Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media

Abstract

Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.

In-Depth Observation on the Microbial and Fungal Community Structure of Four Contrasting Tomato Cultivation Systems in Soil Based and Soilless Culture Systems

“…Several research papers have associated these favorable effects on the microbiome of the soil and the rhizosphere of the plant (Tu et al, 2006;El-Yazeid and Abou-Aly, 2011;Bona et al, 2018;Sellitto et al, 2019). In addition, it has been proven that temporal, biotic and abiotic components have considerable influence on the bulk microbiome and the rhizosphere of tomatoes (Maloney et al, 1997;Grunert et al, 2016a;Grunert et al, 2019). In the presented study, we cultivated tomato plants grown in soil based and soilless culture systems.…”

“…Total DNA was extracted from the growing medium samples using the Power Soil ® DNA Isolation Kit (MoBio Laboratories Inc., Carlsbad, CA, United States). Five hundred milligrams were used from the bulk as previously described ( Grunert et al, 2019 ). High-throughput amplicon sequencing of the V3 – V4 hypervariable region ( Klindworth et al, 2012 ) was performed with the Illumina MiSeq platform (LGC Genomics GmbH, Berlin, Germany) and the following primers were used 338f and the 518 r ( Øvreås et al, 1997 ).…”

“…Variations in tomato cultivation systems and nitrogen dynamics were computed using a repeated measures mixed in SAS (version 9.4, SAS Institute, Cary, United States). P-values for Pearson correlation coefficients and regression coefficients were used to determine significant relations with a significance level of P < 0.05 (Grunert et al, 2019). Multiple Factor Analysis (MFA) was employed to detect how the microbial community composition based on a PLFA analysis and bacterial abundance contributed to the differences between the four different tomato cultivating systems across time points.…”

“…Chao and Bray-Curtis indices were used to check dissimilarity and find out the impact of experimental factors on microbial community composition. Principal Coordinate Analysis (PCoA) visualized the differences between samples, using the vegan package in R (Oksanen et al, 2007), and stratified permutational multivariate analysis of variance (PERMANOVA) with 999 permutations were run to display the significance of each covariate on the microbial community of the bulk soil (Grunert et al, 2019). ANOVA was applied to reveal whether the distribution of the genera was different between treatments (Oksanen et al, 2007).…”

The rhizosphere microbiome: functions, dynamics, and role in plant protection

“…Besides the plant genotype (Marschner et al 2001) and the developmental stage (Micallef et al 2009;Chaparro et al 2014), the soil type is also amongst the main drivers shaping the rhizosphere microbiome structure (Liesack et al 1997;Grayston et al 1998;Micallef et al 2009). Nutrition (Grunert et al 2019), carbon level, soil pH, biogeography, and microbial interactions also shape the bacterial diversity and its abundance in the rhizosphere (Lauber et al 2009;Andrew et al 2012;Marques et al 2014;Wei et al 2015;Qiao et al 2017).…”