Phytobiomes Alliance Newsletter – February 2020


Genome-based circumscription and phenotyping of regulated microbes

The project (funded by the USDA Animal Plant Health Inspection Service – APHIS) began in August 2019 and focuses on the select agent Ralstonia solanacearum (Rs). In this project, high quality sequences of more than 100 Rs will be assembled and a classification system, based on whole genome sequences developed in the project and from public archives, will be used to precisely identify microbes with the goal of distinguishing conclusively between pathogenic and non-pathogenic microbes. If successful, the project will expand to classify other microbial strains. 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. In particular, the Alliance is coordinating with various efforts designed to enhance or build such infrastructure(s) to ensure that the various projects for which databases are developed will complement and not duplicate other efforts. Discussions are also underway to establish at least one international Phytobiomes Alliance repository into which all Alliance-supported projects can deposit microbial genome sequences and metagenomic sequences.

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. The US Ag Microbiome network has published an article in the Phytobiomes Journal entitled “Community-driven Metadata Standards for Agricultural Microbiome Research”. The Alliance will be seeking comments regarding the proposed metadata standards directly from its scientific Coordinating Committee. Additionally, the Alliance is working with the US Culture Collections Research Coordination Network to develop recommended standards for large and small microbial collections used in research and/or distribution.

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. Alliance leaders Kellye Eversole and Boris Vinatzer (Virginia Tech) with Michael Stulberg (USDA-APHIS) will be organizing a workshop entitled “Defining Datapoints for Metagenomic & Microbial Classification to Set Industry Standards” at the 4th MicrobiomeMovement – AgBioTech Summit taking place in Raleigh, NC on Monday 24 February 2020.

Precision and Digital Agriculture

While most of the Alliance projects to date have been focused on efforts related to microbial interactions with the various components of agriculturally relevant phytobiomes, the Alliance is increasing its activities related to precision and digital agriculture, especially as it relates to nutrient and seed management, variable rate technologies, imaging for disease identification and phenotyping, as well as plant genetics and high throughput phenotyping. With the recent addition of The Fertilizer Institute as an Alliance sponsor, activities related to nutrient management are increasing and the goal is to have a session focused on this at the International Phytobiomes Conference in December. Further, we are working to develop various partnerships and alliances with the precision and digital agricultural industries. We will participate for the first time at the World Agri-Tech Innovation Summit in San Francisco on 17-18 March 2020. The Summit is expected to have more than 1,500 attendees and cover the broad range of advancements in agricultural technologies, especially related to a broad range of tools and technologies for precision agriculture.

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. Membership in working groups is open to representatives of the Alliance Coordinating Committee members. The Coordinating Committee is comprised of academicians who are leading Alliance-sponsored or endorsed projects and financial sponsors of Alliance activities.

Food Safety & Quality

At its December 2019 meeting, the scientific Coordinating Committee established a new Food Safety & Quality working group. The working group is now being formed with leadership from Eurofins BioDiagnostics and its members will be announced shortly. Membership in the working groups is open to representatives of the Alliance Coordinating Committee members. The Coordinating Committee is comprised of academicians who are leading Alliance-sponsored or endorsed projects and financial sponsors of Alliance activities.

Alliance Publications

New Coordinating Committee Members

We are pleased to welcome:

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.

Microbiome Movement AgBioTech Summit in Raleigh, NC, 24-26 February

We are excited to be supporting the Microbiome Movement – AgBioTech Summit taking place in Raleigh, NC this February. The meeting will unite the largest agbiological community of ag strategic companies, biotechs, solution providers & academics to advance plant-soil microbe discovery strategies into the next generation of commercially successful products with predictable modes of action, consistent performance & increased yield for crop agriculture.
Phytobiomes Alliance members can benefit from an exclusive 15% discount by quoting code PA15.

World Agri-Tech Innovation Summit in San Francisco, CA, 17-18 March

Join us at the World Agri-Tech Innovation Summit in San Francisco this March where you will hear from over 100 of the brightest minds in agriculture. Don’t miss this opportunity to gather with 1500+ agribusinesses, food brands, producers, investors and entrepreneurs from over 50 counties meet to discuss transformative solutions to the food system and fast-track innovation to the field.
Phytobiomes Alliance members can benefit from $400 discount on a full priced ticket by using code PHA400.

US Biostimulants Summit in Raleigh, NC, 29-30 April

ACI’s US Biostimulants Summit 2020 will be taking place on 29 & 30 April 2020 in Raleigh, North Carolina. The conference will bring together leading executives and experts from across the entire value chain (producers of biostimulant and plant nutrient products, farmers and agriculture suppliers, technology providers, research institutes and government representatives) for two days of informative presentations, interactive discussion and excellent networking opportunities.
Phytobiomes Alliance members can benefit from an exclusive 15% discount. Contact Rafael Krupa to benefit from the special rate.

Our Sponsors

Welcome to our new sponsors : Eurofins BioDiagnostics, Biovante and Aphea.Bio
The Phytobiomes Alliance is sponsored by Bayer CropScience, Eversole Associates, INRAE, Novozymes, Valent BioSciences, Biovante, Colorado State University, Eurofins BioDiagnostics, 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, Apheo.Bio, the American Phytopathological Society, BioConsortia, AIT Austrian Institute of Technology and Karyosoft.