Effects of biocontrol Bacillus and fermentation bacteria additions on the microbial community, functions and antibiotic resistance genes of prickly ash seed oil meal-biochar compost

Ionic liquid coupled plasma promotes acetic acid production during anaerobic fermentation of waste activated sludge: Breaking the restrictions of low bioavailable substrates and altering the metabolic activities of anaerobes

This study explored the potential application of plasma coupling ionic liquid on disintegration of waste activated sludge and enhanced production of short-chain fatty acids (SCFAs) in anaerobic fermentation. Under optimal conditions (dosage of ionic liquid [Emim]OTf = 0.1 g/g VSS (volatile suspended solids) and discharge power of dielectric barrier discharge plasma (DBD) = 75.2 W), the [Emim]OTf/DBD pretreatment increased SCFA production by 302 % and acetic acid ratio by 53 % compared to the control. Mechanistic investigations revealed that the [Emim]OTf/DBD combination motivated the generation of various reactive species (such as H2O2, O3, •OH, 1O2, ONOO-, and •O2-) and enhanced the utilization of physical energies (such as heat). The coupling effects of [Emim]OTf/DBD synergistically improved the disintegration of sludge and biodegradability of dissolved organic matter, promoting the sludge anaerobic fermentation process. Moreover, the [Emim]OTf/DBD pretreatment enriched hydrolysis and SCFAs-forming bacteria while inhibiting SCFAs-consuming bacteria. The net effect was pronounced expression of genes encoding key enzymes (such as alpha-glucosidase, endoglucanase, beta-glucosidase, l-lactate/D-lactate dehydrogenase, and butyrate kinase) involved in the SCFA-producing pathway, enhancing the production of SCFAs from sludge anaerobic fermentation. In addition, [Emim]OTf/DBD pretreatment facilitated sludge dewatering and heavy metal removal. Therefore, [Emim]OTf/DBD pretreatment is a promising approach to advancing sludge reduction, recyclability, and valuable resource recovery.

The regulation pathways of biochar and microorganism in soil-plant system by multiple statistical methods: The forms of carbon participation in coastal wetlands

Coastal wetlands possess significant carbon storage capabilities. However, in coastal soil-plant systems augmented with biochar and microorganisms, the mechanisms of these amendments and carbon participation remain unclear. This study utilized pot experiments to explore how Enteromorpha prolifera biochar and Arbuscular mycorrhizal fungi (AMF) affect soil organic carbon (SOC), carbon-related microbes, photosynthetic and osmotic system of Suaeda salsa. The results showed biochar reduced exchangeable sodium percentage by 6.9% through adsorption and ion exchange, and increased SOC content by 34.4%. The abundance of carbon-related microorganisms (Bacteroidota and Chloroflexi) was increased and carbon metabolizing enzyme (cellulase and sucrase) activity in the soil was enhanced. AMF significantly improved plant growth compared with CK, as evidenced by the enhanced dry weight by 2.34 times. A partial least squares pathway model (PLS-PM) and correlation analysis suggested that the combined effect of biochar and AMF could be outlined as two pathways: soil and plant. Biochar increased SOC, improved the growth of soil carbon metabolizing microorganisms, and further promoted the activity of carbon-related enzymes. Additionally, AMF facilitated nutrient absorption by plants through root symbiosis, with biochar further enhancing this process by acting as a nutrient adsorber. These combined effects of biochar and AMF at soil and plant level enhanced the photosynthetic process of Suaeda salsa. The transport of photosynthetic products to the roots can increase the carbon storage in the soil. This study provides quantitative evidence supporting the increase of carbon storage in coastal wetland soil-plant systems through a combined application of biochar and AMF.

Impact of Ganoderma lucidum fermentation on the nutritional composition, structural characterization, metabolites, and antioxidant activity of Soybean, sweet potato and Zanthoxylum pericarpium residues

One of the major issues in the food sector is the lack of resource utilization and the contamination of the environment caused by by-products. This study aimed to investigate the effects of Ganoderma lucidum (GL) fermentation on the nutritional components, structural characterization, metabolites, and antioxidant activity of soybean residue (SR), sweet potato residue (SPR), and zanthoxylum pericarpium residue (ZPR). The results showed that the nutrient contents of SR, SPR and ZPR increased. The active substances, amino acids (umami, aromatic and basic), metabolites and antioxidant activity (DPPH, ABTS, FRAP) (SR and SPR increased by 11.43, 32.64, 40.19 μmol Trolox/100 g and 19.29, 17.7, 32.35 μmol Trolox/100 g, respectively) of SR and SPR were increased. However, the results of ZPR showed a decrease in the content of bioactive substances, amino acids, and antioxidant activity. The results show that using GL fermentation can provide novel ideas and theoretical basis for improving SR and SPR to obtain new raw materials for antioxidant products.

