Greenhouse gas emission characteristics and influencing factors of agricultural waste composting process: A review.

China, being a major agricultural nation, employs aerobic composting as an efficient approach to handle agricultural solid waste. Nevertheless, the composting process is often accompanied by greenhouse gas emissions, which are known contributors to global warming. Therefore, it is urgent to control the formation and emission of greenhouse gases from composting. This study provides a comprehensive analysis of the mechanisms underlying the production of nitrous oxide, methane, and carbon dioxide during the composting process of agricultural wastes. Additionally, it proposes an overview of the variables that affect greenhouse gas emissions, including the types of agricultural wastes (straw, livestock manure), the specifications for compost (pile size, aeration). The key factors of greenhouse gas emissions during composting process like physicochemical parameters, additives, and specific composting techniques (reuse of mature compost products, ultra-high-temperature composting, and electric-field-assisted composting) are summarized. Finally, it suggests directions and perspectives for future research. This study establishes a theoretical foundation for achieving carbon neutrality and promoting environmentally-friendly composting practices.

High intestinal isoleucine is a potential risk factor for food allergy by regulating the mTOR/AKT pathway in dendritic cells.

Food allergy is a global food safety problem with a growing prevalence. People in industrial regions are more susceptible to allergy, but the mechanisms behind this are not fully understood. In this study, the probiotic Lactobacillus casei Zhang (LcZ) was administered to allergic individuals and the impact on allergy-related factors were determined. LcZ alleviated allergenic responses, and there was a significant correlation between the intestinal isoleucine content and IgE concentration. Metagenomics results suggest that the metabolism of the gut microbiota is a source of isoleucine. In a mouse model of food allergy, a high isoleucine diet exacerbated allergic responses and increased the activity of allergenic dendritic cell. In a dendritic cell model, a protein array revealed that the mTOR/AKT pathway mediated the function of isoleucine, and molecular docking suggested that Sestrin2 could be the potential receptor. Overall, this study revealed the role of isoleucine in promoting food allergy, elucidated the underlying mechanisms, and suggested that a high intake of isoleucine could be a potential risk factor for food allergy.

Carbohydrate polymer-based carriers for colon targeted delivery of probiotics.

Probiotics (PRO) have been recognized for their significant role in promoting human health, particularly in relation to colon-related diseases. The effective delivery of PRO to the colon is a fascinating area of research. Among various delivery materials, carbohydrates have shown great potential as colon-targeted delivery (CTD) carriers for PRO. This review explores the connection between probiotics and colonic diseases, delving into their underlying mechanisms of action. Furthermore, it discusses current strategies for the targeted delivery of active substances to the colon. Unlike other reviews, this work specifically focuses on the utilization of carbohydrates, such as alginate, chitosan, pectin, and other carbohydrates, for probiotic colon-targeted delivery applications. Carbohydrates can undergo hydrolysis at the colonic site, allowing their oligosaccharides to function as prebiotics or as direct functional polysaccharides with beneficial effects. Furthermore, the development of multilayer self-assembled coatings using different carbohydrates enables the creation of enhanced delivery systems. Additionally, chemical modifications of carbohydrates, such as for adhesion and sensitivity, can be implemented to achieve more customized delivery of PRO.

Arecoline alleviated loperamide induced constipation by regulating gut microbes and the expression of colonic genome.

This study aimed to investigate the effects of arecoline on constipation by intervening at different times to explore its preventive and therapeutic effects. Symptoms related to constipation, gut microbes, short-chain fatty acid (SCFA) content in the cecum, and gene expression in the colon were measured to examine the effect of arecoline on relieving constipation. The results showed that arecoline intervention alleviated loperamide-induced constipation, as evidenced by significantly shortened intestinal transit time, increased fecal water content, improved small bowel propulsion, and increased defecation frequency. In addition, arecoline significantly reduced the levels of gastrointestinal regulatory peptides such as somatostatin and vasoactive intestinal peptide in the serum, thereby regulating intestinal peristalsis. Histopathological analysis showed that arecoline ameliorated intestinal injury caused by constipation. Gut microbial analysis indicated that arecoline altered the taxonomic composition and levels of its metabolite SCFAs in the gut microbiota. Furthermore, the colonic transcriptome results indicated that genes expression related to intestinal diseases were significantly down-regulated by arecoline intervention. In conclusion, the results of the correlation analysis propose a possible mechanism of arecoline in alleviating constipation by modulating the gut microbes and their metabolites and regulating the gut genome.

