Comparative analysis of bacterial diversity in the rhizosphere of tomato by culture-dependent and -independent approaches

Abstract

The microbiome in the rhizosphere-the region surrounding plant roots-plays a key role in plant growth and health, enhancing nutrient availability and protecting plants from biotic and abiotic stresses. To assess bacterial diversity in the tomato rhizosphere, we performed two contrasting approaches: culture-dependent and -independent. In the culture-dependent approach, two culture media (Reasoner's 2A agar and soil extract agar) were supplemented with 12 antibiotics for isolating diverse bacteria from the tomato rhizosphere by inhibiting predominant bacteria. A total of 689 bacterial isolates were clustered into 164 operational taxonomic units (OTUs) at 97% sequence similarity, and these were found to belong to five bacterial phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, and Firmicutes). Of these, 122 OTUs were retrieved from the antibiotic-containing media, and 80 OTUs were recovered by one specific antibiotic-containing medium. In the culture-independent approach, we conducted Illumina MiSeq amplicon sequencing of the 16S rRNA gene and obtained 19,215 high-quality sequences, which clustered into 478 OTUs belonging to 16 phyla. Among the total OTUs from the MiSeq dataset, 22% were recovered in the culture collection, whereas 41% of OTUs in the culture collection were not captured by MiSeq sequencing. These results showed that antibiotics were effective in isolating various taxa that were not readily isolated on antibiotic-free media, and that both contrasting approaches provided complementary information to characterize bacterial diversity in the tomato rhizosphere.

Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota

“…The bacterial communities in the five natural field soils DM, JX, HQ, QS and XC, but not the two commercial soils, mostly overlapped with those of the rhizosphere microbiotas in the different cultivar samples. These results were consistent with previous observations of the rhizosphere microbiota of other tomato cultivars, which were dominated by the bacterial orders Sphingomonadales, Rhizobiales, Xanthomonadales, Burkholderiales, Cytophagales and Sphingobacteriales from the bacterial phyla Proteobacteria, Bacteroidetes, and Acidobacteria [15,25]. The result supported the hypothesis that tomato harbors largely conserved communities of rhizosphere microbes that remain stable among cultivars of tomato and even among the field soils from different sources [24][25][26].…”

“…The rhizosphere microbiota of the plant is mainly dominated by the bacterial phyla Proteobacteria, Bacteroidetes, and Acidobacteria [2,5,19,20]. In tomato, some studies on the community composition of the rhizosphere microbiota have reached the same conclusion using both culture-dependent and culture-independent approaches [15,[22][23][24][25][26]. Qiao et al [26] found that the three most abundant core phyla in the tomato (Solanum lycopersicum cv.…”

“…The results demonstrated that the tomato rhizosphere soil was dominated by the bacterial orders Sphingomonadales, Rhizobiales, Xanthomonadales, Burkholderiales, Cytophagales, and Sphingobacteriales in the phyla Proteobacteria, Bacteroidetes and Acidobacteria [15]. In a comprehensive study of 4 tomato cultivars (S. lycopersicum) from 4 geographically separated greenhouses, Lee et al [25] compared rhizobacterial communities by using culture-dependent and culture-independent approaches, revealing that only 22% of the total OTUs in the MiSeq dataset were recovered in the culture collection and the most dominant phylum in the tomato rhizosphere microbiota was Proteobacteria (78.5%), followed by Actinobacteria (8.5%), Bacteroidetes (3.6%), and Acidobacteria (3.5%). Furthermore, Lee et al [24] examined the microbial communities of three compartments of tomato plants collected from a broad range of geographical distributions.…”

“…The assembly and composition of rhizosphere microbial communities in tomato are affected by soil, plant genotype, and root system architecture [24,25,[27][28][29]. In addition, the effects of pathogens, biocontrol microorganisms, and nutrient amendment on the tomato microbiota have been demonstrated [15,22,23].…”

Testing the two-step model of plant root microbiome acquisition under multiple plant species and soil sources

“…We found an overrepresentation of some Sphingobium and Rhizobium species, suggesting that their abundance could be used as a plant health proxy since we did not observe root rot symptoms in any of our individuals (Satour & Butler 1967). Moreover, in a previous work describing tomato roots microbiomes, Sphingomonas and Sphingobium were detected in more than 50% of the 16S rRNA gene OTUs (Lee et al 2016). Sphingobium has been observed as the dominant genus in tomato roots elsewhere (Pii et al 2016).…”