Microbial phylogenetic divergence between surface-water and sedimentary ecosystems drove the resistome profiles

Antibiotic pollution and the evolution of antibiotic resistance genes (ARGs) are increasingly viewed as major threats to both ecosystem security and human health, and have drawn attention. This study investigated the fate of antibiotics in aqueous and sedimentary substrates and the impact of ecosystem shifts between water and sedimentary phases on resistome profiles. The findings indicated notable variations in the concentration and distribution patterns of antibiotics across various environmental phases. Based on the partition coefficient (Kd), the total antibiotic concentration was significantly greater in the surface water (1405.45 ng/L; 49.5 %) compared to the suspended particulate matter (Kd = 0.64; 892.59 ng/g; 31.4 %) and sediment (Kd = 0.4; 542.64 ng/g; 19.1 %). However, the relative abundance of ARGs in surface water and sediment was disproportionate to the abundance of antibiotics concentration, and sediments were the predominant ARGs reservoirs. Phylogenetic divergence of the microbial communities between the surface water and the sedimentary ecosystems potentially played important roles in driving the ARGs profiles between the two distinctive ecosystems. ARGs of Clinical importance; including blaGES, MCR-7.1, ermB, tet(34), tet36, tetG-01, and sul2 were significantly increased in the surface water, while blaCTX-M-01, blaTEM, blaOXA10-01, blaVIM, tet(W/N/W), tetM02, and ermX were amplified in the sediments. cfxA was an endemic ARG in surface-water ecosystems while the endemic ARGs of the sedimentary ecosystems included aacC4, aadA9-02, blaCTX-M-04, blaIMP-01, blaIMP-02, bla-L1, penA, erm(36), ermC, ermT-01, msrA-01, pikR2, vgb-01, mexA, oprD, ttgB, and aac. These findings offer a valuable information for the identification of ARGs-specific high-risk reservoirs.

Comparison analysis of microbial agent and different compost material on microbial community and nitrogen transformation genes dynamic changes during pig manure compost

This study aimed to assess the impact of microbial agent and different compost material, on physicochemical parameters dynamic change, nitrogen-transfer gene/bacterial community interaction network during the pig manure composting. Incorporating a microbial agent into rice straw-mushroom compost reduced the NH3 and total ammonia emissions by 25.52 % and 14.41 %, respectively. Notably, rice straw-mushroom with a microbial agent reduced the total ammonia emissions by 37.67 %. NH4+-N and pH emerged as primary factors of phylum-level and genus-level microorganisms. Microbial agent increased the expression of narG, nirK, and nosZ genes. Rice straw-mushroom elevated the content of amoA, nirK, nirS, and nosZ genes. Alcanivorax, Luteimonas, Pusillimonas, Lactobacillus, Aequorivita, Clostridium, Moheibacter and Truepera were identified as eight core microbial genera during the nitrogen conversion process. This study provides a strategy for reducing ammonia emissions and analyzes the potential mechanisms underlying compost processes.

Microbial organic fertilizer prepared by co-composting of Trichoderma dregs mitigates dissemination of resistance, virulence genes, and bacterial pathogens in soil and rhizosphere

The use of manure, mycelium dregs and other waste as organic fertilizer is the main source of antibiotic resistance genes (ARGs) and pathogens in farmland. Composting of waste may effectively remove ARGs and pathogens. However, the profiles and drivers of changes in metal resistance genes (MRGs), biocide resistance genes (BRGs), and virulence genes (VGs) in soil-crop rhizosphere systems after compost application remain largely unknown. Here, we prepared two kinds of microbial organic fertilizers (MOF) by using Trichoderma dregs (TDs) and organic fertilizer mixing method (MOF1) and TDs co-composting method (MOF2). The effects of different types and doses of MOF on resistance genes, VGs and pathogens in soil-rhizosphere system and their potential mechanisms were studied. The results showed that co-composting of TDs promoted the decomposition of organic carbon and decreased the absolute abundance of ARGs and mobile genetic elements (MGEs) by 53.4-65.0%. MOF1 application significantly increased the abundance and diversity of soil ARGs, BRGs, and VGs, while low and medium doses of MOF2 significantly decreased their abundance and diversity in soil and rhizosphere. Patterns of positive co-occurrence between MGEs and VGs/MRGs/BRGs/ARGs were observed through statistical analysis and gene arrangements. ARGs/MRGs reductions in MOF2 soil were directly driven by weakened horizontal gene transfer triggered by MGEs. Furthermore, MOF2 reduced soil BRGs/VGs levels by shifting bacterial communities (e.g., reduced bacterial host) or improving soil property. Our study provided new insights into the rational use of waste to minimize the spread of resistomes and VGs in soil.

