Temporal Variability in the Rhizosphere Bacterial and Fungal Community Structure in the Melon Crop Grown in a Closed Hydroponic System

Yu-Pin Lin,Hsiao-Feng Lo,Hussnain Mukhtar,Chiao-Ming Lin,Min-Chun Ko,Shu-Jen Wang

doi:10.3390/agronomy11040719

Abstract

Microbes can establish a pathogenetic or symbiotic relationship with plants in soil and aquatic ecosystems. Although change in bacterial and fungal community in soil and their interaction with plants have been widely studied, little is known about their community structure in hydroponic systems across plant growth stages under different nutrient treatments. This study used next-generation sequencing analysis to assess the temporal changes in melon rhizosphere bacterial and fungal community structure across six different nutrient treatments. We found significant changes in the microbial community composition (especially for bacteria) between growth stages (R = 0.25–0.63, p < 0.01) than nutrient treatments. Proteobacteria dominated the bacterial community at the phylum level across melon growth stages (59.8% ± 16.1%). The genera Chryseobacterium, Pseudomonas, and Massilia dominated the rhizosphere in the flowering and pollination stage, while Brevibacillius showed the highest relative abundance in the harvesting stage. However, the rhizosphere was dominated by uncultured fungal taxa, likely due to the application of fungicides (Ridomil MZ). Further, linear regression analysis revealed a weak influence of bacterial community structure on melon yield and quality, while fruit weight and quality moderately responded to Mg and K deficiency. Nevertheless, the relative abundance of bacterial genus Chryseobacterium in the vegetative stage showed a strong correlation with fruit weight (R2 = 0.75, p < 0.05), while genera Brevibacillus, Lysobacter, and Bosea in late growth stages strongly correlated with fruit sweetness. Overall, temporal variability in the microbial (especially bacterial) community structure exceeds the variability between nutrient treatments for the given range of nutrient gradient while having little influence on melon yield.

Highlights

The use of closed hydroponic systems (CHS) for fruit and vegetable production has become widespread in recent decades because of its many advantages over soil cultures [1,2]
Our study found that the major bacteria in nutrient solutions changed to the Brevibacillus group at the harvesting stage
Plant-associated bacterial community was shown to be highly dynamic over time and developmental stage

Summary

Introduction

The use of closed hydroponic systems (CHS) for fruit and vegetable production has become widespread in recent decades because of its many advantages over soil cultures (open loop systems) [1,2]. Microbes are capable of detecting the plant host and colonizing the rhizosphere, and plants are capable of recognizing microbe-derived compounds and initiating their defense and growth strategies depending on the type of microorganisms encountered [17,18]. This change in communication results in different plant–microbe interactions ranging from pathogenesis to symbiosis [19]. The addition of plant growth-promoting microorganisms (PGPMs) has been reported to improve plant quality and productivity, probably by stabilizing the microbial community in the root zone, competing with pathogens, and enhancing plant tolerance to stress conditions [20,21]. The contamination of a CHS with ammonia oxidizers and denitrifiers can potentially reduce the amounts of ammonia and nitrate that are available for plant growth [22,23,24]

Methods

Results

Conclusion