Annual/Termination Reports:

[10/19/2017] [04/28/2018]

Report Information

Participants

Joseph Roberts, University of Maryland
Paul Koch, University of Wisconsin-Madison
John Inguagiato, University of Connecticut
Michelle DaCosta, University of Massachusetts-Amherst
James Murphy, Rutgers University
Bruce Clarke, Rutgers University
Eric Watkins, University of Minnesota
Matthew Elmore, Rutgers University
Kevin Morris, National Turfgrass Federation
Scott Warnke, USDA-ARS
Jenny Koa Kniffen, Cornell University
Emily Merewitz, Michigan State University
Gerald Miller, University of Missouri
Geoffrey Rinehart, National Arboretum
Wei Shi, North Carolina State University
Mary Owen, University of Massachusetts-Amherst
Jason Lanier, University of Massachusetts-Amherst
Christine Strand, University of Massachusetts-Amherst
Jo Anne Crouch, USDA-ARS
Emma Wallace, USDA-ARS
Joseph Doherty, University of Maryland
Mark Carroll, University of Maryland
Hector Bravo, University of Maryland

Brief Summary of Minutes

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

 

 

Accomplishments

<p>Outputs: &nbsp;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.&nbsp; 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.&nbsp;</p>

Publications

<p><em>Crouch, J.A., Carter, Z., Ismaiel, A. and Roberts, J.A.&nbsp; 2017.&nbsp; The US National Mall microbiome:&nbsp; A census of Rhizosphere bacteria inhabiting landscape turf.&nbsp; Crop Science 57: S341-S348.</em></p><br /> <p><em>Doherty, J.R., M. Botti-Marino, J.P. Kerns, and J.A. Roberts.&nbsp; 2017.&nbsp; Response of phyllosphere associated microbial populations in creeping bentgrass to periodic fungicide applications.&nbsp; Plant Health Progress 18:44-49.</em></p>

Impact Statements

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Report Information

Participants

Joseph Roberts, University of Maryland; Paul Koch, University of Wisconsin – Madison; John Inguagiato, University of Connecticut; Emma Buczkowski, University of Wisconsin – Madison; Bruce Clarke, Rutgers University; Dan Dinelli, North Shore Country Club; Joe Doherty, University of Maryland; Matt Elmore, Rutgers University; Glen Groben, Rutgers University; Kurt Hockemeyer, University of Wisconsin – Madison; Jerry Kershasky, Reinders Distribution; Lee Miller, University of Missouri; Michael Millican, University of Wisconsin – Madison; James Murphy, Rutgers University; Florence Sessoms, University of Minnesota; Eric Watkins, University of Minnesota; Emily Merewitz, Michigan State University; Kevin Morris, National Turfgrass Evaluation Program; Jenny Kao-Kniffin, Cornell University; Michelle DaCosta, University of Massachusetts-Amherst, Ning Zhang, Rutgers University

Brief Summary of Minutes

Brief Summary of Minutes of Annual Meeting

The participants listed met at The Pyle Center on the University of Wisconsin – Madison campus in Madison, WI on April 13^th, 2017. The meeting schedule was as follows:

8:30 – 9:15 AM – Dr. Thea Whitman (UW – Madison): An Introduction to the Soil Microbiome from a Soil Biologist’s Perspective

9:15 – 10:00 AM – Group discussion with Dr. Whitman related to how soil microbiome research can be converted into applicable management recommendations for turfgrass managers.

10:15 – 11:15 AM – Dan Dinelli (North Shore Country Club): Putting the Turf Phytobiome in Practice From a Turf Manager’s Perspective

12:15 – 1:15 PM – Discussion on group project updates and potential future funding avenues

• Potential turf phytobiome funding agencies discussed
  
  
  
  • Crop Protection and Pest Manaagement (CPPM)
  
  
  • United States Golf Association
  
  
  • NSF Plant BIO
  
  
  • NSF Water Energy Food Nexus
  
  
  • Organic/soil health initiatives (both public and private)
  
  
  • The Lawn Institute
  
  
  • Wadsworth Institute
  
  
  • OJ Noer Foundation
  
  
  
  


• Also discussed the need to acquire preliminary data to include in future grant proposals and the need to reach out to non-turf scientists to expand the breadth of expertise in our phytobiome research


