Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant‐associated communities of bacteria and fungi

Foliar Application of Vegetal-Derived Bioactive Compounds Stimulates the Growth of Beneficial Bacteria and Enhances Microbiome Biodiversity in Lettuce

(2019) Francesca Luziatelli et al.   Frontiers in Plant Science

Expanding and testing fluorescent amplified fragment length polymorphisms for identifying roots of boreal forest plant species

(2019) Paul Metzler et al.   Applications in Plant Sciences

Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media – A review

(2019) Mohamed S. Sarhan et al.   Journal of Advanced Research

Difference in Some Biological Properties of Saline and Non-saline Soil under Sugarcane Cultivation

(2019) E. Lamizadeh et al.   EURASIAN SOIL SCIENCE

The influence of host genotype and salt stress on the seed endophytic community of salt-sensitive and salt-tolerant rice cultivars

(2018) Denver I. Walitang et al.   BMC PLANT BIOLOGY

Effects of the biocontrol agent Bacillus amyloliquefaciens SN16-1 on the rhizosphere bacterial community and growth of tomato

(2018) Tingting Wan et al.   JOURNAL OF PHYTOPATHOLOGY

Conservation and transmission of seed bacterial endophytes across generations following crossbreeding and repeated inbreeding of rice at different geographic locations

(2018) Denver I. Walitang et al.   MicrobiologyOpen

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Relationship between foliar endophytes and apple cultivar disease resistance in an organic orchard

(2018) Ayumi Hirakue et al.   BIOLOGICAL CONTROL

Hidden mycota of pine needles: Molecular signatures from PCR-DGGE and Ribosomal DNA phylogenetic characterization of novel phylotypes

(2018) Rajesh Jeewon et al.   Scientific Reports

Nitrate Supply-Dependent Shifts in Communities of Root-Associated Bacteria in Arabidopsis

(2017) Noriyuki Konishi et al.   MICROBES AND ENVIRONMENTS

Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change

(2017) Emma J. Sayer et al.   Ecology and Evolution

Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys

(2017) Sofie Thijs et al.   Frontiers in Microbiology

Impact of Transgenic Brassica napus Harboring the Antifungal Synthetic Chitinase (NiC) Gene on Rhizosphere Microbial Diversity and Enzyme Activities

(2017) Mohammad S. Khan et al.   Frontiers in Plant Science

Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem

(2016) Youcai Qin et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Endophytic bacteria with antagonistic traits inhabit the wood tissues of grapevines from Tunisian vineyards

(2016) A. Rezgui et al.   BIOLOGICAL CONTROL

Diversity of endophytic bacteria of Dendrobium officinale based on culture-dependent and culture-independent methods

(2016) Cong Pei et al.   BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT

Rhizobacterial Community Structures Associated with Native Plants Grown in Chilean Extreme Environments

(2016) Milko A. Jorquera et al.   MICROBIAL ECOLOGY

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

(2016) David Johnston-Monje et al.   PLANT AND SOIL

Bacterial community structures and ice recrystallization inhibition activity of bacteria isolated from the phyllosphere of the Antarctic vascular plant Deschampsia antarctica

(2016) Fernanda P. Cid et al.   POLAR BIOLOGY

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity

(2016) Citlali Fonseca-García et al.   Frontiers in Microbiology

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat

(2016) Akitomo Kawasaki et al.   PLoS One

Plant and soil effects on bacterial communities associated with Miscanthus  × giganteus rhizosphere and rhizomes

(2015) Dongfang Li et al.   Global Change Biology Bioenergy

Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards

(2015) Ingrid H. Franke-Whittle et al.   PLANT AND SOIL

Biotic Stress Shifted Structure and Abundance of Enterobacteriaceae in the Lettuce Microbiome

(2015) Armin Erlacher et al.   PLoS One

Transgenic banana plants expressing Xanthomonas wilt resistance genes revealed a stable non-target bacterial colonization structure

(2015) Jean Nimusiima et al.   Scientific Reports

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process

(2014) Daniela Bulgari et al.   BMC MICROBIOLOGY

Impact of swapping soils on the endophytic bacterial communities of pre-domesticated, ancient and modern maize

(2014) David Johnston-Monje et al.   BMC PLANT BIOLOGY

Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait

(2014) Eleonora Rolli et al.   ENVIRONMENTAL MICROBIOLOGY

Community fingerprinting in a sequencing world

(2014) Josie van Dorst et al.   FEMS MICROBIOLOGY ECOLOGY

Analyses of the Temporal Dynamics of Fungal Communities Colonizing the Healthy Wood Tissues of Esca Leaf-Symptomatic and Asymptomatic Vines

(2014) Emilie Bruez et al.   PLoS One

Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies

(2014) Michiel Op De Beeck et al.   PLoS One

Differences between the rhizosphere microbiome of Beta vulgaris ssp. maritima—ancestor of all beet crops—and modern sugar beets

(2014) Christin Zachow et al.   Frontiers in Microbiology

Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants

(2014) Ruth Schmidt et al.   Frontiers in Microbiology

Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce

(2014) Susanne Schreiter et al.   Frontiers in Microbiology

Analysis of plant microbe interactions in the era of next generation sequencing technologies