Microbial agents obtained from tomato straw composting effectively promote tomato straw compost maturation and improve compost quality

Appropriate management of agricultural organic waste (AOW) presents a significant obstacle in the endeavor to attain sustainable agricultural development. The proper management of AOW is a necessity for sustainable agricultural development. This can be done skillfully by incorporating microbial agents in the composting procedure. In this study, we isolated relevant bacteria strains from tomato straw AOW, which demonstrated efficient degradation of lignocellulose without any antagonistic effects in them. These strains were then combined to create a composite microbial agent called Zyco Shield (ZS). The performance of ZS was compared with a commercially effective microorganism (EM) and a control CK. The results indicate that the ZS treatment significantly prolonged the elevated temperature phase of the tomato straw pile, showing considerable degradation of lignocellulosic material. This substantial degradation did not happen in the EM and CK treatments. Moreover, there was a temperature rise of 4-6 ℃ in 2 days of thermophilic phase, which was not the case in the EM and CK treatments. Furthermore, the inoculation of ZS substantially enhanced the degradation of organic waste derived from tomato straw. This method increased the nutrient content of the resulting compost and elevated the enzymatic activity of lignocellulose-degrading enzymes, while reducing the urease enzyme activity within the pile. The concentrations of NH4+-N and NO3--N showed increases of (2.13% and 47.51%), (14.81% and 32.17%) respectively, which is again very different from the results of the EM and CK treatments. To some extent, the alterations observed in the microbial community and the abundance of functional microorganisms provide indirect evidence supporting the fact that the addition of ZS microbial agent facilitates the composting process of tomato straw. Moreover, we confirmed the degradation process of tomato straw through X-ray diffraction, Fourier infrared spectroscopy, and by scanning electron microscopy to analyze the role of ZS microbial inoculum composting. Consequently, reinoculation compost strains improves agricultural waste composting efficiency and enhances product quality.

Searching for Antimicrobial-Producing Bacteria from Soils through an Educational Project and Their Evaluation as Potential Biocontrol Agents

Antimicrobial resistance (AMR) is a serious threat to public health due to the lack of effective drugs to combat infectious diseases, which generates the need to search for new antimicrobial substances. In this study, the potential of soil as a source of antimicrobial-producing bacteria (APB) was investigated and the importance of the connection between education and science was emphasized, using service-learning methodologies. Sixty-one soil samples were collected, and 1220 bacterial isolates were recovered. Eighteen of these isolates showed antimicrobial activity against at least 1 of the 12 indicator bacteria tested (including multidrug-resistant and relevant pathogens). The 18 APB were identified by MALDI-TOF and 6 different genera (Bacillus, Brevibacillus, Lysinobacillus, Peribacillus, Streptomyces, and Advenella) and 10 species were identified. The 18 APB were tested for antifungal activity against four phytopathogenic fungi (Botritis cynerea, Lecanicillium fungicola, Trichoderma harzianum, and Cladobotryum mycophilum). Moreover, the antibiotic susceptibility of APB was tested using the disk-diffusion method as well as their β-hemolytic activity (important safety criteria for potential future applications). A total of 10 of the 18 APB were able to inhibit at least 50% of indicator bacteria tested, including methicillin-resistant Staphylococcus aureus (MRSA), among others. A total of 4 of the 18 APB (3 Bacillus pumilus and 1 Bacillus altitudinis) showed inhibitory activity against two of the four fungal pathogens tested (B. cinerea and L. fungicola), as well as against 5-7 of the 12 bacterial pathogen indicators; these 4 isolates showed susceptibility to the antibiotics tested and lacked β-hemolytic activity and were considered promising APB for use as potential biocontrol agents. In addition, one Brevibacillus laterosporus strain had activity against 83% of indicator bacteria tested including Escherichia coli, MRSA and other methicillin-resistant staphylococci, as well as vancomycin-resistant enterococci (but not against fungi). These results show that soil is a source of APB with relevant antibacterial and antifungal activities, and also emphasize the importance of education and science to raise public awareness of the AMR problem and the strategies to control it.

