From diversity to complexity: Microbial networks in soils

Environmental stress destabilizes microbial networks

(2021) Damian J. Hernandez et al.   ISME Journal

Erosion reduces soil microbial diversity, network complexity and multifunctionality

(2021) Liping Qiu et al.   ISME Journal

Climate warming enhances microbial network complexity and stability

(2021) Mengting Maggie Yuan et al.   Nature Climate Change

Open challenges for microbial network construction and analysis

(2021) Karoline Faust   ISME Journal

A critical perspective on interpreting amplicon sequencing data in soil ecological research

(2021) Lauren V. Alteio et al.   SOIL BIOLOGY & BIOCHEMISTRY

Fungi in Permafrost-Affected Soils of the Canadian Arctic: Horizon- and Site-Specific Keystone Taxa Revealed by Co-Occurrence Network

(2021) Milan Varsadiya et al.   Microorganisms

Soil multitrophic network complexity enhances the link between biodiversity and multifunctionality in agricultural systems

(2021) Shuo Jiao et al.   GLOBAL CHANGE BIOLOGY

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling

(2020) Ching Jian et al.   PLoS One

Multiple elements of soil biodiversity drive ecosystem functions across biomes

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

Co‐occurrence is not evidence of ecological interactions

(2020) F. Guillaume Blanchet et al.   ECOLOGY LETTERS

The Dynamics of Soil Microbial Communities on Different Timescales: A Review

(2020) T. I. Chernov et al.   EURASIAN SOIL SCIENCE

Does Intraspecific Variation in rDNA Copy Number Affect Analysis of Microbial Communities?

(2020) Anton Lavrinienko et al.   TRENDS IN MICROBIOLOGY

Abundance of kinless hubs within soil microbial networks are associated with high functional potential in agricultural ecosystems

(2020) Yu Shi et al.   ENVIRONMENT INTERNATIONAL

Alpha-, beta-, and gamma-diversity of bacteria varies across habitats

(2020) Kendra E. Walters et al.   PLoS One

Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow

(2020) Ruifen Zhu et al.   Scientific Reports

Plant litter decomposition in wetlands is closely associated with phyllospheric fungi as revealed by microbial community dynamics and co-occurrence network

(2020) Pengfei Zhan et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Hidden heterogeneity and co‐occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates

(2020) Márton Szoboszlay et al.   MicrobiologyOpen

A piece of the pie: engineering microbiomes by exploiting division of labor in complex polysaccharide consumption

(2020) Stephen R Lindemann   Current Opinion in Chemical Engineering

Electrochemical biofilm control by reconstructing microbial community in agricultural water distribution systems

(2020) Peng Song et al.   JOURNAL OF HAZARDOUS MATERIALS

Spartina alterniflora invasions reduce soil fungal diversity and simplify co-occurrence networks in a salt marsh ecosystem

(2020) Guangliang Zhang et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Rarity of microbial species: In search of reliable associations

(2019) Arnaud Cougoul et al.   PLoS One

Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales

(2019) Regina L. Wilpiszeski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial network and soil properties are changed in bacterial wilt susceptible soil

(2019) Gaofu Qi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Temperature and soil moisture control microbial community composition in an arctic–alpine ecosystem along elevational and micro-topographic gradients

(2019) K. Frindte et al.   ISME Journal

Difficulty in inferring microbial community structure based on co-occurrence network approaches

(2019) Hokuto Hirano et al.   BMC BIOINFORMATICS

How sample heterogeneity can obscure the signal of microbial interactions

(2019) David W. Armitage et al.   ISME Journal

Use and abuse of correlation analyses in microbial ecology

(2019) Alex Carr et al.   ISME Journal

Toxicity drives facilitation between 4 bacterial species

(2019) Philippe Piccardi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Refining the stress gradient hypothesis in a microbial community

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

Long-term manure application increases soil organic matter and aggregation, and alters microbial community structure and keystone taxa

(2019) Yongxin Lin et al.   SOIL BIOLOGY & BIOCHEMISTRY

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data

(2019) Grace Yoon et al.   Frontiers in Genetics

Grazing Regulates the Spatial Heterogeneity of Soil Microbial Communities Within Ecological Networks

(2019) David J. Eldridge et al.   ECOSYSTEMS

Incorporating phylogenetic metrics to microbial co‐occurrence networks based on amplicon sequences to discern community assembly processes

(2019) Marta Goberna et al.   Molecular Ecology Resources

Soil multifunctionality is affected by the soil environment and by microbial community composition and diversity

(2019) Qing Zheng et al.   SOIL BIOLOGY & BIOCHEMISTRY

Perspectives on the Impact of Sampling Design and Intensity on Soil Microbial Diversity Estimates

(2019) Syrie M. Hermans et al.   Frontiers in Microbiology

Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

(2019) Shuo Jiao et al.   ISME Journal

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

Temporal Dynamics of the Soil Metabolome and Microbiome During Simulated Anaerobic Soil Disinfestation

(2019) Shashika S. Hewavitharana et al.   Frontiers in Microbiology

Fundamental contradictions among observational and experimental estimates of non-trophic species interactions

(2018) Allison K. Barner et al.   ECOLOGY

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Complexity and stability of ecological networks: a review of the theory

(2018) Pietro Landi et al.   POPULATION ECOLOGY

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton et al.   Microbiome

CONTINUOUS-CROPPING TOBACCO CAUSED VARIANCE OF CHEMICAL PROPERTIES AND STRUCTURE OF BACTERIAL NETWORK IN SOILS

(2018) Shu Chen et al.   LAND DEGRADATION & DEVELOPMENT

Soil bacterial networks are less stable under drought than fungal networks

(2018) Franciska T. de Vries et al.   Nature Communications

Geospatial variation in co-occurrence networks of nitrifying microbial guilds

(2018) Christopher M. Jones et al.   MOLECULAR ECOLOGY

Can we predict keystones?

