Bacterial community dynamics of tomato hydroponic greenhouses infested with hairy root disease

Abstract

The rhizosphere is a complex ecosystem consisting of microbes in the interface between growth medium and plant roots, which affects plant productivity and health. This is one of the few studies analysing bacterial communities present in the rhizosphere of hydroponically grown plants. Tomato grown under hydroponic conditions is prone to hairy root disease (HRD) that is caused by rhizogenic Agrobacterium biovar 1 strains. In this study, using high-throughput amplicon sequencing of partial ribosomal RNA (rRNA) genes, we aimed to characterize bacterial communities in rockwool samples obtained from healthy or HRD-infested tomato during an entire growing season. Alpha diversity of rockwool increased in direct relation with time and samples obtained from healthy greenhouses presented a significantly lower alpha diversity than those from HRD-infested greenhouses. Beta diversity showed that bacterial community composition changed throughout the growing season. Amplicon Sequence Variants (ASVs) identified as rhizogenic Agrobacterium bv. 1 were more prevalent in HRD-infected greenhouses. Conversely, ASVs identified as Paenibacillus, previously identified as biocontrol organisms of rhizogenic agrobacteria, were more prevalent in healthy greenhouses. Altogether, our study greatly contributes to the knowledge of bacterial communities in rockwool hydroponics.

Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System

“…Our data revealed that tomato core microbiota was dominated by phyla Proteobacteria, Actinobacteria, and Firmicutes in the substrate, rhizosphere, and fruit samples; comparable bacterial diversity has been reported in numerous studies with tomato plants cultivated in soil-based and SCSs [20,27,[63][64][65][66][67][68][69][70]. Together, these findings suggest that, regardless of the cultivation system, tomato plants have evolved a close biological interaction with members of Proteobacteria, Actinobacteria, and Firmicutes.…”

“…Substrate samples (~5 g) were collected from root-free zones (>1 cm from roots) as previously described [ 18 , 19 ]. Rhizosphere samples (~2 g) were collected ~10 cm away from the stem; roots were shaken to remove loose substrate particles, and only bacterial communities associated within ~1 mm of the root surface remained [ 18 , 26 , 27 ]. A tomato sample was composed of three fruits collected from a single cluster harvested at the pink maturity stage and grade 4, according to the USDA color classification requirements [ 28 ].…”

Exploring the Rhizosphere Microbiome of Hydroponically Grown Leafy Greens

“…We aimed to develop a root scraping procedure that would allow us to maximize the amount of bacterial and fungal DNA in our samples while minimizing the amount of plant DNA. The methods from existing literature on plant rhizospheres included putting the roots straight into DNA isolation tubes or putting the rockwool medium into DNA isolation tubes (Vargas et al, 2021). We observed extremely low DNA concentrations with both of these methods.…”

“…The first objective for our study is to investigate the complete rhizosphere microbiome for each of our four microgreens. The standard procedure for isolating rhizospheric DNA from hydroponically grown plants includes harvesting root material and substrate growing medium like rockwool (Vargas et al, 2021). In an effort to reduce complexity and cost of this procedure, our second objective is to determine the effectiveness of scraping the roots of microgreens in isolating rhizospheric DNA.…”

Endophytic Paenibacillus polymyxa LMG27872 inhibits Meloidogyne incognita parasitism, promoting tomato growth through a dose-dependent effect

“…RS BABA-induced resistance has previously been described to be effective in tomato against M. incognita ( Devran and Baysal, 2018 ) and M. javanica ( Oka et al, 1999 ). Paenibacillus polymyxa displayed antimicrobial activity against many other plant pathogens, such as hairy root disease, caused by rhizogenic Agrobacterium in tomato ( Vanlommel et al, 2020 ; Vargas et al, 2021a , b , and antifungal activity in peanuts ( Arachis villosa ) ( Costa et al, 2021 ) and hemp ( Cannabis sativa ) ( Mahmoud and Jabaji, 2021 ). Other P. polymyxa varieties such as NMA1017 have shown to exert biocontrol activity against Rhizoctonia solani on maize ( Zea mays ) in vitro , while pot experiments with bean ( Phaseolus vulgaris ) exhibited the growth of fungal pathogens such as R. solani and Pythium ultimum ( Chávez-Ramírez et al, 2020 ).…”