Waste seaweed compost and rhizosphere bacteria Pseudomonas koreensis promote tomato seedlings growth by benefiting properties, enzyme activities and rhizosphere bacterial community in coastal saline soil of Yellow River Delta, China

This study investigated the effects of waste seaweed compost and rhizosphere bacteria Pseudomonas koreensis HCH2-3 on the tomato seedlings growth in coastal saline soils and chemical properties, enzyme activities, microbial communities of rhizosphere soil. Microcosmic experiment showed that the seaweed compost and rhizosphere bacteria (SC + HCH2-3) significantly alleviated the negative effects of salinity on the growth of tomato seedlings. SC + HCH2-3 amendment significantly increased the plant height and root fresh biomass of tomato seedling by 105.59% and 55.60% in the coastal saline soils, respectively. The soil properties and enzyme activities were also dramatically increased, indicating that the nutrient status of coastal saline soil was improved by SC + HCH2-3 amendment. In addition, Proteobacteria, Actinobacteriota and Firmicutes were the dominant phyla in the rhizosphere soil after adding seaweed compost and rhizosphere bacteria P. koreensis HCH2-3. The relative abundances of Massilia, Azospira, Pseudomonas and Bacillus increased in treatment SC + HCH2-3. Especially, the beneficial bacteria genera, such as Pseudomonas, Bacillus and Azospira, were significantly correlated with the increases of contents of total nitrogen, nitrate nitrogen and ammonium nitrogen in tomato rhizosphere soil samples. Consequently, adding waste seaweed compost and rhizosphere bacteria P. koreensis HCH2-3 into coastal saline soil was suggested as an effective method to relieve salt stress of tomato plants.

Combinations of waste seaweed liquid fertilizer and biochar on tomato (Solanum lycopersicum L.) seedling growth in an acid-affected soil of Jiaodong Peninsula, China

Biochar application is an effective strategy for improving soil degradation and productivity. However, the effects of the combination of biochar and other fertilizers to improve seedling growth in abiotic stress-affected soils remains unknown. We investigate the effect of biochar derived from reed straw (RBC) and waste seaweed liquid fertilizer (SLF) on tomato (Solanum lycopersicum L.) seedling growth in an acid-affected soil of Jiaodong Peninsula, China. The results revealed RBC, SLF, and the combination of RBC with SLF (RBC+SLF) significantly elevated the dry weight of tomatoes by 23.33 %, 29.93 %, and 63.66 %, respectively. The malondialdehyde content in the tomato seedling roots, stems, and leaves was significantly lower in the RBC+SLF treatment, which might be related to the enhanced contents of proline, soluble sugar, and soluble protein. The synthesis and accumulation of zeatin riboside, indole-3-acetic acid, and gibberellic acid 3 in tomato under RBC+SLF amendment may be attributed to the enhanced plant growth. Moreover, RBC, SLF, and RBC+SLF improved the soil status (including ammonium nitrogen, nitrate nitrogen, laccase, and urease) in the acid-affected soil. Biochar and waste seaweed liquid fertilizer significantly increased the relative abundance of Pseudomonas and Azospira (beneficial bacteria) in tomato rhizosphere. The microbial amino acid metabolism was associated with changes in soil properties and enzyme activities. Consequently, biochar and waste seaweed liquid fertilizer are viable soil conditioners for acid-affected soil.

Effects of different botanical oil meal mixed with cow manure organic fertilizers on soil microbial community and function and tobacco yield and quality

Introduction

The continuous application of cow manure in soil for many years leads to the accumulation of heavy metals, pathogenic microorganisms, and antibiotic resistance genes. Therefore, in recent years, cow manure has often been mixed with botanical oil meal as organic fertilizer applied to farmland to improve soil and crop quality. However, the effects of various botanical oil meal and cow manure mixed organic fertilizers on soil microbial composition, community structure, and function, tobacco yield, and quality remain unclear.

Methods

Therefore, we prepared organic manure via solid fermentation by mixing cow manure with different oil meals (soybean meal, rape meal, peanut bran, sesame meal). Then, we studied its effects on soil microbial community structure and function, physicochemical properties, enzyme activities, tobacco yield and quality; then we analyzed the correlations between these factors.

Results and discussion

Compared with cow manure alone, the four kinds of mixed botanical oil meal and cow manure improved the yield and quality of flue-cured tobacco to different degrees. Peanut bran, which significantly improved the soil available phosphorus, available potassium, and NO₃^--N, was the best addition. Compared with cow manure alone, soil fungal diversity was significantly decreased when rape meal or peanut bran was combined with cow manure, while soil bacterial and fungal abundance was significantly increased when rape meal was added compared with soybean meal or peanut bran. The addition of different botanical oil meals significantly enriched the subgroup_7 and Spingomonas bacteria and Chaetomium and Penicillium fungi in the soil. The relative abundances of functional genes of xenobiotics biodegradation and metabolism, soil endophytic fungi, and wood saprotroph functional groups increased. In addition, alkaline phosphatase had the greatest effect on soil microorganisms, while NO₃^--N had the least effect on soil microorganisms. In conclusion, the mixed application of cow manure and botanical oil meal increased the available phosphorus and potassium contents in soil; enriched beneficial microorganisms; promoted the metabolic function of soil microorganisms; increased the yield and quality of tobacco; and improved the soil microecology.

