Microbial Community Structure in Soilless Substrates Used for Nursery Crops

Abstract

Soilless substrates are widely used for plant cultivation. However, little is known about how soilless substrate components, plant growth, or their interactions impact microbial communities in soilless media. The objectives of this study were to analyze microbial communities in typical pine bark substrates used for nursery crop production and determine the impacts of substituting peat with a compost substrate, and planting, on microbial community dynamics over a production cycle. Three soilless substrate mixtures were compared. The substrate mixes consisted of 80:20:0, 80:10:10, and 80:0:20 (volume:volume:volume) ratios of pine bark:peatmoss:leaf compost, respectively. One set of each treatment was planted with a single birch (Betula nigra ‘Cully’) liner and another set was not planted. The treatments (n = 3) were maintained in a nursery production setting, and samples were taken after 0, 1, 2, 3, and 4 months. Bacterial and fungal communities were characterized by sequencing polymerase chain reaction-amplified 16s rRNA genes and internal transcribed spacer regions. Initially, the two substrate mixtures that contained compost had more phyla than the substrate mixture that only contained peat and bark. After 1 month, microbial communities in all treatments contained similar phyla, but at different relative abundances based on the amount of compost they contained. Over time, Nitrosomonadaceae and Acetobacteraceae were the most abundant bacterial families in substrate mixes containing 10% and 20% compost, but they were absent from treatments without compost. The communities were dynamic and changed the most over the first 2 months. Microbial communities and their dynamics were similar between planted and unplanted treatments. Planting had less of an effect on microbial communities than compost amendment. Among the fungal communities, differences were observed based on both compost amendment and plant presence. Ascomycota and Basidiomycota were the most abundant fungal phyla and resembled those originally in the peat and compost, respectively. These findings could be used to understand the importance and dynamics of specific microbial communities present in substrate components and how they develop during greenhouse production.