Bio-fertilizer and rotten straw amendments alter the rhizosphere bacterial community and increase oat productivity in a saline-alkaline environment

Soil saline-alkalization strongly limits microbial functioning and crop productivity in arid and semi-arid regions. Organic amendments such as bio-fertilizers and decomposed plant residues are proposed to improve soil physicochemical properties, enhance beneficial microbial communities, and increase yields more effectively than inorganic amendments. Plant genotypes may differentially influence rhizosphere microbiomes and amendment responses, yet effects across oat cultivars differing in saline-alkaline tolerance have not been tested. This study asked whether adding bio-fertilizer and rotten straw to saline-alkaline soil alters rhizosphere soil properties and bacterial communities and improves productivity of two oat cultivars (tolerant Baiyan2 and sensitive Caoyou1). Hypothesis: organic amendments will reduce pH, increase nutrient availability, shift rhizosphere bacterial diversity and composition, and enhance yields, with cultivar-specific responses. Objectives: evaluate amendment effects on (1) rhizosphere physicochemical properties, (2) enzyme activities, (3) productivity of both cultivars, and (4) rhizosphere bacterial diversity and composition.

Prior work indicates organic amendments can improve saline soil properties and yields by modifying nutrient status and pH, with reported increases in disease-suppressive taxa (e.g., Acidobacteria, Firmicutes) and bacterial diversity following bio-fertilizer applications. Straw additions have altered microbial community structure and enzyme activity; decomposed (rotten) straw releases nutrients faster than fresh straw and can increase soil organic carbon, potassium, and enzyme activities. Amendment-driven changes in pH and nutrient availability are key drivers of bacterial community assembly in alkaline soils. Plant genotype can shape rhizosphere microbiota in some species, though not universally across crops. For oats, genotypes vary in saline-alkaline tolerance and productivity, but interactions with organic amendments on rhizosphere bacteria were previously untested.

Site and period: Field experiment in 2016–2017 at Tumote Zuoqi Hailiu village, Hohhot, Inner Mongolia, China (mean annual temperature 13.2 °C; rainfall 410 mm). Baseline soil properties were measured in April 2016. Amendments: Rotten corn straw was anaerobically fermented (Sep–Apr) before each season; bio-fertilizer and straw properties were characterized similarly to soils. Experimental design: 4×2 factorial in a randomized complete block design with three replicates per year. Plots: 5 m × 4 m. Cultivars: Caoyou1 (sensitive, A) and Baiyan2 (tolerant, B). Treatments: CK (A1/B1, no amendment), F (A2/B2, 1500 kg ha⁻¹ yr⁻¹ bio-fertilizer), R (A3/B3, 12,000 kg ha⁻¹ yr⁻¹ rotten straw), RF (A4/B4, combined 1500 kg ha⁻¹ yr⁻¹ bio-fertilizer + 12,000 kg ha⁻¹ yr⁻¹ rotten straw). Management: Oats seeded at 150 kg ha⁻¹ yr⁻¹, 25 cm rows; diammonium phosphate (18-46-0) at 150 kg ha⁻¹ yr⁻¹ applied to all plots. Amendments were broadcast and incorporated to ~15 cm before sowing. Sampling: Soil sampled pre-seeding and at heading. Rhizosphere soil collected by shaking off bulk soil and brushing soil within 2 mm of roots. Soils sieved (2 mm) and split: fresh (4 °C), air-dried (physicochemical, enzymes), and −80 °C (DNA). Measurements: SW by oven-drying (105 °C); pH in 1:5 soil:water; salt via EC in 1:2.5 soil:water; AK by 1 M NH₄OAc and flame photometry; AP by 0.5 M NaHCO₃ extraction and molybdenum blue; AN by diffusion. Enzymes: catalase (KMnO₄ titration), alkaline phosphatase (disodium phenyl phosphate), urease (colorimetric), sucrase (DNS method). Microbiome: DNA extraction (MO BIO kit). 16S rRNA V4 amplified with 515F/806R; sequenced on Illumina HiSeq2500. Reads processed with FLASH and QIIME; chimeras removed with UCHIME; OTUs clustered at 97% with UPARSE; taxonomy assigned with SILVA using RDP classifier. Statistics: GLM for yields, soil properties, α-diversity; means separated by Fisher’s LSD at 5%. Bray–Curtis PERMANOVA (adonis) and PCA assessed community differences; RDA related communities to soil and productivity variables after removing collinear variables (VIF>10). Spearman correlations examined taxa–soil–yield relationships; Pearson correlations for soil–yield relationships.

