Microbiome - based agents can optimize composting of agricultural wastes by modifying microbial communities

Suppressiveness of spent mushroom substrate amendment against eggplant Verticillium wilt

BACKGROUND

Verticillium wilt, caused by Verticillium dahliae, is a devastating soil-borne disease. Spent mushroom substrate (SMS) has shown potential as a soil amendment for controlling soil-borne diseases. However, the mechanisms underlying its disease-suppressive effects remain poorly understood. Here, the efficacy of SMS in suppressing eggplant Verticillium wilt and mechanisms related to rhizosphere microbiome regulation were investigated.

RESULTS

We tested different SMS sources (Pleurotus ostreatus, Hypsizygus marmoreus, Lentinus edodes), particle sizes (45, 75, 150, 300 μm), and addition ratios (0.5-8%, w/w). The fungus control efficacy ranged from 26 to 66%, with best results from 2% SMS of L. edodes at 150 μm. This treatment resulted in 5.7-fold reduction in the Verticillium dahliae population in eggplant rhizosphere. Eggplant fresh and dry weights of shoots and roots, and plant height, significantly increased with 2% SMS amendment. 16S rDNA sequencing revealed alterations in rhizosphere bacterial communities, with an increase in indigenous beneficial bacteria, particularly Bacillus spp., following SMS amendment. Spent mushroom substrate co-inoculated with exogenous biocontrol strain Bacillus subtilis NCD-2 achieved a synergistic effect against Verticillium wilt than both SMS or NCD-2 alone.

CONCLUSIONS

Results revealed that SMS protects eggplants against Verticillium wilt, largely by recruiting Bacillus spp. to the rhizosphere. The enrichment effect of indigenous Bacillus spp. in the rhizosphere mediated by SMS similarly applies to Bacillus inoculum, enhancing its efficacy in controlling eggplant Verticillium wilt. These findings enhance our understanding of the protective effects of SMS and its role in the biocontrol of Verticillium wilt. © 2025 Society of Chemical Industry.

Applying bio-organic fertilizer improved saline alkaline soil properties and cotton yield in Xinjiang

Bio-organic fertilizers have demonstrated significant potential in enhancing saline-alkali soil properties, boosting crop yield, and reducing chemical fertilizer dependency. However, the extent of improvement and optimal application rates for varying saline-alkali soil conditions remain unclear. We conducted a 2-year field experiment (2022-2023) to evaluate the effects of different bio-organic fertilizer application rates on soil properties, nutrient availability, and cotton yield across three saline-alkali cotton fields with varying salinity levels 4.58, 9.07, and 12.76 g·kg⁻¹ (T1-T3). Four treatments were implemented, involving chemical fertilizer reductions of 0% (CK), 20% (F1), 40% (F2), and 60% (F3). Results indicated that, compared to CK, bio-organic fertilizer application reduced soil bulk density, salinity, and pH by an average of 15.84%, 53.86%, and 7.5%, respectively. Concurrently, soil moisture content, organic matter, nitrogen, phosphorus, potassium, and cotton yield increased by 36.72%, 58.4%, 59.4%, 77.9%, 88.7%, and 50.32%, respectively. Notably, the improvements in soil properties and cotton yield were more pronounced in 2023 compared to 2022. Principal component analysis revealed that a 60% bio-organic fertilizer application rate was optimal for mild, moderate, and severely salinized cotton fields. These findings provide a scientific basis for reducing chemical fertilizer use while improving the productivity and sustainability of saline-alkali soils.

