Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Metabolic Capacity Differentiates Plenodomus lingam from P. biglobosus Subclade ‘brassicae’, the Causal Agents of Phoma Leaf Spotting and Stem Canker of Oilseed Rape (Brassica napus) in Agricultural Ecosystems

(2022) Magdalena Frąc et al.   Pathogens

Artificial microbial consortia for bioproduction processes

(2022) Fabian Mittermeier et al.   ENGINEERING IN LIFE SCIENCES

From diversity to complexity: Microbial networks in soils

(2022) Ksenia Guseva et al.   SOIL BIOLOGY & BIOCHEMISTRY

Soil microbial inoculants for sustainable agriculture: Limitations and opportunities

(2022) Maureen O'Callaghan et al.   SOIL USE AND MANAGEMENT

Biological Control of Plant Pathogens: A Global Perspective

(2022) Rachid Lahlali et al.   Microorganisms

Microencapsulating Alginate-Based Polymers for Probiotics Delivery Systems and Their Application

(2022) Xiaochen Wang et al.   Pharmaceuticals

Review and Perspectives of the Use of Alginate as a Polymer Matrix for Microorganisms Applied in Agro-Industry

(2022) Betsie Martínez-Cano et al.   MOLECULES

Nanopore-based metagenomic analysis of the impact of nanoparticles on soil microbial communities

(2022) Sangeeta Chavan et al.   Heliyon

Current Challenges and Pitfalls in Soil Metagenomics

(2022) Marcio F. A. Leite et al.   Microorganisms

Long-Term Fertilization Strategy Impacts Rhizoctonia solani–Microbe Interactions in Soil and Rhizosphere and Defense Responses in Lettuce

(2022) Loreen Sommermann et al.   Microorganisms

Trichoderma enriched compost, BCAs and potassium phosphite control Fusarium wilt of lettuce without affecting soil microbiome at genus level

(2022) Alessio Bellini et al.   APPLIED SOIL ECOLOGY

A versatile microfluidic platform measures hyphal interactions between Fusarium graminearum and Clonostachys rosea in real-time

(2021) Alejandro Gimeno et al.   Communications Biology

Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing

(2021) Rahul Vijay Kapoore et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Microbiome Modulation—Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants

(2021) Gabriele Berg et al.   Frontiers in Microbiology

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil

(2021) Andrea Manfredini et al.   Frontiers in Microbiology

Realities and hopes in the application of microbial tools in agriculture

(2021) Bruna D. Batista et al.   Microbial Biotechnology

Metagenomic Analysis of Bacterial Communities in Agricultural Soils from Vietnam with Special Attention to Phosphate Solubilizing Bacteria

(2021) Anna Hegyi et al.   Microorganisms

Studying Microbial Communities through Co-Occurrence Network Analyses during Processes of Waste Treatment and in Organically Amended Soils: A Review

(2021) José A. Siles et al.   Microorganisms

Microfluidic chips provide visual access to in situ soil ecology

(2021) Paola Micaela Mafla-Endara et al.   Communications Biology

The effect of soil sample size, for practical DNA extraction, on soil microbial diversity in different taxonomic ranks

(2021) Hiroki Morita et al.   PLoS One

Predicting measures of soil health using the microbiome and supervised machine learning

(2021) Roland C. Wilhelm et al.   SOIL BIOLOGY & BIOCHEMISTRY

Microbial Consortia for Effective Biocontrol of Root and Foliar Diseases in Tomato

(2021) Zhivko Minchev et al.   Frontiers in Plant Science

Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation

(2021) Carlos Arellano-Caicedo et al.   Communications Biology

Metagenomic insights into seasonal variations in the soil microbial community and function in a Larix gmelinii forest of Mohe, China

(2020) Tong Bao et al.   JOURNAL OF FORESTRY RESEARCH

Formulation of Microbial Inoculants by Encapsulation in Natural Polysaccharides: Focus on Beneficial Properties of Carrier Additives and Derivatives

(2020) Nikolay Vassilev et al.   Frontiers in Plant Science

Plant–microbiome interactions: from community assembly to plant health

(2020) Pankaj Trivedi et al.   NATURE REVIEWS MICROBIOLOGY

Development of a low-cost culture medium for the rapid production of plant growth-promoting Rhodopseudomonas palustris strain PS3

(2020) Kai-Jiun Lo et al.   PLoS One

An Optimized Method to Assess Viable Escherichia coli O157:H7 in Agricultural Soil Using Combined Propidium Monoazide Staining and Quantitative PCR

(2020) Yulong Fu et al.   Frontiers in Microbiology

Field Exploitation of Multiple Functions of Beneficial Microorganisms for Plant Nutrition and Protection: Real Possibility or Just a Hope?