Lactobacillus fermentum HNU312 alleviated oxidative damage and behavioural abnormalities during brain development in early life induced by chronic lead exposure.

Lead exposure is a global public health safety issue that severely disrupts brain development and causes damage to the nervous system in early life. Probiotics and gut microbes have been highlighted for their critical roles in mitigating lead toxicity. However, the underlying mechanisms by which they work yet to be fully explored. Here, we designed a two-stage experiment using the probiotic Lactobacillus fermentum HNU312 (Lf312) to uncover how probiotics alleviate lead toxicity to the brain during early life. First, we explored the tolerance and adsorption of Lf312 to lead in vitro. Second, the adsorption capacity of the strain was determined and confirmed in vivo. The shotgun metagenome sequencing showed lead exposure-induced imbalance and dysfunction of the gut microbiome. In contrast, Lf312 intake significantly modulated the structure of the microbiome, increased the abundance of beneficial bacteria and short-chain fatty acids (SCFAs)-producing bacteria, and upregulated function-related metabolic pathways such as antioxidants. Notably, Lf312 enhanced the integrity of the blood-brain barrier by increasing the levels of SCFAs in the gut, alleviated inflammation in the brain, and ultimately improved anxiety-like and depression-like behaviours induced by lead exposure in mice. Subsequently, the effective mechanism was confirmed, highlighting that Lf312 worked through integrated strategies, including ionic adsorption and microbiota-gut-brain axis regulation. Collectively, this work elucidated the mechanism by which the gut microbiota mitigates the toxic effects of lead in the brain and provides preventive measures and intervention measures for brain damage due to mass lead poisoning in children.

Short-term arecoline exposure affected the systemic health state of mice, in which gut microbes played an important role.

Arecoline is a critical bioactive component in areca nuts with toxicity and pharmacological activities. However, its effects on body health remain unclear. Here, we investigated the effects of arecoline on physiologic and biochemical parameters in mouse serum, liver, brain, and intestine. The effect of arecoline on gut microbiota was investigated based on shotgun metagenomic sequencing. The results showed that arecoline promoted lipid metabolism in mice, manifested as significantly reduced serum TC and TG and liver TC levels and a reduction in abdominal fat accumulation. Arecoline intake significantly modulated the neurotransmitters 5-HT and NE levels in the brain. Notably, arecoline intervention significantly increased serum IL-6 and LPS levels, leading to inflammation in the body. High-dose arecoline significantly reduced liver GSH levels and increased MDA levels, which led to oxidative stress in the liver. Arecoline intake promoted the release of intestinal IL-6 and IL-1ß, causing intestinal injury. In addition, we observed a significant response of gut microbiota to arecoline intake, reflecting significant changes in diversity and function of the gut microbes. Further mechanistic exploration suggested that arecoline intake can regulate gut microbes and ultimately affect the host's health. This study provided technical help for the pharmacochemical application and toxicity control of arecoline.

Occurrence, distribution and risk assessment of antibiotics at various aquaculture stages in typical aquaculture areas surrounding the Yellow Sea.

The pollution of antibiotics commonly existed throughout the entire aquaculture process, but the residues of antibiotics at different aquaculture stages have rarely been studied. This study investigated the occurrence, distribution and risk assessment of antibiotics at different aquaculture stages (the non-aquaculture stage, the early aquaculture stage, the middle aquaculture stage, and the late aquaculture stage) in two typical marine aquaculture areas (Mahegang River and Dingzi Bay) surrounding the Yellow Sea. Fluoroquinolones and tetracyclines were commonly used antibiotics in the aquaculture of these areas with high detection frequencies (17% to 83%). Compared among four aquaculture stages, the highest concentration of antibiotics (9032.08 ng/L) in aquaculture ponds was detected at the late aquaculture stage. And the antibiotic pollution level of natural water was directly related to the aquaculture stages. Similarly, at the aquaculture stages, the detection frequency of antibiotics in sediments was higher than that at the non-aquaculture stage. Based on the correlation analysis, the concentration of main antibiotics in water showed a positive correlation with total nitrogen (p<0.05) and chlorophyll a (p<0.01), while it showed a negative correlation with salinity (p<0.01) in coastal water of the Dingzi Bay. According to the risk assessment, with the development of aquaculture stages, the selection pressure of fluoroquinolones and tetracyclines on resistant bacteria had increased. And the ecological risks caused by sulfonamides and tetracyclines to aquatic organisms had also increased markedly. Overall, this study may provide a reference for formulating regulatory policies regarding antibiotic use at different aquaculture stages.

