Effects of single- and mixed-bacterial inoculation on the colonization and assembly of endophytic communities in plant roots

Abstract

The introduction and inoculation of beneficial bacteria in plants have consistently been considered as one of the most important ways to improve plant health and production. However, the effects of bacterial inoculation on the community assembly and composition of the root endophytic microbiome remain largely unknown. In this study, 55 strains were randomly isolated from tomato roots and then inoculated into wheat seeds singly or in combination. Most of the isolated bacterial strains showed an ability to produce lignocellulose-decomposing enzymes and promote plant growth. The results demonstrated that bacterial inoculation had a significant effect on the wheat root endophytic microbiome. The wheat root samples inoculated with single-bacterial species were significantly separated into two groups (A and B) that had different community structures and compositions. Among these, root endophytic communities for most wheat samples inoculated with a single-bacterial strain (Group A) were predominated by one or several bacterial species, mainly belonging to Enterobacterales. In contrast, only a few of the root samples inoculated with a single-bacterial strain (Group B) harbored a rich bacterial flora with relatively high bacterial diversity. However, wheat roots inoculated with a mixed bacterial complex were colonized by a more diverse and abundant bacterial flora, which was mainly composed of Enterobacterales, Actinomycetales, Bacillales, Pseudomonadales, and Rhizobiales. The results demonstrated that inoculation with bacterial complexes could help plants establish more balanced and beneficial endophytic communities. In most cases, bacterial inoculation does not result in successful colonization by the target bacterium in wheat roots. However, bacterial inoculation consistently had a significant effect on the root microbiome in plants. CAP analysis demonstrated that the variation in wheat root endophytic communities was significantly related to the taxonomic status and lignocellulose decomposition ability of the inoculated bacterial strain (p < 0.05). To reveal the role of lignocellulose degradation in shaping the root endophytic microbiome in wheat, four bacterial strains with different colonization abilities were selected for further transcriptome sequencing analysis. The results showed that, compared with that in the dominant bacterial species Ent_181 and Ent_189 of Group A, the expression of lignocellulose-decomposing enzymes was significantly downregulated in Bac_133 and Bac_71 (p < 0.05). In addition, we found that the dominant bacterial species of the tomato endophytic microbiome were more likely to become dominant populations in the wheat root microbiome. In general, our results demonstrated that lignocellulose-decomposing enzymes played a vital role in the formation of endophytes and their successful colonization of root tissues. This finding establishes a theoretical foundation for the development of broad-spectrum probiotics.

Impact of conservation tillage on wheat performance and its microbiome

“…Main bacterial genera in roots were Lechevalieria , Promicromonospora , Actinoplanes , Streptomyces , and Pseudomonas . These genera belong to Actinomycetales or Pseudomonadales orders, which are well known to colonize roots of different crops such as tomato and wheat ( Aleklett et al., 2022 ; Zhang et al., 2022 ). Furthermore, Streptomyces and Pseudomonas have been described for their plant growth-promoting potential ( Romano et al., 2020 ; Chouyia et al., 2022 ; Quiroz-Carreño et al., 2022 ).…”

Interaction studies of Serendipita indica and Zhihengliuella sp. ISTPL4 and their synergistic role in growth promotion in rice

“…In general, plant–microorganism interactions in the rhizospheric region are critical for nutrient uptake, stress alleviation, and plant development ( Ali et al., 2022 ). The inoculation and introduction of beneficial bacteria into plants has long been regarded as the most important method of improving plant health and productivity ( Zhang et al., 2022 ). This study examined the effects of S. indica and Z. sp.…”

Genomics assisted functional characterization of Bacillus velezensis E as a biocontrol and growth promoting bacterium for lily

“…Each treatment consisted of three replicates, and each replicate consisted of three plantlets. The root colonization of strain E was detected using previously reported methods with minor modifications ( Thomas, 2004 ; Valdameri et al, 2015 ; Zhang et al, 2022 ). To evaluate the epiphytic colonization ability of strain E, 1 g of the lily root from plantlets was collected, cleaned with sterilized water to remove the peat on the root surface, and then agitated in a vortex for 1 min in 5 ml of sterilized water containing 0.03% Tween 80 seven days after inoculation.…”