- Productivity: Baiyan2 out-yielded Caoyou1 overall. Bio-fertilizer increased grain yield for both cultivars, with maximum grain yields under combined bio-fertilizer + rotten straw (RF). For Caoyou1, RF significantly increased grass biomass to levels similar to Baiyan2. Two-way ANOVA: grain yield affected by amendment (P<0.0001) and cultivar (P=0.0001); dry biomass affected by amendment (P=0.003) and cultivar (P<0.0001); fresh biomass affected by cultivar (P<0.0001) and marginally by amendment (P=0.053); C×M interaction significant for dry biomass (P=0.039). - Rhizosphere soil properties (overall M effects): RF reduced pH (CK 8.11±0.01 vs RF 7.94±0.01) and increased SW (CK 5.68±0.10% vs RF 9.26±1.55%), salt (CK 0.47±0.01% vs RF 0.75±0.04%), AK (CK 71.67±10.06 mg kg⁻¹ vs RF 199.17±13.38), AP (CK 27.39±0.41 vs RF 61.44±0.10), and AN (CK 17.02±1.59 vs RF 40.78±2.15). Rotten straw alone (R) also increased AK (192.50±13.39), AP (52.95±0.26), AN (27.55±1.35). Cultivar effect: Baiyan2 had higher AP than Caoyou1. - Enzymes: Rotten straw increased catalase and sucrase; bio-fertilizer increased catalase and alkaline phosphatase for Caoyou1; RF decreased urease activity relative to other treatments according to text; overall enzyme responses varied by cultivar and amendment. - Bacterial α-diversity: Baiyan2 exhibited higher richness and Shannon diversity than Caoyou1 (Chao1: 3413±112 vs 3169±70; Shannon: 9.09±0.13 vs 8.58±0.11). Amendments with rotten straw tended to reduce diversity: overall Shannon decreased from CK 9.17±0.14 to RF 8.45±0.04. Treatment effects varied by cultivar: all amendments reduced richness for Baiyan2, while RF increased observed richness for Caoyou1. - Community composition: PERMANOVA showed significant effects of cultivar (R²=0.091, P=0.001), amendment (R²=0.467, P=0.001), and C×M (R²=0.234, P=0.001). PCA separated rotten straw-containing treatments along PC1 (20.36%) and cultivars along PC2 (12.25%). - Dominant phyla across treatments: Proteobacteria (27.28–41.09%), Actinobacteria (24.17–30.36%), Firmicutes (2.82–22.95%). Baiyan2 had higher Proteobacteria (e.g., Azotobacter, Massilia, Pseudomonas) and lower Firmicutes than Caoyou1. Rotten straw increased Firmicutes (e.g., Bacillus, Planomicrobium) and decreased Proteobacteria (Massilia) and Actinobacteria (Nocardioides). Bio-fertilizer increased Massilia and Nocardioides for Caoyou1, and Azotobacter and Pseudomonas for Baiyan2. - Correlations and RDA: Treatments with rotten straw correlated positively with soil salt, AK, AP, and grass yield. Soil salt, AK, AP, and AN were positively associated with Bacillus, Pseudarthrobacter, Planomicrobium and negatively with Sphingomonas, Massilia, Nocardioides, Pseudomonas. Grain yield, salt, AK, AP, and AN were positively intercorrelated and negatively correlated with soil pH and urease.

The study confirmed that organic amendments, particularly the combination of bio-fertilizer and rotten straw, increased oat productivity in saline-alkaline soil by reducing pH and enhancing nutrient availability, with concurrent shifts in rhizosphere bacterial diversity and composition. The tolerant cultivar Baiyan2 supported higher α-diversity and a greater relative abundance of potentially beneficial Proteobacteria taxa (Azotobacter, Pseudomonas), which may contribute to its superior performance under stress. Rotten straw strongly shaped communities toward Firmicutes enrichment and Proteobacteria/Actinobacteria reductions, consistent with higher salinity and nutrient availability driving community assembly. Enzyme activity enhancements (catalase, alkaline phosphatase, sucrase) reflected improved nutrient cycling potential, while reduced urease under combined amendments may relate to increased salinity or N inputs. Overall, amendment-driven improvements in soil conditions and microbiome restructuring addressed the hypothesis by demonstrating cultivar-dependent and amendment-specific microbial and agronomic responses that are relevant for saline-alkaline soil remediation and sustainable production.

Combined application of rotten straw and bio-fertilizer in saline-alkaline soil maximized oat yields, decreased soil pH, increased nutrient availability, and reshaped rhizosphere bacterial communities toward taxa associated with improved soil function. Tolerant cultivar Baiyan2 harbored more diverse and beneficial microbiota than sensitive Caoyou1, yet the combined amendment elevated Caoyou1 productivity to levels comparable to Baiyan2. Implementing tolerant cultivars with combined organic amendments is an effective strategy for rehabilitating saline-alkaline soils in semi-arid regions. Future research should include long-term studies to assess sustainability, salinity dynamics, microbiome stability, and optimization of amendment rates to balance nutrient gains with salt management.

- Increased soil salt content under the combined amendment may pose a risk for salinity build-up; management of salt dynamics requires attention. - The study spanned two growing seasons; long-term effects on soil salinity, microbial community stability, and yield sustainability remain uncertain. - Enzyme activity responses did not consistently translate to yield differences and urease inhibition under combined amendments may limit N cycling. - Results are specific to the site conditions, amendment formulations, and application rates used; generalizability to other soils and climates may be limited.