Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land.

Crop residue and animal manure as a soil amendment have been recognized as a feasible agricultural practice owing to its contribution in improving the soil fertility (SF). The primary advantages of this practice are determined by the activities of soil microorganisms. However, goat manure (M), sugarcane straw (S), and goat manure plus straw (MS) amendments influence soil bacteria, their activities, and SF in clay-loam soil remains undefinable. Therefore, this study distinguished the efficacy of M, MS, and S amendment on soil enzyme activities and the availability of nutrients, including various bacterial populations in clay-loamy soil with respect to two different phases (50 and 100 days). In order to analyze the bacterial structure and their activities, we employed high-throughput sequencing (HTS) and soil enzyme activity (SEA) tests. Soil amended with M and MS not only significantly enhanced nutrient availability, including C, P, and N, soil pH, as well as SEA for C and N cycles in both phases. Additionally, the increase in nutrient availability was greater in M- and MS-amended soils in the second phase (100 days) compared to the M- and S-amended soils in the first phase (50 days). Moreover, plant growth promoting and lignocellulose degrading bacterial genera were enhanced under M- and MS-amended soil compared to S-amended soil in both phases. Distance-based redundancy analysis (dbRDA) showed that soil pH, carbon-nitrogen ratio (C:N), and nitrates (NO₃⁻) were inducing the fewest changes, while total nitrogen (TN), total carbon (TC), available nitrogen (AN), available phosphorus (AP), total phosphorus (TP), available potassium (AK), and ammonium (NH₄⁺) were the main operators in terms of change in bacterial populations. In general, we observed that M and MS are better amendment sources as compared to S amendment in order to enhance the SF in the clay-loamy soil in both phases, but greater fertility was exhibited in the second phase.