Phytobiomes Alliance Newsletter – July 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, approximately 140 Rs strains have been sequenced and assembled, with complete, closed sequenced genomes of 48 strains via long-read technology and 96 strains sequenced to draft quality with short-read technology. A classification system, based on whole genome sequences from the project and public archives, will be used to precisely identify microbes with the goal of distinguishing conclusively between pathogenic and non-pathogenic microbes. Two key deliverables, a metadata “checklist” for microbial genome sequences and recommendations for USDA-APHIS have been delayed as a result of Covid-19. If success is reached, 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. The project is now expected to be completed in 2021. Project page

Classification System for Risk Prediction

We did not receive funding last year for the Alliance proposal 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 BacillusPseudomonas, and Burkholderia for which plant growth promoting activity and biocontrol activity has been identified. We are continuing to seek funding for this project as it would allow us to build 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

Efforts to establish a database to support correlation studies between biological and geophysical phytobiome components have stalled due to Covid-19. We will continue to coordinate the efforts designed to enhance or build such infrastructure(s) to ensure that the 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, the 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 EU MicrobiomeSupport project has led the development of a published article entitled “Microbiome definition re-visited: old concepts and new challenges” and has a paper regarding requirements for biobanking that has been accepted for publication. Additionally, the Alliance is working with the US Culture Collections Research Coordination Network to develop recommended standards, protocols, and checklists for large and small microbial collections used for research and/or distribution. The Alliance will be seeking comments regarding the metadata standards, checklists, and recommendations to regulatory agencies directly from its scientific Coordinating Committee.

Regulatory Working Group

Alliance leaders Kellye Eversole and Boris Vinatzer (Virginia Tech) along with Michael Stulberg (USDA-APHIS) led a workshop entitled “Defining Datapoints for Metagenomic & Microbial Classification to Set Industry Standards” at the 4th MicrobiomeMovement – AgBio Tech Summit in Raleigh, North Carolina, on 24 February 2020. Workshop presentations by Eversole, Vinatzer, and Stulberg are available on the Alliance website. Eversole has recently discussed with potential funders the development of a regulatory science proposal which could include several regulatory science studies, the development of the regulatory science roadmap, and a practical workshop on biostimulant regulations and standards.

Controlled Environment Working Group

Trevor Charles, University of Waterloo and chair of the working group, recently received funding from the Ontario Ministry of Agriculture, Food and Rural Affairs for Metagenom Bio, a two-year project for a microbiome survey of Ontario vegetable greenhouses and the development of novel approaches for analyses of controlled environment microbiomes. If you are leading a controlled environment project and want to become involved in the working group, please contact Kellye Eversole or Trevor Charles.

Food Safety & Quality Working Group

The Food Safety & Quality Working Group is still looking for members so that the group can be launched. The group is chaired by Farhad Ghavami, Eurofins BioDiagnostics. If you have a food safety or food quality research project and want to be involved, please contact Kellye Eversole or Farhad Ghavami.

New Coordinating Committee Members

We are pleased to welcome:

  • Kirsty Bayliss, Murdoch University, Australia – Topical Leader in horticultural research
  • Davide Bulgarelli, University of Dundee, UK – EU Innovation project CIRCLES
  • Paul Cotter, TEAGASC, Ireland – EU Innovation project MASTER
  • Ann Hirsch, University of California, Los Angeles, USA – Topical Leader in Nitrogen-fixing bacteria
  • Isabel Vercauteren, representing, a new sponsoring partner

Alliance Publications

Alliance Webinar Series

Recordings of Alliance webinars are available on the Alliance YouTube channel. Subscribe to the channel to never miss an upload.

Upcoming webinars
Past webinars

Alliance Events

  • On 15 January 2020, the Alliance organized the workshop “Exploring Phytobiomes” during the Plant and Animal Genome Conference in San Diego, CA, USA. Slides of the presentations made during the workshop are available on this page.
  • On 24 February 2020 , the Alliance organized a workshop entitled “Defining Datapoints for Metagenomic & Microbial Classification to Set Industry Standards” during the 4th MicrobiomeMovement – AgBioTech Summit that took in Raleigh, NC, USA. Slides of the presentations are available on the Alliance website.
  • International Phytobiomes Conference – Due to the ongoing Covid-19 pandemic, the Phytobiomes Conference, originally scheduled for 1-4 December 2020 in Denver, CO, USA, has been postponed to 14-17 September 2021.

Upcoming events

list of events is available on the website.

If you are aware of an event 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 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.

Advancing Vertical Farming, 24-26 August

The inaugural Advancing Vertical Farming Summit, the industry’s first meeting designed ALONGSIDE commercial growers FOR commercial growers, will take place from 24 to 26 August and will be accessible from anywhere, on any device. The Advancing Vertical Farming Summit is set to unite indoor farming industry leaders, academic scientists, investors, policymakers, and buyers to tackle the industries greatest challenges, enabling you to optimize your farms’ productivity, sustainability and maximize profitability.
Across three days content will be spread between three key learning modules focused on the following topics: 1) Plant Growth & Development; 2) Business Case & Investment; 3) Farm Design, Automation & Upscaling. This will be an unrivalled opportunity to join like-minded thought-leaders from cross-disciplines in the indoor farming sector and foster new connections and partnerships. Download the full digital event guide. Phytobiomes Alliance members can benefit from an exclusive 10% discount by quoting the code PHYAVF10.

World Agri-Tech Innovation Summit, 15-16 September

The World Agri-Tech Innovation Summit is going virtual! This year’s summit will be live online on 15-16 September 2020, providing a 1-1 meeting platform for our global agtech network, focused discussion groups, interactive panel discussions, start-up pitches, and critical intelligence from industry leaders on how our industry will emerge from the current crisis.
An expert international speaking faculty will present live, before hosting breakout virtual roundtables on the trends, opportunities and challenges that will shape your business in 2021.
Key themes addressed will be: Carbon Neutrality, Sustainable Inputs, Automation and Robotics, Supply Chain Resiliency, Soil Health, Digital Platforms, Localised Food Systems, and Investment Outlook.
Partnership and collaboration are critical as we strive to create a stronger, more sustainable agri-food system. We may not be able to meet in person right now, but we still need to come together to share knowledge and make new connections to help our businesses grow.Phytobiomes Alliance members can benefit from a 10% discount on the full registration fee by quoting the code PHYTO10.

US Biostimulants Summit in Raleigh, NC, 1-2 October

ACI’s US Biostimulants Summit 2020 will be taking place on 1-2 October 2020 in Raleigh, North Carolina, USA. 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.

Microbiome for Agriculture Congress USA, Raleigh, NC, 19-20 October

The Microbiome for Agriculture Congress that will take place in Raleigh, NC, USA, from 19 to 20 October, will examine the symbiotic relationships between microbes and plants through case studies in plant and soil microbiomes. Academic and industry leaders will discuss new research into the rhizosphere, phyllosphere and endosphere and the application of plant and soil microbiome research in improving disease resistance, nutrient acquisition and crop yield, and tolerance to multiple stressors including nematodes, insects and drought. With dedicated space in the schedule to network, this conference is the ideal forum to share knowledge and build partnerships. Visit the event page to download the full agenda.

Our Sponsors

Welcome to our new sponsor:  Aphea.Bio

The Phytobiomes Alliance is sponsored by Bayer Crop Science, Eversole Associates, INRAE, Novozymes, Valent BioSciences, Biovante, Colorado State University, Eurofins BioDiagnostics, Indigo, IRD, Joyn Bio, 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, Aphea.Bio, the American Phytopathological Society, BioConsortia, AIT Austrian Institute of Technology and Karyosoft.