Core species impact plant health by enhancing soil microbial cooperation and network complexity during community coalescence

Top-down and bottom-up cohesiveness in microbial community coalescence

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Chimeric plants favor asynchrony of conditionally rare bacterial species facilitating functional complementarity in rhizosphere

(2022) Yang Ruan et al.   BIOLOGY AND FERTILITY OF SOILS

The diversity of biotic interactions complements functional and phylogenetic facets of biodiversity

(2022) Pierre Gaüzère et al.   CURRENT BIOLOGY

Trophic interactions between predatory protists and pathogen-suppressive bacteria impact plant health

(2022) Sai Guo et al.   ISME Journal

Sucrose addition directionally enhances bacterial community convergence and network stability of the shrimp culture system

(2022) Haipeng Guo et al.   npj Biofilms and Microbiomes

Long-term watermelon continuous cropping leads to drastic shifts in soil bacterial and fungal community composition across gravel mulch fields

(2022) Xin Gu et al.   BMC MICROBIOLOGY

Core phylotypes enhance the resistance of soil microbiome to environmental changes to maintain multifunctionality in agricultural ecosystems

(2022) Shuo Jiao et al.   GLOBAL CHANGE BIOLOGY

Identifying thresholds of nitrogen enrichment for substantial shifts in arbuscular mycorrhizal fungal community metrics in a temperate grassland of northern China

(2022) Hui Wu et al.   NEW PHYTOLOGIST

Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease

(2022) Xin Zhou et al.   Nature Communications

Environmental stress destabilizes microbial networks

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

Climate warming enhances microbial network complexity and stability

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

Soil microbial community coalescence and fertilization interact to drive the functioning of the legume–rhizobium symbiosis

(2021) Josep Ramoneda et al.   JOURNAL OF APPLIED ECOLOGY

Pseudomonas Inoculation Stimulates Endophytic Azospira Population and Induces Systemic Resistance to Bacterial Wilt

(2021) Xian-chao Shang et al.   Frontiers in Plant Science

Transmission of Seed and Soil Microbiota to Seedling

(2021) Aude Rochefort et al.   mSystems

Guided by Microbes: Applying Community Coalescence Principles for Predictive Microbiome Engineering

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Vertical environmental gradient drives prokaryotic microbial community assembly and species coexistence in a stratified acid mine drainage lake

(2021) Zhixiang She et al.   WATER RESEARCH

The meta-gut: community coalescence of animal gut and environmental microbiomes

(2021) Christopher L. Dutton et al.   Scientific Reports

A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance

(2021) Zhefei Li et al.   Microbiome

Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth

(2020) Sajjad Asaf et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Community coalescence: an eco-evolutionary perspective

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

Microbiome-Mediated Stress Resistance in Plants

(2020) Hongwei Liu et al.   TRENDS IN PLANT SCIENCE

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer

(2020) Ohana Y. A. Costa et al.   Microbiome

Plant Grafting Shapes Complexity and Co-occurrence of Rhizobacterial Assemblages

(2020) Yang Ruan et al.   MICROBIAL ECOLOGY

Effect of enriched thermotolerant nitrifying bacteria inoculation on reducing nitrogen loss during sewage sludge composting

(2020) Yi Zhao et al.   BIORESOURCE TECHNOLOGY

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

(2020) Chengyuan Tao et al.   Microbiome

Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum

(2020) Hyun S. Gweon et al.   ENVIRONMENTAL MICROBIOLOGY

Invader-resident relatedness and soil management history shape patterns of invasion of compost microbial populations into agricultural soils

(2020) Kelly Gravuer et al.   APPLIED SOIL ECOLOGY

The Super-Donor Phenomenon in Fecal Microbiota Transplantation

(2019) Brooke C. Wilson et al.   Frontiers in Cellular and Infection Microbiology

Soil functionality produced by soil mixing: The role of inoculum and substrate

(2019) Pantelitsa D. Kapagianni et al.   ECOLOGICAL RESEARCH

FEAST: fast expectation-maximization for microbial source tracking

(2019) Liat Shenhav et al.   NATURE METHODS

Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

(2019) Norma M. Morella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of Long-term Cotton Continuous Cropping on Soil Microbiome

(2019) Hui Xi et al.   Scientific Reports

Application of the microbial community coalescence concept to riverine networks

(2018) India Mansour et al.   BIOLOGICAL REVIEWS

Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities?

