Brief Summary of Minutes of Annual Meeting

The participants listed met at the National Arboretum in Washington, DC on March 31, 2017.  The meeting schedule was as follows

8:30-9:30am - Dr. Hector Corrada Bravo: Current and future challenges and opportunities in metagenomic data analysis

9:30-11:30am - Research Updates from Participating Institutions

• University of Maryland – Dr. Joseph Roberts
• USDA – Dr. Jo Anne Crouch
• University of Wisconsin-Madison – Dr. Paul Koch
• NC State University – Dr. Wei Shi
• University of Connecticut – Dr. John Inguagiato
• Cornell University – Dr. Jenny Koa Kniffen
• University of Massachusetts – Dr. Michelle DaCosta
• Rutgers University – Dr. Bruce Clarke
• University of Minnesota – Dr. Eric Watkins
• 1:00-3:00pm - Discussion of Future Project Directions

1:00-3:00pm - Future Directions for NE1602 Project

Topic: Technical Details Surrounding Turfgrass Labs Getting Started with Microbiome Analysis (Initial Overview by Jo Anne Crouch)

Consideration 1:  In-house vs. Service Provider

• Outsourcing:  Possibly cheaper in sending to provider
• Outsourcing:  Some platforms only available through service provider
• In-house:  Generate data faster on your own schedule and provide students/Post-docs with NGS training
• Other tools needed:  Library prep requires some peripheral tools/equipment in addition to sequencing

 Consideration 2:  Which NGS technology

• Sanger sequencing not suitable for heterogenous environmental data
• PacBio Sequel
• Illumina NextSeq
• Illumina MiSeq
• Illumina MiniSeq
• Illumina NovaSeq
• Oxford Nanopore Minlon

 MiSeq Reagent Kits

• One MiSeq Run uses a single use (RFID Chipped) Reagent Kit
• Different MiSeq Kits available, depending on the length of sequences desired (50 bp, 150 bp, 300 bp, and 600 bp)
• Different kits carry different costs

 How to determine how many samples per cartridge

• Support.illumina.com/downloads/sequencing_coverage_calculator.html
• Example – 3 Sclerotinia homoeocarpa isolates on a single 600 bp MiSeq Chip
• Coverage details are much less clear with environmental DNA systems
• Sample number significantly impacts results – Predictive models on previous research by Beirn et al. suggested that 12 samples had no significance, but increasing sample number to 20 and 30 resulted in significance.

Additional technical details for sampling and microbiome analysis

        Replications in microbiome studies – How many are needed?

Unpublished data suggests management intensity can overcome spatial variance.  Sampling of golf course fairways impacted more by management intensity vs. spatial differences

Many participants focusing on soil and rhizosphere communities.  Less work on foliar communities.  Suggestions by Bruce Clarke to examine thatch communities, specifically with plant pathogens as many foliar pathogens reside in thatch. 

 Standardized research protocols

• Shaking samples to determine rhizosphere samples – One Shake removes bulk soil based on the extensive, dense root system with established turfgrass. 
• Additional projects are needed to develop standardized research procedures

Proposed multi-state research experiment - (MD, MN, WI, CT, MI, and NY Participating)

In order to better understand how sampling methods impact results, multiple participants decided to develop a research trial: Simple 2 treatment design with same sampling protocol across each institution.  Organic input (i.e., Worm Power) and/or fumigation (i.e., Basamid). 

Additonal resources for developing research

New database tools for use in analysis possibly developing at NC State University.  Wei Shi will share with group if available. 

Other areas to develop future research studies 

Identify what regions of the soil are important.

•             Pesticide inputs
•             Drought tolerance
•             Effluent Irrigation – Recycled Water
•             Beneficial vs. Detrimental vs. Neutral

Funding Opportunities

General group discussion on potential avenues for funding.  Some of the major topics covered included.

CPPM Webinar on April 9 – Tough for preliminary nature of the microbiome project

•             Strategic tasks – Improving community health
•             Biocontrol Introduction – Soil Health

Separate SCRI Project

Block Grants

Northeast IPM

NSF grant – Breeding, Genomes,

AFRI grants – Tough for Turf projects

CARE – Critical Agricultural Research and Extension projects

Outreach and Extension - Pesticide Regulations

Organic management practices vs. Conventional – Microbial Community Responses related to management

Sports Turf – Impcat of field management on small kids utilizing fields

Critical Steps in Planning/Developing Funding Proposals

• What are the real-world questions we are trying to answer?  Engage with sharp minded practitioners to broadcast
• Survey developed to understand practitioner knowledge of microbial groups - Plan to engage with stakeholders to better understand stakeholder needs moving forward.
• Identify Key Management practices utilized by different practitioner groups (i.e., Landscape contractors, golf course superintendents, sports turf managers, etc.)
• Coordinated fashion for achieving preliminary data.  Many of the studies discussed have been designed to get preliminary data

Outputs:  One of the first projects developed between participants Roberts and Crouch was aimed at understanding the changes in the microbial communities associated with the National Mall turfgrass restoration project in Washington, DC.  In 2017, Crouch et al. published a manuscript outlining the impacts of the renovation on the bacterial community of the soil at the National Mall both pre and post-renovation. 

Crouch, J.A., Carter, Z., Ismaiel, A. and Roberts, J.A.  2017.  The US National Mall microbiome:  A census of Rhizosphere bacteria inhabiting landscape turf.  Crop Science 57: S341-S348.

Doherty, J.R., M. Botti-Marino, J.P. Kerns, and J.A. Roberts.  2017.  Response of phyllosphere associated microbial populations in creeping bentgrass to periodic fungicide applications.  Plant Health Progress 18:44-49.