Plant, Root, and Soil Microbiome

Updated May 2018. If you have suggestions for more key papers, please let me know in the comments.

Research papers

A global atlas of the dominant bacteria found in soil – Manuel Delgado-Baquerizo – Science – January 2018

A communal catalogue reveals Earth’s multiscale microbial diversity – Thompson and the Earth Microbiome Project Consortium – Nature – November 2017

Next-Generation Sequencing of the Bacterial 16S rRNA Gene for Forensic Soil Comparison: A Feasibility Study – Ellen M. Jesmok – Journal of Forensic Sciences – February 2016

Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China – Bin Ma – The ISME Journal – January 2016

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition – Andrzej Tkacz – The ISME Journal – November 2015

Red Pepper: Rhizobacterial Communities and Red Pepper (Capsicum annum) Yield under Different Cropping Systems – Byung Kwon Jung – International Journal of Agriculture & Biology – August 2015

The Soil Microbiome Influences Grapevine-Associated Microbiota – Iratxe Zarraonaindia – mBio – March 2015

Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally – Kelly S. Ramirez – Proceedings of the Royal Society B – November 2014

Metatranscriptomic Analysis of Arctic Peat Soil Microbiota – Alexander T. Tveit – Applied Environmental Microbiology – September 2014

Diversity and heritability of the maize rhizosphere microbiome under field conditions – Jason A. Peiffer – PNAS – April 2013

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens – Kevin J. Forsberg – Science – August 2012

Roof gardens

Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks – Krista L. McGuire – PLOS ONE – March 2013

Manipulating soil microbial communities in extensive green roof substrates – Chloe J. Molineux – Science of the Total Environment – September 2014



Disease Suppressive Soils: New Insights from the Soil Microbiome – 
Daniel Schlatter- Phytopathology – November 2017
(PDF here )

Embracing the unknown: disentangling the complexities of the soil microbiome
Noah Fierer – Nature Reviews in Microbiology – August 2017

Global Change and the Soil Microbiome: A Human-Health Perspective – Raúl Ochoa-Hueso – Frontiers in Ecology and Evolution – July 2017

Research priorities for harnessing plant microbiomes in sustainable agriculture – Posy E. Busby – PLOS Biology – March 2017

Evaluating the diversity of soil microbial communities in vineyards relative to adjacent native ecosystems – Taylor C. Holland – Applied Soil Ecology – December 2015

A review: what is the spermosphere and how can it be studied? – S. Schiltz – Journal of Applied Microbiology – October 2015

Microbiota and Host Nutrition across Plant and Animal Kingdoms – Stéphane Hacquard – Cell Host & Microbe – May 2015

Role of root microbiota in plant productivity – Andrzej Tkacz – Journal of Experimental Botany

The Plant Microbiome at Work – Klaus Schlaeppi – Molecular Plant-Microbe Interactions – March 2015

Functional Soil Microbiome: Belowground Solutions to an Aboveground Problem – Venkatachalam Lakshmanan et al. – Plant Physiology – October 2014

The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants – Vanessa C. Coats – Frontiers in Microbiology – July 2014

The microbiome of medicinal plants: diversity and importance for plant growth, quality, and health – Martina Köberl – Frontiers in Microbiology – December 2013

Plant growth-promoting rhizobacteria and root system functioning – Jordan Vacheron – Frontiers in Microbiology – September 2013

Going back to the roots: the microbial ecology of the rhizosphere – Laurent Philippot – Nature Reviews Microbiology – September 2013

Inside the root microbiome: Bacterial root endophytes and plant growth promotion – Jonathan R. Gaiero – American Journal of Botany – September 2013

The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms – Rodrigo Mendes – FEMS Microbiology Reviews – September 2013

Mobile elements, zoonotic pathogens and commensal bacteria: conduits for the delivery of resistance genes into humans, production animals and soil microbiota – Steven P. Djordjevic – Frontiers in Microbiology – April 2013

Structure and Functions of the Bacterial Microbiota of Plants – Davide Bulgarelli – Annual Review of Plant Biology – April 2013

A review of molecular methods to study the microbiota of soil and the mycosphere
J.D. van Elsas – European Journal of Soil Biology – March 2011

Popular Press


Dirt has a microbiome, and it may double as an antidepressant – Zoë Schlanger – Quartz -May 30, 2017

Healthy Soil Microbes, Healthy People. The microbial community in the ground is as important as the one in our guts – Mike Amaranthus and Burce Allyn – The Atlantic – June 2013