Fertilization influences the soil microbiome. However, little is known about the effects of long-term fertilization on soil microbial metabolic pathways. In this study, we investigated the soil microbiome composition and function and microbial participation in the N cycle according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) functional annotation of different genes in a metagenomic analysis after long-term fertilization. Fertilizer application significantly changed the soil C/N ratio. Chemical fertilizer (NPK) treatment decreased soil pH, and chemical fertilizer combined with straw (NPK+S0.5) treatment increased ammonium nitrogen (NH₄⁺-N) but decreased nitrate nitrogen (NO₃⁻-N). NPK, NPK+S0.5 and S0.5 applications did not change the soil microbiome composition or dominant phylum but changed the relative abundances of microbiome components. Moreover, fertilizer significantly influenced metabolic processes, cellular processes and single-organism processes. Compared with a no-fertilizer treatment (CK), the NPK treatment resulted in more differentially expressed gene (DEG) pathways than the NPK+S0.5 and S0.5 treatments, and these pathways significantly correlated with soil nitrate nitrogen (NO₃⁻-N), available phosphorus (AP) and the moisture content of soil (MC). KEGG analysis found that fertilizer application mainly affected the ribosome, photosynthesis and oxidative phosphorylation pathways. S0.5 and NPK+S0.5 increased microbial nitrogen fixation, and NPK and NPK+S0.5 decreased amoA and amoB and accelerated denitrification. Thus, organic fertilizer increased N fixation and nitrification, and inorganic N fertilizer accelerated denitrification. We found that the function of the soil microbiome under different fertilizer applications could be important for the rational application of fertilizer and for environmental and sustainable development.

Returning crop straw to the soil is an effective measure to increase soil fertility and maintain crop yield in agroecosystems. In this study, we conducted a 34-year field experiment (1984–2017) to investigate the relationships among the impacts of straw return on soil nutrients, phosphorus (P) fractions, phosphorus transformation-related functional microbial communities, and key genes in black soil. The results of the soil chemical properties showed that straw return could slow the decline in soil pH and increase soil nutrients, i.e., soil organic carbon (SOC), available K (AK), and available P (AP) concentrations, with the straw addition (PKS) treatment resulting in the highest soil AP and AK contents. Compared with conventional fertilizer (NPK) and conventional fertilizer with straw (NPKS), straw return alone (S) significantly increased the soil AP and AK contents by 1.1–42.8 and 38.3–114.3 mg/kg (p < 0.05), respectively. The results of the phosphorus fraction experiment indicated that long-term straw return promoted labile and moderately stable phosphorus content by altering the composition and increasing the relative abundances of functional genes regulating soil P activation (ugpQ, ppk, phoD, and gcd). The compositional changes in the phosphorus-cycling-related functional genes of the soil were affected mostly by soil total P (TP), AK, and NO₃⁻-N, whereas pH, SOC, and available N (AN) were the main environmental factors influencing the phosphorus-cycling-related microbial community composition. These direct measurements provide insight into the soil phosphorus fractions, phosphorus-cycling-related functional genes, and microbial communities associated with straw returning, which enhances our understanding of the chemical and biogeochemical behavior of soil phosphorus upon straw incorporation.

Soil improvement methods can result in changes in the microbial community in blueberry soil. Bacterial communities play an important role in soil fertilizer and plant nutrient acquisition. In this study, the response of microbial community composition, microbial function, and the nitrogen (N) cycle to different improvement methods was analyzed using high-throughput sequencing to investigate the best soil improvement method from a microbial perspective. The results showed that the highest microbial diversity was observed in the treatment involving peat combined with mushroom bran (T2), followed by the peat combined with acidified rice husk (T2) both in the rhizosphere and roots. The dominant phyla were Proteobacteria and Actinobacteria both in the blueberry rhizosphere soil and roots. Interestingly, Acidobacterium and Paludibaculum, belonging to the Acidobacteria phylum, exhibited the most significant influence and were most predominant in the T2 treatment rhizosphere soil. The T2 treatment promoted the growth of N fixation functional bacteria both in the rhizosphere soil and roots. At the module level, the T2 treatment enhanced N fixation and suppressed the assimilatory and dissimilatory nitrate reduction reactions, denitrification, and nitrification in the blueberry rhizosphere. Additionally, the T2 treatment increased the abundance of root endophytic microbes involved in N fixation. Overall, our findings suggest that the addition of peat combined with acidified rice husk is the optimal soil improvement method for blueberry cultivation.