Exogenous microbial antagonism affects the bioaugmentation of humus formation under different inoculation using Trichoderma reesei and Phanerochaete chrysosporium

This study was aimed at exploring the effect of antagonism of Trichoderma reesei (T.r) and Phanerochaete chrysosporium (P.c) on humification during fermentation of rice (RS) and canola straw (CS). Results showed that exogeneous fungi accelerated straw degradation and enzyme activities of CMCase, xylanase and LiP. P.c inhibited the activity of LiP when co-existing with T.r beginning, it promoted the degradation of lignin and further increased the production of humus-like substances (HLS) and humic-like acid (HLA) in later fermentation when nutrients were insufficient. The HLS of RTP was 54.9 g/kg RS, higher than the other treatments, and displayed more complex structure and higher thermostability. Brucella and Bacillus were the main HLA bacterial producers. P.c was the HLA fungal producer, while T.r assisted FLA and polyphenol transformation. Therefore, RTP was recommended to advance technologies converting crop straw into humus resources.

Response characteristics of antibiotic resistance genes and bacterial communities during agricultural waste composting: Focusing on biogas residue combined with biochar amendments

This research investigated biogas residue and biochar addition on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and changes in bacterial community during agricultural waste composting. Sequencing technique investigated bacterial community structure and ARGs, MGEs changes. Correlations among physicochemical factors, ARGs, MGEs, and bacterial community structure were determined using redundancy analysis. Results confirmed that biochar and biogas residue amendments effectively lowered the contents of ARGs and MGEs. The main ARGs detected was sul1. Proteobacteria and Firmicutes were the main host bacteria strongly associated with the dissemination of ARGs. The dynamic characteristics of the bacterial community were strongly correlated with pile temperature and pH (P < 0.05). Redundancy and network analysis revealed that nitrate, intI1, and Firmicutes mainly affected the in ARGs changes. Therefore, regulating these key variables would effectively suppress the ARGs spread and risk of compost use.

Combined use of biochar and microbial agent can promote lignocellulose degradation and humic acid formation during sewage sludge-reed straw composting

This study investigated the effects of corn straw biochar (CSB) and effective microorganisms (EM) added individually or combinedly on lignocellulose degradation, compost humification, and microbial communities during sewage sludge-reed straw composting process. All the additive practices were found to significantly elevate the humification degree of compost products. The degradation rates of cellulose, hemicellulose, and lignin in different additive treatments were 20.8-31.2 %, 36.2-44.8 %, and 19.9-25.7 %, respectively, which were greatly higher than those of the control. Compared with the single uses of CSB or EM, the combined use of CSB and EM generated greater promotions in lignin and hemicellulose degradations and increase in humic acid content. By comparing the differences in microbial communities among different treatments, the CSB-EM demonstrated greater increases in activity and diversity of lignocellulose degradation-related microbes, especially for fungus. Lastly, the combined use of CSB and EM was highly recommended as a high-efficient improvement strategy for organic compost production.

Biochar-amended composting of lincomycin fermentation dregs promoted microbial metabolism and reduced antibiotic resistance genes

Improper disposal of antibiotic fermentation dregs poses a risk of releasing antibiotics and antibiotic resistant bacteria to the environment. Therefore, this study evaluated the effects of biochar addition to lincomycin fermentation dregs (LFDs) composting. Biochar increased compost temperature and enhanced organic matter decomposition and residual antibiotics removal. Moreover, a 1.5- to 17.0-fold reduction in antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) was observed. Adding biochar also reduced the abundances of persistent ARGs hosts (e.g., Streptomyces, Pseudomonas) and ARG-related metabolic pathways and genes (e.g., ATP-binding cassette type-2 transport, signal transduction and multidrug efflux pump genes). By contrast, compost decomposition improved due to enhanced metabolism of carbohydrates and amino acids. Overall, adding biochar into LFDs compost reduced the proliferation of ARGs and enhanced microbial community metabolism. These results demonstrate that adding biochar to LFDs compost is a simple and efficient way to decrease risks associated with LFDs composting.

