Response of bacterial community structure to different ecological niches and their functions in Korean pine forests

Abstract

A healthy plant microbiome is diverse, taxonomically-structured, and gives its plant host moderate advantages in growth, development, stress tolerance, and disease resistance. The plant microbiome varies with ecological niches and is influenced by variables that are complex and difficult to separate from each other, such as the plant species, soil, and environmental factors. To explore the composition, diversity, and functions of the bacterial community of Korean pine forests, we used high-throughput sequencing to study five areas with different forest ages from June to October 2017 in northeast China. We obtained 3,247 operational taxonomic units (OTUs) based on 16S rRNA gene sequencing via an Illumina Hi-seq platform. A total of 36 phyla and 159 known genera were classified. The Shannon index of the bacterial community from the rhizospheric soil was significantly higher (p < 0.01, n = 10) than that of the root tips. Beta-diversity analysis confirmed that the bacterial community of the rhizospheric soil was significantly different (p < 0.001) from the root tips. Nine bacterial phyla were dominant (relative richness > 1%) in the rhizospheric soil, but there were six dominant phyla in the root tips. Proteobacteria was the core flora in the root tips with a relative abundance of more than 50%. It is known that the formation of bacterial communities in the rhizospheric soil or the root is mainly caused by the processes of selection, and we found a relatively high abundance of a few dominant species. We further analyzed the correlations between the bacterial community from the rhizospheric soil with that of the root tips, as well as the correlations of the bacterial community with soil physicochemical properties and climate factors. We used Functional Annotation of the Prokaryotic Tax (FAPROTAX) to predict the functions of the bacterial community in the rhizospheric soil and root tips. Five related phototrophic functions, nine nitrogen cycle functions, two related chemoheterotrophic functions, and two others were predicted. The abundance of the bacteria phyla performing relevant functions was different in the rhizospheric soil than in the root tips. These functions were significantly influenced by the contents of nitrogen, phosphorus, and potassium in the soil habitat. The bacterial composition and functions in the rhizospheric soil and root tips of Korean pine were analyzed, and the results demonstrated the importance of soil and plant species on the bacterial community in the below ground plant microbiome.

Fungal–Bacterial Networks in the Habitat of SongRong (Tricholoma matsutake) and Driving Factors of Their Distribution Rules

“…Soil can be seen as a factor that directly affects microbial communities and the structures within them [ 26 , 27 ]. T. matsutake in Japan appears in nutrient-poor soils, such as granite, chert and sandstone, which are acidic, with pH values of 4.5–5.0 [ 28 ].…”

Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds

“…FAPROTAX was reported as a helpful tool to highlight functions related to biogeochemical dynamics especially on N and C cycles [ 50 ]. It was, for instance used in Ji et al (2022), to predict bacterial functions in Korean pine root tips and rhizosphere soil [ 51 ]. Tax4fun is suitable to target changes in gene expressions or in potential enzymatic activities.…”

Soil microbiomes of hardwood‐ versus pine‐dominated stands: Linkage with overstory species

“…Their most apparent component—the woody overstory—is actually the least diverse with respect to numbers of species, whereas the plant community of smallest physical stature—the herbaceous layer—can represent 80%–90% of forest plant diversity (Gilliam, 2007, 2014). Less apparent still is the biotic community of highest diversity—the forest microbiome (Mishra et al, 2020; Uroz et al, 2016), especially that of soil (Ji et al, 2022). Estimates have been made that 1 g of soil can support 10 10 –10 11 bacteria representing between 6000 and 50,000 species (van der Heijden et al, 2008).…”

“…Using a meta‐analysis of published studies, Liu et al (2022) compared rhizosphere versus bulk soil and found higher microbial biomass and essential plant nutrients in the rhizosphere, especially in infertile soils. Ji et al (2022) demonstrated the importance of soil fertility and plant species on soil bacterial communities in Korean pine forests. Thus, despite the contention of Fierer and Jackson (2006) that edaphic factors primarily affect soil microbiomes, it is clear that tree species can exert a profound influence on composition and biomass of soil microbial communities, especially at finer spatial scales (Prescott & Grayston, 2013).…”