.   NEW PHYTOLOGIST

Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests

(2014) Karina E. Clemmensen et al.   NEW PHYTOLOGIST

Soil water availability strongly alters the community composition of soil protists

(2014) Geisen Stefan et al.   PEDOBIOLOGIA

Spatial Ecology of Bacteria at the Microscale in Soil

(2014) Xavier Raynaud et al.   PLoS One

Microbial Growth and Carbon Use Efficiency in the Rhizosphere and Root-Free Soil

(2014) Evgenia Blagodatskaya et al.   PLoS One

A theoretical analysis of microbial eco-physiological and diffusion limitations to carbon cycling in drying soils

(2014) S. Manzoni et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

(2014) Ali N. Ebrahimi et al.   WATER RESOURCES RESEARCH

Weaker soil carbon–climate feedbacks resulting from microbial and abiotic interactions

(2014) Jinyun Tang et al.   Nature Climate Change

Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil

(2013) Steven J. Blazewicz et al.   ECOLOGY

In and out: an analysis of epibiotic vs periplasmic bacterial predators

(2013) Z Pasternak et al.   ISME Journal

Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm

(2013) Kai Wei Kelvin Lee et al.   ISME Journal

Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition

(2013) Nana Yaw D Ankrah et al.   ISME Journal

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

(2013) E. Tisserant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Active microorganisms in soil: Critical review of estimation criteria and approaches

(2013) Evgenia Blagodatskaya et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial cell-envelope fragments and the formation of soil organic matter: a case study from a glacier forefield

(2012) Christian Schurig et al.   BIOGEOCHEMISTRY

Development of microbial-enzyme-mediated decomposition model parameters through steady-state and dynamic analyses

(2012) Gangsheng Wang et al.   ECOLOGICAL APPLICATIONS

A trait-based approach for modelling microbial litter decomposition

(2012) S. D. Allison   ECOLOGY LETTERS

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?

(2012) M. Francesca Cotrufo et al.   GLOBAL CHANGE BIOLOGY

SOM genesis: microbial biomass as a significant source

(2011) Anja Miltner et al.   BIOGEOCHEMISTRY

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Low Pore Connectivity Increases Bacterial Diversity in Soil

(2010) J. K. Carson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Shifting carbon flow from roots into associated microbial communities in response to elevated atmospheric CO2

(2010) B. Drigo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics

(2010) Sara Vieira-Silva et al.   PLoS Genetics

Impact of wheat straw decomposition on successional patterns of soil microbial community structure

(2008) Fabiola Bastian et al.   SOIL BIOLOGY & BIOCHEMISTRY

Dynamics of litter carbon turnover and microbial abundance in a rye detritusphere

(2007) Christian Poll et al.   SOIL BIOLOGY & BIOCHEMISTRY