Diversity Shifts in the Root Microbiome of Cucumber Under Different Plant Cultivation Substrates

Abstract

Application of plant artificial cultivation substrates lead to alteration of rhizosphere environment. Whether this alteration could lead to root microbiome variation was limitedly investigated. This work aims to determine the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates and predict corresponding function of these different root bacterial microbiota. Cucumber root samples cultivated with two artificial cultivation substrates and greenhouse soils were prepared. Subsequently, high throughput sequencing and bioinformatics analysis were applicated to compare the root bacterial diversity of cucumber cultivated in different substrates and their corresponding function. In total, 311,039 sequences were obtained, and they were annotated to 42 operational taxonomic units (OTUs), belonging to 28 genera, 18 families, 12 orders, four classes, and three phyla. The α and β diversity of samples from the two cultivation substrates and greenhouse soils were significantly different. Only 2–3 bacterial species were found to be discrepancy between cucumber root samples from artificial cultivation substrates and from greenhouse soils. The relative abundance of genus Asticcacaulis, Methylophilus, Massilia, Dyella, and Devosia in samples of artificial cultivation substrates was significantly higher than that of soils, while the relative abundance of genus Phenylobacterium, Noviherbaspirillum, and Arenimonas was significantly lower than that of soils. Besides, compared to cucumber root bacterial community cultivated in soils, the abundance of synthetic pathways for flavonoids and flavonols, bile acids, indole alkaloids, lactose, and neolactose increased by 41.6-, 28.7-, 5.9-, and 5.5-fold, respectively, in the bacterial community of the substrate 1-cultivated roots, and the abundance of clavulanic acid, receptor interaction, sesquiterpenoid, bile acid, flavonoid and flavonol, indole alkaloid, lactose, and neolactose synthetic pathways increased by 42.3-, 32.4-, 32.4-, 13.9-, 10.3-, 6.3-, and 5.2-fold, respectively, in the bacterial community of the substrate two-cultivated roots. This paper verified the diversity shifts in the root microbiome of cucumber under different plant cultivation substrates. Besides, the corresponding function difference of these different root bacterial microbiota was predicted. This work would provide theoretical support for discovering microbial resources and building artificial microbial flora.

Effects of different cultivation media on root bacterial community characteristics of greenhouse tomatoes

“…The results indicated that the tomato root tended to recruit the genus that benefited plant’s growth during its continuous growth in different environments. This study also showed that the genera with higher abundance had significant abundance differences in the three cultivation media, similar to differences observed in bacterial colonies in cucumber roots in previous studies ( Zhou et al, 2022 ). For example, the abundance of some facultative anaerobes in soil (such as Aquabacteria , Acidoborax , and Flavobacillium ) ( Dahal et al, 2021 ; Li et al, 2021 ; Liu L. et al, 2021 ) was significantly higher than those in the two substrates.…”

“…According to Venn analysis, the same 79 genera accounted for 68.70, 76.70, and 71.17% of the total genera were existing in soil, substrate 1, and substrate 2 community, respectively. The above results were similar to the characteristic of the cucumber root bacteria community ( Zhou et al, 2022 ). The results indicated that a batch of bacteria colonized on the tomato roots, which were relatively stable in different cultivation media; however, the abundance difference was significant.…”

“…In this study, 79 bacterial genera in tomatoes in different media overlapped with only 3 genera ( Pseudomonas , Methylobacterium , and Sphingomonas ) that were mentioned above. Interestingly, in our previous study, we compared and analyzed the bacterial community in the cucumber roots under different cultivation medium conditions in the same greenhouse as in this study, and 26 common genera were obtained; of which 16 genera were the same as the common genera in tomato roots (except for three genera: Devosia , Bradyrhizobium , and Pseudomonas , most of which did not have any reported effects on plants), and four same common families that could not be identified to genus ( Zhou et al, 2022 ). These phenomena suggest that similar growth environments may produce similar core groups; however, most of the bacterial genera that are potentially beneficial to plants are determined to a greater extent by different plant types.…”

“…Thus, further research in the above field is required to support rhizosphere engineering technology in the transplanting mode in greenhouse agriculture. Previously, we demonstrated the bacterial community characteristics of a typical facility crop cucumber in the substrate and soil ( Zhou et al, 2022 ). In this study, we compared the differences in the root bacterial community of another typical greenhouse crop tomato in the substrate and soil cultivation.…”

Accurate prediction of huanglongbing occurrence in citrus plants by machine learning-based analysis of symbiotic bacteria

“…The plant phytobiome, consisting of the rhizosphere, phyllosphere, and endosphere, harbors diverse microbes that affect plant growth and health ( Berendsen et al., 2012 ; Liu et al., 2019 ; Liu et al., 2020 ). Considerable research has been carried out on the diversity, composition, and function of the phytobiome of various plant species, including rice ( Edwards et al., 2015 ), maize ( Peiffer et al., 2013 ), corn ( Jat et al., 2021 ), soybean ( Zhang et al., 2018 ), cucumber ( Zhou et al., 2022a ), citrus ( Xu et al., 2018 ), and tomato ( Oyserman et al., 2022 ). Microbes inhabiting plant surfaces or internal tissues produce metabolites that support plant growth by regulating physiological processes (e.g., nutrient absorption and pathogen suppression) ( Trivedi et al., 2020 ).…”