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ARS Home » Midwest Area » Wooster, Ohio » Application Technology Research » Research » Research Project #435412

Research Project: Understanding the Container Media Microbiome and its Effects on Plant Health

Location: Application Technology Research

Project Number: 5082-21000-018-18-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 15, 2018
End Date: Sep 14, 2023

Objective:
The objective of this research is to analyze microbial community structure in pine bark/peat plant growth media substrates used for nursery crop production and determine the effects of compost amendment on these communities and on plant health.

Approach:
As part of this investigation, substrates made from pine bark, peat and various types of compost will be used in nursery containers and planted with common vegetable and ornamental crops. The plants will be grown in a greenhouse or outdoor planting area, in a randomized plot block design. Replicate plants will be sacrificed at each sampling period and the total media in a pot removed, mixed and analyzed periodically from various treatments. Plant growth will be assessed regularly by measuring plant height, leaf number, plant weight, root weight, flower or product yield and size. Representative samples will be taken from containers throughout the growing season and chemical and physical properties will be measured. The microbial consortia in the potting media samples will be characterized using nucleic acid based high-throughput ribosomal RNA gene (bacteria) and intergenic spacer region (fungi) sequencing. DNA will be extracted using available soil DNA extraction kits and purified using column gel purification to remove PCR interfering humic acids. Universal, as well as population-specific, bacterial and fungal PCR primers will be used to amplify, identify and quantify individual ribotypes within each sample. The obtained sequences will be compared to those in 16S gene and ITS gene sequence databases. The data will be processed using an open-source bioinformatics pipeline developed by the cooperator. Microbial communities overt time and in different treatments will be compared using cluster analysis and seqeunces that correlate to specific plant growth responses will be identified. To investigate disease suppression, powdery mildew or other pathogen, will be inoculated onto healthy plants. The severity of disease as a function of the amount of compost and the microbial communities in the media will be investigated. Results will be used to understand how communities change throughout the growing season, with compost amendment and plant growth, whether correlations exist between members of microbial communities and growth response, and if specific groups could be used to assess substrate quality or used to improve disease suppression. The effectiveness of bio stimulants and their similarity to members of beneficial communities identified in potting media and composts will also be investigated.