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Litter decomposition plays a key role in nutrient cycling across ecosystems. The presence of Epichloë endophytes in grass plants affects litter decomposition. The overall effects of leaf litter containing Epichloë endophytes on the chemical and biological properties in non‐rhizosphere soils have not previously been examined. The current study is aimed to understand the effect of direct incorporation of leaf litter from Epichloë endophyte‐infected perennial ryegrass (Lolium perenne) on soil chemical characteristics, and fungal and bacterial biodiversity. Firstly, fresh leaf litter of the endophyte Epichloë festucae var. lolii‐infected (E+) and endophyte‐free (E−) L. perenne were incorporated into the soil, and then samples were collected from E+ and E− litter incorporated soil at T0, T1, T2 and T3 (0, 120, 240 and 360 days) for chemical and sequencing analyses. The Epichloë‐containing leaf litter incorporation changed the soil microbial environment by enhancing the soil organic carbon (SOC), total nitrogen (TN), total phosphorus, NH4+–N and NO3−–N contents, and acidifying soil pH. The endophyte had stronger effects on soil bacteria than soil fungi when the litter was determined with and without the endophyte. Litter containing the Epichloë endophyte significantly increased the absolute abundance of the 16S rRNA gene and relative abundances of the Actinobacteria, Nitrospirae and Gemmatimonadetes, while significantly decreasing the relative abundances of the Planctomycetes and Rokubacteria and the diversity in soil bacteria community. There was no significant effect of endophyte‐containing leaf litter incorporation on the absolute abundance and diversity of the soil fungal community except the increment in the relative abundance of Rozellomycota. Soil pH and the SOC‐to‐TN ratio (C:N) were the main factors influencing the soil bacterial community, and the presence of E. festucae var. lolii was directly and positively related to the soil bacterial diversity. The current study established that Epichloë endophyte‐infection altered the abundance and diversity of the soil bacterial community by affecting leaf litter quality and increasing soil chemical properties after litter incorporation. Highlights: Soil microbial habitat was changed by leaf litter with Epichloë endophyte incorporation.Litter containing endophytes increased the absolute abundance of the 16S rRNA gene.Epichloë endophytes altered the diversity of bacteria during litter incorporation.The response of soil bacteria to a litter containing endophytes was greater than that of soil fungi. [ABSTRACT FROM AUTHOR]

Although Epichloë endophytes are present only in aboveground tissues of grasses they indirectly influence soil biological characteristics through increased litter incorporation and root exudation. Epichloë endophytes have been reported to affect the decomposition rates of litter by altering litter quality and microbial decomposers to affect soil characteristics. However, it is not well-studied that underlying effects on functional genes involved in nitrification and denitrification after incorporation of litter containing Epichloë endophytes into soil. We collected soil samples at S 0 (first litter incorporation), S 1 (second litter incorporation), S 2 (third litter incorporation) and S 3 (120 days after the third litter incorporation) times after incorporation of litter that was either infected with the fungal endophyte Epichloë festucae var. Lolii or free of Epichloë endophyte, respectively.. We sampled the soil fororganic carbon (OC), total nitrogen (TN), total phosphorus (TP), ammonium nitrogen (NH 4 +-N: AN), nitrate nitrogen (NO 3 −-N: NN), soil microbial biomass carbon (MBC), nitrogen (MBN), ammonia-oxidizing bacteria (AOB- amoA) and ammonia-oxidizing archaea (AOA- amoA) functional genes for nitrification, nitrite reduction (nirS and nirK) and nitrous oxide reduction (nosZ) functional genes for denitrification. We found that Epichloë -infected plant increased the soil properties (OC, TN, AN, NN) and microbial biomass C in S 1 to S 3 times, and microbial biomass N in S 2 and S 3 times, but reduced soil pH in S 1 times and the C_N ratio in S 2 and S 3 times by litter incorporation. The absolute abundance of the AOB- amoA functional gene at S 1 and S 3 times and relative abundances of Planctomycetes, Methylobacterium, Nitosomonas, Gemmata, Geodermatophilus and Sinorhizobium in the nirK functional gene community were significantly higher in soil with Epichloë -infected litter compared to soil with Epichloë -free litter at S 1 and S 3 times. While the absolute abundance at S 1 and S 3 times and diversity at S 3 times of the nirK functional gene, and the absolute abundance at S 1 to S 3 times and diversity at S 1 times of the nosZ functional gene, and relative abundance of Proteobacteria in the AOB- amoA functional gene were significantly lower in soil with litter containing Epichloë endophyte than that of soil with litter without the endophyte. The soil moisture, and the contents of TP, OC, AN and MBN were the best explanatory variables for the altered microbial community. Our results provide a new understanding of the responses of soil nitrification and denitrification genes through incorporation of litter containing Epichloë endophytes into soil. • Soil microbial habitat environment was changed by litter incorporation. • We observed an increase in the absolute abundance of AOB- amoA in EI compared to EF soil. • The composition of nirK functional gene communities differed in EI and EF soil. • Endophyte reduced the diversity of nosZ functional gene following litter incorporation. • Soil properties were explained best the difference in functional genes. [ABSTRACT FROM AUTHOR]