(2020) Jolanta Kowalska et al.   Frontiers in Microbiology

A Compost Treatment Acts as a Suppressive Agent in Phytophthora capsici – Cucurbita pepo Pathosystem by Modifying the Rhizosphere Microbiota

(2020) Alessio Bellini et al.   Frontiers in Plant Science

Towards Better Understanding of the Interactions and Efficient Application of Plant Beneficial Prebiotics, Probiotics, Postbiotics and Synbiotics

(2020) Maria Vassileva et al.   Frontiers in Plant Science

Microbiome definition re-visited: old concepts and new challenges

(2020) Gabriele Berg et al.   Microbiome

Effects of biocontrol agents and compost against the Phytophthora capsici of zucchini and their impact on the rhizosphere microbiota

(2020) Maria Alexandra Cucu et al.   APPLIED SOIL ECOLOGY

Achieving similar root microbiota composition in neighbouring plants through airborne signalling

(2020) Hyun Gi Kong et al.   ISME Journal

Microfluidic monitoring of the growth of individual hyphae in confined environments

(2020) Claire Baranger et al.   Royal Society Open Science

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Recommendations for soil microbiome analyses

(2019) P. Nannipieri et al.   BIOLOGY AND FERTILITY OF SOILS

Composts from green sources show an increased suppressiveness to soilborne plant pathogenic fungi: Relationships between physicochemical properties, disease suppression, and the microbiome

(2019) Ugo De Corato et al.   CROP PROTECTION

Techno-economic analysis of the industrial production of a low-cost enzyme using E. coli: the case of recombinant β-glucosidase

(2018) Rafael da Gama Ferreira et al.   Biotechnology for Biofuels

Biotechnological potential of microbial consortia and future perspectives

(2018) Shashi Kant Bhatia et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

The soil microbiome — from metagenomics to metaphenomics

(2018) Janet K Jansson et al.   CURRENT OPINION IN MICROBIOLOGY

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

(2018) Shin Haruta et al.   CURRENT GENOMICS

Influence of different biological control agents and compost on total and nitrification-driven microbial communities at rhizosphere and soil level in a lettuce - Fusarium oxysporum f. sp. lactucae pathosystem

(2018) M.A. Cucu et al.   JOURNAL OF APPLIED MICROBIOLOGY

Nursery treatments with resistant inducers, soil amendments and biocontrol agents for the management of the Fusarium wilt of lettuce under glasshouse and field conditions

(2018) Giovanna Gilardi et al.   JOURNAL OF PHYTOPATHOLOGY

Microbial Consortium Design Benefits from Metabolic Modeling

(2018) Karoline Faust   TRENDS IN BIOTECHNOLOGY

Encapsulation of Lactobacillus acidophilus in moist-heat-resistant multilayered microcapsules

(2017) Panithan Pitigraisorn et al.   JOURNAL OF FOOD ENGINEERING

Innovative liquid formulation of digestates for producing a biofertilizer based on Bacillus siamensis : Field testing on sweet pepper

(2017) Raquel Pastor-Bueis et al.   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Disease Suppressive Soils: New Insights from the Soil Microbiome

(2017) Daniel Schlatter et al.   PHYTOPATHOLOGY

Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks

(2017) David A. Bohan et al.   TRENDS IN ECOLOGY & EVOLUTION

Microbiome-on-a-Chip: New Frontiers in Plant–Microbiota Research

(2017) Claire E. Stanley et al.   TRENDS IN MICROBIOLOGY

Biostimulants in Plant Science: A Global Perspective

(2017) Oleg I. Yakhin et al.   Frontiers in Plant Science

Co-inoculum of Beauveria brongniartii and B. bassiana shows in vitro different metabolic behaviour in comparison to single inoculums

(2017) L. Canfora et al.   Scientific Reports

Microbial inoculation of seed for improved crop performance: issues and opportunities

(2016) Maureen O’Callaghan   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Potential application of glycerol in the production of plant beneficial microorganisms

(2016) Nikolay Vassilev et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples

(2016) Janine Heise et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Soil-on-a-Chip: microfluidic platforms for environmental organismal studies

(2016) Claire E. Stanley et al.   LAB ON A CHIP

Phenotype MicroArray™ system in the study of fungal functional diversity and catabolic versatility

(2016) Flavia Pinzari et al.   RESEARCH IN MICROBIOLOGY

Soil immune responses

(2016) J. M. Raaijmakers et al.   SCIENCE

Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression

(2016) Jie Hu et al.   mBio

Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut

(2016) Eveline Adam et al.   Frontiers in Microbiology

Nutritional niche overlap potentiates the use of endophytes in biocontrol of a tree disease

