Linking Bacterial-Fungal Relationships to Microbial Diversity and Soil Nutrient Cycling

Multiple elements of soil biodiversity drive ecosystem functions across biomes

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

Compared to conventional, ecological intensive management promotes beneficial proteolytic soil microbial communities for agro-ecosystem functioning under climate change-induced rain regimes

(2020) Martina Lori et al.   Scientific Reports

Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives

(2020) Haiyan Chu et al.   mSystems

Environmental heterogeneity determines the ecological processes that govern bacterial metacommunity assembly in a floodplain river system

(2020) Paula Huber et al.   ISME Journal

Microbial carbon use efficiency in grassland soils subjected to nitrogen and phosphorus additions

(2020) Meike Widdig et al.   SOIL BIOLOGY & BIOCHEMISTRY

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

(2020) Bin Ma et al.   Microbiome

Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling

(2019) Shuo Jiao et al.   mSystems

Consistent trade-offs in fungal trait expression across broad spatial scales

(2019) Daniel S. Maynard et al.   Nature Microbiology

Diversifying livestock promotes multidiversity and multifunctionality in managed grasslands

(2019) Ling Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions in self-assembled microbial communities saturate with diversity

(2019) Xiaoqian Yu et al.   ISME Journal

Use and abuse of correlation analyses in microbial ecology

(2019) Alex Carr et al.   ISME Journal

The global soil community and its influence on biogeochemistry

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

Volatile‐mediated antagonism of soil bacterial communities against fungi

(2019) Xiaogang Li et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2019) Shuo Jiao et al.   ISME Journal

Diversity-triggered deterministic bacterial assembly constrains community functions

(2019) Weibing Xun et al.   Nature Communications

Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning

(2019) Cameron Wagg et al.   Nature Communications

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

(2018) Mara A. Freilich et al.   ECOLOGY

Distinct patterns and processes of abundant and rare eukaryotic plankton communities following a reservoir cyanobacterial bloom

(2018) Yuanyuan Xue et al.   ISME Journal

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

A global atlas of the dominant bacteria found in soil

(2018) Manuel Delgado-Baquerizo et al.   SCIENCE

Soil pH correlates with the co-occurrence and assemblage process of diazotrophic communities in rhizosphere and bulk soils of wheat fields

(2018) Kunkun Fan et al.   SOIL BIOLOGY & BIOCHEMISTRY

β-Diversity, Community Assembly, and Ecosystem Functioning

(2018) Akira S. Mori et al.   TRENDS IN ECOLOGY & EVOLUTION

Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain

(2018) Yu Shi et al.   Microbiome

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

(2018) Shuo Jiao et al.   Microbiome

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

Facilitation promotes invasions in plant‐associated microbial communities

(2018) Mei Li et al.   ECOLOGY LETTERS

Habitat-specific patterns and drivers of bacterial β-diversity in China’s drylands

(2017) Xiao-Bo Wang et al.   ISME Journal

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Biodiversity effects in the wild are common and as strong as key drivers of productivity

(2017) J. Emmett Duffy et al.   NATURE

Leaf bacterial diversity mediates plant diversity and ecosystem function relationships

(2017) Isabelle Laforest-Lapointe et al.   NATURE

OUP accepted manuscript

(2017)   NUCLEIC ACIDS RESEARCH

Competitive network determines the direction of the diversity–function relationship

(2017) Daniel S. Maynard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GSA: Genome Sequence Archive *

(2017) Yanqing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

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Local loss and spatial homogenization of plant diversity reduce ecosystem multifunctionality

(2017) Yann Hautier et al.   Nature Ecology & Evolution

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages

(2016) Shengjing Shi et al.   ECOLOGY LETTERS

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau

(2016) Haiyan Chu et al.   ENVIRONMENTAL MICROBIOLOGY

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China

(2016) Bin Ma et al.   ISME Journal

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

(2016) Pankaj Trivedi et al.   ISME Journal

Understanding the value of plant diversity for ecosystem functioning through niche theory