Potential utilization of vitamin C industrial effluents in agriculture: Soil fertility and bacterial community composition

The potential of industrial effluents from vitamin C (VC) production was assessed for agricultural applications by monitoring plant growth, soil properties, and microbial community structure. The results demonstrated that two types of effluents-residue after evaporation (RAE) and concentrated bacterial solution after ultrafiltration (CBS)-had positive effects on the yield and VC content of pak choi. The highest yield and VC content were achieved with a combined RAE-CBS treatment (55.82 % and 265.01 % increase, respectively). The soil fertility was also enhanced by the application of RAE and CBS. Nitrate nitrogen and organic carbon contents in the soil were positively correlated with the RAE addition, while ammonium nitrogen and available phosphorus were positively correlated with the CBS addition. The diversity of bulk and rhizosphere soil bacterial communities increased significantly after the addition of RAE-CBS. The abundance of Sphingomonas and Rhizobium significantly increased after the RAE-CBS treatment, which affected aromatic compound hydrolysis and nitrogen fixation positively. Changes in plant growth and soil fertility were closely related to the upregulation of functional gene expression related to C, N, and P cycling. RAE and CBS application exerted various positive synergistic effects on plant growth, soil fertility, and bacterial community structure. Consequently, the study results confirmed the potential of RAE and CBS application in agriculture. This study provides an innovative solution for utilizing VC industrial wastewater in agriculture in a resourceful and economically beneficial manner while alleviating the corresponding environmental burden.

Exploring the impact of biochar supplement on the dynamics of antibiotic resistant fungi during pig manure composting

The purpose of this study was to investigate antibiotic resistant fungal (ARF) communities in pig manure (PM) composting employing two different biochar (coconut shell-CSB and bamboo biochar-BB) as amendment. Three treatments (Control, 10% CSB and 10% BB) were designed and indicated with T1 to T3. Experimental results declared that the fungal abundance significantly reduced among the both biochar applied treatments but three dominant phyla Ascomycota, Basidiomycota and Mucoromycota were still relatively greater abundance present. There were significant differences (p < 0.05) in the relative abundance and diversity of fungi among all three treatments. Interestingly, biochar addition regulated the overall fungal community in final compost. Compared with the control group, the abundance of fungi was positively mobilized, and especially CSB showed a better effect. Conclusively, biochar has potential to inhibit and reduce the ARGs population and mobility in compost. Thus, these findings offer new insight to understand the succession of ARFs during PM composting.

Characteristics of carbon, nitrogen, phosphorus and sulfur cycling genes, microbial community metabolism and key influencing factors during composting process supplemented with biochar and biogas residue

Carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling functional genes and bacterial and fungal communities during composting with biochar and biogas residue amendments were studied. Correlations between microbial community structure, functional genes and physicochemical properties were investigated by network analysis and redundancy analysis. It was shown that the gene of acsA abundance accounted for about 50% of the C-related genes. Biogas residue significantly decreased the abundance of denitrification gene nirK. Biogas residues can better promote the diversity of bacteria and fungi during composting. Biochar significantly increased the abundance of Humicola. Redundancy analysis indicated that pile temperature, pH, EC were the main physicochemical factors affecting the microbial community. WSC and NO₃^--N have significant correlation with C, N, P, S functional genes. The research provides a theoretical basis for clarifying the metabolic characteristics of microbial communities during composting and for the application of biochar and biogas residues in composting.

Biochar amendment of aerobic composting for the effective biodegradation of heavy oil and succession of bacterial community

Soil pollution caused by petroleum pollutants from production trade activities in petroleum-related factories contributes serious threat to the environment and human health. Composting is technically-feasible and cost-effective in the biodegradation of heavy oil pollutants. This composting experiment was developed with four rice husk biochar (RHB) concentrations of 0 wt% (CK), 5 wt% (S1), 10 wt% (S2) and 15 wt% (S3) for the degradation of heavy oil. The results showed that RHB amendment could strengthen the degradation performance of heavy oil, and the degradation efficiencies for CK, S1, S2 and S3 were 59.67%, 65.00%, 73.29% and 74.82%, respectively. Microbial community succession process was investigated through high-throughput sequencing technology, and the RHB addition regulated bacterial community succession and further effectively facilitated the biodegradation of heavy oil in composting. This study substantiated that biochar materials-amended aerobic composting would be a promising strategy for the biodegradation of petroleum pollutants.

