Friends and Foes: Bacteria of the Hydroponic Plant Microbiome

Abstract

Hydroponic greenhouses and vertical farms provide an alternative crop production strategy in regions that experience low temperatures, suboptimal sunlight, or inadequate soil quality. However, hydroponic systems are soilless and, therefore, have vastly different bacterial microbiota than plants grown in soil. This review highlights some of the most prevalent plant growth-promoting bacteria (PGPB) and destructive phytopathogenic bacteria that dominate hydroponic systems. A complete understanding of which bacteria increase hydroponic crop yields and ways to mitigate crop loss from disease are critical to advancing microbiome research. The section focussing on plant growth-promoting bacteria highlights putative biological pathways for growth promotion and evidence of increased crop productivity in hydroponic systems by these organisms. Seven genera are examined in detail, including Pseudomonas, Bacillus, Azospirillum, Azotobacter, Rhizobium, Paenibacillus, and Paraburkholderia. In contrast, the review of hydroponic phytopathogens explores the mechanisms of disease, studies of disease incidence in greenhouse crops, and disease control strategies. Economically relevant diseases caused by Xanthomonas, Erwinia, Agrobacterium, Ralstonia, Clavibacter, Pectobacterium, and Pseudomonas are discussed. The conditions that make Pseudomonas both a friend and a foe, depending on the species, environment, and gene expression, provide insights into the complexity of plant-bacterial interactions. By amalgamating information on both beneficial and pathogenic bacteria in hydroponics, researchers and greenhouse growers can be better informed on how bacteria impact modern crop production systems.

Keywords: food production; greenhouses; hydroponics; plant growth-promoting bacteria; plant pathogens; plant stress.

Figure 1

Summary of common plant-growth promotion mechanisms exhibited by PGPB. ACC: 1-aminocyclopropane-1-carboxylate; Fe: iron; IAA: Indole-3-acetic acid; ISR: induced systemic resistance; K: potassium; N: nitrogen; NH4: ammonium; NO3: nitrate; PO4: phosphate; VOCs: volatile organic compounds.

Figure 2

A circular phylogram of the pangenome of sixteen Pseudomonas reference strains, eight of which are considered plant growth-promoting (P. protegens, P. migulae, P. jessenii, P. fluorescens, P. chloroaphis, P. putida, P. azotifigens, and P. stutzeri) and eight that are considered phytopathogenic (P. viridiflava, P. syringae, P. savastanoi, P. cichorii, P. avellanae, P. marginalis, P. corrugata, and P. salomonii). The black shading of a cell represents the presence of a gene cluster in the genome of the species. Tables below the phylogram highlight KEGG modules and genes of interest that are enriched in either the PGPB or phytopathogenic species of Pseudomonas.