(2018) Lisa Röttjers et al.   NATURE REVIEWS MICROBIOLOGY

Reply to ‘Can we predict microbial keystones?’

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Microbial diversity and ecological networks as indicators of environmental quality

(2017) Battle Karimi et al.   Environmental Chemistry Letters

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Where less may be more: how the rare biosphere pulls ecosystems strings

(2017) Alexandre Jousset et al.   ISME Journal

gCoda: Conditional Dependence Network Inference for Compositional Data

(2017) Huaying Fang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Effects of threshold on the topology of gene co-expression networks

(2017) Cynthia Martins Villar Couto et al.   Molecular BioSystems

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Using null models to infer microbial co-occurrence networks

(2017) Nora Connor et al.   PLoS One

The importance of being modular

(2017) Marta Sales-Pardo   SCIENCE

Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation

(2017) Shany Ofaim et al.   Frontiers in Microbiology

Analysis of Microbiome Data in the Presence of Excess Zeros

(2017) Abhishek Kaul et al.   Frontiers in Microbiology

Inference of Environmental Factor-Microbe and Microbe-Microbe Associations from Metagenomic Data Using a Hierarchical Bayesian Statistical Model

(2017) Yuqing Yang et al.   Cell Systems

The multilayer nature of ecological networks

(2017) Shai Pilosof et al.   Nature Ecology & Evolution

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

High-Throughput Single-Cell Cultivation on Microfluidic Streak Plates

(2016) Cheng-Ying Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial interactions and community assembly at microscales

(2016) Otto X Cordero et al.   CURRENT OPINION IN MICROBIOLOGY

A network approach for inferring species associations from co-occurrence data

(2016) Naia Morueta-Holme et al.   ECOGRAPHY

Evidence of structural balance in spatial ecological networks

(2016) Hugo Saiz et al.   ECOGRAPHY

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Air pollution below WHO levels decreases by 40 % the links of terrestrial microbial networks

(2016) Battle Karimi et al.   Environmental Chemistry Letters

Describe, understand and predict: why do we need networks in ecology?

(2016) Timothée Poisot et al.   FUNCTIONAL ECOLOGY

Network modules and hubs in plant-root fungal biomes

(2016) Hirokazu Toju et al.   Journal of the Royal Society Interface

Dimensions of biodiversity in the Earth mycobiome

(2016) Kabir G. Peay et al.   NATURE REVIEWS MICROBIOLOGY

Community detection in networks: A user guide

(2016) Santo Fortunato et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis

(2016) Ning Ling et al.   SOIL BIOLOGY & BIOCHEMISTRY

Modularity and stability in ecological communities

(2016) Jacopo Grilli et al.   Nature Communications

Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism

(2016) Tim A. Hoek et al.   PLOS BIOLOGY

Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects

(2015) Tadashi Fukami   Annual Review of Ecology Evolution and Systematics

16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies

(2015) Matthew Perisin et al.   ISME Journal

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

Microbial hotspots and hot moments in soil: Concept & review

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

What do you mean, ‘resilient’?

(2015) Dave Hodgson et al.   TRENDS IN ECOLOGY & EVOLUTION

Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health

(2015) Zhong Wei et al.   Nature Communications

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Below-ground plant-fungus network topology is not congruent with above-ground plant-animal network topology

(2015) H. Toju et al.   Science Advances

Modularity Reveals the Tendency of Arbuscular Mycorrhizal Fungi To Interact Differently with Generalist and Specialist Plant Species in Gypsum Soils

(2014) Emma Torrecillas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The geographic scaling of biotic interactions

(2014) Miguel B. Araújo et al.   ECOGRAPHY

Beyond species loss: the extinction of ecological interactions in a changing world

(2014) Alfonso Valiente-Banuet et al.   FUNCTIONAL ECOLOGY

Community assembly, coexistence and the environmental filtering metaphor

(2014) Nathan J. B. Kraft et al.   FUNCTIONAL ECOLOGY

Spatial Ecology of Bacteria at the Microscale in Soil

(2014) Xavier Raynaud et al.   PLoS One

Demonstrating microbial co-occurrence pattern analyses within and between ecosystems

(2014) Ryan J. Williams et al.   Frontiers in Microbiology

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Patterns and Processes of Microbial Community Assembly

(2013) D. R. Nemergut et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Fungal networks in yield-invigorating and -debilitating soils induced by prolonged potato monoculture

(2013) Lihua Lu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

The network structure of plant-arbuscular mycorrhizal fungi

(2012) A. Montesinos-Navarro et al.   NEW PHYTOLOGIST

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Using network analysis to explore co-occurrence patterns in soil microbial communities

(2011) Albert Barberán et al.   ISME Journal

Advances, challenges and a developing synthesis of ecological community assembly theory

(2011) E. Weiher et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Stochastic blockmodels and community structure in networks

(2011) Brian Karrer et al.   PHYSICAL REVIEW E

Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO2

(2011) J. Zhou et al.   mBio

Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks

(2010) E. Thebault et al.   SCIENCE

Functional Molecular Ecological Networks

(2010) J. Zhou et al.   mBio

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Generalized Models Reveal Stabilizing Factors in Food Webs

(2009) T. Gross et al.   SCIENCE

Disentangling the Web of Life

(2009) Jordi Bascompte   SCIENCE

Network structural properties mediate the stability of mutualistic communities

(2008) Toshinori Okuyama et al.   ECOLOGY LETTERS