Occurrence of polycyclic aromatic compounds and interdomain microbial communities in oilfield soils

Soil polycyclic aromatic compound (PAC) pollution as a result of petroleum exploitation has caused serious environmental problems. The unclear assembly and functional patterns of microorganisms in oilfield soils limits the understanding of microbial mechanisms for PAC elimination and health risk reduction. This study investigated the polycyclic aromatic hydrocarbons (PAHs) and substituted PAHs (SPAHs) occurrence, and their impact on the bacteria-archaea-fungi community diversity, co-occurrence network and functionality in the soil of an abandoned oilfield. The results showed that the PAC content in the oilfield ranged from 3429.03 μg kg^-1 to 6070.89 μg kg^-1, and risk assessment results suggested a potential cancer risk to children and adults. High molecular weight PAHs (98.9%) and SPAHs (1.0%) contributed to 99.9% of the toxic equivalent concentration. For microbial analysis, the abundantly detected degraders and unigenes indicated the microbial potential to mitigate pollutants and reduce health risks. Microbial abundance and diversity were found to be negatively correlated with health risk. The co-occurrence network analysis revealed nonrandom assembly patterns of the interdomain microbial communities, and species in the network exhibited strong positive connections (59%). The network demonstrated strong ecological linkages and was divided into five smaller coherent modules, in which the functional microbes were mainly involved in organic substance and mineral component degradation, biological electron transfer and nutrient cycle processes. The keystone species for maintaining microbial ecological functions included Marinobacter of bacteria and Neocosmospora of fungi. Additionally, benzo [g,h,i]pyrene, dibenz [a,h]anthracene, indeno [1,2,3-cd]perylene and total phosphorus were the key environmental factors driving the assembly and functional patterns of microbial communities under pollution stress. This work improves the knowledge of the functional pattern and environmental adaptation mechanisms of interdomain microbes, and provides valuable guidance for the further bioremediation of PAC-contaminated soils in oilfields.

Deciphering the internal driving mechanism of microbial community for carbon conversion and nitrogen fixation during food waste composting with multifunctional microbial inoculation

In this study, the effects of multifunctional microbial inoculation on food waste composting based on the synergistic property between organic matter degradation and nitrogen fixation were investigated. The results showed that inoculation simultaneously strengthened organic matter degradation by 9.9% and improved the nitrogen content by 20.6% compared with that of the control group. Additionally, spectral analysis demonstrated that inoculation was conducive to the enhanced humification, which was supported by the improvement in polyphenol oxidase activity. Microbial analysis showed that most of the introduced microorganisms (Bacillus, Streptomyces, Saccharomonospora) successfully colonized, and stimulated the growth of other indigenous microorganisms (Enterobacter, Paenibacillus). Meanwhile, the change in microbial community structure was accompanied by the enhanced tricarboxylic acid cycle and amino acid metabolism. Furthermore, network analysis and structural equation model revealed that the enhanced cooperation of microorganisms, in which more carbon sources could be provided by cellulose decomposition for nitrogen fixation.

Coupling of desorption of phenanthrene from marine sediments and biodegradation of the sediment washing solution in a novel biochar immobilized-cell reactor

The recurrent dredging of marine sediments needs the use of ex-situ technologies such as sediment washing (SW) to effectively remove polycyclic aromatic hydrocarbons. Notwithstanding, the large volumes of generated spent SW effluents require adequate treatment by employing highly-efficient, inexpensive and environmentally-friendly solutions. This study proposes the phenanthrene (PHE) desorption from sediments using Tween® 80 (TW80) as extracting agent and the treatment of the resulting spent SW solution in a biochar (BC) immobilized-cell bioreactor. The SW process reached the highest PHE removal of about 91% using a surfactant solution containing 10,800 mg L^-1 of TW80. The generated amount of spent PHE-polluted SW solution can be controlled by keeping a solid to liquid ratio of 1:4. A PHE degradation of up to 96% was subsequently achieved after 43 days of continuous reactor operation, aerobically treating the TW80 solution in the BC immobilized-cell bioreactor with a hydraulic retention time of 3.5 days. Brevundimonas, Chryseobacterium, Dysgonomonas, Nubsella, and both uncultured Weeksellaceae and Xanthobacteraceae genera were mainly involved in PHE biodegradation. A rough economic study showed a total cost of 342.60 € ton^-1 of sediment, including the SW operations, TW80 and BC supply and the biological treatment of the SW solution.