(2015) Kathrin Blumenstein et al.   BIOCONTROL

Soil-Borne Microbiome: Linking Diversity to Function

(2015) Lucas W. Mendes et al.   MICROBIAL ECOLOGY

Ecological communities by design

(2015) J. K. Fredrickson   SCIENCE

Microbial consortium-mediated plant defense against phytopathogens: Readdressing for enhancing efficacy

(2015) Birinchi Kumar Sarma et al.   SOIL BIOLOGY & BIOCHEMISTRY

Effects of arbuscular mycorrhizal fungus, humic acid, and whey on wilt diseasecaused by Verticillium dahliae Kleb. in three solanaceous crops

(2015) Semra DEMİR et al.   Turkish Journal of Agriculture and Forestry

Utilization of different waste proteins to create a novel PGPR-containing bio-organic fertilizer

(2015) Yan Huang et al.   Scientific Reports

Arbuscular Mycorrhizal Fungi for the Biocontrol of Plant-Parasitic Nematodes: A Review of the Mechanisms Involved

(2015) Nele Schouteden et al.   Frontiers in Microbiology

Phenotype microarray technology and its application in industrial biotechnology

(2014) Darren Greetham   BIOTECHNOLOGY LETTERS

Natural polymers for the microencapsulation of cells

(2014) L. Gasperini et al.   Journal of the Royal Society Interface

The role of soil microbes in the global carbon cycle: tracking the below-ground microbial processing of plant-derived carbon for manipulating carbon dynamics in agricultural systems

(2014) Christos Gougoulias et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Exploring the transfer of recent plant photosynthates to soil microbes: mycorrhizal pathway vs direct root exudation

(2014) Christina Kaiser et al.   NEW PHYTOLOGIST

Arbuscular mycorrhiza and nitrogen: implications for individual plants through to ecosystems

(2014) Angela Hodge et al.   PLANT AND SOIL

Biological control agents (BCAs) of verticillium wilt: influence of application rates and delivery method on plant protection, triggering of host defence mechanisms and rhizosphere populations of BCAs

(2014) D. J. Angelopoulou et al.   PLANT PATHOLOGY

An introduction to the analysis of shotgun metagenomic data

(2014) Thomas J. Sharpton   Frontiers in Plant Science

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

Temporal variability in soil microbial communities across land-use types

(2013) Christian L Lauber et al.   ISME Journal

Biochar of animal origin: a sustainable solution to the global problem of high-grade rock phosphate scarcity?

(2013) Nikolay Vassilev et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Advances in plant growth-promoting bacterial inoculant technology: formulations and practical perspectives (1998–2013)

(2013) Yoav Bashan et al.   PLANT AND SOIL

Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

(2013) Darine Trabelsi et al.   Biomed Research International

Application of phenotypic microarrays to environmental microbiology

(2012) Sharon Borglin et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Technologies for Beneficial Microorganisms Inocula Used as Biofertilizers

(2012) E. Malusá et al.   TheScientificWorldJOURNAL

Have biopesticides come of age?

(2012) Travis Glare et al.   TRENDS IN BIOTECHNOLOGY

Evaluating novel microbe amended composts as biocontrol agents in tomato

(2011) Ajinath Shridhar Dukare et al.   CROP PROTECTION

Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

(2011) Nathalie Lombard et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2011) Albert Barberán et al.   ISME Journal

Microbial consortium-mediated reprogramming of defence network in pea to enhance tolerance against Sclerotinia sclerotiorum

(2011) A. Jain et al.   JOURNAL OF APPLIED MICROBIOLOGY

Detection and identification of bacteria in clinical samples by 16S rRNA gene sequencing: comparison of two different approaches in clinical practice

(2011) C. Jenkins et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Biocontrol of Fusarium head blight: interactions between Trichoderma and mycotoxigenic Fusarium

(2011) F. Matarese et al.   MICROBIOLOGY-SGM

Bacillus thuringiensis: a century of research, development and commercial applications

(2011) Georgina Sanahuja et al.   PLANT BIOTECHNOLOGY JOURNAL

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Extraction of mRNA from Soil

(2010) C. Mettel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Optimization of thermostable α- amylase production by Streptomyces erumpens MTCC 7317 in solid-state fermentation using cassava fibrous residue

(2010) Kar Shaktimay et al.   BRAZILIAN ARCHIVES OF BIOLOGY AND TECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Evaluation of arbuscular mycorrhizal fungus, fluorescent Pseudomonas and Trichoderma harzianum formulation against Fusarium oxysporum f. sp. lycopersici for the management of tomato wilt

(2009) Rashmi Srivastava et al.   BIOLOGICAL CONTROL

Facilitation in the conceptual melting pot

(2009) Rob W. Brooker et al.   JOURNAL OF ECOLOGY

Disintegration of the Ecological Community

(2008) Robert E. Ricklefs   AMERICAN NATURALIST