Silicon-based additive on heavy metal remediation in soils: Toxicological effects, remediation techniques, and perspectives.

Chemical fertilizer is gaining increasing attention and has been the center of much research which indicating complex beneficial and harmful effects. Chemical fertilizer might cause some environmental hazards to the biosphere, especially in the agricultural ecosystem. The application of silicon (Si) fertilizer in agriculture has been proved to be able to create good economic and environmental benefits. Si is the second most abundant earth crust element. Si fertilizer improves soil quality and alleviates biotic and abiotic crop stress. It is of great significance to understand the function of Si fertilizer in agricultural utilization and environmental remediation. This paper reviews the Si-based fertilizer in farmland use and summarizes prior research relevant with characterization, soil quality improvement, and pollution remediation effects. Its use in agriculture enhances plant silicon uptake, mediates plant salt and drought stress and remediates heavy metals such as Al, As, Cd, Cu, Zn and Cr. This article also summarizes the detoxification mechanism of silicon and its effects on plant physiological activity such as photosynthesis and transpiration. Fertilizer materials and crop fertilizer management were also considered. Foliar spraying is an effective method to improve crop growth and yield and reduce biotic or abiotic stress. Silicon nanoparticle material provides potential with great potential and prospects. More investigation and research are prospected to better understand how silicon impacts the environment and whether it is a beneficial additive.

The characteristics of alkaline phosphatase activity and phoD gene community in heavy-metal contaminated soil remediated by biochar and compost.

This research was carried out to determine the influence of biochar and compost addition on the characteristics of potential alkaline phosphatase (ALP) activity and phoD gene community in heavy metal polluted soils. The ALP activity, the abundance and structure of phoD gene were systematically determined. Results showed that biochar and compost significantly changed soil properties, and promoted the microbial transformation of phosphorus. Compost addition significantly increased the ALP activity. Biochar and compost addition markedly increased the phoD gene abundance. The addition of biochar increased the proportion of Actinobacteria, Euryarchaeota, and Proteobacteria. By contrast, Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were the dominant taxa in soils with compost addition. Electrical conductivity critically controlled the expression of phoD and changed the structure of phoD-coding microbial communities in heavy-metal polluted soils that remediated by biochar and compost.

Effects of different carbon sources on the removal of ciprofloxacin and pollutants by activated sludge: Mechanism and biodegradation.

This research investigated the effects of ciprofloxacin (CIP) (0.5, 5, and 20 mg/L) on SBR systems under different carbon source conditions. Microbial community abundance and structure were determined by quantitative PCR and high-throughput sequencing, respectively. The biodegradation production of CIP and possible degradation mechanism were also studied. Results showed that CIP had adverse effects on the nutrient removal from wastewater. Compared with sodium acetate, glucose could be more effectively used by microorganisms, thus eliminating the negative effects of CIP. Glucose stimulated the microbial abundance and increased the removal rate of CIP by 18%-24%. The mechanism research indicated that Proteobacteria and Acidobacteria had a high tolerance for CIP. With sodium acetate as a carbon source, the abundance of nitrite-oxidizing bacterial communities decreased under CIP, resulting in the accumulation of nitrite and nitrate. Rhodanobacter and Microbacterium played a major role in nitrification and denitrification when using sodium acetate and glucose as carbon sources. Dyella and Microbacterium played positive roles in the degradation process of CIP and eliminated the negative effect of CIP on SBR, which was consistent with the improved removal efficiency of pollutants.

Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava.