(2018) Mara A. Freilich et al.   ECOLOGY

Disease-induced assemblage of a plant-beneficial bacterial consortium

(2018) Roeland L. Berendsen et al.   ISME Journal

Genomic characterization of Nitrospirillum amazonense strain CBAmC, a nitrogen-fixing bacterium isolated from surface-sterilized sugarcane stems

(2018) Stefan Schwab et al.   MOLECULAR GENETICS AND GENOMICS

Role of priority effects in the early-life assembly of the gut microbiota

(2018) Daniel Sprockett et al.   Nature Reviews Gastroenterology & Hepatology

Keystone taxa as drivers of microbiome structure and functioning

(2018) Samiran Banerjee et al.   NATURE REVIEWS MICROBIOLOGY

Biological control of plant pathogens by Bacillus species

(2018) Djordje Fira et al.   JOURNAL OF BIOTECHNOLOGY

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

Streptomyces: implications and interactions in plant growth promotion

(2018) Oluwaseyi Samuel Olanrewaju et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

Potential for synergy in soil inoculation for nature restoration by mixing inocula from different successional stages

(2018) E. R. Jasper Wubs et al.   PLANT AND SOIL

Cohesion: a method for quantifying the connectivity of microbial communities

(2017) Cristina M Herren et al.   ISME Journal

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

(2017) Benjamin J Callahan et al.   ISME Journal

Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome

(2017) Wu Xiong et al.   SOIL BIOLOGY & BIOCHEMISTRY

Probiotic Pseudomonas communities enhance plant growth and nutrient assimilation via diversity-mediated ecosystem functioning

(2017) Jie Hu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Distinct roles for soil fungal and bacterial communities associated with the suppression of vanilla Fusarium wilt disease

(2017) Wu Xiong et al.   SOIL BIOLOGY & BIOCHEMISTRY

Network structure embracing mutualism–antagonism continuums increases community robustness

(2017) Alicia Montesinos-Navarro et al.   Nature Ecology & Evolution

Relationships of decomposability and C/N ratio in different types of organic matter with suppression of Fusarium oxysporum and microbial communities during reductive soil disinfestation

(2016) Liangliang Liu et al.   BIOLOGICAL CONTROL

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Host species and environmental variation can influence rhizobial community composition

(2016) Holly B. Vuong et al.   JOURNAL OF ECOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Soil microbes and community coalescence

(2016) Matthias C. Rillig et al.   PEDOBIOLOGIA

Assessment of bacterial populations associated with banana tree roots and development of successful plant probiotics for banana crop

(2016) Iris-Esther Marcano et al.   SOIL BIOLOGY & BIOCHEMISTRY

Evolving Perspectives on Monopolization and Priority Effects

(2016) Luc De Meester et al.   TRENDS IN ECOLOGY & EVOLUTION

Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression

(2016) Jie Hu et al.   mBio

Microbial Community Coalescence for Microbiome Engineering

(2016) Matthias C. Rillig et al.   Frontiers in Microbiology

Nitrospirillum irinus sp. nov., a diazotrophic bacterium isolated from the rhizosphere soil of Iris and emended description of the genus Nitrospirillum

(2015) Eu Jin Chung et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Rapid local adaptation mediates zooplankton community assembly in experimental mesocosms

(2015) Jelena H. Pantel et al.   ECOLOGY LETTERS

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

The response of root-associated bacterial community to the grafting of watermelon

(2015) Ning Ling et al.   PLANT AND SOIL

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) K. Z. Coyte et al.   SCIENCE

Interchange of entire communities: microbial community coalescence

(2015) Matthias C. Rillig et al.   TRENDS IN ECOLOGY & EVOLUTION

Engineering Microbiomes to Improve Plant and Animal Health

(2015) U.G. Mueller et al.   TRENDS IN MICROBIOLOGY

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

(2015) Zhong Wei et al.   Nature Communications

Diversity of nitrogen-fixing, ammonia-oxidizing, and denitrifying bacteria in biological soil crusts of a revegetation area in Horqin Sandy Land, Northeast China

(2014) Ying Zhang et al.   ECOLOGICAL ENGINEERING

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

(2014) Albert Barberán 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

Long-term exposure to elevated CO2 enhances plant community stability by suppressing dominant plant species in a mixed-grass prairie

(2014) T. J. Zelikova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The dynamics of community assembly under sudden mixing in experimental microcosms

(2013) George Livingston et al.   ECOLOGY

Molecular ecological network analyses

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Pseudomonas fluorescens F113 Mutant with Enhanced Competitive Colonization Ability and Improved Biocontrol Activity against Fungal Root Pathogens

(2011) Emma Barahona et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Using SiZer to detect thresholds in ecological data

(2008) Derek L Sonderegger et al.   FRONTIERS IN ECOLOGY AND THE ENVIRONMENT

Trichoderma–plant–pathogen interactions

(2007) Francesco Vinale et al.   SOIL BIOLOGY & BIOCHEMISTRY