Structure and diversity of bacterial community in different niches of garden plant Ligustrum lucidum Ait.

Abstract:

[Objective] Ligustrum lucidum Ait., a plant with landscaping and medical values as well as an excellent host plant for the resource insect Ericerus pela, is widely distributed in China. This study aims to investigate the community structure, species composition, and diversity of bacteria in four niches (leaf, stem, root, and rhizosphere soil) of L. lucidum, and to lay a foundation for the interaction between L. lucidum and its associated microbiota, so as to provide a scientific basis for exploiting and utilizing endophytic and rhizospheric bacterial resources. [Methods] The leaf, stem, root, and rhizosphere soil samples of L. lucidum were collected, and the V5-V7 region of bacterial 16S rRNA gene was sequenced with the Illumina MiSeq platform. The bacterial community structure, species composition, and function in different niches were compared with bioinformatics tools. [Results] The high-throughput sequencing generated 168 229 valid sequences for the four samples of L. lucidum. A total of 977 OTUs were annotated, belonging to 23 phyla, 54 classes, 138 orders, 227 families, and 399 genera. The bacterial community diversity decreased gradually in the order of rhizosphere soil, root, stem, and leaf, with the Shannon indexes of 4.514, 3.856, 2.704, and 1.908, respectively. The β-diversity analysis indicated that there were significant differences in bacterial community structure among four niches (R=0.842 6, P<0.05). The bacterial community structure was similar between leaf and stem (R=0.481 5, P>0.05) as well as between root and rhizosphere soil (R=0.888 9, P>0.05). At the level of phylum, Proteobacteria and Actinobacteriota were dominant in leaf, stem, and root, while Chloroflexi had the highest relative abundance in rhizosphere soil. The dominant genera mainly included Rhodococcus, Massilia, Sphingomonas, Burkholderia, Bradyrhizobium, and Acidothermus, some of which, like Bradyrhizobium and Burkholderia, were plant probiotics. Chemoheterotrophy was the predominant function in each niche. The bacterial community in the aboveground part (leaf and stem) mainly played a role in carbon and hydrogen cycle, while that in the underground part (root and rhizosphere soil) mainly played a role in nitrogen cycle. [Conclusion] The bacterial community diversity in different niches of L. lucidum showed a selective filtration mechanism from bottom to top. The niche differentiation of bacterial community structure was obvious in different samples, and plant compartment specificity existed in species composition. There were a variety of plant probiotics in L. lucidum-associated microbiota, which were worthy of further study and utilization.