Cassava is one of the most important staple food crops in tropical regions. To date, an understanding of the relationship between microbial communities and disease resistance in cassava has remained elusive. In order to explore the relationship among microbiome and phenotypes for further targeted design of microbial community, 16S rRNA and ITS of microbiome of ten cassava varieties were analysed, and a distinctive microbial community in the rhizosphere showed significant interdependence with disease resistance. Shotgun metagenome sequencing was performed to elucidate the structure of microbiomes of cassava rhizosphere. Comprehensive microbiome studies were performed to assess the correlation between the rhizosphere microbiome and disease resistance. Subsequently, the metagenome of rhizosphere microbiome was annotated to obtain taxonomic information at species level and identify metabolic pathways that were significantly associated with cassava disease resistance. Notably, cassava disease resistance was significantly associated with Lactococcus sp., which specifically produces nisin. To definitively explain the role of nisin and underlying mechanism, analysis of nisin biosynthesis-associated genes together with in vitro and in vivo experiments highlighted the effect of nisin on inhibiting the growth of Xanthomonas axonopodis pv. manihotis (Xam) and activating immune response in cassava. The new insights between cassava rhizosphere microbiome especially Lactococcus sp. and disease resistance provide valuable information into further control of cassava disease.

Alternation of soil bacterial and fungal communities by tomato-rice rotation in Hainan Island in Southeast of China.

Tomato-rice rotation is prevalent in subtropical and tropical regions in China. This practice enhances crop productivity and the disease suppression property of soils against soil-borne plant pathogens. To explore the variations and dynamics of bacterial and fungal communities, bulk soil samples were collected during two consecutive years under a rotation system between tomato and rice originated from the year of 2010 in Hainan Island, and 16S rDNA and ITS amplicons were sequenced by Illumina MiSeq. The results demonstrated that potentially beneficial bacterial phyla Acidobacteria, Chloroflexi and genus Paenibacillus, as well as the fungal genus Mortierella were significantly enriched, while the potentially pathogenic fungal genus Fusarium was significantly decreased during the crop rotation. Measurements of soil physicochemical properties indicated that the soil acidification was improved. Redundancy analysis (RDA) revealed the correlation of the microbial community with soil pH and identified soil total phosphorus (TP) level as the highest determinant factor for both bacterial and fungal communities. This work provides a preliminary description of changes of the bacterial and fungal communities related to tomato-rice rotation in China and offered experimental evidences for exploring the effects of this agricultural practice on soil ecology.

Metagenomic Analyses Expand Bacterial and Functional Profiling Biomarkers for Colorectal Cancer in a Hainan Cohort, China.

This study was conducted for the metagenomic analysis of stool samples from CRC affected individuals to identify biomarkers for CRC in Hainan, the only tropical island province of China. The gut microbiota of CRC patients differed significantly from that of healthy and reference database cohorts based on Aitchison distance and Bray-Cutis distance but there was no significant difference in alpha diversity. Furthermore, at the species level, 68 species were significantly altered including 37 CRC-enriched, such as, Fusobacterium nucleatum, Parvimonas micra, Gemella morbillorum, Citrobacter portucalensis, Alloprevotella sp., Shigella sonnei, Coriobacteriaceae bacterium, etc. Sixty-seven different metabolic pathways were acquired, and pathways involved in the synthesis of many amino acids were significantly declined. Besides, 2 identified antibiotic resistance genes performed well (area under the receive-operation curve AUC = 0.833, 95% CI 58.51-100%) compared with virulence factor genes. The results of the present study provide region-specific bacterial and functional biomarkers of gut microbiota for CRC patients in Hainan. Microbiota is considered as a non-invasive biomarker for the detection of CRC. Gut microbiota of different geographic regions should be further studied to expand the understanding of markers, especially for the China cohort due to diverse nationalities and lifestyles.

Responses of ammonia-oxidizing microorganisms to biochar and compost amendments of heavy metals-polluted soil.

