Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering

Zonation of bulk and rhizosphere soil bacterial communities and their covariation patterns along the elevation gradient in riparian zones of three Gorges reservoir, China

Zonation is a typical pattern of soil distribution and species assembly across riparian habitats. Microorganisms are essential members of riparian ecosystems and whether soil microbial communities demonstrate similar zonation patterns and how bulk and rhizosphere soil microorganisms interact along the elevation (submergence stress) gradient remain largely unknown. In this study, bulk and rhizosphere (dominant plant) soil samples were collected and investigated across riparian zones where the submergence stress intensity increased as the elevation decreased. Results showed that the richness of bacterial communities in bulk and rhizosphere soil samples was significantly different and presented a zonation pattern along with the submergence stress gradient. Bulk soil at medium elevation that underwent moderate submergence stress had the most abundant bacterial communities, while the species richness of rhizobacteria at low elevation that experienced serious submergence stress was the highest. Additionally, principal coordinate analysis (PCoA) and significance tests showed that bulk and rhizosphere soil samples were distinguished according to the structure of bacterial communities, and so were bulk or rhizosphere soil samples from different elevations. Redundancy analysis (RDA) and Mantel test suggested that bacterial communities of bulk soil mainly relied on the contents of soil organic matter, total carbon (TC), total nitrogen (TN), sodium (Na), calcium (Ca) and magnesium (Mg). Contrastingly, the contents of Na and Mg were the main factors explaining the variation in rhizobacterial community composition. Correlation and microbial source tracking analyses showed thatthe relationship of bulk and rhizosphere soil bacteria became much stronger, and the rhizosphere soil may get more bacterial communities from bulk soil with the increase in submergence severity. Our results suggest that the abiotic and biotic components of the riparian ecosystem are closely covariant along the submergence stress gradient and imply that the bacterial community may be a key node linking soil physiochemical properties and vegetation communities.

Response of abundance, diversity, and network of rhizosphere fungal community to monoculture of cut chrysanthemum

The effects of different monoculture years on rhizosphere fungal communities (abundance, diversity, structure, and cooccurrence network) of cut chrysanthemum were determined. Three different monoculture years were (i) planting for only 1 year (Y1), (ii) continuous monoculture for 6 years (Y6), and (iii) continuous monoculture for 12 years (Y12). Compared to the Y1 treatment, the Y12 treatment significantly decreased the rhizosphere fungal gene copy numbers but increased the potential pathogen Fusarium oxysporum (P < 0.05). Both the Y6 and Y12 treatments significantly increased fungal diversity (Shannon and Simpson indices), but Y6 had great potential to enhance fungal richness (Chao1 index) relative to the Y12 treatment. Monoculture treatments decreased the relative abundance of Ascomycota but increased that of Mortierellomycota. Four ecological clusters (Modules 0, 3, 4, and 9) were observed in the fungal cooccurrence network across the Y1, Y6, and Y12 treatments, and only Module 0 was significantly enriched in the Y12 treatment and associated with soil properties (P < 0.05). RDA (redundancy analysis) and Mantel analysis showed that soil pH and soil nutrients (organic carbon, total nitrogen, and available phosphorus) were the key factors affecting fungal communities during monoculture of cut chrysanthemum. Overall, the changes in soil properties were responsible for shaping rhizospheric soil fungal communities in long-term rather than short-term monoculture systems. KEY POINTS: • Both short- and long-term monocultures reshaped the soil fungal community structure. • Long-term monoculture enhanced the network complexity of the fungal community. • Soil pH, C and N levels mainly drove modularization in the fungal community network.