Microbiome, Transcriptome, and Metabolomic Analyses Revealed the Mechanism of Immune Response to Diarrhea in Rabbits Fed Antibiotic-Free Diets

In this study, diarrhea was induced in rabbits by feeding them antibiotic-free feed. The gut provides important defense against the barriers of the body, of which the duodenum is an important part to help digest food and absorb nutrients. However, the mechanisms underlying the roles of the gut microbiome and fecal metabolome in rabbit diarrhea caused by feeding an antibiotic-free diet have not been characterized. Recently, only a single study has been conducted to further characterize the antibiotic-free feed additives that caused diarrhea in weaned rabbits. The multi-omics techniques, including 16S rRNA sequencing, transcriptome sequencing, and LC-MS analysis, were combined to analyze the gut microbial compositions and functions. They also determined the fecal metabolomic profiles of diarrhea in rabbits caused by feeding antibiotic-free feed. The results showed that the liver, duodenal, and sacculus rotundus tissues of diarrhea rabbits were diseased, the composition of intestinal microbes was significantly changed, the diversity of intestinal microbes was decreased, and the distribution of intestinal microbe groups was changed. Functional analysis based on the cluster of GO and KEGG annotations suggested that two functional GO categories belonged to the metabolism cluster, and five KEGG pathways related to the metabolic pathways were significantly enriched in diarrhea rabbits. Moreover, real-time quantitative PCR (RT-qPCR) was used to verify the significant expression of genes related to diarrhea. Metabolomics profiling identified 432 significantly differently abundant metabolites in diarrhea rabbits, including amino acids and their derivatives. These amino acids were enriched in the tryptophan metabolic pathway. In addition, the functional correlation analysis showed that some altered gut microbiota families, such as Parasutterella, significantly correlated with alterations in fecal metabolites. Collectively, the results suggested that altered gut microbiota was associated with diarrhea caused by antibiotic-free feed additives in weaned rabbit pathogenesis.

A Review of Current Bacterial Resistance to Antibiotics in Food Animals

The overuse of antibiotics in food animals has led to the development of bacterial resistance and the widespread of resistant bacteria in the world. Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in food animals are currently considered emerging contaminants, which are a serious threat to public health globally. The current situation of ARB and ARGs from food animal farms, manure, and the wastewater was firstly covered in this review. Potential risks to public health were also highlighted, as well as strategies (including novel technologies, alternatives, and administration) to fight against bacterial resistance. This review can provide an avenue for further research, development, and application of novel antibacterial agents to reduce the adverse effects of antibiotic resistance in food animal farms.

Integrated meta-omics study on rapid tylosin removal mechanism and dynamics of antibiotic resistance genes during aerobic thermophilic fermentation of tylosin mycelial dregs

For efficient treatment of tylosin mycelial dregs (TMDs), rapid tylosin removal mechanism and dynamics of ARGs during TMDs fermentation were investigated using integrated meta-omics (genomics, metaproteomics and metabolomics) and qPCR approaches. The results showed that over 86% of tylosin was degraded on day 7 regardless of the type of bulking agents. The rapid removal of tylosin was mainly attributed to de-mycarose reaction (GH3) and esterase hydrolysis (C7MYQ7) of Saccharomonospora, and catalase-peroxidase oxidation of Bacillus (A0A077JB13). In addition, the moisture content and mobile genetic elements were vital to control the rebound of ARGs. The removal efficiency of antibiotic resistant bacteria (Streptomyces, Pseudomonas, norank_f__Sphingobacteriaceae, and Paenalcaligenes) and Intl1 (98.8%) in fermentation treatment TC21 with corncob as the bulking agent was significantly higher than that in other three treatments (88.3%). Thus, appropriate bulking agents could constrain the abundance of antibiotic resistant bacteria and Intl1, which is crucial to effectively reduce the resistance.

The relationship between material transformation, microbial community and amino acids and alkaloid metabolites in the mushroom residue-prickly ash seed oil meal composting with biocontrol agent addition

This study investigated the effects of adding biocontrol microbes on metabolites and pathogenic microorganisms during mushroom residue composting and the relationships of metabolite changes with microbes and material transformation. The results showed that the addition of Bacillus subtilis (BS) and Trichoderma harzianum (TH) with mushroom residue promoted the conversion of organic carbon and nitrogen. The abundance of pathogenic microbes was increased in biocontrol microbial treatments. BS or TH treatments increased the levels of amino acids, carbohydrates, and bacteriostatic alkaloid metabolites. Network analysis revealed that the main microorganisms significantly related to alkaloid metabolites were Rhabdanaerobium, Atopostipes, Planifilum and Ureibacillus. The increased bacterial abundance and decreased NO₃^--N and TOC were closely related to the increases in amino acid and alkaloid metabolites after biocontrol agent treatments. Generally, adding biocontrol microbes is an effective way to increase the levels of antibacterial metabolites, but there is a risk of increasing the abundance of pathogenic microbes.