Heavy metal pollution affects soil ecological function. Biochar and compost can effectively remediate heavy metals and increase soil nutrients. The effects and mechanisms of biochar and compost amendments on soil nitrogen cycle function in heavy-metal contaminated soils are not fully understood. This study examined how biochar, compost, and their integrated use affected ammonia-oxidizing microorganisms in heavy metal polluted soil. Quantitative PCR was used to determine the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Ammonia monooxygenase (AMO) activity was evaluated by the enzyme-linked immunosorbent assay. Results showed that compost rather than biochar improved nitrogen conversion in soil. Biochar, compost, or their integrated application significantly reduced the effective Zn and Cd speciation. Adding compost obviously increased As and Cu effective speciation, bacterial 16S rRNA abundance, and AMO activity. AOB, stimulated by compost addition, was significantly more abundant than AOA throughout remediation. Correlation analysis showed that AOB abundance positively correlated with NO3--N (r = 0.830, P < 0.01), and that AMO activity had significant correlation with EC (r = -0.908, P < 0.01) and water-soluble carbon (r = -0.868, P < 0.01). Those seem to be the most vital factors affecting AOB community and their function in heavy metal-polluted soil remediated by biochar and compost.

The effects of exopolysaccharides and exopolysaccharide-producing Lactobacillus on the intestinal microbiome of zebrafish (Danio rerio).

BACKGROUND: Numerous studies have reported the health-promoting effects of exopolysaccharides (EPSs) in in vitro models; however, a functional evaluation of EPSs will provide additional knowledge of EPS-microbe interactions by in vivo intestinal microbial model. In the present study, high-throughput amplicon sequencing, short-chain fatty acid (SCFAs) and intestinal inflammation evaluation were performed to explore the potential benefits of exopolysaccharides (EPSs) and EPS-producing Lactobacillus (HNUB20 group) using the healthy zebrafish (Danio rerio) model. RESULTS: The results based on microbial taxonomic analysis revealed that the abundance of four genera, Ochrobactrum, Sediminibacterium, Sphingomonas and Sphingobium, were increased in the control group in comparison to HNUB20 group. Pelomonas spp. levels were significantly higher and that of the genera Lactobacillus and Brachybacterium were significantly decreased in EPS group compared with control group. PICRUSt based functional prediction of gut microbiota metabolic pathways indicated that significantly lower abundance was found for transcription, and membrane transport, whereas folding, sorting and degradation and energy metabolism had significantly higher abundance after HNUB20 treatment. Two metabolic pathways, including metabolism and endocrine functions, were more abundant in the EPS group than control group. Similar to the HNUB20 group, transcription was also decreased in the EPS group compared with the control group. However, SCFAs and immune indexes indicated EPS and HNUB20 performed limited efficacy in the healthy zebrafish. CONCLUSIONS: The present intestinal microbial model-based study indicated that EPSs and high-yield EPS-producing Lactobacillus can shake the structure of intestinal microbiota, but cannot change SCFAs presence and intestinal inflammation.

Spatial variation of sediment bacterial community in an acid mine drainage contaminated area and surrounding river basin.

Microbial community is sensitive to the variations of environment, and it plays an important role in biogeochemical cycling in acid mine drainage (AMD). In this study, an integrated high-throughput absolute abundance quantification (iHAAQ) method was applied to study the dynamics of microbial community and the characteristics of microorganism. The results showed a significant difference in bacterial community with diversity being higher in watershed area. The main influential factors for bacterial communities in watershed were physicochemical properties (e.g., pH and potassium), while in mining areas the main driving factors were metals/metalloids (e.g., As, Zn, and Pb). Notably, the major functions of microbial community were transporter and ABC transporter in mining area, while two-component system was more abundant in watershed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis (level 3). In particular, Phyllobacterium, Bacteroides, and Sulfurovum were demonstrated to be potentially useful bacterial species for bioremediation, which should be a good choice for future studies. These results could facilitate our understanding of microbial diversity in different sediments of mining areas and identify microbial communities for bioremediation projects.

Carbon-based materials as adsorbent for antibiotics removal: Mechanisms and influencing factors.

With the development of the removal of organic pollutants in the soil and water environment, antibiotics have been considered as emerging pollutants and received considerable attention among the scientific community. Thus, there is a need for an effective, economical, fast, operational feasible and environmental-friendly technology to remove antibiotics. Adsorption technology would be one of the most promising option on the basis that it best meets the criteria we set out above. From the most primitive activated carbon to the most innovative modified biochar, carbon-based materials have played a significant role in the adsorption process of antibiotics all the time. This paper reviews the adsorption behavior of some representative antibiotics (e.g., chloramphenicols, sulfonamides, tetracyclines, flouroquinolones) over various carbonaceous materials (i.e., activated carbon, carbon nanotubes, graphene, and biochar). Nevertheless, in addition to the structural characteristics and adsorption capacities of carbon-based materials, a special emphasis was placed on the underlying adsorption mechanisms and roles of different influencing factors in the adsorption process. Moreover, the knowledge gaps and research challenges have been highlighted, including design and optimization of the carbonaceous materials for antibiotics adsorption.