(2014) Claudia Knief   Frontiers in Plant Science

Different pioneer plant species select specific rhizosphere bacterial communities in a high mountain environment

(2014) Sonia Ciccazzo et al.   SpringerPlus

Bacterial endophytes enhance competition by invasive plants

(2013) Marnie E. Rout et al.   AMERICAN JOURNAL OF BOTANY

Design and application of specific 16S rDNA-targeted primers for assessing endophytic diversity in Dendrobium officinale using nested PCR-DGGE

(2013) Jie Yu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Diagnostic assessment of mycodiversity in environmental samples by fungal ITS1 rDNA length polymorphism

(2013) Alfons R. Weig et al.   MYCOLOGICAL PROGRESS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Distinct Phyllosphere Bacterial Communities on Arabidopsis Wax Mutant Leaves

(2013) Eva E. Reisberg et al.   PLoS One

Catch the Best: Novel Screening Strategy to Select Stress Protecting Agents for Crop Plants

(2013) Christin Zachow et al.   Agronomy-Basel

Molecular and culture-dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (Oryza sativa) varieties

(2012) Lucía Ferrando et al.   FEMS MICROBIOLOGY ECOLOGY

Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica)

(2012) Tristan Cordier et al.   Fungal Ecology

Application of Trichoderma harzianum SQR-T037 bio-organic fertiliser significantly controls Fusarium wilt and affects the microbial communities of continuously cropped soil of cucumber

(2012) Li-Hua Chen et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Combining ecophysiological and microbial ecological approaches to study the relationship between Medicago truncatula genotypes and their associated rhizosphere bacterial communities

(2012) A. Zancarini et al.   PLANT AND SOIL

Summer season and long-term drought increase the richness of bacteria and fungi in the foliar phyllosphere ofQuercus ilexin a mixed Mediterranean forest

(2012) J. Peñuelas et al.   PLANT BIOLOGY

Dynamics of Seed-Borne Rice Endophytes on Early Plant Growth Stages

(2012) Pablo R. Hardoim et al.   PLoS One

Effect of Biocontrol Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere Using T-RFLP and DGGE

(2012) Guanpeng Gao et al.   PLoS One

Assessment of Variation in Bacterial Composition among Microhabitats in a Mangrove Environment Using DGGE Fingerprints and Barcoded Pyrosequencing

(2012) Daniel F. R. Cleary et al.   PLoS One

A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming

(2012) Ramona Marasco et al.   PLoS One

Methylobacterium-Induced Endophyte Community Changes Correspond with Protection of Plants against Pathogen Attack

(2012) Pavlo Ardanov et al.   PLoS One

Influence of nitrogen fertilization on diazotrophic communities in the rhizosphere of the Jerusalem artichoke (Helianthus tuberosus L.)

(2012) Xianfa Meng et al.   RESEARCH IN MICROBIOLOGY

Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica)

(2012) Neus Garcias-Bonet et al.   Frontiers in Microbiology

Plant and soil properties determine microbial community structure of shared Pinus-Vaccinium rhizospheres in petroleum hydrocarbon contaminated forest soils

(2011) Susan J. Robertson et al.   PLANT AND SOIL

Conservation and Diversity of Seed Associated Endophytes in Zea across Boundaries of Evolution, Ethnography and Ecology

(2011) David Johnston-Monje et al.   PLoS One

Desert Farming Benefits from Microbial Potential in Arid Soils and Promotes Diversity and Plant Health

(2011) Martina Köberl et al.   PLoS One

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

Molecular community analysis of arbuscular mycorrhizal fungi associated with five selected plant species from heavy metal polluted soils

(2010) Liang Kun Long et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Diversity of endophytic bacteria from the cuprophytes Haumaniastrum katangense and Crepidorhopalon tenuis

(2010) Alfred Cubaka Kabagale et al.   PLANT AND SOIL

Selection of Enzymes for Terminal Restriction Fragment Length Polymorphism Analysis of Fungal Internally Transcribed Spacer Sequences

(2009) P. Alvarado et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Increased Diversity of Arbuscular Mycorrhizal Fungi in a Long-Term Field Experiment via Application of Organic Amendments to a Semiarid Degraded Soil

(2009) M. del Mar Alguacil et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search of environmental descriptors to explain the variability of the bacterial diversity from maize rhizospheres across a regional scale

(2009) Thelma Castellanos et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Analyzing salt-marsh fungal diversity: comparing ARISA fingerprinting with clone sequencing and pyrosequencing

(2009) Patrick M. Gillevet et al.   Fungal Ecology

Development of a Bacterial Cell Enrichment Method and its Application to the Community Analysis in Soybean Stems

(2009) Seishi Ikeda et al.   MICROBIAL ECOLOGY

Endophytic bacteria in long-term in vitro cultivated “axenic” pineapple microplants revealed by PCR–DGGE

(2009) Monita F. Abreu-Tarazi et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

TRiFLe, a Program for In Silico Terminal Restriction Fragment Length Polymorphism Analysis with User-Defined Sequence Sets

(2008) P. Junier et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities

(2008) Ursel M. E. Schütte et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

(2008) Stephen J Bent et al.   ISME Journal