• Group project update
  
  
  
  • Participating institutions: Maryland, Minnesota, Wisconsin, Connecticut, Michigan, and New York
  
  
  • All participating institutions conducted the experiment and collected the samples in 2017 and placed into a -20°C or -80°C to await extraction
  
  
  • We initiated a multi-state field study in collaboration with scientists from Maryland, New York, Michigan, Connecticut, and Wisconsin. The objective of this study is to determine optimum sampling procedures for turfgrass microbiome research studies. We established a perennial ryegrass turf (cultivar ‘Stellar 3GL’). Once established, plots were mowed once each week at 5.1 cm with clippings returned. Fertilizer was applied using a granular source (18-5-9).  The first application occurred 2 weeks post germination and subsequent applications were 24.4 kg N ha^-1 monthly following first application.  Subsequent applications of 24.4 kg N ha^-1 occurred at 42 d, 70 d, and 98 d post germination. Acclaim Extra (1.46 L ha^-1) in a spray solution with nonionic surfactant (0.25% v/v) was applied approximately 4 weeks after seed germination for crabgrass control and Speedzone (3.5 L ha^-1) was applied approximately 5 weeks after germination for broadleaf weed control.
  
  
  • We established two treatments: (1) microbial inoculant (Worm Power) and (2) no treatment. The study was arranged as a randomized complete block design with four replications. Plots size was 1.83 m x 1.83 m with a 0.3 m border between plots. Microbial inoculant (Worm Power) was applied at 50.9 L ha^-1 at 28, 56, and 84 days after seedling emergence. Untreated plots did not receive an application. Soil samples (1.9 cm diameter by 5.0 cm depth) were taken from each plot (8 sub-samples per individual plot) prior to seeding, and then again just prior to initial microbial inoculant application and then again 56 and 112 days post-emergence. Each soil core was sectioned to remove foliar material and the rhizosphere portion of each core will be used for environmental DNA extraction at the conclusion of the study.  Foliar tissue was removed by clipping the tissue at the chlorophyll line, placing in a coin envelope, and storing at -20 C for later testing. Partitioned rhizosphere samples were stored at -80 C before extraction. Turf performance was evaluated every 14 days for quality (1 to 9 scale; 9 = best), NDVI, and disease development. Clipping yield was assessed at 8 and 16 weeks post emergence.
  
  
  • All participating institutions agreed to repeat the experiment in 2018
  
  
  • The goal of this project is to create a standardized method for analyzing the turfgrass phytobiome. Currently UW-Madison employs a couple extra steps during the soil extraction procedure to analyze only soil that is most tightly adhered to the turfgrass root. No other institution conducts these additional steps and UW will compare their procedure with the Maryland procedure to see if any differences in microbiome results are observed.
  
  
  • By the fall of 2018 a standardized sample handling and extraction procedure should be in place and all the samples from 2017 and 2018 can be extracted and prepared for analysis.
  
  
  
  

1:15 – 3:00 PM – Research Updates from Participating Institutions

• University of Wisconsin – Madison - Michael Millican


• University of Minnesota – Florence Sessoms


• University of Maryland – Joe Doherty


• Rutgers University - Glenn Groben


• Rutgers University – Matt Elmore


• University of Connecticut – John Inguagiato


• University of Missouri – Lee Miller

Reinders Distribution – Jerry Kershasky

Accomplishments

<p>Outputs:</p><br /> <p>The multistate group project will provide a nice overview of the variability of soil turfgrass microbiomes across a large span of the Northeastern and Midwestern United States over a 2-year span. The data collected from this project will be submitted to a peer-reviewed journal. See prior update for more detailed information.</p><br /> <p>Funding of turf phytobiome research is difficult because the immediate applicability is not always clear and the sequencing and bioinformatics is expensive. However we continued to discuss potential funding avenues and brainstormed both public and private funding sources that can contribute to conducting this research.</p><br /> <p>The focus of the morning portion of the meeting was on applying turf phytobiome results for the end user. While there is no single method to accomplish this, the discussion was beneficial in developing studies and analyzing the results in a manner that will be beneficial for turfgrass managers.</p>

Publications

Impact Statements

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