Diagnosis of soil contamination using microbiological indices: A review on heavy metal pollution.

Heavy metal contamination of soil has become a serious global issue because of their persistence in the environment and the non-biodegradable nature leading to their accumulation to toxic levels. In order to achieve early warning and prevent soil quality from deteriorating, it is necessary to select suitable indices to diagnose heavy metal pollution. Microbiological indices for monitoring soil pollution by heavy metals are gaining attention. However, the related researches are scattered, and critical review is imperative. This review is mainly to provide readers with an in-depth understanding of the merits and limitations of microbiological indices for heavy metals contaminated and remediated soils. Microbiological indicators include microbial abundance, community diversity and structure, functional activity. The changes of different microbiological indices and the mechanism of microbial response to heavy metal stress in soils are comprehensively summarized. Furthermore, research gaps and future directions of the microbial ecotoxicological diagnosis of soil contamination by heavy metals are also proposed and discussed.

Selenium contamination, consequences and remediation techniques in water and soils: A review.

Selenium (Se) contamination in surface and ground water in numerous river basins has become a critical problem worldwide in recent years. The exposure to Se, either direct consumption of Se or indirectly may be fatal to the human health because of its toxicity. The review begins with an introduction of Se chemistry, distribution and health threats, which are essential to the remediation techniques. Then, the review provides the recent and common removal techniques for Se, including reduction techniques, phytoremediation, bioremediation, coagulation-flocculation, electrocoagulation (EC), electrochemical methods, adsorption, coprecipitation, electrokinetics, membrance technology, and chemical precipitation. Removal techniques concentrate on the advantages, drawbacks and the recent achievements of each technique. The review also takes an overall consideration of experimental conditions, comparison criteria and economic aspects.

Whole-genome sequencing reveals the mechanisms for evolution of streptomycin resistance in Lactobacillus plantarum.

In this research, we investigated the evolution of streptomycin resistance in Lactobacillus plantarum ATCC14917, which was passaged in medium containing a gradually increasing concentration of streptomycin. After 25 d, the minimum inhibitory concentration (MIC) of L. plantarum ATCC14917 had reached 131,072 µg/mL, which was 8,192-fold higher than the MIC of the original parent isolate. The highly resistant L. plantarum ATCC14917 isolate was then passaged in antibiotic-free medium to determine the stability of resistance. The MIC value of the L. plantarum ATCC14917 isolate decreased to 2,048 µg/mL after 35 d but remained constant thereafter, indicating that resistance was irreversible even in the absence of selection pressure. Whole-genome sequencing of parent isolates, control isolates, and isolates following passage was used to study the resistance mechanism of L. plantarum ATCC14917 to streptomycin and adaptation in the presence and absence of selection pressure. Five mutated genes (single nucleotide polymorphisms and structural variants) were verified in highly resistant L. plantarum ATCC14917 isolates, which were related to ribosomal protein S12, LPXTG-motif cell wall anchor domain protein, LrgA family protein, Ser/Thr phosphatase family protein, and a hypothetical protein that may correlate with resistance to streptomycin. After passage in streptomycin-free medium, only the mutant gene encoding ribosomal protein S12 remained; the other 4 mutant genes had reverted to the wild type as found in the parent isolate. Although the MIC value of L. plantarum ATCC14917 was reduced in the absence of selection pressure, it remained 128-fold higher than the MIC value of the parent isolate, indicating that ribosomal protein S12 may play an important role in streptomycin resistance. Using the mobile elements database, we demonstrated that streptomycin resistance-related genes in L. plantarum ATCC14917 were not located on mobile elements. This research offers a way of combining laboratory evolution techniques and whole-genome sequencing for evaluating antibiotic resistance in probiotics.