(2016) Lindsay A. Turnbull et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Positive biodiversity-productivity relationship predominant in global forests

(2016) J. Liang et al.   SCIENCE

An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability

(2016) S. Franz Bender et al.   TRENDS IN ECOLOGY & EVOLUTION

Microbial diversity drives multifunctionality in terrestrial ecosystems

(2016) Manuel Delgado-Baquerizo et al.   Nature Communications

Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment

(2015) Tao He et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Low multifunctional redundancy of soil fungal diversity at multiple scales

(2015) Akira S. Mori et al.   ECOLOGY LETTERS

Volatile affairs in microbial interactions

(2015) Ruth Schmidt et al.   ISME Journal

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

(2015) Adam R Burns et al.   ISME Journal

Consistent and Clear Reporting of Results from Diverse Modeling Techniques: The A3 Method

(2015) Scott Fortmann-Roe   Journal of Statistical Software

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

(2015) Francisco Dini-Andreote et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deterministic processes vary during community assembly for ecologically dissimilar taxa

(2015) Jeff R. Powell et al.   Nature Communications

The links between ecosystem multifunctionality and above- and belowground biodiversity are mediated by climate

(2015) Xin Jing et al.   Nature Communications

lavaan: AnRPackage for Structural Equation Modeling

(2015) Yves Rosseel   Journal of Statistical Software

Belowground biodiversity and ecosystem functioning

(2014) Richard D. Bardgett et al.   NATURE

Soil biodiversity and soil community composition determine ecosystem multifunctionality

(2014) C. Wagg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Changes in community assembly may shift the relationship between biodiversity and ecosystem function

(2014) Joseph E. Knelman et al.   Frontiers in Microbiology

Patterns and Processes of Microbial Community Assembly

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

Increasing antagonistic interactions cause bacterial communities to collapse at high diversity

(2012) Joachim Becker et al.   ECOLOGY LETTERS

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

New method for isolating antibiotic-producing fungi

(2012) Mio Kawaguchi et al.   JOURNAL OF ANTIBIOTICS

Erratum: Corrigendum: Biodiversity loss and its impact on humanity

(2012) Bradley J. Cardinale et al.   NATURE

Biodiversity loss and its impact on humanity

(2012) Bradley J. Cardinale et al.   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Spatial and Temporal Variation of Archaeal, Bacterial and Fungal Communities in Agricultural Soils

(2012) Michele C. Pereira e Silva et al.   PLoS One

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impacts of Biodiversity Loss Escalate Through Time as Redundancy Fades

(2012) P. B. Reich et al.   SCIENCE

Plant Species Richness and Ecosystem Multifunctionality in Global Drylands

(2012) F. T. Maestre et al.   SCIENCE

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Do assembly history effects attenuate from species to ecosystem properties? A field test with wood-inhabiting fungi

(2011) Ian A. Dickie et al.   ECOLOGY LETTERS

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Antibiotic Production by Myxobacteria Plays a Role in Predation

(2011) Y. Xiao et al.   JOURNAL OF BACTERIOLOGY

Biodiversity improves water quality through niche partitioning

(2011) Bradley J. Cardinale   NATURE

Disentangling the importance of ecological niches from stochastic processes across scales

(2011) J. M. Chase et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

Stochastic Community Assembly Causes Higher Biodiversity in More Productive Environments

(2010) J. M. Chase   SCIENCE

How understanding aboveground–belowground linkages can assist restoration ecology

(2010) Paul Kardol et al.   TRENDS IN ECOLOGY & EVOLUTION

Mechanisms that promote bacterial fitness in fungal-affected soil microhabitats

(2009) Rashid Nazir et al.   FEMS MICROBIOLOGY ECOLOGY

Integrating Soil Ecological Knowledge into Restoration Management

(2008) Liam Heneghan et al.   RESTORATION ECOLOGY

Functional Traits and Niche-Based Tree Community Assembly in an Amazonian Forest

(2008) N. J. B. Kraft et al.   SCIENCE