Study of the mechanism by which Bacillus subtilis improves the soil bacterial community environment in severely saline-alkali cotton fields

Soil salinization severely damages the soil bacterial community environment. Bacillus subtilis can improve bacterial communities and enhance crop nutrient absorption. However, the mechanism by which B. subtilis improves the bacterial community environment in heavily saline-alkali-treated cotton fields is currently unclear. Therefore, this study adopted a field plot experiment and established four bacterial treatments (0, 9, 12, and 15 kg·ha-1) to investigate the environmental improvement mechanism of B. subtilis on soil bacterial communities in severely saline alkali cotton fields was studied. Compared with the CK treatment, the application of B. subtilis significantly increased the available nitrogen (25.34 %), available phosphorus (50.894 %), available potassium (86.87 %), and urease (112.961 %) contents but significantly reduced the soil pH (1.07 %) and salt content (39.73 %) and significantly increased the proline (245.116 %) and superoxide dismutase (237.46 %) contents in the leaves and significantly reduced the malondialdehyde content (47.30 %). This is mainly because B. subtilis enhances the diversity of bacterial communities and affects catalase, urease, phosphatase, and protease activities, thereby promoting nutrient release in the soil and improving soil fertility; specifically, B. subtilis promotes the secretion of oxalic acid, formic acid, malic acid, and soluble total sugars in cotton roots. The organic acids in root exudates lower the soil pH and chelate with salt ions in the soil, reducing the concentration of soluble salts and providing a suitable environment for B. subtilis. Soluble total sugars can provide energy and carbon sources for bacteria, maintaining the health and diversity of rhizosphere bacterial communities. The results of the principal component analysis revealed that the application rate of B. subtilis was 12 kg·ha-1, which had the greatest effect on improving the soil bacterial community in severely saline-alkali cotton fields. The research results provide a theoretical basis and practical reference for microbial improvement in severely saline-alkali land in arid areas.

Revealing the interplay of dissolved organic matters variation with microbial symbiotic network in lime-treated sludge landscaping

Lime pretreatment is commonly used for sludge hygienization. Appropriate lime dosage is crucial for achieving both sludge stabilization (lime dosage >0.2 g/g-TS) and promoting plant and soil health during subsequent landscaping (lime dosage <0.8 g/g-TS). While much research has been conducted on sludge lime treatment, few studies have examined the effects of lime dosing on integrating sludge stabilization and plant growth promotion during landscaping. In this study, we investigated microbial dynamics and dissolved organic matter (DOM) transformation during sludge landscaping with five lime dosage gradients (0, 0.2, 0.4, 0.6, 0.8 g lime/g-TS) over 90 days. Our results showed that a lime dosage of 0.4 g/g-TS is the lower threshold for achieving waste activated sludge (WAS) stabilization during landscaping, leading to maximum humic substance formation and minimal phytotoxicity. Specifically, at 0.4 g/g-TS lime dosage, protein degradation and decarboxylation-induced humification were significantly enhanced. The predominant microbial genera shifted from Aromatoleum to Exiguobacterium and Romboutsia (both affiliated with the phylum Firmicutes). Reactomics analysis further indicated that a 0.4 g/g-TS lime dosage promoted the hydrolysis of proteins (lyase reactions on C-C, C-O, and C-N bonds), amino acid metabolism, and decarboxylation-induced humification (e.g., C1H2O2, C2H4O2, C5H4O2, C6H4O2). The co-occurrence network analysis suggested that the phyla Firmicutes, Proteobacteria, and Bacteroidetes were key players in DOM transformation. This study provides an in-depth understanding of microbe-mediated DOM transformation during sludge landscaping and identifies the optimal lime dosage for improving sludge landscaping efficiency.

Compost derived from olive mill cake: Effects on isohumic soil quality based on humic acids characterization

The compost effects on soil organic matter (SOM) stability were evaluated. Manure at 10 % ratio and compost at 10 %, 20 % and 40 % ratios (v/v) were added to the soil and their effects were compared to unamended control soil after 90-days of greenhouse-experiment. Humic acids (HA) and fulvic acids (FA) were extracted from two different soil-sample layers at 0-15 and 15-30 cm depth. The CHA/CFA ratio and the humification parameters were determined, and the soil-HA were characterized by spectroscopic methods (E4/E6 and FTIR). The humification parameters progress with time were affected by the amendment concentration. After 90 days, the treated soils HA' FTIR spectra showed an increase in aromatic carbon polycondensation and O-containing groups reflecting the high degrees of molecular associations and humification of soil HA. Compared to 10 % manure application and 40 % compost ratio use, the applications of 10 % and 20 % compost ratios induced higher humification level and highly oxidized HA structure. Moreover, changes in the HA compositional and functional groups were noticed at the upper layer which exhibited higher reactivity compared to the lower layer which displayed more humified SOM. Through the humification process, the HA fraction was improved to reach more stable and complex macromolecules, where aromatic structures were bio-converted into highly functionalized compounds.

