Soil bacterial community composition is more stable in kiwifruit orchards relative to phyllosphere communities over time

Land use modification causes slow, but predictable, change in soil microbial community composition and functional potential

(2023) Z. Louisson et al.   Environmental Microbiome

Insights into the microbiome assembly during different growth stages and storage of strawberry plants

(2022) Expedito Olimi et al.   Environmental Microbiome

Distinct and Temporally Stable Assembly Mechanisms Shape Bacterial and Fungal Communities in Vineyard Soils

(2022) Stefano Larsen et al.   MICROBIAL ECOLOGY

Land‐use drives the temporal stability and magnitude of soil microbial functions and modulates climate effects

(2021) Julia E. Kostin et al.   ECOLOGICAL APPLICATIONS

Kiwifruit bacterial canker: an integrative view focused on biocontrol strategies

(2021) Carla Pereira et al.   PLANTA

Bacterial Community Structure and the Dominant Species in Imported Pollens for Artificial Pollination

(2021) Su-Hyeon Kim et al.   Plant Pathology Journal

Storage of soil microbiome for application in sustainable agriculture: prospects and challenges

(2021) Annapurna Bhattacharjee et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Assembly processes of abundant and rare microbial communities in orchard soil under a cover crop at different periods

(2021) Zhiyuan Zhao et al.   GEODERMA

Pseudomonas syringae pv. actinidiae: Ecology, Infection Dynamics and Disease Epidemiology

(2020) Irene Donati et al.   MICROBIAL ECOLOGY

Microbial community overlap between the phyllosphere and rhizosphere of three plants from Yongxing Island, South China Sea

(2020) Lijun Bao et al.   MicrobiologyOpen

Using soil bacterial communities to predict physico-chemical variables and soil quality

(2020) Syrie M. Hermans et al.   Microbiome

The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time

(2020) Pablo Aguilar et al.   MOLECULAR ECOLOGY

Plant–microbiome interactions: from community assembly to plant health

(2020) Pankaj Trivedi et al.   NATURE REVIEWS MICROBIOLOGY

Heterosis of leaf and rhizosphere microbiomes in field‐grown maize

(2020) Maggie R. Wagner et al.   NEW PHYTOLOGIST

Role of Dominant Phyllosphere Bacteria with Plant Growth–Promoting Characteristics on Growth and Nutrition of Maize (Zea mays L.)

(2020) Vahid Alah Jahandideh Mahjen Abadi et al.   Journal of Soil Science and Plant Nutrition

Temporal variation in soil bacterial communities can be confounded with spatial variation

(2020) Syrie M Hermans et al.   FEMS MICROBIOLOGY ECOLOGY

Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective

(2020) Kai Wang et al.   MOLECULAR ECOLOGY

Phyllosphere microbiota: Community dynamics and its interaction with plant hosts

(2020) Tianyu Gong et al.   Journal of Integrative Plant Biology

Hormones as go‐betweens in plant microbiome assembly

(2020) Ruth Eichmann et al.   PLANT JOURNAL

Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

(2020) Prasun Ray et al.   Frontiers in Microbiology

Soil pH and temperature regulate assembly processes of abundant and rare bacterial communities in agricultural ecosystems

(2019) Shuo Jiao 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

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

(2019) Keara L. Grady et al.   Nature Communications

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Field study reveals core plant microbiota and relative importance of their drivers

(2018) Kelly Hamonts et al.   ENVIRONMENTAL MICROBIOLOGY

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes

(2018) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

(2018) Binu M. Tripathi et al.   ISME Journal

Stochastic processes govern invasion success in microbial communities when the invader is phylogenetically close to resident bacteria

(2018) Marta Kinnunen et al.   ISME Journal

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

(2018) Kateryna Zhalnina et al.   Nature Microbiology

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

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

(2017) Benjamin J Callahan et al.   ISME Journal

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

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

Propagule pressure increase and phylogenetic diversity decrease community’s susceptibility to invasion

(2017) T. Ketola et al.   BMC ECOLOGY

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Bacteria as emerging indicators of soil condition

(2016) Syrie M. Hermans et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes

(2016) Florence Mus et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Leaf economics spectrum-productivity relationships in intensively grazed pastures depend on dominant species identity

(2016) Norman W.H. Mason et al.   Ecology and Evolution

Temporal and Spatial Variation of Soil Bacteria Richness, Composition, and Function in a Neotropical Rainforest

(2016) Stephanie N Kivlin et al.   PLoS One

Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice

(2016) Yoshiaki Ueda et al.   PLoS One

Using a Control to Better Understand Phyllosphere Microbiota

(2016) Andrea R. Ottesen et al.   PLoS One

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome

(2016) Rafael Soares Correa de Souza et al.   Scientific Reports

Biodiversity increases the resistance of ecosystem productivity to climate extremes

(2015) Forest Isbell et al.   NATURE

The Soil Microbiome Influences Grapevine-Associated Microbiota

(2015) Iratxe Zarraonaindia et al.   mBio

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

(2015) Zhong Wei et al.   Nature Communications

Estimating and mapping ecological processes influencing microbial community assembly

(2015) James C. Stegen et al.   Frontiers in Microbiology

Niche construction initiates the evolution of mutualistic interactions

(2014) Claudia C. Buser et al.   ECOLOGY LETTERS

Ecological Succession and Stochastic Variation in the Assembly of Arabidopsis thaliana Phyllosphere Communities

(2014) L. Maignien et al.   mBio

A meta-analysis of changes in bacterial and archaeal communities with time

(2013) Ashley Shade et al.   ISME Journal

Quantifying community assembly processes and identifying features that impose them

(2013) James C Stegen et al.   ISME Journal

Rhizosphere microbiome assemblage is affected by plant development

(2013) Jacqueline M Chaparro et al.   ISME Journal

Patterns and Processes of Microbial Community Assembly

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Going back to the roots: the microbial ecology of the rhizosphere

(2013) Laurent Philippot et al.   NATURE REVIEWS MICROBIOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Temporal variation in surface and subsoil abundance and function of the soil microbial community in an arable soil

(2013) Susanne Kramer et al.   SOIL BIOLOGY & BIOCHEMISTRY

Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing

(2012) Feng Guo et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Stochastic and deterministic assembly processes in subsurface microbial communities

(2012) James C Stegen et al.   ISME Journal

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

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

Microbial diversity determines the invasion of soil by a bacterial pathogen

(2012) J. D. van Elsas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variation partitioning involving orthogonal spatial eigenfunction submodels

(2011) Pierre Legendre et al.   ECOLOGY

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

Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture

(2011) P. N. Bhattacharyya et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Using null models to disentangle variation in community dissimilarity from variation in α-diversity

(2011) Jonathan M. Chase et al.   Ecosphere

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

Insect overwintering in a changing climate

(2010) J. S. Bale et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Conceptual Synthesis in Community Ecology

(2010) Mark Vellend   QUARTERLY REVIEW OF BIOLOGY

Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture

(2009) Gabriele Berg   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

A distinct population ofSaccharomyces cerevisiaein New Zealand: evidence for local dispersal by insects and human-aided global dispersal in oak barrels

(2009) Matthew R. Goddard et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal variation in soil microbial communities in Alpine tundra

(2007) Robert G. Björk et al.   SOIL BIOLOGY & BIOCHEMISTRY