Phytobiomes Alliance Newsletter – October 2019


Genome-based circumscription and phenotyping of regulated microbes

The Alliance project has received funding from the USDA Animal Plant Health Inspection Service (APHIS). In this project, a classification system, based on whole genome sequences, will be used to precisely identify microbes and conclusively distinguish pathogenic and non-pathogenic microbes. The project began in August and focuses initially on the select agent Ralstonia solanacearum (Rs). Over the long-term, it is hoped that this method will be beneficial for accelerating the regulatory pathway for international and interstate shipments as well as commercialization of microbial products. Project page

Classification System for Risk Prediction

The Alliance has submitted a “proposal” (Farm Bill suggestion) to USDA-APHIS to develop a risk prediction method for beneficial plant bacteria by integrating genome-based circumscription and phenotypic data with an initial focus on Bacillus, Pseudomonas, and Burkholderia for which plant growth promoting activity and biocontrol activity has been identified. If approved, this project would start building a comprehensive database that links bacterial genomes with genome-based taxonomic information, gene content, and phenotypes, including, most importantly, potential pathogenicity on animals and plants.

Database to Support Correlation Studies

The Alliance is beginning efforts to establish a database to support correlation studies between biological and geophysical phytobiome components.

Standards Development

The Alliance is working with the US Ag Microbiome network, the International Metagenomics and Microbiome Standards Alliance, French PhytoMic Network, and the EU’s MicrobiomeSupport project to develop standards to advance our knowledge in fundamental phytobiomes science, especially as it relates to microbiomes, and to support commercialization of agricultural microbials as solutions to the challenges facing agriculture.

Regulatory Science Roadmap for Microbials

The Alliance established a Regulatory Working Group tasked with continuing efforts to identify gaps and priorities in regulatory science that if addressed may facilitate regulatory approvals for agricultural microbials. The Alliance is working to understand the regulatory science needs of industry, academia, and governmental agencies. While we have already identified some of the gaps and are leading research to fill them, the regulatory science roadmap will outline further gaps, priorities, and opportunities for research and will then be used to guide the development, funding, and implementation of research that could support changes or improvements in state, national, and international regulations.

Indoor Agriculture/Controlled Environment

The Alliance has set up an Indoor Agriculture/Controlled Environment Working Group focused on research to enhance the understanding of the various components of controlled environment phytobiomes, and to support the development of microbial products that may enhance the productivity of plants in such environments.


Press releases and announcements

Alliance Events

Upcoming events

A list of events is available on the website.
If you are going to or are aware of a conference, workshop, or seminar on phytobiome-related topics and if that event is not listed on the website, please let us know.
In case you could not join us at an event, PDFs of the latest presentations made by the Alliance Leadership team are available on the website.
We developed a set of standards slides about phytobiomes, the Alliance, its goals and priorities. Contact us if you wish to receive those slides to add to your presentations.

New Coordinating Committee Members

We are pleased to welcome:

  • Richard Broglie, as representative of Pivot Bio, a financial sponsor
  • Arun Manoharan, as new representative of Prime Discoveries, a financial sponsor
  • Nathan Pumplin, as representative of Joyn Bio, a financial sponsor
  • Marci Surpin, as representative of Valent BioSciences, a financial sponsor

Our Sponsors

Welcome to our new sponsors: Valent BioSciences, Joyn Bio and Pivot Bio

The Phytobiomes Alliance is sponsored by Bayer CropScience, Eversole Associates, INRA, Novozymes, Valent BioSciences, Colorado State University, Indigo, IRD, Joyn Bio, the University of Maryland, the University of Nebraska-Lincoln, NewLeaf Symbiotics, the Noble Research Institute, Penn State College of Agricultural Sciences, Pivot Bio, The Fertilizer Institute, the Waterloo Centre for Microbial Research, the American Phytopathological Society, BioConsortia, Prime Discoveries, the Austrian Institute of Technology, and Karyosoft.