Application of cold-adapted microbial agents in soil contaminate remediation: biodegradation mechanisms, case studies, and safety assessments

The microbial agent technology has made significant progress in remediating nitro-aromatic compounds (NACs), such as p-nitrophenol, 2,4-dinitrophenol, and 2,4,6-Trinitrotoluene, in farmland soil over the past decade. However, there are still gaps in our understanding of the bioavailability and degradation mechanisms of these compounds in low-temperature environments. In this review, we provide a comprehensive summary of the strategies employed by cold-adapted microorganisms and elucidate the degradation pathways of NACs pollutants. To further analyze their metabolic mechanisms, we propose using mass balance to improve our understanding of biochemical processes and refine the degradation pathways through stoichiometry analysis. Additionally, we suggest employing 13C-metabolic flux analysis to track enzyme activity and intermediate products during bio-degradation processes with the aim of accelerating the remediation of nitro-aromatic compounds, particularly in cold regions. Through a comprehensive analysis of pollutant metabolic activities and a commitment to the 'One Health' approach, with an emphasis on selecting non-pathogenic strains, the environmental management strategies for soil remediation could be positioned to develop and implement safe and effective measure.

Control of nitrogen and odor emissions during chicken manure composting with a carbon-based microbial inoculant and a biotrickling filter

Although aerobic composting is usually utilized in livestock manure disposal, the emission of odorous gases from compost not only induces harm to the human body and the environment, but also causes loss of nitrogen, sulfur, and other essential elements, resulting in a decline in product quality. The impact of biotrickling filter (BTF) and insertion of carbon-based microbial agent (CBMA) on compost maturation, odor emissions, and microbial population during the chicken manure composting were assessed in the current experiment. Compared with the CK group, CBMA addition accelerated the increase in pile temperature (EG group reached maximum temperature 10 days earlier than CK group), increased compost maturation (GI showed the highest increase of 41.3% on day 14 in EG group), resulted in 36.59% and 14.60% increase in NO3--N content and the total nitrogen retention preservation rate after composting. The deodorization effect of biotrickling filter was stable, and the removal rates of NH3, H2S, and TVOCs reached more than 90%, 96%, and 56%, respectively. Furthermore, microbial sequencing showed that CBMA effectively changed the microbial community in compost, protected the ammonia-oxidizing microorganisms, and strengthened the nitrification of the compost. In addition, the nitrifying and denitrifying bacteria were more active in the cooling period than they were in the thermophilic period. Moreover, the abundance of denitrification genes containing nirS, nirK, and nosZ in EG group was lower than that in CK group. Thus, a large amount of nitrogen was retained under the combined drive of BTF and CBMA during composting. This study made significant contributions to our understanding of how to compost livestock manure while reducing releases of odors and raising compost quality.

Composting municipal solid waste and animal manure in response to the current fertilizer crisis - a recent review

The dynamic price increases of fertilizers and the generation of organic waste are currently global issues. The growth of the population has led to increased production of solid municipal waste and a higher demand for food. Food production is inherently related to agriculture and, to achieve higher yields, it is necessary to replenish the soil with essential minerals. A synergistic approach that addresses both problems is the implementation of the composting process, which aligns with the principles of a circular economy. Food waste, green waste, paper waste, cardboard waste, and animal manure are promising feedstock materials for the extraction of valuable compounds. This review discusses key factors that influence the composting process and compares them with the input materials' parameters. It also considers methods for optimizing the process, such as the use of biochar and inoculation, which result in the production of the final product in a significantly shorter time and at lower financial costs. The applications of composts produced from various materials are described along with associated risks. In addition, innovative composting technologies are presented.

