Bacterial Community Structure of Pinus Thunbergii Naturally Infected by the Nematode Bursaphelenchus Xylophilus

Abstract

Pine wilt disease (PWD) caused by the nematode Bursaphelenchus xylophilus is a devastating disease in conifer forests in Eurasia. However, information on the effect of PWD on the host microbial community is limited. In this study, the bacterial community structure and potential function in the needles, roots, and soil of diseased pine were studied under field conditions using Illumina MiSeq coupled with Phylogenetic Investigation of Communities by Reconstruction of Unobserved states (PICRUSt) software. The results showed that the community and functional structure of healthy and diseased trees differed only in the roots and needles, respectively (p < 0.05). The needles, roots, and soil formed unique bacterial community and functional structures. The abundant phyla across all samples were Proteobacteria (41.9% of total sequence), Actinobacteria (29.0%), Acidobacteria (12.2%), Bacteroidetes (4.8%), and Planctomycetes (2.1%). The bacterial community in the healthy roots was dominated by Acidobacteria, Planctomycetes, and Rhizobiales, whereas in the diseased roots, Proteobacteria, Firmicutes, and Burkholderiales were dominant. Functionally, groups involved in the cell process and genetic information processing had a higher abundance in the diseased needles, which contributed to the difference in functional structure. The results indicate that PWD can only affect the host bacteria community structure and function in certain anatomical regions of the host tree.

The Impact of Pine Wood Nematode Infection on the Host Fungal Community

“…macroporum genera in the needles of diseased trees in our study. Moreover, our previous study showed that the abundance of bacteria involved in cellular processes was higher in PWD-affected needles, whereas bacteria with environmental information processing had a higher abundance in healthy needles [ 55 ]. The interaction between fungi and bacteria in PWD-affected needles should not be neglected due to their shared niches.…”

“…Samples were delivered to the lab on ice and kept at −20 °C for subsequent analysis. The soil physical and chemical properties around diseased and healthy trees were published in our previous study by Ma et al [ 55 ] and were cited as supplementary Table S1 .…”

“…Following the manufacturer’s instructions, genomic DNA from the soil was extracted using Soil DNA kits (OMEGA BIO TEK, Norcross, GA, USA), and genomic DNA from the needles and roots was extracted using Plant Genomic DNA Kits (TIANGEN BIOTECH (BEIJING) CO., LTD, Beijing, China). The procedure was previously described in detail [ 55 ]. A NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) was used to measure DNA concentrations.…”

“…To correct differences in sample size, a rarified subset of data with the smallest size of the sample across all datasets were analyzed to calculate the diversity index including α diversity (Shannon), species richness (Chao1), evenness (Shannon evenness), and Good’s coverage to ensure comparable comparison across samples [ 55 ]. One-way ANOVA tests were used to identify differences in community diversity index (richness, α diversity, and evenness) by IBM SPSS Statistics 20.0 software.…”

Taisui TS-2007S, a Large Microbial Mat Discovered in Soil in China

“…The predominant fungal phylum in Taisui TS-2007S was Ascomycota (relative abundance 87.43%), and the predominant genera were Cyphellophora (10.91%), Cordyceps (10.12%), and Anthopsis (9.46%). However, no microbial phyla or genera with such high levels of abundance have been observed in water and soil (Gilbert et al, 2009;Carvajal et al, 2016;Ma et al, 2020). The microbial community structure of Taisui TS-2007S was obviously different from that in the surrounding environment.…”