Mechanisms of nitrogen transformation driven by functional microbes during thermophilic fermentation in an ex situ fermentation system

Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation

Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4+-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.

Biochar's role in improving pakchoi quality and microbial community structure in rhizosphere soil

Background

Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes.

Methods

The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq.

Results

The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significantly negatively correlated with the relative abundance of Ilumatobacter. Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application.

Conclusion

Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (e.g., Gemmatimonadetes and Ilumatobacter), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.

Key genes of electron transfer, the nitrogen cycle and tetracycline removal in bioelectrochemical systems

BACKGROUND

Soil microbial fuel cells (MFCs) can remove antibiotics and antibiotic resistance genes (ARGs) simultaneously, but their removal mechanism is unclear. In this study, metagenomic analysis was employed to reveal the functional genes involved in degradation, electron transfer and the nitrogen cycle in the soil MFC.

RESULTS

The results showed that the soil MFC effectively removed tetracycline in the overlapping area of the cathode and anode, which was 64% higher than that of the control. The ARGs abundance increased by 14% after tetracycline was added (54% of the amplified ARGs belonged to efflux pump genes), while the abundance decreased by 17% in the soil MFC. Five potential degraders of tetracycline were identified, especially the species Phenylobacterium zucineum, which could secrete the 4-hydroxyacetophenone monooxygenase encoded by EC 1.14.13.84 to catalyse deacylation or decarboxylation. Bacillus, Geobacter, Anaerolinea, Gemmatirosa kalamazoonesis and Steroidobacter denitrificans since ubiquinone reductase (encoded by EC 1.6.5.3), succinate dehydrogenase (EC 1.3.5.1), Coenzyme Q-cytochrome c reductase (EC 1.10.2.2), cytochrome-c oxidase (EC 1.9.3.1) and electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) served as complexes I, II, III, IV and ubiquinone, respectively, to accelerate electron transfer. Additionally, nitrogen metabolism-related gene abundance increased by 16% to support the microbial efficacy in the soil MFC, and especially EC 1.7.5.1, and coding the mutual conversion between nitrite and nitrate was obviously improved.

CONCLUSIONS

The soil MFC promoted functional bacterial growth, increased functional gene abundance (including nitrogen cycling, electron transfer, and biodegradation), and facilitated antibiotic and ARG removal. Therefore, soil MFCs have expansive prospects in the remediation of antibiotic-contaminated soil. This study provides insight into the biodegradation mechanism at the gene level in soil bioelectrochemical remediation.

Effects of microplastics on denitrification and associated N2O emission in estuarine and coastal sediments: insights from interactions between sulfate reducers and denitrifiers

Global estuarine and coastal zones are facing severe microplastics (MPs) pollution. Sulfate reducers (SRB) and denitrifiers (DNB) are two key functional microorganisms in these zones, exhibiting intricate interactions. However, whether and how MPs modulate the interactions between SRB and DNB, with implications for denitrification and associated N2O emissions, remains poorly understood. Here, we simultaneously investigated the spatial response patterns of SRB-DNB interactions and denitrification and associated N2O emissions to different MPs exposure along an estuarine gradient in the Yangtze Estuary. Spatial responses of denitrification to polyvinyl chloride (PVC) and polyadipate/butylene terephthalate (PBAT) MPs exposure were heterogeneous, while those of N2O emissions were not. Gradient-boosted regression tree and multiple regression model analyses showed that sulfide, followed by nitrate (NO3-), controlled the response patterns of denitrification to MPs exposure. Further mechanistic investigation revealed that exposure to MPs resulted in a competitive and toxic (sulfide accumulation) inhibition of SRB on DNB, ultimately inhibiting denitrification at upstream zones with high sulfide but low NO3- levels. Conversely, MPs exposure induced a competitive inhibition of DNB on SRB, generally promoting denitrification at downstream zones with low sulfide but high NO3- levels. These findings advance the current understanding of the impacts of MPs on nitrogen cycle in estuarine and coastal zones, and provide a novel insight for future studies exploring the response of biogeochemical cycles to MPs in various ecosystems.

Effects of different fermentation synergistic chemical treatments on the performance of wheat straw as a nursery substrate

Wheat straw is rich in organic matter and nutrients and has the potential to replace peat as the primary raw material in organic nurseries. Using straw as a peat substitute can also aid in reducing the CO₂ emissions that result from peat mining. Furthermore, this can avoid resource wastage and eliminate the practice of burning wheat straw, thereby causing pollution. The conventional composting treatment has a long cycle and inability to control substrate properties in a targeted manner. Thus, this study analyzed the physicochemical properties, material science properties, and biological toxicity of straw substrate at the end of fermentation to achieve rapid and targeted regulations of the substrate's overall performance. Wheat straw treated with two types of fermentation (aerobic/anaerobic) and five chemical conditioners (1% CH₃COOH, 1% H₂SO₄, 1% NaOH, 1% K₂CO₃, and H₂O) under different temperature conditions was used. Adjusting the pH of straw substrate to acidic levels (4.47-6.51) reduced the organic matter consumption by 0.27-5.82% under anaerobic digestion than under aerobic composting. Meanwhile, aerobic composting retained more nitrogen (0.12-8.23 mg/g) than anaerobic digestion. The co-fermentation of wheat straw pretreated with 1% H₂SO₄ resulted in 14.18-46.12% hemicellulose degradation. Co-aerobic straw composting with H₂SO₄ and K₂CO₃ at 35 °C reduced the crystallinity of the straw substrate by 6.66 and 7.33%, respectively, as compared to other conditioning agents. CH₃COOH lowered the electrical conductivity values of the straw substrate at the end of fermentation (2.33-3.49 mS/cm). Overall, the findings revealed that CH₃COOH-cooperative aerobic composting pretreatment at 35 °C is a suitable replacement for the traditional composting process as a method of utilizing straw substrate.

Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting

Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM= 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.

Existence of antibiotic pollutant in agricultural soil: Exploring the correlation between microbiome and pea yield

Due to sewage irrigation, manure fertilizer application or other agricultural activities, antibiotics have been introduced into farmland as an emerging contaminant, existing with other agrochemicals. However, the potential influences of antibiotics on the efficiency of agrochemicals and crops health are still unclear. In this work, the effect of antibiotics on fertilization efficiency and pea yield was evaluated, and the mechanism was explored in view of soil microbiome. Nitrogen utilization and pea yield were decreased by antibiotics. In specific, the weight of seeds decreased 9.5 % by 5 mg/kg antibiotics and decreased 25.1 % by 50 mg/kg antibiotics. For N nutrient in pea, antibiotics resulted in 62.5 %-63.7 % decrease in amino acid content and 8.3 %-35.3 % decrease in inorganic-N content. Further research showed that antibiotics interfered with N cycle in soil, inhibiting urea decomposition and denitrification process by reducing function genes ureC, nirK and norB in soil, thus decreasing N availability. Meanwhile, antibiotics destroyed the enzyme function in N assimilation. This work evaluated the environmental risk of antibiotics from fertilization efficiency and N utilization in crop. Antibiotics could not only affect N cycle, limiting the decomposition of N fertilizer, but also affect N utilization in plants, thus affecting the yield and even the quality of leguminous crops.

Impacts of exogenous quorum sensing signal molecule-acylated homoserine lactones (AHLs) with different addition modes on Anammox process

Anammox was proved having the quorum sensing ability, and several acylated homoserine lactones (AHLs) signal molecules were detected in the system. In this study, the impact of exogenous N-dodecanoyl homoserine lactone (C12-HSL) with different addition modes on the nitrogen removal, key enzymes' activity, and microbial revolution were investigated in Anammox system. Results showed that once-addition of C12-HSL had no obvious impact on Anammox. Daily-addition with 40 nM slightly improved the TN removal from 71.1 % to 74.5 %, while 80 and 200 nM significantly decreased it to 62.7 % and 61.8 %, respectively. The enzyme activity of ammonia monooxygenase increased from 0.015 to 0.068, nitrite reductase increased from 0.25 to 1.23, and nitrate reductase increased from 0.05 to 0.11 μg NO₂^--N mg^-1 Protein min^-1. Arenimonas abundance showed positive correlation with TN removal while Candidatus Kuenenia was continuously suppressed. C12-HSL was beneficial for partial nitrification, and it could be adopted for regulating the nitrite production.

Role of the rhizosphere bacterial community in assisting phytoremediation in a lead-zinc area

Heavy metals (HMs) contamination and vegetation destruction in the mining area caused by mining activities are severely increasing. It is urgent to restore vegetation and stabilize HMs. In this study, we compared the ability of HMs phytoextraction/phytostabilization of three dominant plants, including Artemisia argyi (LA), Miscanthus floridulus (LM), and Boehmeria nivea (LZ) in a lead-zinc mining area in Huayuan County (China). We also explored the role of the rhizosphere bacterial community in assisting phytoremediation using 16S rRNA sequencing technology. Bioconcentration factor (BCF) and translocation factor (TF) analysis showed that LA preferred accumulating Cd, LZ preferred accumulating Cr and Sb, and LM preferred accumulating Cr and Ni. Significant (p < 0.05) differences were found among the rhizosphere soil microbial communities of these three plants. The key genera of LA were Truepera and Anderseniella, that of LM were Paracoccus and Erythrobacter, and of LZ was Novosphingobium. Correlation analysis showed some rhizosphere bacterial taxa (e.g., Actinomarinicola, Bacillariophyta and Oscillochloris) affected some soil physicochemical parameters (e.g., organic matter and pH) of the rhizosphere soil and enhanced the TF of metals. Functional prediction analysis of soil bacterial community showed that the relative abundances of genes related to the synthesis of some proteins (e.g., manganese/zinc-transporting P-type ATPase C, nickel transport protein and 1-aminocyclopropane-1-carboxylate deaminase) was positively correlated with the phytoextraction/phytostabilization capacity of plants for heavy metals. This study provided theoretical guidance on selecting appropriate plants for different metal remediation applications. We also found some rhizosphere bacteria might enhance the phytoremediation of multi-metals, which could provide a reference for subsequent research.

Effects of segmented aerobic and anaerobic fermentation assisted with chemical treatment on comprehensive properties and composition of wheat straw

Traditional aerobic composting used for straw treatment shows limited regulation effects and unstable properties, and it is necessary to introduce some co-processing methods to optimize its performance. Herein, segmented aerobic/anaerobic fermentation, combined with chemical treatment with wood vinegar/NaOH, was used to treat wheat straw. The results showed that anaerobic fermentation when used as the first stage could stabilize the wheat straw pH between 5.19 and 6.13 and improve nutrient contents. All treatments had greater effects on substrate aeration porosities (range of 14%) than on total porosity (range of 6%), and the water-holding porosities were improved to a greater extent by NaOH than by wood vinegar. The hemicellulose degradation rate of aerobic-anaerobic treatment was higher than that achieved with anaerobic-aerobic treatment, while the latter method was more effective at removing the neutral detergent-soluble as well as remaining organic matter, which was generated due to a higher KCl content in the ash.