[Objective] Saprophytic fungi can convert complex organic substances into available components, which is closely related to soil nutrient availability and carbon (C) sequestration. Mortierella has been reported to be substantially enhanced after long-term fertilization in agricultural soils. Studies in the past demonstrated that some species of Mortierella did make important contributions to soil nutrient transformation and availability, and were able to degrade hemicellulose, cellulose and lignin, and hence could directly affect straw decomposition and alter nutrient status of the soil. Furthermore, Mortierella species show great ability to excrete a large volume of polyunsaturated fatty acids, which contained abundant C sources, thus altering the soil microhabitat. It was therefore, presumed that Mortierella inoculants could affect soil microbial communities in part by changing their nutrient uptake, thus indirectly influencing soil nutrient transformation and availability in the soil. However, empirical evidence of the effects of Mortierella inoculants on the soil microbial communities under planting conditions is seldom available. The objective of this study was to explore how indigenous strains of Mortierella affect soil nutrient availability during the process of straw decomposition.[Method] Two strains of Mortierella (Mortierella alpina and Mortierella elongata) were isolated from two types of agricultural soils (red soil and Shajiang black soil) that had been applied with organic manure for decades. A pot experiment, designed to have three treatments, i.e. no inoculation (Control); inoculation with Mortierella alpina (Ma); and inoculation with Mortierella elongata (Me), and three replicates for each treatment, was conducted with the two soils packed in the pots separately and incorporated with straw. Availability of C, nitrogen (N) and phosphorus (P) and activities of β-glucosidase, N-acetyl-β-glucosaminidase and phosphatase were determined. Chemical C structure of the residual straw and bacterial community composition in the soil was analyzed with the aid of the solid state ¹³C-nuclear magnetic resonance (¹³C-NMR) spectroscopy and the technique of 16S rRNA gene amplicon sequencing, respectively.[Result] In red soil, Treatment Ma increased the content of soil available P by 29.0%, while Treatment Me did the content of soil available N and the activity of β-glucosidase by 15.5% and 81.3%, respectively. In Shajiang black soil, both Mortierella treatments notably increased the content of soil available N and the activity of β-glucosidase. In addition, Treatment Ma significantly increased the activity of phosphatase, while Treatment Me did the content of dissolved organic C and soil available P by 16.2% and 11.5%, respectively. In red soil, Mortierella inoculants inhibited straw decomposition and significantly altered composition and metabolic functions of the bacterial community, while in Shajiang black soil, they promoted straw degradation but had little effect on bacterial community structure. Ochrobactrum, Achromobacter and Streptomyces were the most influential taxa contributing to differences in bacterial community between the treatments and the control in red soil. Network analysis showed that the interactions between soil microbes were more complex connectedness in red soil than in Shajiang black soil. Lysobacter, Stenotrophomonas, Pantoea, Phyllobacteriaceae and Solirubrobacterales were identified as the keystone taxa in red soil, while Comamonadaceae, Lysobacter, Cytophagaceae and Serpens flexibilis were in Shajiang black soil. These keystone taxa acted as decomposers or biocontrol agents, and played important roles in maintaining microbial interactions and in potential processes of straw decomposition.[Conclusion] The present study has demonstrated that Mortierella alpina and Mortierella elongata can improve soil C, N and P availability and associated enzyme activities, and provide evidence of roles of indigenous strains of Mortierella strains on straw decomposition and nutrient transformation in agricultural soils.