Evaluation of immobilized microspheres of Clonostachys rosea on Botrytis cinerea and tomato seedlings

Tomato (Solanum lycopersicum L.) is a popular vegetable crop which is widely cultivated around the world. However, the production of tomatoes is threatened by several phytopathogenic agents, including gray mold (Botrytis cinerea Pers.). Biological control using fungal agents such as Clonostachys rosea plays a pivotal role in managing gray mold. However, these biological agents can negatively be influenced by environmental factors. However, immobilization is a promising approach to tackle this issue. In this research, we used a nontoxic chemical material, sodium alginate as a carrier to immobilize C. rosea. For this, sodium alginate microspheres were prepared using sodium alginate prior to embedding C. rosea. The results showed that C. rosea was successfully embedded in sodium alginate microspheres, and immobilization enhanced the stability of the fungi. The embedded C. rosea was able to suppress the growth of gray mold efficiently. In addition, the activity of stress related enzymes, peroxidase superoxidase dismutase and polyphenol oxidation was promoted in tomatoes treated with the embedded C. rosea. By measuring photosynthetic efficiency, it was noted that the embedded C. rosea has positive impacts on tomato plants. Taken together, these results indicate that immobilization of C. rosea improved its stability without detrimentally affecting its efficiency on gray mold suppression and tomato growth. The results of this research can be used as a basis for research and development of new immobilized biocontrol agents.

Microbial inoculants enhance the persistence of antibiotic resistance genes in aerobic compost of food waste mainly by altering interspecific relationships

The effects of microbial inoculants on ARG removal in composting are poorly understood. Here, a co-composting method for food waste and sawdust amended with different microbial agents (MAs) was designed. The results show that the compost without MA unexpectedly achieved the best ARG removal. The addition of MAs markedly increased the abundance of tet, sul and multidrug resistance genes (p < 0.05). Structural equation modeling demonstrated that MAs can enhance the contribution of the microbial community to ARG changes by reshaping community structure and altering the ecological niche, causing the proliferation of individual ARGs, an effect related to the MA component. Network analysis revealed that inoculants weakened the correlation between ARGs and community but increased the linkage between ARGs and core species, suggesting that inoculant-induced ARG proliferation may correspond with gene exchange occurring mainly between core species. The outcome provides new insights into MA application for ARG removal in waste treatment.

Effect of biodrying of lignocellulosic biomass on humification and microbial diversity

By optimizing the carbon to nitrogen (C/N) ratio, this study accomplished an improved level of humification and microbial diversity in the biodrying process of lignocellulosic biomass. The results demonstrated that C/N ratio of 20 accelerated the decomposition of refractory lignocellulose, resulting in lower greenhouse gas emissions and the production of highly mature fertilizer with a germination index of 119.0% and a humic index of 3.2. Moreover, C/N ratio of 20 was found to diversify microbial communities, including Pseudogracilibacillus, Sinibacillus, and Georgenia, which contributed to the decomposition of lignocellulosic biomass and the production of humic acid. Hence, it is recommended to regulate the C/N ratio to 20:1 during the biodrying of biogas residue and wood chips to promote the economic feasibility and bioresource recycling.

Addition of exogenous microbial agents increases hydrogen sulfide emissions during aerobic composting of kitchen waste by improving bio-synergistic effects

The effect of microbial agents (MA) on hydrogen sulfide (H₂S) emissions in the compost is still a controversial issue. This study examined the effects and microbial mechanisms of MA on H₂S emissions during the composting of kitchen waste. The results showed that MA addition can promote sulfur conversion to elevate H₂S emissions by approximately 1.6 ∼ 2.8 times. Structural equations demonstrated that microbial community structure was the dominant driver on H₂S emissions. Agents reshaped the compost microbiome, showing more microorganisms participated in sulfur conversion, and enhanced the connection between microorganisms and functional genes. The relative abundance of keystone species associated with H₂S emissions increased after adding MA. Particularly, the sulfite and sulfate reduction processes were intensified, as evidenced by an increasing in the abundance and pathways cooperation of sat and asrA after MA addition. The outcome provides deeper insights into MA on regulating the mitigation of H₂S emissions in compost.