Declining soil fertility and reduced microbial diversity due to intensive farming threaten sustainable agriculture. This study aimed to assess the effects of B. japonicum inoculation and biochar amendment, applied individually and in combination, on soil properties, microbial communities, and soybean yield under field conditions in Jilin Province, China. A field experiment was established with four treatments: control (CK), B. japonicum alone (RH), biochar alone (CK2), and their combination (RHB). Observations were recorded at flowering (FS), seed-filling (SFS), and harvesting (HS) stages. Soil physicochemical properties, microbial diversity, and soybean yield were evaluated to determine treatment responses. The RHB treatment significantly improved soil fertility. Soil pH increased from 5.77 in CK to 6.20 in RHB, total nitrogen rose from 0.12% to 0.19%, and available phosphorus increased from 32.4 to 45.3 mg/kg. Available potassium and soil organic matter increased by 18.2% and 27.7%, respectively. Soybean yield was highest in RHB (3798 kg/ha) compared to CK (3158 kg/ha) and correlated strongly with total nitrogen (TN) ( r = 0.84), nitrate nitrogen ( r = 0.75), and available nitrogen ( r = 0.67). Microbial analysis revealed enrichment of beneficial genera, including Pseudomonas and Beauveria, along with higher populations of nitrogen-cycling bacteria and mycorrhizal fungi, thereby enhancing nutrient cycling. B. japonicum inoculation combined with biochar significantly enhanced soil fertility, improved microbial diversity, and increased soybean yield, offering a sustainable strategy to strengthen soil health and productivity in intensive farming systems.

Straw returning enhances soil fertility and increases corn yield, but the impact on soil fertility varies with different incorporation methods. To explore the optimal straw-returning method, this study, based on a long-term field experiment, investigated the following different corn-straw-returning methods: deep plowing and straw returning (B), rotary tillage and straw returning (RT), crushing and mixing straw returning (TM), pulverized cover straw returning (C), high-stubble-retention straw returning (LHS), strip cover (S), and flat no-tillage without straw returning (CK). High-throughput sequencing technology was employed to analyze the soil bacterial community composition and structural changes under different straw-returning methods. The study further explored the relationships between the soil bacterial community and nutrient content. The results indicated that different straw-returning methods altered the composition and structure of the soil bacterial community. The TM treatment significantly increased the richness and diversity of the soil bacterial communities. Shredding and covering (C and TM) effectively improved the soil nutrient content and bacterial community structure. In the C treatment, the abundance of Blastococcus, Nocardioides, and Microvirga increased the most, by 241.02%, 77.79%, and 355.08%, respectively, compared with CK. In the TM treatment, Pseudarthrobacter showed the highest abundance, increasing by 343.30%. The genes involved in soil carbon hydrolysis (pulA), nitrification (hao), organic nitrogen degradation and synthesis (gudB), and the nitrogen limitation response (glnR) significantly decreased by 56.21%, 78.75%, 66.46%, and 67.40%, respectively, in the C treatment. The genes involved in soil carbon hydrolysis (IMA), carbon fixation (pccB-A), methane metabolism (moxF), nitrate reduction in soil (nirD), organic nitrogen degradation and synthesis (gdh, ureAB, ureE), and phosphate absorption (glpT) significantly increased by 93.37%, 92.68%, 95.00%, 23.42%, 35.40%, 114.21%, 59.14%, and 75.86%, respectively, in the C treatment. The nitrate reduction gene (nrfA) significantly increased by 80.27% in the TM treatment. Therefore, we concluded that straw primarily stimulates the activity of bacterial communities and regulates the bacterial community by changing the relative abundance of the soil microorganisms and functional genes, thereby improving the soil nutrient content. This study considered pulverized cover straw returning and crushing and mixing straw returning to be the most reasonable methods.